Biochimica et Biophysica Acta 1858 (2016) 1688–1709

Contents lists available at ScienceDirect

Biochimica et Biophysica Acta

journal homepage: www.elsevier.com/locate/bbamem

Computational and experimental approaches for investigating

nanoparticle-based drug delivery systems☆
M. Ramezanpour a, S.S.W. Leung b, K.H. Delgado-Magnero a, B.Y.M. Bashe c, J. Thewalt b,c, D.P. Tieleman a
a
Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
b
Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
c
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada

a r t i c l e i n f o a b s t r a c t

Article history: Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting,
Received 23 January 2016 and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of
Received in revised form 20 February 2016 overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer
Accepted 23 February 2016
cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies
Available online 27 February 2016
have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions
Keywords:
with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and dis-
Drug delivery system cuss how computer modeling can assist in rational design of DDSs with improved and optimized properties.
Gene nanocarrier We summarize commonly used experimental techniques for the study of DDSs. Then we review computational
Nanoparticle studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-,
Biological membrane nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled:
Computer modeling Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Experimental techniques © 2016 Elsevier B.V. All rights reserved.

1. Introduction [1,2]. Practically, an ideal DDS is cheap and straightforward to make,

In medicine, the delivery of a drug can be as important as the drug
itself. Physiology poses key challenges to effective drug delivery; an ad-
ministered drug must penetrate obstacles such as endo- or epithelial
membranes and also survive the host's defenses in order to be effective.
Addressing such challenges requires some form of drug encapsulation,
and the entity forming the capsule, which has a defined molecular ar-
chitecture, is known as a “drug delivery system (DDS).” From a func-
tional point of view, an ideal DDS is easy to administer, non-toxic,
carries the drug to its desired destination, and then releases it (Fig. 1)
Abbreviations: 5-FU, 5-fluorouracil; AuNPs, gold nanoparticles; BSA, bovine serum
albumin; CD, cyclodextrin; CG, coarse-grained; CNP, carbon-based nanoparticle; CNT,
carbon nanotube; CPe, inverse-phosphatidylcholine; CPNT, cyclic peptide based nano-
tube; CPP, cell penetrating peptide; DDS, drug delivery system; DLS, dynamic light scat-
tering; DOX, doxorubicin; DPD, Dissipative Particle Dynamics; DPPC,
dipalmitoylphosphatidylcholine; DSC, differential scanning calorimetry; ESR, electron
spin resonance spectroscopy; FT-IR, Fourier transform-infrared spectroscopy;
gamma-PGA, poly(gamma-glutamic acid); HSA, human serum albumin; IDP, intrinsi-
cally disordered proteins; IFN, interferon alpha-1b; IR, infrared; ITC, isothermal titra-
tion calorimetry; LD, laser diffraction; LNP, lipid nanoparticle; MD, Molecular
Dynamics; NMR, nuclear magnetic resonance spectroscopy; NP, nanoparticle; p-
THPP, 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin; PAMAM, poly(amido amine);
PEI, polyethylenimine; PPI, poly(propylene imine); QD, quantum dot; SAXS, small
angle X-ray scattering; SCPs, star copolymers; SEM, scanning electron microscopy;
SSMs, sterically stabilized micelles; TAT, trans-activator of transcription; TEM, trans-
mission electron microscopy; VIP, vasoactive intestinal peptide; WAXS, wide angle
X-ray scattering; XRD, X-ray diffraction.
☆ This article is part of a Special Issue entitled: Membrane Proteins edited by J.C.
Gumbart and Sergei Noskov.
as well as stable prior to its administration. Intense research into DDS
design is providing increasingly effective disease treatment.
A central aim for specialized DDS development is the optimization of
tiny drug encapsulation vehicles known as nanoparticles (NPs). NPs typ-
ically have diameters in the range of 10 to 100 nm [3]. These small DDS
can circulate freely even in capillaries [4], and are intrinsically better at
traversing biological barriers than larger DDS. It is worth mentioning
that nanomedicines, however, have a more complicated and time con-
suming FDA approval process than parent unimolecular therapeutics
[5]. In addition to efficacy and side effect evaluations common between
both small molecules and nanomedicines, there are other concerns
about nanocarriers which need further evaluation. Nanocarrier aggrega-
tion in vivo and their drug release, as well as evaluation of each compo-
nent of the formulation are some of those concerns. FDA regulations for
nanomedicines, the complexity of nanocarriers, and the prospect of
only a small increase in performance upon reformulating small drugs in
nanocarriers can discourage pharmaceutical companies from investing
in these systems. In fact, it seems that investigations into DDS are much
more successful in generating papers than in developing new treatment
methods [5]. However, considering the number of approved drugs and
current ones in clinical trials [6,7], as well as clearer guidelines for
nanomedicine approval by the FDA, there is growing momentum in
transferring these systems from publication to clinical development [5].
Many different types of NPs exist, including liposomes [7,8],
dendrimers [9–11], carbon nanotubes (CNTs) [12–14], inorganic
[15–20], and polymer-based [21,22] NPs, with each having its own

http://dx.doi.org/10.1016/j.bbamem.2016.02.028
0005-2736/© 2016 Elsevier B.V. All rights reserved.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709 1689

Fig. 1. Drug delivery pathway for a drug-nanocarrier system. After the DDSs enter the bloodstream (1), drug (green circle) leakage might occur if the drug–DDS complex is unstable (2).
Depending on the surface chemistry, DDSs might interact with biomolecules (3) and ions (4) in circulation. Eventually, they will extravasate to the extracellular space (5). After reaching
the target cell, they interact with the cell membrane (6) and can be internalized either via direct penetration (7) or endocytosis (8). In the latter case, the nanocarrier will be entrapped in
endosomes and must be released (9) before endosomal maturation. Drug–DDS dissociation (10) is necessary for drugs to be effective in the cytoplasm or nucleus (11). This dissociation can
be mediated by interactions with endogeneous biomolecules (12). Not drawn to scale.

unique properties (Fig. 2). Physicochemical properties including size,
shape, deformability, surface charge and chemical composition affect
how well they evade phagocytosis and how they interact with vascula-
ture, traverse cell membranes and escape from endosomes prior to drug
degradation [1]. Thus, physical characterization of NPs is an important
step in the DDS design process.
Despite the increasing sophistication of experimental efforts to mea-
sure, design and optimize the structure and dynamics of NPs, such re-
search inevitably faces intrinsic and practical limitations. Resolution of
structural details can be difficult or impossible, and systematic variation
of properties such as composition, size and surface charge can be pro-
hibitively time consuming and expensive. As a result, general biophysi-
cal principles connecting the effectiveness of a DDS with its composition
are difficult to elucidate. Predicting optimum DDS design solely on the
basis of experimental research is therefore unlikely. Another challenge
in DDS development is that many DDSs show promise in vitro but fail
in vivo [6]. This is mainly because of the lack of mechanistic insight
obtainable by experiments which are based on trial and error. Theoret-
ical methods, both analytical and computational, can allow primary
screening of variables in order to predict suitable conditions for further
experiments [23]. Computer modeling techniques provide detailed in-
formation about molecular interactions and other physicochemical
properties of drugs and carriers (Table 1) and have found broad applica-
tions in biology, biochemistry, and biophysics [24]. Computer simula-
tion is capable of complementing experiments and assisting in the
rational design of new formulations with improved efficacies. In this re-
view, we describe the main experimental approaches to characterize
NP-based DDSs and focus in more detail on current applications of com-
puter simulations aimed at understanding molecular aspects of DDSs.
In the next sections, we first give a brief overview of commonly used
experimental techniques, followed by a section that describes several
common computational approaches. Section 4 highlights recent com-
putational studies of what currently are the major classes of NP-based
DDSs. We conclude with a brief outlook on the role of computer simula-
tions in drug delivery technology.
2. Commonly used experimental techniques for nanoparticle
characterization
Here we provide a brief summary of techniques regularly used to
characterize NP size, zeta potential, surface morphology, and the exis-
tence of colloidal structures (Table 2). We first describe the importance
of each of these properties and the experimental techniques used to
measure them. Next we describe some sophisticated physical chemistry
tools that are used in DDS development to provide data that can param-
eterize and validate computational simulations. Experiments used to vi-
sualize cellular uptake, NP–cell interactions, as well as those used to
determine cell viability will be omitted, even though they are vital to
pharmaceutical development and are also commonly performed, since
details on these can be found elsewhere (e.g. [25]).
Particle size is an important property because the size of the carrier
can affect circulation time, encapsulation efficiency, and cellular uptake
[1,26,27]. For example, in the case of cancer treatment, nano-drug car-
riers of the appropriate sizes can extravasate from the bloodstream to
tumor tissues (380–780 nm) [1,28], but not from the tighter capillaries
(50–200 nm) in healthy tissues [29]. This contributes to the well-known
enhanced permeability and retention effect [30–33]. Light scattering
techniques such as laser diffraction (LD) and dynamic light scattering
(DLS) can be used to measure NP size [34]. In both of these experiments,
a laser beam is directed at a dilute sample (e.g. a suspension or solution
of NPs). In LD, the diffraction angle is used to determine the particle size
[35]. In DLS, the time dependence of the scattered light intensity is
1690 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709

Fig. 2. Examples of nanoparticulate DDS. From top-left to bottom-right, monolayer-protected gold nanoparticle, polymeric micelle, DNA cage, carbon nanotube, solid lipid nanoparticle,
polymer, dendrimer and dendron, liposome, and protein-based DDS. For dendrimer: orange, green, red, and blue represents G0, G1, G2, and G3, respectively. Dendron has also been
shown as black branch. Not drawn to scale.

detected at a known scattering angle. The Brownian motion of scattering techniques with a separation technique, such as field flow
suspended particles causes the scattered light intensity to fluctuate. fractionation [37,38].
These fluctuations are correlated with the particle's velocity, and can Microscopy techniques such as transmission electron microscopy
be used to determine particle size via an appropriate theoretical (TEM), scanning electron microscopy (SEM), and atomic force micros-
model (e.g. Stokes–Einstein equation). Most models assume the parti- copy can be used to measure NP size, as well as size distribution
cles are spherical and monodisperse; artifacts may arise if they are (dispersity), shape, and surface morphology. Dispersity – also known
not. DLS can be used to measure the size of particles in the 2 nm–3 μm as polydispersity in older literature – in a formulation can result in vary-
range, and LD can be used in the 20 nm–2 mm range [34,36]. Resolution ing body-residence time and immunogenicity [39,40]. Particle shape
of small differences in particle size can be improved by combining light can affect cellular uptake mechanisms and kinetics [41–45] as well as
margination dynamics — the lateral drift of NPs to endothelial walls
Table 1
[1]. The particle surface is the first point of contact between the NP
Questions relevant to drug delivery system design that can be answered by computational and its environment, and surface morphology is known to affect drug
simulations. release kinetics [46]. In electron microscopy, an electron beam is direct-
ed at the sample, and differences in electron density in the sample gives
Drug delivery step Properties of interest
contrast to structures. Since electron microscopy can give high-
Physicochemical characterization Self-assembly of DDS components
resolution images approaching molecular resolution, all motions on
Structure and dynamics of drug–DDS complex
Drug loading the supramolecular scale have to be halted. For SEM, the NPs are depos-
Drug distribution ited onto a carbon conductive tape, dried, and covered with a thin layer
Drug–DDS interactions of metal [47]. In cryo-TEM, samples are applied onto an electron micros-
Functionalization copy grid, plunge-frozen rapidly in ethane to prevent the formation of
Drug leakage
Aggregation
damaging cubic ice and then imaged under cryogenic conditions to pre-
Circulation Interaction with biomolecules vent radiation damage to the sample during imaging [48]. Magnifica-
Stability tions on the order of 50,000 ×, with a resolution of 0.3 nm, are
Interaction with ions possible [49]. Atomic force microscopy probes surface terrain using a
Cell-membrane Interactions with membrane
nanoscale mechanical probe with a vertical resolution as small as
Cellular internalization
Interaction with membrane proteins 0.01 nm [35].
Intracellular Drug–DDS dissociation A NP's shape can influence the physiological fate of its cargo [1].
Drug release from endosome Particle shape can be an indication of undesirable aggregate structures.
Interaction with endogenous molecules Aggregate structures can also cause inaccurate particle size determina-
Nucleus translocation
tion by LD or DLS [34]. Light microscopy can be used for determining
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
if microparticles are aggregates of smaller particles [36,50], even though
it cannot be used for directly observing NP structure due to limitations
in optical resolution (~200 nm). Isothermal titration calorimetry (ITC),
which will be described in greater detail below, has been used to
study aggregate formation in polycationic nucleic acid carriers [51].
Aggregation of NPs can be prevented via electrostatic repulsion [31,
52]. Surface charge measurements can be a predictor of aggregation be-
havior, and consequently a predictor of colloidal dispersion stability
during storage.
Surface charge can affect cellular uptake, cytotoxicity, and circula-
tion times [1,31,53,54]. Zeta potential is used to characterize the surface
charge of NPs. When a particle moves in a liquid, a thin layer of liquid
moves with it. The zeta potential is defined as the electrical potential
at the boundary of this moving liquid, defined as the shear plane. It is
a function of surface charge density, shear plane location, and surface
structure [55]. Zeta potential is determined by measuring light scatter-
ing caused by particle motion in an applied electric field. Charged parti-
cles with larger zeta potential (|zeta| N 25 mV) are less likely to form
aggregates but neutral particles generally have longer circulation
times [56]. Surface charge effects are very complex; positive and nega-
tive zeta potentials correlate with higher cellular uptake in non-
phagocytic and phagocytic cells, respectively [54]. Future DDS designs
may require NPs to switch zeta potential at the target site to maximize
circulation time while targeting a particular type of cell [1]. It should
be noted that protein adsorption in cellular media can change the
surface charge [52]. Conclusions on surface-charge effects, therefore,
are only valid when comparing functionalized or non-functionalized
particles of similar sizes [54].
Encapsulation efficiency – the ratio of encapsulated drug to the
amount of drug used during formulation preparation – is an important
parameter [46]. Low encapsulation efficiency implies that more carrier
material is needed, heightening the risk of carrier material toxicity [2,
57]. Encapsulation efficiency can be determined in a number of ways,
depending on the particular type of NP. Drug loading can be determined
by weight [16]. Gel electrophoresis has been used to determine encap-
sulation efficiency by analyzing protection from RNase degradation in
siRNA lipid nanoparticles (LNPs). Physical chemistry techniques can
also be used to identify and quantify the degree to which components
have been encapsulated. For example, fluorescence spectroscopy can
be used if the drug is fluorescent [16]. Ultraviolet–visible (UV–Vis)
light spectroscopy can be used to determine the amount of cargo (e.g.
siRNA, anticancer drug doxorubicin (DOX)) present [58,59]. High per-
formance liquid chromatography can be used to separate, identify, and
quantify the components of a mixture [46,60]. Novel single molecule
measurements have been applied to measure encapsulation efficiency
in individual lipid vesicles [61].
An array of physical chemistry techniques has been instrumental in
evaluating the chemical and physical properties of NP components.
Dendrimer structures have been simulated based on experimental
data from nuclear magnetic resonance spectroscopy (NMR) and X-ray
[62]. LNP matrix state, polymorphism, and phase behavior have been
characterized by differential scanning calorimetry (DSC), X-ray diffrac-
tion (XRD), and neutron scattering [63]. Lipid crystallinity of solid
LNPs has been studied using X-ray scattering, DSC, NMR, and electron
spin resonance spectroscopy (ESR) [64]. CNTs have been characterized
using XRD, UV–Vis spectroscopy, Fourier transform-infrared spectros-
copy (FT-IR), ESR, SEM, and energy dispersive X-ray diffraction [65].
Iron oxide NPs, which are magnetic, can be studied using magnetome-
try, NMR relaxation dispersion profiles [55], and magnetic field flow
fractionation [66]. Some more common physical chemistry tools will
be briefly described here.
In optical spectroscopy, the absorption of electromagnetic radiation
by NPs occurs at frequencies characteristic of the molecular structures
present. UV–Vis light is absorbed if it supplies the right amount of ener-
gy to excite valence electrons, while infrared (IR) light is absorbed if it
excites bond vibrations. FT-IR is a more efficient variant of IR
1691
spectroscopy where all frequencies are sampled simultaneously. It has
been used to monitor cholesterol-induced changes in liposomal mem-
brane structure [67] and to verify conjugation of block copolymers
onto iron oxide NPs [68]. UV–Vis spectroscopy has been used extensive-
ly in NP characterization. For example it was used to confirm the pres-
ence of cleavable disulfide bond in CNT-nucleic acid conjugates [69];
monitor the metal to ligand charge transfer band (5d(Pt11) to
π*(diimine)) in dendrimer synthesis [70]; measure dye and drug encap-
sulation in poly(lactic-co-glycolic acid) polymeric carriers [71,72] and
study drug release kinetics of liposomal formulations [67].
NMR and ESR both rely on spin manipulations in the presence of an
applied external magnetic field. NMR monitors the nuclear spin of
nuclei with non-zero nuclear spins, and ESR monitors the electron
spin of excited unpaired electrons [73]. NMR can provide a wealth of in-
formation on molecular arrangements. NMR is sensitive to small chang-
es in the local environment: it can be used to differentiate between
various layers up to the fourth generation in dendrimers [74], and be-
tween neighboring carbon atoms in lipids [75]. 2D NMR techniques
can be used to ascertain chemical connectivity (e.g. COSY, HMQC,
HSQC) and distances (e.g. NOESY and ROESY) between specific atoms
[74,76,77]. Dynamic information is also accessible to NMR. Pulsed
field-gradient spin echo 1H NMR and diffusion-ordered spectroscopy
have been used to determine diffusion coefficients in aliphatic polyester
and poly(propylene imine) (PPI) dendrimers [74,78]. 31P NMR has been
used to determine the mobility of siRNA encapsulated in LNPs [79].
NMR relaxation was used to monitor molecular tumbling activities
[80] and this information, in turn, was used to determine the location
of a spin-labeled anticancer drug in micelles formed by PEG modified
with long alkyl groups and of paclitaxel in cyclodextrin (CD) vesicles
[77,80]. Most DDSs are invisible to ESR, requiring the addition of para-
magnetic spin probes [81]. Lipophilic ESR probes have been used as
model lipophilic drugs to help determine where these drugs localized
in solid LNPs [35]. In gadolinium poly(amido amine) (PAMAM) dendri-
mer containing spin probes, ESR was used to determine the location and
concentration of the magnetic resonance imaging contrast agent gado-
linium [78]. ESR has also been used to prove that the terminal inter-
branch H-bonded groups preclude backfolding in PAMAM dendrimers
[78]. Since ESR can probe membrane fluidity, ESR has been used to
study interactions between polymeric micelles and lipid membranes,
which are models for cell membranes [68]. ESR can also give
microviscosity and micropolarity information [81]. Viscoelastic proper-
ties of dispersions can affect DDS interactions with the body. For exam-
ple, capillary blockage can occur with solid LNPs, which are less
deformable than nano-emulsions [64].
Scattering techniques can be used to study the structure of colloidal
systems. In scattering studies, a monochromatic beam of light, neutrons,
or X-ray is focused on the sample, and the intensity of the scattered
beam is measured. Light scattering was covered earlier in this section.
X-ray scattering results from variations in electron density and neutron
scattering results from variations in the spatial distribution of atomic
nuclei [82]. The interference pattern formed by the scattered beam
can be used to determine characteristic lengths using Bragg's Law. Larg-
er angle measurements contain information for shorter length scales:
small and wide angle X-ray scattering (SAXS and WAXS) are used to
look at liquids and solids with structures on the length scale of 1–
200 nm and sub-nm, respectively. For example, SAXS is used to monitor
monolayer and bilayer repeat spacing, and hydrophobic thickness in
lipid membranes, while WAXS is used to determine chain packing and
extent of lipid motion [83,84]. SAXS has been used to study NPs with
cubosome structures [85,86], to provide micelle shape, size and density
of nonsteroidal anti-inflammatory drug celecoxib-loaded protein mi-
celles [50], and to observe in situ shell growth of polymeric
nanocapsules [87]. WAXS has been used to study lipid polymorphic
transformations in solid LNPs and crystallinity of encapsulated drugs
[88], and crystallinity of polyelectrolyte complexes made with polysac-
charides [89]. SANS, useful for studying structures of 1–100 nm [90], has
1692 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709

been used to determine molecular weight and end group locations of
dendrimers [74]. Neutron scattering can also be used to study drug dif-
fusion and internal molecular motions in LNPs [63].
Fluorescence comprises a family of spectroscopy and microscopy
techniques relying on excitation of fluorescent species. An extrinsic
fluorescent probe is added when no fluorescent moieties are present
in the material of interest. Absorption of a photon excites the
fluorophore and fluorescence occurs when a photon is later emitted. Be-
tween excitation and emission, the fluorophore's motions and local en-
vironment (e.g. viscosity, polarity, temperature, pH, ion concentration)
influence the fluorophore's spectrum [91]. Polarity sensitive fluorescent
probes are commonly used to determine the critical association concen-
tration of polymeric micelles – analogous to the critical micellar concen-
tration of surfactant micelles [92]. Fluorescence quenching assays have
been done to evaluate nucleic acid-polycation binding in polycationic
nucleic acid carriers [51] and dye leakage assays have been used to eval-
uate drug release characteristics [93].
Thermal analysis is a versatile tool for DDS characterization [94,95].
DSC measures enthalpy changes — the heat required for a sample to un-
dergo a physical phase transition (e.g. glass transition, melting, decom-
position, isomerization or heats of solution, water sorption–desorption)
[95,96]. DSC was used to monitor the physical state of the antineoplastic
drug paclitaxel inside polymeric microspheres, for example [46]. More
specific to DDS design, DSC has been used to measure the gel-to-liquid
crystalline transition temperature of lipids in liposomal formulations,
which can be used to predict release rates of encapsulated drugs [95,
97]. In a closely related technique, ITC, the evolved heat is measured
as concentrated aliquots of one substance are added to a solution of a
second substance. The released heat is directly proportional to the
amount of substance added, and can be used to measure enthalpy
changes, stoichiometry, and binding constants. ITC has been used to
measure cyclodextran–guest molecule interactions, micelle–drug inter-
actions, and polyelectrolyte aggregation [98].
NP DDSs are complex systems that can evolve over time. Dynamic
processes cannot be captured in steady-state measurements, and can
pose as a challenge to characterization [35]. For example, PEGylated
NPs are known to lose their PEG coating before reaching target cells
[99–101]. Time-resolved DLS combined with TEM was used to inves-
tigate morphology transition kinetics of multiblock copolymer mi-
celles [102]. Time-resolved fluorescence lifetime measurements
have been used to follow the release of fluorescent compounds
from polymeric carriers [71], and fluorescence lifetime imaging mi-
croscopy could extend drug release studies to cellular systems
[103,104].
3. Computational approaches to study nanoparticles
Computer simulations in general describe the physics of materials at a
suitable level of detail for a particular application. A simulation is de-
scribed by the level of detail in the physics used to model the system of
interest, and the algorithms used to generate enough simulation data to
draw statistically valid conclusions about the behavior of the system of in-
terest. NPs can be described at different levels of detail (Fig. 3), but for
most of the applications in this review the appropriate levels of detail
are limited to atomistic and semi-atomistic, slightly coarser, levels.
At the highest level of detail, a system is described by quantum me-
chanics in one of its approximations. Quantum mechanical calculations
have been widely applied to CNTs and play a role in optimizing less de-
tailed simulations, but in practice they are only useful for small systems
with limited degrees of freedom and generally not in solution. They are

Fig. 3. Categories of simulation methods and their respective spatio-temporal domains of applicability. The question of interest dictates the level of resolution required. Briefly, if electronic
motion play an important role in the property we are studying, quantum mechanics (QM) level is appropriate. However, if there is no bond formation and cleavage, all atom (AA) level
works well; we can safely ignore electronic motion by assigning point charges to each atom. If electrostatic and hydrophobic interactions are the dominant contributors, coarse grain
models (CG) can be used: individual atoms can be ignored and a group of atoms (e.g. 4 heavy atoms in MARTINI) can be treated as one interaction point/bead. CG models allow the
exploration of a larger area in phase space, at the expense of losing atomistic details. Coarser levels of simulations (e.g. DPD and continuum models) are appropriate for systems and
processes which require longer times and lengths.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709 1693

essential to correctly model electronic properties and can be used to cal- Table 2
culate electrical, optical, magnetic and mechanical properties of CNTs, Experimental methods used to study drug delivery systems.

quantum dots (QDs), magnetic NPs and similar systems. For soft- Experimental technique Abbreviation Properties
condensed matter systems such as liposomes or dendrimers in solution Dynamic light scattering DLS Particle size, aggregation
their usefulness is currently limited. Laser diffraction LD Particle size, aggregation
If we average over electronic properties by representing electrons as Transmission electron TEM Particle size, dispersity, shape, surface
partial charges on atoms rather than taking them into account explicitly, microscopy morphology
Scanning electron SEM Particle size, dispersity, shape, surface
we significantly simplify calculations. At this level of detail, atoms are
microscopy morphology
described as point charges that interact through simplified empirical Atomic force microscopy AFM Particle size, dispersity, shape, surface
potential terms including Coulomb interactions, Van der Waals interac- morphology
tions, and simplified terms describing bonds, angles, and dihedrals as Fluorescence FLIM Drug release
harmonic terms and cosine expansions [105]. The resulting technique Zeta potential – Surface charge
Gel electrophoresis – Encapsulation efficiency of nucleic acids
is called Molecular Dynamics (MD) and is widely used for biological Ultraviolet–visible light UV–vis Encapsulation efficiency
and soft-condensed matter systems. The vast majority of the papers spectroscopy
reviewed below use this approach, which accounts for a substantial Fourier FT-IR Bond vibrations
fraction of super computer time on the worlds' major academic comput- transform-infrared
light spectroscopy
er centers. MD is a mature technique that is implemented in a number
X-ray scattering SAXS and Repeat spacing, chemical connectivity
of widely-used software packages, including GROMACS [106], NAMD WAXS
[107], LAMPPS [108], CHARMM [109], and AMBER [110]. MD simula- Neutron scattering – Crystallinity
tions essentially generate a movie of a set of molecules over time, incor- High performance liquid HPLC Separate, identify and quantify
porating every degree or nearly every degree of freedom, from which chromatography components in mixture
Nuclear magnetic NMR Crystallinity, molecular mobility,
through statistical mechanics thermodynamic properties can be calcu-
resonance chemical connectivity
lated. Its main limitations include the computational cost and the corre- spectroscopy
sponding limited time scale (realistically, microseconds in most cases) Electron spin resonance ESR Carrier fluidity, gadolinium
and length scale (~10 nm per dimension) and the limitations implicit spectroscopy concentration, microviscosity,
micropolarity
in the physics that describes the interactions between atoms: point
Fluorescence – Viscosity, polarity, concentration, drug
charges mean electronic effects like polarization, pi-electron clouds spectroscopy release
possibly important for CNTs, and charge transfer are typically ignored. Differential scanning DSC Phase transitions
In addition, the simplified interaction function sometimes imposes calorimetry
other limitations. Isothermal calorimetry ITC Phase transitions

For many properties of interest, especially in mesoscopic-scale sys-

tems like NPs with a size of 20–200 nm, atomistic detail may not always
be necessary. Many papers below use coarse-grained (CG) simulations,
often based on the MARTINI model [111]. Here CG means that several
atoms have been grouped into interaction sites, which are no longer rec-
ognizable as atoms but instead are ‘beads’ that represent molecular
fragments. Depending on the level of coarse-graining, these beads can
still maintain a significant amount of chemical specificity, or they can
represent very generic properties such as those that represent a lipid
by one head group bead and two tail beads. The same physics applies
as in atomistic simulations, and sufficient conformations of a system of
interest have to be generated by a sampling algorithm to accurately
calculate thermodynamic and structural properties. This can be done
by MD, Monte Carlo, or various other algorithms including Langevin
dynamics or Dissipative Particle Dynamics (DPD) [105].
At the CG level, individual molecules and usually fragments of mol-
ecules are still clearly recognizable. In material science, there exists a
whole hierarchy of additional models. Beyond molecules, DPD solves
hydrodynamics equations for materials by representing materials as
discrete particles that can be much larger than individual molecules.
DPD blurs the line with CG MD a little by its choice of particle volume:
if the volume is chosen to coincide with molecules or molecular frag-
ments its resolution is similar to CG MD, although it typically treats
problems that are more generic. Beyond DPD there are many other pos-
sibilities, including field-based treatments where a system is described
by density fields. Simulations coarser than DPD are beyond the scope
of this review.
4. Computational studies on drug and gene delivery systems
Computer modeling, as complementary tools to experiments, is ex-
cellent in shedding light into the structural and dynamical properties
of systems of interest at atomistic or molecular levels of detail [112,
113]. Applied to DDSs, computer simulations have been used to address
a broad range of questions (Table 1). Computer simulations can be used
to study self-assembly [114–116], the structural and dynamical
characteristics of the resulting aggregates [117,118], drug loading ca-
pacity, mechanism and rate [119–121], drug distribution/localization
in DDS [121], complex stability [118,122], drug retention, release mech-
anism and release rate [123–125], dominant drug–DDS interactions
[119,126,127], and to design or optimize DDSs targeting capabilities
[128,129]. Environmental conditions, e.g. pH, temperature, salt type
and concentration, counterions [126,130], and external stimulus such
as external magnetic fields [131–133], as well as interactions with
other biomolecules (e.g. serum proteins, miRNA, heparin), all might af-
fect the aforementioned aspects of DDSs [126,134–137] and can be
studied computationally.
The way DDSs interact with cell membranes is one of the most com-
monly studied steps in drug delivery by computational studies [138,
139]. Computer modeling can investigate the driving forces for NP-
membrane interactions, as well as how factors such as design parameters
and environmental conditions affect these. These parameters include size,
shape, surface chemistry, and concentration of NPs, as well as mechanical
and elastic properties of both NPs and membranes [138–143]. Surface
chemistry refers to NPs hydrophobicity/hydrophilicity, charge density
and distribution, as well as coating ligand's length, grafting density and
distribution, rigidity, and their affinity to receptors [144–147]. Since, in
real systems the membrane often interacts with more than one NP simul-
taneously, NP aggregation and interaction of multiple NPs with the mem-
brane also is a relevant factor [138,139]. Membrane properties such as
lipid phase, membrane composition, surface tension, charge density, re-
ceptor types and density also play important roles [148–150]. In addition
to all of these, external macromolecules, e.g. proteins in the bloodstream,
and different environmental conditions in different cell types [134], as
well as differences between external and internal cellular environments,
are also of great importance and worth further investigation. Of course,
many of these factors are coupled and have to be taken into account to-
gether in the design of NPs [138,139].
NPs are usually functionalized by coating with polymers, lipids, or li-
gands, to increase their stability, targeting capability, cellular uptake
1694 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
efficiency, and also to reduce their toxicity [131]. Both the type of coating
molecule and the coating pattern and density strongly affect the physico-
chemical properties of these NPs, and as a result their interactions with
their cargo and target lipid membranes [147,151–155]. Simulations can
be used to study these coatings, how they affect NP properties including
their interactions with other molecules [152,156], and can be used to op-
timize these coatings towards DDS with improved delivery capabilities
[151,154]. Functionalization with PEG polymers, a process called
PEGylation, is a good example of functionalization [157,158]. Drugs/pro-
teins/nucleic acids and NPs' surfaces are usually PEGylated to improve
their water solubility, stability, and circulation lifetime, and to reduce
their aggregation, toxicity, and immune response [157,159].
Considering the importance of PEG and its wide usage in drug deliv-
ery applications, PEG is worth further discussion. PEG is the most com-
monly used non-ionic polymer with stealth behavior for drug delivery
purposes [160]. These biocompatible hydrophilic polymers can solubi-
lize hydrophobic molecules, and reduce renal clearance and toxicity of
drugs and nanoparticles. They also inhibit the aggregation of PEGylated
agents by steric stabilization, as well as mask therapeutic agents from
the host immune system and consequently suppress immunogenicity
and antigenicity. This protective polymer layer, which is known as
stealth sheath, can reduce the fast recognition by the immune system
and reduce the non-specific interactions with blood components,
resulting in longer blood circulation times. These properties have
made it the gold standard polymer for drug delivery and other biomed-
ical applications and have been the topic of several computational
modeling studies reviewed in more detail below. Despite the wide-
spread use of PEG, there are several drawback to PEG including immu-
nogenicity and antigenicity, e.g. hypersensitivity reactions and the
development of antibodies against PEGs [160], which adversely affects
pharmacokinetics [161], and the search for alternatives, e.g. poly(amino
acids), continues, in part aided by computer simulations.
In addition to different aspects of DDS mechanism, different types of
DDS have been simulated. There are many types of nanoparticulate DDS.
DDSs based on polymers, peptides, nucleic acids, lipids, carbon,
dendrimers and dendrons, and gold have been investigated via comput-
er modeling and are described in more detail below. Combined, these
applications show that computer simulation has become a powerful
technique for rational design and optimization of DDS, and demon-
strates the growing importance of computational pharmaceutics.
For the rest of this review, we will present examples of computation-
al studies on each aspect of interest for each nanoparticulate DDS type in
separate sections, and then comment on challenges in this field. We will
focus on atomistic, CG MD simulations, and DPD simulations of
nanoparticulate DDSs; these fall mainly in categories defined as
dendrimers/dendrons, polymer-, protein/peptide-, nucleic acid-, lipid-,
and carbon-based DDSs, as well as gold nanoparticles (AuNPs). We em-
phasize studies published since 2010. There are computational studies
on other DDSs that are outside the scope of this review, e.g. graphene
oxides and reduced graphene oxides [19,162], silicon NPs [19,163],
nanodiamond [164,165], layered drug delivery carriers [166,167], zeo-
lites [168–170], metal–organic frameworks [171,172], and other porous
materials. These are excluded because they are not NPs, there are limit-
ed computational studies available, or because their focus is different
from the studies described below.
4.1. Dendrimers and dendrons
Dendrimers are a class of branched globular materials with broad
application in nanotechnology and nanomedicine, including for drug/
gene delivery [9–11]. Their monodispersity, modifiable surface, shell
and core characteristics, and their high loading capacity make them
suitable carriers for therapeutic agents, with promising applications in
gene delivery through complex formation with nucleic acids, so-called
dendriplexes [173–177]. Drugs can be covalently or noncovalently
incorporated in dendrimers to overcome solubility problems and to
improve targeting and cellular uptake. Dendrimers have been studied
in many computational papers to characterize their structure in solu-
tion, their interactions with drugs and biomolecules [62,175], and
their response to external stimuli [178]. All parts of dendrimers can be
modified chemically; core, shell and surface. The surface can be opti-
mized for different biological activities by functionalizing the terminal
groups. Thus dendrimers are a flexible class of materials with the poten-
tial for almost infinite variation.
Different dendrimers have been modeled including PPI, triazines
and PAMAM. Simulations can be used to investigate their interactions
with other molecules, the effect of solvents and counter-ions, pH, salt
concentration, different generation number, the nature of terminal
groups and chemical modifications. Computer simulations have also
been used to study deformation and conformational changes of
dendrimers upon interaction with nanopores [179], lipid membranes
[180], and nucleic acids [181] as a function of generation number, pH,
functionalization, and ionic strength. For example, Nandy et al. [181]
simulated a 38 base pair double stranded DNA and three different gen-
erations of PAMAM dendrimer (G3, G4, G5). They found that DNA
caused deformations in lower-generation dendrimers (G3) while
higher generation PAMAM (G5) bent DNA (Fig. 4). Generation number,
pH, and architecture have been shown to affect dendron's flexibility and
rigidity, and as a result influence their binding efficiency to nucleic acids
[182,183]. Several studies have investigated the effect of chemical mod-
ification on self-assembly, conformation, and drug/gene binding
[184–186].
Self-assembly of Janus dendrimers, comprised of hydrophobic and
hydrophilic parts, has been studied both experimentally and computa-
tionally. They form onion-like dendrimers and other complex architec-
tures [187,188].
Computer simulation has been used to study how chemical modifi-
cation and surface functionalization (e.g. PEGylation, acetylation, folic
acid groups, peptides, and targeting ligands of the surface) influences
the structure [189], and the interactions with cargos [190,191]. Comput-
er modeling can also be used to determine the optimal grafting densities
and patterns based on structural and drug-loading properties, and inter-
actions with target membranes [154,192–195]. Effect of PEGylation size
and grafting density on the structure of dendrimers, and also the struc-
ture of the PEG layer itself have been widely studied [154,196–198].
PEGylation expands the core of dendrimers, effectively reduces their
surface charge density and increases the overall size of dendrimers
[196]. The effect of PEGylation on structure and drug loading capacity
of PAMAM-G4 dendrimers was investigated by an all-atom MD simula-
tion [154]. Different PEG densities (25%, 50%, 75% and 100%), were test-
ed for complexation and loading capacity for 5-fluorouracil (5-FU), as a
model anticancer drug. The simulations suggested that 25% PEG is the
most suitable PEGylation density for drug delivery purposes. This
grafting density can retain the internal drug complexation capability,
and also assist in retaining drugs. For higher PEGylation degrees than
25%, 5-FU molecules to a high extent interact with external PEG chains
than dendrimer branches. Pearson et al. [193] used MD simulation to
understand why PEGylated dendron-based copolymers functionalized
with different terminal groups, –NH2, –COOH, and –Ac, do not exhibit
a charge-dependent cellular interaction. Simulations suggest that inter-
actions between positively charged terminal groups with PEG mole-
cules sequester the charges, and cause this low level of cellular
interaction for NH2 terminated micelles.
Interactions between dendrimers with lipid membranes, permeation
of dendrimers as a function of generation number (size), protonation
state, functionalization, and dendrimer concentration, as well as the effect
of bilayer asymmetry, bilayer tension, lipid tail length, and lipid phase
(temperature) all have been studied by simulations [124,180,195,
199–204]. Tian and Ma [124] studied interactions of G4-PAMAM
dendrimers with both symmetric and asymmetric negatively charged bi-
layers, with and without tension, at both neutral and low pH. It was
shown that both membrane tension and electrostatic interactions
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709 1695

Fig. 4. PAMAM Dendrimer-DNA interaction and deformation as a function of generation number. (a) For the G3 dendrimer, very little deformation in DNA was observed, while the
dendrimer was bent considerably by the DNA. (b) For G4, both DNA and dendrimer were deformed. (c) For G5, DNA was deformed, but the dendrimer behaved almost as a rigid body.
Adapted with permission from B. Nandy, P.K. Maiti, A. Bunker, Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA, (2013).
Copyright 2013 American Chemical Society.

between charged dendrimers and tensed membrane play important role
in dendrimer penetration through membrane. Based on their simulation
results authors proposed a mechanism of endosomal escape for pH-
responsive gene delivery vectors (Fig. 5). Xie et al. [204] found that low
generations leave gel-phase membranes intact while higher generations
fluidize the membrane and cause a gel-fluid phase transition around the
dendrimer binding site. Higher generation cationic dendrimers are capa-
ble of membrane disruption in both low and high temperatures [204].
Functionalization can influence these interactions since it affects the
physicochemical properties of dendrimers [195].
Dendrimers can condense DNA and siRNA, and stabilize small mole-
cules in their core, shell and interface. Several studies have considered

Fig. 5. Proposed mechanism of endosomal escape for pH-responsive dendrimers. In endosomes (pH ~ 5), dendrimers are protonated, leading to increasing osmotic pressure and dendrimer
swelling, putting the membrane under tension. Meanwhile, electrostatic interactions between charged dendrimers and asymmetric negatively charged endosomal membrane cause a
drop in the critical membrane tension required for membrane disruption, allowing NP escape from endosomes. Bottom row: snapshots of a MARTINI simulation of interactions
between a G4 dendrimer (orange beads) and a membrane (with lipid tails represented with cyan beads, and lipid headgroups represented with green and blue beads) at different pH
levels. Reproduced from [124] with permission from The Royal Society of Chemistry.
1696 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
the loading, release, interactions and distribution of small molecules in
dendrimers [174,205–213]. For example, Jain et al. [206] used all atom
MD simulations and molecular mechanics Poisson-Boltzmann surface
area analysis to study the solubility and drug release profile of the hy-
drophobic drugs famotidine and indomethacin in G5 ethylenediamine
cored PPI dendrimers under different pH conditions. They found fast
drug release in low pH, intermediate values in neutral pH and a slow re-
lease in high pH. These results and further simulations on the effect of
dendrimer chemistry and topology on drug loading and release suggest
that both the pKa of the drug and pH-dependent changes in the dendri-
mer influence these dendrimer–drug interactions and complex stability.
Loading and release of the antibiotic rifampicin, from G4-PAMAM den-
drimer has been studied by Bellini et al. [205] in a combined experimen-
tal and simulation approach. Experimentally, approximately 20 drug
molecules were found as the maximum potential loading capacity of
this dendrimer at neutral pH. In simulation, the model of the dendrimer
with 20 drug molecules in neutral pH was more stable than in low pH,
where drug molecules got expelled rapidly and simultaneously to the
solvent. This suggests a pH dependent drug release desirable for drug
delivery applications. Simulations can also be used to study the effect
of PEG lipids on loading capacity of dendrimers, and on surface
ligand's targeting capability [154,211,214].
Based on a comparison of several generations of PAMAM
dendrimers, G4 PAMAM might be optimal as vector for gene delivery,
based on PAMAM interactions with bilayers and siRNA complexation
[203,215]. For gene delivery applications, generation number (size),
flexibility, hydrogen bonding capability, pH, ion concentration and salt
type have been considered in simulations [183,216–219]. Electrostatic
interactions and the entropy gain from counterion release upon binding
have been proposed as important driving forces determining the inter-
actions between dendrimers and nucleic acids [181,212,213].
As one final example, we would like to design drug specific
nanocarriers by including optimal drug-binding molecules in the struc-
ture. Shi et al. [220] used de novo design of dendrimers via optimizing
building blocks and including optimal drug-binding molecules with a
final goal the design of a drug-specific nanocarrier. They combined
virtual screening with molecular docking and MD simulations on
DOX-dendrimer complexes. Using Rhein, a molecule with strong DOX
binding, they achieved Rhein-containing nanocarriers with a suitable
DOX profile.
4.2. Polymer-based delivery systems
Polymeric NPs are of interest in drug delivery applications and more
generally because of their stability and easily modifiable surface [21,31].
Block-copolymers [92] composed of hydrophobic and hydrophilic parts
can form a variety of self-assembled structures [221] of interest in drug
delivery applications. These structures, e.g. polymeric micelles [222], are
capable of accumulating drug molecules in their core, interface and shell
[121]. There are several reviews of computational studies on different
aspects or specific type of polymers [23,221,223–225]. Here, we will dis-
cuss some examples.
Amphiphilic polymers form a variety of structures in solvents, e.g.
core–shell, Janus particles, micelles, and rod-like micelles [102,226,
227]. Several factors affecting aggregate structures, stability and phase
transitions between different structures have been studied: for exam-
ple, solvent polarity [130], polymer architecture, concentration and
physicochemical properties [226,228,229], mixture components and
mixing ratios of comprising polymers [230,231], pH, temperature
[226,232], and the addition of components, e.g. lipids, cholesterol and li-
gands [102,233,234]. Huynh et al. [122] performed all atom MD simula-
tions on star copolymers (SCPs) to understand why SCP micelles are
unstable and form multimolecular micelles in solution, and to assist in
the rational design of stable SCP unimolecular micelles in solution.
Each SCP has a central connecting part and six attached arms, with
each arm comprised of a hydrophilic part (PEG) and a hydrophobic
one (PCL). These SCPs were different in their PCL and PEG length and
the resulting molecular weight. They form core–shell structures, in
which PCL blocks form a dense hydrophobic core while PEG blocks
form a shell around the PCL core. The simulations suggested that partial
water exposure of the PCL core drives aggregation into multimolecular
micelles. Increasing PEG length protects the PCL core from exposure to
the water but it also increases the size of micelles. Therefore, since
smaller micelles are preferred in DDS applications, predicting the mini-
mum number of PEG units for a specific number of PCL blocks required
to fully protect the PCL core is important. The authors found a quantita-
tive relation between hydration of PCL core and both number and mo-
lecular weight of PEG and PCL blocks [122].
The internal structure of the thermoresponsive polymer blend NPs,
and the phase transition between core–shell and Janus structures
were investigated by DPD simulations by Guo et al. [226]. Chen and
Ruckenstein [230] looked at the structure and mechanism of formation
and the degradation process of multicomponent multicore micelles via
DPD simulations. Taresco et al. [231] used a combined computational/
experimental approach to study the self-assembly and structure of co-
polymer micelles formed by two different types of monomers. Wang
et al. [233] studied the structural characterization of cholesterol-
functionalized CD micelles by all-atom MD simulation. Tan et al. [102]
by both experiment and DPD simulations showed that introducing a
second hydrophilic phosphatidylcholine group into the polymer chains
causes a phase transition from sphere to rod-like in multiblock polyure-
thane micelles.
Hybrid systems composed of polymers and other NPs, e.g. AuNPs
and QDs, also show interesting structural and phase transition behavior
[227,235]. Using both experiments and DPD simulations, Cai et al. [227]
studied the effect of adding AuNPs on block copolymer self-assembly.
Adding AuNPs caused a transformation from long cylindrical micelles
to short cylindrical micelles and finally to spherical micelles.
Interactions with and translocation through cell membranes for
polymer-based DDSs have been studied both by experiment and simu-
lations [236–238]. Li et al. [236] studied the interactions between a
novel amphiphilic polymer, PMAL, and siRNAs, combining experiment
and CG MD simulations. Potential of mean force calculations showed
that siRNA by itself experiences a large free energy barrier for transloca-
tion while the siRNA–PMAL complex entered the membrane spontane-
ously, consistent with experiment. The PMAL polymers induced pore
formation to facilitate siRNA translocation. Srinivas et al. [237] used
CG MD simulation and showed that these patchy polymeric micelles
are capable of accommodating and transporting hydrophilic contents
across a lipid membrane into a lipid vesicle.
Ding and Ma [238], using DPD simulations, investigated receptor-
mediated endocytosis for a new type of pH-responsive DDS composed
of NP (radius of 4 nm) and some pH-sensitive polymers (of twelve
beads length). Beads on the NP surface were treated as ligands and
assigned +e charges. The polymer had N randomly distributed nega-
tively charged (−e) beads, where N depends on the pKa of the polymer
and the system's pH. Half of the model lipids in the membrane were
treated as receptors by replacing charged beads in the lipid's head
group with neutral beads. They introduced a modified Lennard–Jones
potential to account for receptor–ligand interactions. Eighteen-
microsecond simulations for three different pH conditions combined
with potential of mean force calculations showed a triple-pH-response.
The NP can only be engulfed by cell membrane when the pH is higher or
lower than the polymer's pKa, whereas endocytosis is blocked when the
pH equals the polymer's pKa. It was also found that the properties of
NPs, pH-sensitive polymer and cell membranes, and the external envi-
ronment, all affect NP engulfment by the membrane, at least in this sim-
plified DPD model (Fig. 6).
The effect of functionalization on interactions with the membrane,
uptake mechanism, as well as effect on the structure and conformation
of drugs/polymer complexes have been studied by simulation [118,
239–243]. Liao et al. [240] used both experiment and all atom MD
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709 1697

Fig. 6. Time evolution of nanoparticle-polymer complex endocytosis as a function of pH. The endocytosis process of a nanoparticle-polymer complex (nanoparticle with pH-sensitive
polymers absorbed on its surface) depends on the pH. For pH values lower (a) and higher (c) than the polymer's pKa, the nanoparticle can be fully engulfed by the membrane.
However, for pH = pKa (b), endocytosis is blocked. Membrane lipid head groups are shown in green, purple, and blue correspond to +e, −e, and neutral beads, respectively. Lipid
tails are in orange, receptor heads are in red, and nanoparticle beads are in yellow. Polymer beads are in cyan (−e) and pink. Reprinted by permission from Macmillan Publishers Ltd.:
Scientific reports H. Ding, Y. Ma, Controlling Cellular Uptake of Nanoparticles with pH-Sensitive Polymers., Sci. Rep. 3 (2013) 2804., Copyright 2013.

simulations to study the uptake of chitosan/DNA complexes coated with
anionic poly(gamma-glutamic acid) (gamma-PGA). This coating en-
hanced the cellular uptake of chitosan/DNA complexes via a specific
protein-mediated endocytosis. Both the structure of this ternary com-
plex (CS/DNA/PGA), and the interaction between gamma-PGA and
glutamyl transpeptidase proteins were studied by MD simulations.
Sun. et al. [239,244] studied the effect of polyethylenimine polymer
(PEI) modification by lipids on nucleic acid compaction and aggrega-
tion. They found that lipid association as an additional mechanism of ag-
gregation resulted in more compact and stable structures.
Several studies have focused on interactions between polymeric
DDS and small molecule cargos, investigating driving forces for
partitioning [60,245–249], complex stability [250], drug loading capac-
ity and rate, and drug distribution and release [121,247,251–255] as a
function of temperature [256], pH [228,232,257,258], concentration of
drugs [232], physicochemical and structural properties of polymers
and cargos [259,260]. CD is a well-known family of cyclic oligosaccha-
rides with great promise as solubilizing agent for poorly soluble drugs
[246,261]. He et al. [246] performed MD simulations to investigate the
binding mode and affinities of the antifungal drug amphotericin B
drug with γ- and β-CD. Consistent with experiments, simulations
showed a significantly higher binding affinity for γ-CD than β-CD. The
binding mechanism of the drugs bexarotene and human vasoactive
intestinal peptide (VIP) to highly PEGylated sterically stabilized micelles
(SSMs) has been investigated by Vukovic et al. [121] both experimental-
ly and computationally. Using free energy profiles, they predicted the
drug distribution in SSMs. Single bexarotene, as a poorly water-
soluble drug, resides in the ionic interface with its polar end exposed

Fig. 7. Solubilization of bexarotene in sterically stabilized micelles (SSM). (Left) Free energy profiles for systems composed of 1, 3, and 5 bexarotenes in SSMs. SSMs are either composed of
10 (small) or 90 (large) monomers, in water and 0.16 M NaCl, respectively. Single drugs prefer the ionic interface, represented with vertical arrows, in both SSMs. For multiple drugs
accumulated in the SSM core (shown as a gold surface), a deeper minimum develops in the core. This is because several bexarotene (e.g. 5) cluster together (Right) via a hydrogen
bond network between their –COOH groups. Reprinted (adapted) with permission from L. Vukovic, A. Madriaga, A. Kuzmis, A. Banerjee, A. Tang, K. Tao, et al., Solubilization of
Therapeutic Agents in Micellar Nanomedicines, (2013). Copyright 2013 American Chemical Society.
1698 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
to solvent. With multiple bexarotene molecules, the preferred distribu-
tion is as clusters in the alkane core of SSM (Fig. 7). Dominated by elec-
trostatic interactions, VIP molecules, with two regions with positively
charged residues, interact with negatively charged − PO4 groups in
the ionic interface. These simulations suggest the importance of the bal-
ance between hydrophobic and Coulomb interactions between drugs
and phospholipid polymers in stabilization of drugs in SSMs.
The interaction and complexation of nucleic acids, including DNA and
siRNA with cationic polymers have been studied extensively [223]. PEI, as
an example of cationic polymers, is one of the most promising polymers
which have been widely utilized in studies for gene delivery applications.
Both experimental and computational studies have provided a better un-
derstanding of PEIs' binding modes with DNA/siRNA [223]. Molecular
modeling has had a significant impact on our understanding of critical
steps in gene delivery, including complexation of carriers with nucleic
acids, as well as nucleic acid condensation and aggregation by gene car-
riers [177]. Simulations can be used to investigate the factors determining
interactions between cationic polymers and nucleic acids, including com-
plexation and decomplexation. Such factors, similar to those in other
DDSs, include chemical surface composition as amine-to-phosphate
ratio [51,262], charge density, protonation state, polymer molecular
weight, polymer chemical structure and charge distribution [262–267],
the effect of endogenous molecules [136], and multivalent ions, e.g.
Fe(III) [137,268]. miRNA as endogenous molecule might cause
decomplexation. To test this hypothesis, Meneksedag-Erol et al. [136]
used both experiment and all atom MD to study the interactions between
miRNA and pre-formed PEI-siRNA complexes. PEI was found to bind
more strongly to miRNA than siRNA. However, miRNA could not disrupt
the integrity of PEI-siRNA but formed a layer on the complex, leading to
a siRNA-PEI-miRNA complex.
Interactions between polymeric DDS and nucleic acids for gene de-
livery purposes can be studied indirectly using polymers. Polycations
and polyanions can be considered as models for DDS and nucleic
acids, respectively [269–271]. Zhao et al. [270] utilized polycations and
polyanions and studied the effect of charge distribution along the
chain on complexation behavior and the structure of the resulting com-
plexes. They found that charge distribution has a significant influence
on aggregation and the complex structure.
4.3. Peptide- and nucleic acid-based delivery systems
There are several peptide-based DDSs, e.g. protein- [272] and cyclic
peptide-based [273,274], and cell penetrating peptides (CPPs) [275].
Fig. 8. DNA nanocage with temperature-controlled conformational transition capability. The cage is closed at 4 °C (a), and in a more open conformation at 37 °C (b). Heating the nanocage
to 37 °C in presence of horseradish peroxidase (HRP), followed by cooling to 4 °C, allows HRP enzymes to be encapsulated in nanocages. Reheating to 37 °C causes enzyme (orange) release
(not shown). Reprinted with permission from S. Juul, F. Iacovelli, M. Falconi, S.L. Kragh, B. Christensen, R. Frøhlich, et al., Encapsulation and Release of an Active Enzyme in the Cavity of a
Self-Assembled DNA Nanocage, (2013) 9724–9734. Copyright 2013 American Chemical Society.
There are also DDSs based on nucleic acids. RNA and DNA have been
used as either building blocks or surface ligands to design a variety of
three-dimensional nanostructures, including rings, tubes, cubes, cages,
and spheres [276–279]. As with other DDSs, the structural properties
of these systems, and their interactions with endogeneous biological
molecules, as a function of environmental conditions are of interest
[280–282]. Badu et al. [281] performed atomistic MD simulations on
RNA nanotubes and investigated their structural properties. Juul et al.
[282] studied DNA cages loaded with active enzymes both experimen-
tally and by all-atom MD simulation, and found a temperature-
dependent conformational change from an ‘open’ to a ‘closed’ state, in
principle enabling controllable encapsulation and release (Fig. 8).
Protein-based NPs are promising because of their unique character-
istics, including biocompatibility, biodegradability, low cytotoxicity, and
non-antigenicity [283,284]. Some proteins, e.g. albumin, can be used for
targeted delivery to tumor cells and inflamed tissues since they are pref-
erentially taken up by these types of cells [284]. Luo et al. [272] using
both theory and experimentations investigated the binding mode, affin-
ity and interactions between bovine serum albumin (BSA) and interfer-
on alpha-1b (IFN) as delivery system and protein drug, respectively.
Simulations predicted domain III of BSA as the most probable binding
sites, as well as hydrogen bonds and salt bridges as the main contribu-
tors in binding between BSA and IFN. Cyclic peptide based nanotubes
(CPNTs) can be used as a transporter for ions and small molecules
[273,274]. Vijayaraj et al. [273] investigated the transport mechanism
of 5-FU through a variety of CPNTs and determined the driving forces
and free energy barriers affecting this transport. They found that trans-
port was driven by direct or water-mediated hydrogen bonding and hy-
drophobic interactions between CPNT and 5-FU.
CPPs are of interest because of their intrinsic ability to enter cells,
their low cytotoxicity, and their versatility. They can facilitate the trans-
port of small molecules (e.g. drugs, imaging agents), macromolecules
(e.g. DNA, siRNA, proteins, peptides) and NPs/DDS. Therefore, CPPs
can be used as drug/gene delivery systems, as well as carriers for imag-
ing agents, proteins and peptides [275]. Recently, it has been of great in-
terest to combine the benefits of nanomaterials and CPPs. CPPs can be
functionalized with other delivery systems, like QDs, liposomes, and
dendrimers, potentially improving CPPs intracellular drug release abili-
ty and decreasing their toxicity. DDSs such as polymeric micelles,
dendrimers, liposomes, QDs, and inorganic nanocarriers (e.g. gold-,
silver-, and iron-based NPs) can be functionalized with CPPs to enable
their cellular uptake [275]. CPPs' unique physicochemical properties,
their uptake mechanisms, classifications, and applications in medicine
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
and biotechnology have recently been reviewed by Durzynska et al.
[275].
Key elements involved in CPPs' roles in drug delivery have been stud-
ied computationally [285–288]. Atomistic MD simulations revealed the
importance of arginine, lysine and tryptophan in the interaction between
two CPPs, penetratin [285] and transportan [286], and
dipalmitoylphosphatidylcholine (DPPC) membranes, as well as their
translocation mechanism. CPP conjugation can help translocate hydro-
phobic and hydrophilic drugs across lipid membranes [289,290]. Teixeira
et al. [290], via both MD simulations and experiments, found that lysine-
based surfactants enhanced the transdermal permeation of two topically
administered hydrophilic drugs, tetracaine and ropivacaine hydrochlo-
ride. As mentioned earlier, NPs can be functionalized with CPPs. The con-
centration and distribution of CPPs on the NP's surface influence the
conformation of the peptide layer, which in turn affects the CPP-
functionalized NPs' activity and the efficiency of cellular internalization.
So, designing a DDS of desired activity requires knowledge of the struc-
ture and dynamics of CPPs on NPs in solution prior to interacting with
membranes. Todorova et al. [291] using both experimental and atomistic
MD simulations investigated the effect of the grafting density and surface
distribution of HIV-derived trans-activator of transcription (TAT) peptide
on NPs cell internalization. They found a correlation between the surface
properties, e.g. positive charge distribution, of these TAT conjugated NPs
in solution, and their membrane permeation.
New DDS design strategies combine the benefits of several systems
such as block copolymers and CPPs [292], or mimic natural systems
such as intrinsically disordered proteins (IDPs) [293]. Sanchez-
Sanchez et al. [293], using both experiments and MD simulations,
designed and characterized single chain NPs called artificial IDP
mimetics. These IDP mimetics are capable of simultaneous release of
two dermal bioactive molecules, folic acid and hinokitiol, into aqueous
solution in a pH-dependent manner.
Computer simulations can provide insight into drug loading, distri-
bution/complex structure and release from peptide self-assemblies
[294,295], as well as the influence of pH and temperature [282,294,
296] on these processes. Guo et al., using both experiments and DPD
simulations investigated the effect of pH on microstructure of peptidic
micelles [296]. Micelles were self-assemblies of HR-20 (Histidine10-Ar-
ginine10) peptides conjugated with cholesterol, either loaded or not
with DOX. Micelles had more compact structure at pH N 6 (Fig. 9). For
pH b 6, channels in swollen micelles might cause drugs to diffuse out
of micelles. This was verified experimentally as the DOX release rate
was influenced by pH values, consistent with simulation results.
Finally, physicochemical properties of peptides and solvent condi-
tions can govern self-assembly and structural properties of peptide-
based carriers. Computer simulation can be used to design peptides
which can self-assemble, and to study the mechanism of self-assembly
into nanostructures. Computational approaches can also be used to
Fig. 9. Effect of pH on microstructure of self-assembled micelles. Starting from a homogeneous state (a), cholesterol conjugated peptides form compact core/shell micelles at pH N 6.0 (b).
Decreasing the pH loosens these micelles (c) and the swelling facilitates DOX release. Arginine, histidine, and cholesterol, are shown in green, brawn, and black, respectively. Water has not
been shown for clarity. Reprinted with permission from X.D. Guo, L.J. Zhang, Z.M. Wu, Y. Qian, Dissipative Particle Dynamics Studies on Microstructure of pH-Sensitive Micelles for
Sustained Drug Delivery, Macromolecules. 43 (2010) 7839–7844. Copyright 2010 American Chemical Society.
1699
study how factors such as solvent and temperature influence both
self-assembly and transitions between different morphologies
[297–301].
4.4. Carbon-based delivery systems
Several different types of carbon-based nanoparticles (CNPs) have
the potential to act as DDS [12,302]. Here we focus on DDS based on
CNTs and fullerenes but DDS using graphene, graphene oxide, and
nanodiamond [19,162,165,168] are also of interest.
Computational research has played a major role in exploring drug
loading of [164,303] and release [132,133,304,305] from CNPs, as well
as interactions of cargos with carbon nanocarriers [306] as a function of
internal and external stimulus, e.g. pH, temperature, torsion, and external
magnetic field. CNTs are capable of loading therapeutic agents on their
surface or inside their cylindrical hollow [19,307]. Saikia et al. [305] per-
formed MD simulation to study the C60 fullerene-mediated release of
multiple pyrazinamide molecules from the interior of a single walled
CNT as a function of temperature. Chaban et al. [304] investigated the ef-
fect of temperature and concentration on drug release from CNTs using
MD simulations. The effect of external magnetic fields has been studied
on hybrid systems composed of CNTs with magnetic NP caps [132].
Understanding the interactions of CNTs with biological macromole-
cules is also of great interest [308–313]. Wu et al. [313] studied DNA
ejection from CNTs as a function of temperature, torsion loading and
CNT size by MD simulation. Santosh et al. [309] studied the binding of
siRNA and DNA to the surface of single walled CNTs via MD simulations.
Chen et al. [311] studied the dynamic mechanism of encapsulation of
HIV replication inhibitor peptide into CNTs using MD simulation. It is
also important to understand the interactions of carbon-based DDS
with human serum albumin (HSA), the most abundant protein in
blood. Interaction of DDS with HSA is crucial in DDS absorption, distri-
bution and metabolism [314].
The membrane associations of carbon-based DDS have been studied
by computer simulation [315–317]. Several factors affect these associa-
tions: DDS structural properties [318–321]; clustering [320–322];
functionalization [319,323,324]; concentration [319] and lipid mem-
brane properties [321,325]. The effects of size and clustering of fullerene
NPs, and fullerene concentration on a DPPC monolayer as a model for
pulmonary surfactant was investigated by CG MD simulation by Chiu
et al. [321]. Free energy calculations suggest that all fullerene systems
in this study (C60, C180, C540, and cluster of five C60 fullerenes) spon-
taneously diffuse into the hydrophobic region of both monolayer and bi-
layer membranes. Large fullerene molecules were found to prefer
partitioning into bilayers rather than monolayers, however, which can
influence the monolayer-to-bilayer transition in the respiratory cycle.
This may suggest a possible mechanism of internalization of CNPs
through lung inhalation.
1700 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709

The effects of using polymers, peptides, and lipids as surface
functionalization agents in carbon-based DDS were studied by compu-
tational methods. Chehel Amirani and Tang [308] comprehensively
reviewed studies, mainly at the quantum mechanical level, of graphene
and CNT functionalization, and their binding energies with nucleobases.
Lai and Barnard [131] have reviewed recent studies on functionalized
nanodiamonds and their importance for biomedical applications.
Functionalization can prevent NPs from aggregating [323,326], increase
their stability [327], and influence their interactions with lipid mem-
branes [323,326,328]. Surface functionalization can also promote drug
delivery through improving translocation across lipid bilayers [328].
Sridhar et al. [328] used CG MD simulations to look at effects on fuller-
ene (C60) translocation through the membrane due to polar and non-
polar functionalization, temperature, and fullerene concentration.
Although none of their models showed complete translocation, they
found that Janus particles having half the surface modified by polar
groups were the most promising form of functionalized fullerenes in
terms of bilayer translocation.
A NP's behavior depends on the conformation of the functionalization
layer on its surface. The coating mechanism used to functionalize the NP,
e.g. covalent vs. non-covalent attachment, as well as the grafting density
are two factors which can affect this conformation [329,330]. For exam-
ple, Lee [330] found, using CG MD simulation, that the PEGylation method
can influence PEG distribution on CNTs. They also found that PEG size and
grafting density affected the PEG layer's conformation (Fig. 10). Designing
functionalized NPs with desired properties will require a detailed
understanding of these factors.
4.5. Lipid-based delivery system
Recently, lipid-based DDS such as liposomes, micelles and LNPs have
attracted much attention [7,8,331,332] due to their ability to encapsu-
late and transport drugs as well as biomolecules, the versatility of
their structures and compositions, and their inherent selectivity to
tumor cells and inflammation sites. There are currently more than ten
approved lipid-based drug formulations and many more in clinical trials
[7,8]. Specifically, sterically stabilized liposomes, i.e. PEGylated lipo-
somes, are widely used as DDS. PEGylation achieves long circulation
times for liposomes in vivo due to the formation of a protective PEG
layer over the liposomal surface. This layer sterically prevents the coat-
ing of liposomes by opsonins, thus reducing drug uptake by cells of the
immune system [333]. However, the mechanism through which
PEGylated lipids interact with different components in the liposomes,
its function in drug distribution, localization and retention as well as
the influence of external environmental factors such as salt concentra-
tion are not completely understood.
Since atomistic simulations of full liposomes are computationally ex-
pensive, a common approach is to infer results on liposomes from lipid bi-
layer simulations. Dzieciuch et al., [334] for instance, performed atomistic
MD simulation to study the effect of liposome PEGylation on their drug-
loading efficiency. They compared the effect of zwitterionic and
PEGylated membranes on the location and orientation of a model hydro-
phobic compound, 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (p-
THPP). p-THPP enters both types of lipid bilayers, which agreed with ex-
perimental results, but in PEGylated liposomes p-THPP also localizes to
the outer PEG corona where porphyrins are wrapped by PEG chains.
Thus, in PEGylated liposomes p-THPP showed a greater exposure to the
water than in zwitterionic liposomes. These results highlight that
PEGylation enhances the drug-loading efficiency of membranes and sup-
port fluorescence experiments carried out in this study [334]. Simulations
also predicted strong interaction between PEG lipids and porphyrin [334].
This interaction is particularly important in drug delivery studies as it may
be an extra barrier to drug release. This finding supports previous compu-
tational studies that showed that PEG interacts with hydrophobic mole-
cules [127,335,336]. Similarly, MD simulations combined with free
energy calculations were used to elucidate binding mechanisms and di-
vulge the exact location and organization of two small drugs, bexarotene
and human VIP, within PEGylated micellar nanocarriers [121].
PEGs strongly interact with salts. This property has been utilized in
lithium ion batteries with PEGs as polymer electrolytes [337,338].
PEGs are soluble in a wide variety of both polar and nonpolar solvents
[339]. Although both of these general properties have been shown pre-
viously by computational studies [337,338,340] and experiments [341,
342], for DDS applications it is important to understand how the PEG
layer on DDS, e.g. PEGylated liposomes, interacts with salts in physiolog-
ical conditions and how these interactions affect the structure of the
PEG layer [118,343,344]. Stepniewski et al. [344] modeled the effect of
NaCl on the surface structure of PEGylated liposomes. They varied the
salt concentration in Langmuir monolayer film experiments and
added ions at the physiological level in atomistic MD simulation studies.
The results showed that the PEG surface layer should not be treated as
generic hydrophilic molecules completely outside the bilayer, nor

Fig. 10. Effect of PEGylation method, and PEG chain size and grafting density on the conformation of PEG layer on carbon nanotube. Non-covalently modified single walled CNT (SWNT)
(Left) is more exposed to water than covalently modified SWNT (Right). PEG (red) size and grafting density also influence the conformation of PEG layer on SWNT (gray cylinder). RF is the
mushroom radius and L is the thickness of brush state. SWNT is shown as gray cylinders. Reprinted with permission from H. Lee, Molecular Dynamics Studies of PEGylated Single-Walled
Carbon Nanotubes: The Effect of PEG Size and Grafting Density, (2013). Copyright 2013 American Chemical Society.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
should it be considered as totally neutral as was previously accepted.
PEG molecules are able to penetrate into the liquid-crystalline lipid
bilayer, which may affect the permeability and structure of the mem-
brane. It was also noted that Na+ ions bind to PEG chains, changing
the surface charge of the liposome and enhance opsonization, whereas
Ca2+ did not interact with PEG [343]. These results are not surprising,
however. In fact, when PEGs are attached on DDS surface, e.g. liposomes,
they seem to show similar properties as previously reported for other
applications [337,338,340–342]. As another example, Pannuzo et al.
[345] performed CG simulations to study the effect of Ca2 + and PEG
molecules on membrane fusion. They showed that for a rapid fusion be-
tween negatively charged apposed membranes both Ca2 + and PEG
were required.
An important property governing drug release from liposomal DDS
is bilayer permeability [346,347]. Magarkar et al. [346] performed atom-
istic simulations using the OPLS-AA force field to investigate the high
permeability observed for “inverse-phosphatidylcholine” (CPe) lipo-
somes in experimental studies [348]. CPe is a synthetic analog of phos-
phatidylcholine (PC) with a reversed zwitterionic headgroup and has
been proposed for use in liposomal DDS formulations. The larger surface
area observed for the CPe bilayer compared with the PC bilayer may
cause CPe's higher permeability. Adding cholesterol to liposomal formu-
lations reduces leakage from liposomes due to its well-known role in
lipid packing and stability, but the mechanism for this is not understood.
Magarkar et al. [336], by performing MD simulation using OPLS force
field, proposed a model to explain the interaction between PEG mole-
cules and cholesterol. PEG molecules tend to interact with the ß side
of cholesterol, disrupting the membrane structure. Contrary to the ex-
pectation that cholesterol should make the membranes more stable
and compact, adding cholesterol in the presence of PEG caused mem-
brane destabilization. This result may explain possible effects of choles-
terol on the permeability and compressibility of PEGylated liposomes.
Self-assembly is another feature of special interest in nanotechnolo-
gy and nanomedicine as its understanding provides a framework for
developing new nanoscale materials with desirable properties [116].
CG and DPD simulations have been performed for the investigation of
lipid-based aggregates relevant for drug delivery [115,349–352]. For ex-
ample, Lee and Pastor [349] used the Martini CG force field to study mix-
tures of lipids and PEGylated lipids in water at different sizes and
concentrations of PEGylated lipids. They found that the mixtures self-
assembled to liposomes, bicelles and micelles. The analyses and simula-
tions indicated that the average aggregate sizes decreased when the
concentration of PEGylated lipid increased, in agreement with experi-
mental results. Janke et al. [352] used CG MD simulations to study the
phase behavior of oleic acid aggregation at various concentration and
protonation states. They observed a range of structures including
micelles, vesicles and oil phases depending on the protonation state of
the oleic acid head group.
Simulations can be used to calculate drug release rates from lipid-
based DDS [353,354]. For instance, the release of encapsulated materials
from systems including emulsions (100% liquid lipid phase) and nano-
structured lipid carriers, which have a combination of solid and liquid
lipid domains, was investigated by Dan using Monte Carlo simulations
[353]. The results obtained suggest that the size of lipid domains does
not significantly affect the rate of release, but the location and distribution
of the solid domains have a notable impact. When solid domains are con-
centrated near the solution interface, transport is inhibited due to a reduc-
tion in the accessible surface area. However, when the solid domain is
located in the center of the LNP the release rate is increased and may
even be higher than in the corresponding emulsion particle. In another
study by Dan [354], Monte Carlo simulations were performed to study
drug release in response to electric field-induced liposome pores.
There are also other interesting studies, three of which are mentioned
briefly here. Computer simulations were combined with experiments to
investigate the effect of penetration and membrane behavior of three ter-
penes, which are effective chemical permeation enhancers in
1701
nanostructured lipid carriers [355]. A detailed model of the distribution
of drug molecules inside a liposome was obtained using the Martini
force field [356]. Jämbeck et al. [356] performed large scale simulations
of hypericin, a photosensitizing drug, in a DPPC liposome (Fig. 11) and cal-
culated the distribution and orientation of the drugs in the lipid bilayer.
Hoof et al. [357] studied the encapsulation of proteins in spontaneously
forming vesicles using MD simulation with a CG force field. They showed
that the interactions of proteins with membranes govern the encapsula-
tion efficiency, but the size of the encapsulated proteins and the speed
of the vesicle formation did not seem to have a significant effect.
A promising gene therapy approach is based on siRNA. Sophisticated
delivery systems are required to protect and deliver siRNA effectively to
the target tissues [358,359]. CG molecular simulations together with a va-
riety of experimental techniques were able to give a more detailed view of
the structure of a LNP containing siRNA (Fig. 12) [79,360]. Simulations of
small systems containing 8 duplex 12 base pair DNA complexes, DLinKC2-
DMA (an ionizable cationic lipid), DSPC, cholesterol, a PEG-lipid, water
and ion molecules were performed. These molecules self-assembled and
organized in an ordered structure where, for instance, the PEG-lipids
were distributed in the outer layer of the LNP. This was the first study
to show that LNP siRNA systems likely have a nanostructured core, with
the encapsulated siRNA located in internalized inverted micelles com-
plexed to cationic lipids. The in silico finding agreed with 31P NMR,
FRET, cryo-TEM, and RNase digestion data and it was possible to under-
stand the mechanism whereby LNP siRNA systems are formed. This in-
sight is being applied to the design and construction of new LNP
systems. In addition, both CG and atomistic computer simulation have
been used to study the DNA adsorption onto anionic lipid membranes in-
duced by multivalent cations [361].
4.6. Gold-nanoparticles
AuNPs are of particular importance in drug delivery research due to
their unique properties including their stability, ease of synthesis, and
the ability to manufacture a range of sizes [15,362]. They can be loaded
with various therapeutics including small molecules, peptides, proteins,
and nucleic acids [19], either conjugated to AuNPs covalently or
noncovalently. There are several computational studies on the properties
of AuNPs and their interactions with other molecules [135,227,363–370].
The effect of AuNP conjugation on peptide conformational flexibility
and structure was studied by Lee and Ytreberg [366]. They examined
the structure and dynamics of six peptides that were either free or
conjugated to AuNPs in water. Conjugation affected both structure and
dynamics in an amino acid sequence dependent way. Peptides with little
or no secondary structure in solution were adsorbed on the AuNP surface.
This causes peptides to lose their specific interactions with cell compo-
nents. For drug delivery purposes, this suggests that peptides with signif-
icant secondary structures in solution are suitable candidates for peptide-
NP conjugation. Interactions between ubiquitin and AuNPs have also been
studied by Brancolini et al. [135] using computer simulation.
Van Lehn and co-workers performed a series of computational stud-
ies on AuNPs coated by lipids. Among other properties, they investigat-
ed the structure of the monolayer coating the AuNP under different
conditions [369], lipid composition and AuNP size [368], the interac-
tions of a monolayer-coated AuNP with model membranes relevant
for uptake [367], suggesting similarities in uptake process with
bilayer-bilayer fusion [371], and interactions between AuNPs [370].
5. Conclusions and future perspectives
We have reviewed common biophysical and computational ap-
proaches to studying DDSs, focusing in particular on computational
studies of several major classes of NPs used in drug delivery research.
The strength of computer simulations in general is their ability to give
very detailed insight into the structure of NPs and their interactions
with drugs and model membranes under a range of conditions. Clearly,
1702 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709

Fig. 11. Distribution and orientation of hypericin within liposome. a) Snapshots from MD simulations taken after 10 μs. Phosphorus groups (orange), choline groups (blue) and
hydrophobic tails (green) of the lipids are represented, with different numbers of drug molecules (yellow). b) Liposomes with some lipids removed to show the binding of hypericin
to DPPC; the hydrophilic parts of hypericin are shown in red and the hydrophobic parts in yellow. Reprinted with permission from J.P.M. Jämbeck, E.S.E. Eriksson, A. Laaksonen, A.P.
Lyubartsev, L.A. Eriksson, Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation and Simulations with a Coarse-Grained Model,
(2013). Copyright 2013 American Chemical Society.

the efficiency of DDSs depends on a large number of other parameters, can characterize important aspects of DDSs, a major challenge for the
including stability in the bloodstream, targeting to the desired tissues, near future is to go beyond individual drug carriers and to investigate
uptake by endocytosis or other mechanisms, and final release of the at a mechanistic level the larger-scale processes that determine the suc-
drugs. Although experimental biophysical and computational studies cess of DDSs.

Fig. 12. Lipid nanoparticle. External and a cross-sectional view of the LNP (top). Components are represented by their molecular densities: protective PEG-lipid (magenta), therapeutic
siRNA (red), cholesterol (green), DSPC (yellow), ionizable cationic lipid (DLin-KC2-DMA) (blue) and water (cyan). Adapted from D. Rozmanov, S. Baoukina, D.P. Tieleman, Density
Based Visualization for Molecular Simulation., Faraday Discuss. 169 (2014) 225–43. doi:10.1039/c3fd00124e. Under a Creative Commons Attribution 3.0 Unported License.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
At the computational level, currently we are limited by some of the
standard limitations of biomolecular simulation. In general, these in-
volve limited sampling time, limited length scale, and expensive or dif-
ficult access to important thermodynamic variables. Simulations can
access time scales of the order of microseconds or for coarser models
tens or hundreds of microseconds, at length scales of ca. 10 × 10 nm
for atomistic and up to 150 × 150 nm for CG simulations. Thus it is
now possible to simulate entire nanocarriers, which will open up new
areas of study for simulations. However, the process of NP formation
by e.g. microfluidics remains outside reach of direct detailed simula-
tions. Questions regarding drug loading, the stability of complexes,
and the interactions of NPs with membranes essentially involve free en-
ergies of binding, partitioning, and membrane pore formation. These
can all be studied by free energy methods, but the current state of the
literature remains somewhat qualitative. This is an obvious area for fu-
ture work, which is already feasible with current methods and compu-
tational resources. Some of the most interesting simulations currently
available use CG MD or DPD. This is an exciting development, but also
comes with its own limitations; in particular, CG models need to be
carefully tested for their ability to reproduce the effect of important fac-
tors in DDSs such as salt concentration, the distribution of chemical
functional groups over the surface of a DDS, and the effect of pH.
DDSs are an interesting example of multi-scale computational prob-
lems, with a growing amount of data from biophysical characterization.
They have an obvious biomedical and biotechnological importance, and
bridge chemistry, nanoscience, materials, basic biology and medical ap-
plications in a unique way. Although there already is a large body of lit-
erature as reviewed in this paper, in our assessment the impact of
computational work in this important area is likely to grow significantly
in the near future as model systems become more realistic and more
tightly coupled to experiment.
Conflict of interest
The authors declare no conflicts of interest.
Acknowledgments
This work was supported by a Natural Sciences and Engineering Coun-
cil (Canada) Strategic Project Grant (DPT, JT) (STPGP/463247-2014). DPT
is an Alberta Innovates Health Solutions Scientist and Alberta Innovates
Technology Futures Strategic Chair in (Bio)Molecular Simulation.
References
[1] E. Blanco, H. Shen, M. Ferrari, Principles of nanoparticle design for overcoming bi-
ological barriers to drug delivery, Nat. Biotechnol. 33 (2015) 941–951.
[2] T.M. Allen, P.R. Cullis, Drug delivery systems: entering the mainstream, Science 303
(2004) 1818–1822.
[3] S. Parveen, R. Misra, S.K. Sahoo, Nanoparticles: a boon to drug delivery, therapeu-
tics, diagnostics and imaging, Nanomed. Nanotechnol. Biol. Med. 8 (2012)
147–166.
[4] D.S. Kohane, Microparticles and nanoparticles for drug delivery, Biotechnol.
Bioeng. 96 (2007) 203–209.
[5] V.J. Venditto, F.C. Szoka Jr., Cancer nanomedicines: so many papers and so few
drugs! Adv. Drug Deliv. Rev. 65 (2013) 80–88.
[6] Y. Zhang, H.F. Chan, K.W. Leong, Advanced materials and processing for drug deliv-
ery: the past and the future, Adv. Drug Deliv. Rev. 65 (2013) 104–120.
[7] B.S. Pattni, V.V. Chupin, V.P. Torchilin, New developments in liposomal drug deliv-
ery, Chem. Rev. 115 (2015) 10938–10966.
[8] T.M. Allen, P.R. Cullis, Liposomal drug delivery systems: from concept to clinical ap-
plications, Adv. Drug Deliv. Rev. 65 (2013) 36–48.
[9] E.R. Gillies, J.M.J. Frechet, Dendrimers and dendritic polymers in drug delivery,
Drug Discov. Today 10 (2005) 35–43.
[10] C.C. Lee, J.A. MacKay, J.M.J. Fréchet, F.C. Szoka, Designing dendrimers for biological
applications, Nat. Biotechnol. 23 (2005) 1517–1526.
[11] S. Svenson, D.A. Tomalia, Dendrimers in biomedical applications—reflections on
the field, Adv. Drug Deliv. Rev. 57 (2005) 2106–2129.
[12] A. Bianco, K. Kostarelos, M. Prato, Applications of carbon nanotubes in drug deliv-
ery, Curr. Opin. Chem. Biol. 9 (2005) 674–679.
[13] L. Lacerda, A. Bianco, M. Prato, K. Kostarelos, Carbon nanotubes as nanomedicines:
from toxicology to pharmacology, Adv. Drug Deliv. Rev. 58 (2006) 1460–1470.
1703
[14] A. Bianco, K. Kostarelos, C.D. Partidos, M. Prato, Biomedical applications of
functionalised carbon nanotubes, Chem. Commun. 571–577 (2005).
[15] P. Ghosh, G. Han, M. De, C.K. Kim, V.M. Rotello, Gold nanoparticles in delivery ap-
plications, Adv. Drug Deliv. Rev. 60 (2008) 1307–1315.
[16] T.K. Jain, M.A. Morales, S.K. Sahoo, D.L. Leslie-Pelecky, V. Labhasetwar, Iron oxide
nanoparticles for sustained delivery of anticancer agents, Mol. Pharm. 2 (2005)
194–205.
[17] G. Bao, S. Mitragotri, S. Tong, Multifunctional nanoparticles for drug delivery and
molecular imaging, Annu. Rev. Biomed. Eng. 15 (2013) 253–282.
[18] C. Sun, J.S.H. Lee, M. Zhang, Magnetic nanoparticles in MR imaging and drug deliv-
ery, Adv. Drug Deliv. Rev. 60 (2008) 1252–1265.
[19] X. Sun, Z. Feng, T. Hou, Y. Li, Computational simulation of inorganic nanoparticle
drug delivery systems at the molecular level, Computational Pharmaceutics: Appli-
cation of Molecular Modelling in Drug Delivery, John Wiley & Sons 2015,
pp. 149–168.
[20] C.S. Kim, G.Y. Tonga, D. Solfiell, V.M. Rotello, Inorganic nanosystems for therapeutic
delivery: status and prospects, Adv. Drug Deliv. Rev. 65 (2013) 93–99.
[21] R. Duncan, The dawning era of polymer therapeutics, Nat. Rev. Drug Discov. 2
(2003) 347–360.
[22] K.S. Soppimath, T.M. Aminabhavi, A.R. Kulkarni, W.E. Rudzinski, Biodegradable
polymeric nanoparticles as drug delivery devices, J. Control. Release 70 (2001)
1–20.
[23] L. Huynh, C. Neale, R. Pomès, C. Allen, Computational approaches to the rational de-
sign of nanoemulsions, polymeric micelles, and dendrimers for drug delivery,
Nanomed. Nanotechnol. Biol. Med. 8 (2012) 20–36.
[24] W.F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura,
et al., Biomolecular modeling: goals, problems, perspectives, Angew. Chem. Int. Ed.
45 (2006) 4064–4092.
[25] B. Kann, H.L. Offerhaus, M. Windbergs, C. Otto, Raman microscopy for cellular in-
vestigations — from single cell imaging to drug carrier uptake visualization, Adv.
Drug Deliv. Rev. 89 (2015) 71–90.
[26] A. Sharma, U.S. Sharma, Liposomes in drug delivery: progress and limitations, Int. J.
Pharm. 154 (1997) 123–140.
[27] R.W. Niven, M. Speer, H. Schreier, Nebulization of liposomes. II. The effects of
size and modeling of solute release profiles, Pharm. Res. 8 (1991) 217–221.
[28] S.K. Hobbs, W.L. Monsky, F. Yuan, W.G. Roberts, L. Griffith, V.P. Torchilin, et al., Reg-
ulation of transport pathways in tumor vessels: role of tumor type and microenvi-
ronment, Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 4607–4612.
[29] C.R. Dass, Drug delivery in cancer using liposomes, Drug Delivery Systems,
Humana Press 2008, pp. 177–182.
[30] P.Y. Lu, M.C. Woodle, Delivering small interfering RNA for novel therapeutics, Drug
Delivery Systems, Humana Press 2008, pp. 93–107.
[31] R. Singh, J.W. Lillard, Nanoparticle-based targeted drug delivery, Exp. Mol. Pathol.
86 (2009) 215–223.
[32] S.H. Jang, M.G. Wientjes, D. Lu, J.L.S. Au, Drug delivery and transport to solid tu-
mors, Pharm. Res. 20 (2003) 1337–1350.
[33] A.R. Kirtane, R.A. Siegel, J. Panyam, A pharmacokinetic model for quantifying the ef-
fect of vascular permeability on the choice of drug carrier: a framework for person-
alized nanomedicine, J. Pharm. Sci. 104 (2015) 1174–1186.
[34] S.K. Brar, M. Verma, Measurement of nanoparticles by light-scattering techniques,
Trends Anal. Chem. 30 (2011) 4–17.
[35] W. Mehnert, K. Mäder, Solid lipid nanoparticles: production, characterization and
applications, Adv. Drug Deliv. Rev. 64 (2012) 83–101.
[36] S.A. Kübart, C.M. Keck, Laser diffractometry of nanoparticles: frequent pitfalls &
overlooked opportunities, J. Pharmacol. Technol. Drug Res. 2 (2013) 17.
[37] A. Moquin, F.M. Winnik, The use of field-flow fractionation for the analysis of drug
and gene delivery systems, Field-Flow Fractionation in Biopolymer Analysis,
Springer Vienna 2012, pp. 187–206.
[38] A. Zattoni, B. Roda, F. Borghi, V. Marassi, P. Reschiglian, Flow field-flow fraction-
ation for the analysis of nanoparticles used in drug delivery, J. Pharm. Biomed.
Anal. 87 (2014) 53–61.
[39] F.M. Veronese, G. Pasut, PEGylation, successful approach to drug delivery, Drug
Discov. Today 10 (2005) 1451–1458.
[40] N.S. Berchane, K.H. Carson, A.C. Rice-Ficht, M.J. Andrews, Effect of mean diameter
and polydispersity of PLG microspheres on drug release: experiment and theory,
Int. J. Pharm. 337 (2007) 118–126.
[41] C.M. Beddoes, C.P. Case, W.H. Briscoe, Understanding nanoparticle cellular
entry: a physicochemical perspective, Adv. Colloid Interf. Sci. 218C (2015)
48–68.
[42] M. Müllner, S.J. Dodds, T.-H. Nguyen, D. Senyschyn, C.J.H. Porter, B.J. Boyd, et al.,
Size and rigidity of cylindrical polymer brushes dictate long circulating properties
in vivo, ACS Nano 9 (2015) 1294–1304.
[43] S.E.A. Gratton, P.A. Ropp, P.D. Pohlhaus, J.C. Luft, V.J. Madden, M.E. Napier, et al., The
effect of particle design on cellular internalization pathways, Proc. Natl. Acad. Sci.
U. S. A. 105 (2008) 11613–11618.
[44] J.A. Champion, S. Mitragotri, Role of target geometry in phagocytosis, Proc. Natl.
Acad. Sci. U. S. A. 103 (2006) 4930–4934.
[45] S. Fusco, H.W. Huang, K.E. Peyer, C. Peters, M. Häberli, A. Ulbers, et al., Shape-
switching microrobots for medical applications: the influence of shape in drug
delivery and locomotion, ACS Appl. Mater. Interfaces 7 (2015) 6803–6811.
[46] G. Ruan, S.S. Feng, Preparation and characterization of poly(lactic acid)–poly(ethyl-
ene glycol)–poly(lactic acid) (PLA–PEG–PLA) microspheres for controlled release
of paclitaxel, Biomaterials 24 (2003) 5037–5044.
[47] E. Fattal, H. Hillaireau, S. Mura, J. Nicolas, N. Tsapis, Targeted delivery using biode-
gradable polymeric nanoparticles, Fundamentals and Applications of Controlled
Release Drug Delivery, Springer US 2012, pp. 255–288.
1704 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
[48] J.L.S. Milne, M.J. Borgnia, A. Bartesaghi, E.E.H. Tran, L.A. Earl, D.M. Schauder, et al.,
Cryo-electron microscopy —a primer for the non-microscopist, FEBS J. 280
(2013) 28–45.
[49] A. Bartesaghi, A. Merk, S. Banerjee, D. Matthies, X. Wu, J.L.S. Milne, et al., 2.2 Å res-
olution cryo-EM structure of β-galactosidase in complex with a cell-permeant in-
hibitor, Science 348 (2015) 1147–1151.
[50] T. Turovsky, R. Khalfin, S. Kababya, A. Schmidt, Y. Barenholz, D. Danino, Celecoxib
encapsulation in β-casein micelles: structure, interactions, and conformation,
Langmuir 31 (2015) 7183–7192.
[51] M. Zheng, G.M. Pavan, M. Neeb, A.K. Schaper, A. Danani, G. Klebe, et al., Targeting
the blind spot of polycationic nanocarrier-based siRNA delivery, ACS Nano 6
(2012) 9447–9454.
[52] A.M. Alkilany, C.J. Murphy, Toxicity and cellular uptake of gold nanoparticles: what
we have learned so far? J. Nanoparticle Res. 12 (2010) 2313–2333.
[53] K. Murugan, Y.E. Choonara, P. Kumar, D. Bijukumar, L.C. du Toit, V. Pillay, Parame-
ters and characteristics governing cellular internalization and trans-barrier traf-
ficking of nanostructures, Int. J. Nanomedicine 10 (2015) 2191–2206.
[54] E. Fröhlich, The role of surface charge in cellular uptake and cytotoxicity of medical
nanoparticles, Int. J. Nanomedicine 7 (2012) 5577–5591.
[55] M. Di Marco, C. Sadun, M. Port, I. Guilbert, P. Couvreur, C. Dubernet, Physicochem-
ical characterization of ultrasmall superparamagnetic iron oxide particles (USPIO)
for biomedical application as MRI contrast agents, Int. J. Nanomedicine 2 (2007)
609–622.
[56] K. Xiao, Y. Li, J. Luo, J.S. Lee, W. Xiao, A.M. Gonik, et al., The effect of surface charge
on in vivo biodistribution of PEG-oligocholic acid based micellar nanoparticles, Bio-
materials 32 (2011) 3435–3446.
[57] L.P. Mendes, J.M.F. Delgado, A.D.A. Costa, M.S. Vieira, P.L. Benfica, E.M. Lima, et al.,
Biodegradable nanoparticles designed for drug delivery: the number of nanoparti-
cles impacts on cytotoxicity, Toxicol. in Vitro 29 (2015) 1268–1274.
[58] M. Law, M. Jafari, P. Chen, Physicochemical characterization of SiRNA-peptide com-
plexes, Biotechnol. Prog. 24 (2008) 957–963.
[59] A.M. Chen, M. Zhang, D. Wei, D. Stueber, O. Taratula, T. Minko, et al., Co-delivery of
doxorubicin and bcl-2 siRNA by mesoporous silica nanoparticles enhances the ef-
ficacy of chemotherapy in multidrug-resistant cancer cells, Small 5 (2009)
2673–2677.
[60] X.Y. Wang, L. Zhang, X.H. Wei, Q. Wang, Molecular dynamics of paclitaxel encapsu-
lated by salicylic acid-grafted chitosan oligosaccharide aggregates, Biomaterials 34
(2013) 1843–1851.
[61] B. Sun, D.T. Chiu, Determination of the encapsulation efficiency of individual vesi-
cles using single-vesicle photolysis and confocal single-molecule detection, Anal.
Chem. 77 (2005) 2770–2776.
[62] N. Martinho, H. Florindo, L. Silva, S. Brocchini, M. Zloh, T. Barata, Molecular model-
ing to study dendrimers for biomedical applications, Molecules 19 (2014)
20424–20467.
[63] H. Bunjes, T. Unruh, Characterization of lipid nanoparticles by differential scanning
calorimetry, X-ray and neutron scattering, Adv. Drug Deliv. Rev. 59 (2007)
379–402.
[64] W. Mehnert, Solid lipid nanoparticles: production, characterization and applica-
tions, Adv. Drug Deliv. Rev. 47 (2001) 165–196.
[65] M. Deborah, A. Jawahar, T. Mathavan, M.K. Dhas, A.M.F. Benial, Spectroscopic stud-
ies on sidewall carboxylic acid functionalization of multi-walled carbon nanotubes
with valine, Spectrochim. Acta Part A. 139 (2015) 138–144.
[66] P.S. Williams, F. Carpino, M. Zborowski, Magnetic nanoparticle drug carriers and
their study by quadrupole magnetic field-flow fractionation, Molecules 6 (2009)
1290–1306.
[67] M.L. Briuglia, C. Rotella, A. McFarlane, D.A. Lamprou, Influence of cholesterol on
liposome stability and on in vitro drug release, Drug Deliv. Transl. Res. 5 (2015)
231–242.
[68] J. Wang, Y. Wang, W. Liang, Delivery of drugs to cell membranes by encapsulation
in PEG–PE micelles, J. Control. Release 160 (2012) 637–651.
[69] N.W.S. Kam, Z. Liu, H. Dai, Functionalization of carbon nanotubes via cleavable
disulfide bonds for efficient intracellular delivery of siRNA and potent gene silenc-
ing, J. Am. Chem. Soc. 127 (2005) 12492–12493.
[70] S. Achar, R.J. Puddephatt, Organoplatinum dendrimers formed by oxidative addi-
tion, Angew. Chem. Int. Ed. 33 (1994) 847–849.
[71] M.L. Viger, W. Sheng, C.L. McFearin, M.Y. Berezin, A. Almutairi, Application of time-
resolved fluorescence for direct and continuous probing of release from polymeric
delivery vehicles, J. Control. Release 171 (2013) 308–314.
[72] A.A. Metwally, R.M. Hathout, Computer-assisted drug formulation design: novel
approach in drug delivery, Mol. Pharm. 12 (2015) 2800–2810.
[73] M.B. Sankaram, T.E. Thompson, Interaction of cholesterol with various
glycerophospholipids and sphingomyelin, Biochemistry 29 (1990)
10670–10675.
[74] A. Caminade, R. Laurent, J. Majoral, Characterization of dendrimers, Adv. Drug
Deliv. Rev. 57 (2005) 2130–2146.
[75] Y.W. Hsueh, M. Zuckermann, J. Thewalt, Phase diagram determination for phos-
pholipid/sterol membranes using deuterium NMR, Concepts Magn. Reson. Part A.
26A (2005) 35–46.
[76] T. Io, T. Fukami, K. Yamamoto, T. Suzuki, J. Xu, K. Tomono, et al., Homogeneous
nanoparticles to enhance the efficiency of a hydrophobic drug, antihyperlipidemic
probucol, characterized by solid-state NMR, Mol. Pharm. 7 (2009) 299–305.
[77] T. Sun, Q. Guo, C. Zhang, J. Hao, P. Xing, J. Su, et al., Self-assembled vesicles pre-
pared from amphiphilic cyclodextrins as drug carriers, Langmuir 28 (2012)
8625–8636.
[78] D. Astruc, E. Boisselier, C. Ornelas, Dendrimers designed for functions: from phys-
ical, photophysical, and supramolecular properties to applications in sensing,
catalysis, molecular electronics, photonics, and nanomedicine, Chem. Rev. 110
(2010) 1857–1959.
[79] A.K.K. Leung, I.M. Hafez, S. Baoukina, N.M. Belliveau, I.V. Zhigaltsev, E.
Afshinmanesh, et al., Lipid nanoparticles containing siRNA synthesized by
microfluidic mixing exhibit an electron-dense nanostructured core, J. Phys.
Chem. C 116 (2012) 18440–18450.
[80] E.V. Mathias, X. Liu, O. Franco, I. Khan, Y. Ba, J.A. Kornfield, Model of drug-loaded
fluorocarbon-based micelles studied by electron-spin induced 19F relaxation
NMR and molecular dynamics simulation, Langmuir 24 (2008) 692–700.
[81] G. Martini, L. Ciani, Electron spin resonance spectroscopy in drug delivery, Phys.
Chem. Chem. Phys. 11 (2009) 211–254.
[82] H. Wennerström, D.F. Evans, The Colloidal Domain: Where Physics, Chemistry, Bi-
ology, and Technology Meet, New York, Wiley-VCH, 1999.
[83] C. Nicolini, J. Kraineva, M. Khurana, N. Periasamy, S.S. Funari, R. Winter, Tem-
perature and pressure effects on structural and conformational properties of
POPC/SM/cholesterol model raft mixtures—an FT-IR, SAXS, DSC, PPC and
Laurdan fluorescence spectroscopy study, Biochim. Biophys. Acta 1758
(2006) 248–258.
[84] T.T. Mills, S. Tristram-Nagle, F.A. Heberle, N.F. Morales, J. Zhao, J. Wu, et al., Liquid–
liquid domains in bilayers detected by wide angle X-ray scattering, Biophys. J. 95
(2008) 682–690.
[85] V. Meli, C. Caltagirone, A.M. Falchi, S.T. Hyde, V. Lippolis, M. Monduzzi, et al.,
Docetaxel-loaded fluorescent liquid-crystalline nanoparticles for cancer
theranostics, Langmuir 31 (2015) 9566–9575.
[86] A. Angelova, B. Angelov, R. Mutafchieva, S. Lesieur, P. Couvreur, Self-assembled
multicompartment liquid crystalline lipid carriers for protein, peptide and nucleic
acid drug delivery, Acc. Chem. Res. 44 (2010) 147–156.
[87] R.H. Utama, M. Dulle, S. Förster, M.H. Stenzel, P.B. Zetterlund, SAXS analysis of shell
formation during nanocapsule synthesis via inverse miniemulsion periphery RAFT
polymerization, Macromol. Rapid Commun. 1267-1271 (2015).
[88] R.H. Müller, S.A. Runge, V. Ravelli, A.F. Thünemann, W. Mehnert, E.B. Souto,
Cyclosporine-loaded solid lipid nanoparticles (SLN®): drug–lipid physicochemical
interactions and characterization of drug incorporation, Eur. J. Pharm. Biopharm.
68 (2008) 535–544.
[89] A.F. Martins, A.G.B. Pereira, A.R. Fajardo, A.F. Rubira, E.C. Muniz, Characterization of
polyelectrolytes complexes based on N,N,N-trimethyl chitosan/heparin prepared
at different pH conditions, Carbohydr. Polym. 86 (2011) 1266–1272.
[90] J. Pan, F.A. Heberle, R.S. Petruzielo, J. Katsaras, Using small-angle neutron
scattering to detect nanoscopic lipid domains, Chem. Phys. Lipids 170-171
(2013) 19–32.
[91] J.R. Lakowicz, Principles of Fluorescence SpectroscopySpringer Sceince & Business
Media 2006.
[92] K. Kataoka, A. Harada, Y. Nagasaki, Block copolymer micelles for drug delivery:
design, characterization and biological significance, Adv. Drug Deliv. Rev. 64
(2012) 37–48.
[93] S.R. Pygall, J. Whetstone, P. Timmins, C.D. Melia, Pharmaceutical applications of
confocal laser scanning microscopy: the physical characterisation of pharmaceuti-
cal systems, Adv. Drug Deliv. Rev. 59 (2007) 1434–1452.
[94] C. Dubernet, Thermoanalysis of microspheres, Thermochim. Acta 248 (1995)
259–269.
[95] D. Giron, Applications of thermal analysis and coupled techniques in pharmaceuti-
cal industry, J. Therm. Anal. Calorim. 68 (2002) 335–357.
[96] H. Reinl, T. Brumm, T.M. Bayerl, The physical properties of the liquid-ordered phase
with temperature in binary mixtures of DPPC with cholesterol: A 2H-NMR, FT-IR,
DSC, and neutron scattering study, Biophys. J. 61 (1992) 1025–1035.
[97] N.R. Labiris, M.B. Dolovich, Pulmonary drug delivery. Part I: Physiological factors
affecting therapeutic effectiveness of aerosolized medications, Br. J. Clin.
Pharmacol. 56 (2003) 588–599.
[98] K. Bouchemal, New challenges for pharmaceutical formulations and drug delivery
systems characterization using isothermal titration calorimetry, Drug Discov.
Today 13 (2008) 960–972.
[99] R. Gref, A. Domb, P. Quellec, T. Blunk, R.H. Müller, J.M. Verbavatz, et al., The con-
trolled intravenous delivery of drugs using PEG-coated sterically stabilized nano-
spheres, Adv. Drug Deliv. Rev. 64 (2012) 316–326.
[100] K. Avgoustakis, A. Beletsi, Z. Panagi, P. Klepetsanis, A.G. Karydas, D.S. Ithakissios,
PLGA-mPEG nanoparticles of cisplatin: in vitro nanoparticle degradation, in vitro
drug release and in vivo drug residence in blood properties, J. Control. Release 79
(2002) 123–135.
[101] B.L. Mui, Y.K. Tam, M. Jayaraman, S.M. Ansell, X. Du, Y.Y.C. Tam, et al., Influence of
polyethylene glycol lipid desorption rates on pharmacokinetics and pharmacody-
namics of siRNA lipid nanoparticles, Mol. Ther. Acids 2 (2013) e139.
[102] H. Tan, Z. Wang, J. Li, Z. Pan, M. Ding, Q. Fu, An approach for the sphere-to-rod tran-
sition of multiblock copolymer micelles, ACS Macro Lett. 2 (2013) 146–151.
[103] A. Almutairi, W.J. Akers, M.Y. Berezin, S. Achilefu, J.M.J. Frechet, Monitoring the bio-
degradation of dendritic near-infrared nanoprobes by in vivo fluorescence imag-
ing, Mol. Pharm. 5 (2008) 1103–1110.
[104] X. Dai, Z. Yue, M.E. Eccleston, J. Swartling, N.K.H. Slater, C.F. Kaminski, Fluorescence
intensity and lifetime imaging of free and micellar-encapsulated doxorubicin in
living cells, Nanomed. Nanotechnol. Biol. Med. 4 (2008) 49–56.
[105] D. Frenkel, B. Smit, Understanding Molecular Simulation: From Algorithms to Ap-
plications, Academic Press, 2001.
[106] B. Hess, C. Kutzner, D. Van Der Spoel, E. Lindahl, GROMACS 4: algorithms for highly
efficient, load-balanced and scalable molecular simulation, J. Chem. Theory
Comput. 4 (2008) 435–447.
[107] J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, et al., Scalable
molecular dynamics with NAMD, J. Comput. Chem. 26 (2005) 1781–1802.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
[108] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J.
Comput. Phys. 117 (1995) 1–19.
[109] B.R. Brooks, C.L. Brooks, A.D. MacKerell, L. Nilsson, R.J. Petrella, B. Roux, et al.,
CHARMM: the biomolecular simulation program, J. Comput. Chem. 30 (2009)
1545–1614.
[110] D.A. Case, T.E. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, et al., The Amber
biomolecular simulation programs, J. Comput. Chem. 26 (2005) 1668–1688.
[111] S.J. Marrink, D.P. Tieleman, Perspective on the Martini model, Chem. Soc. Rev. 42
(2013) 6801–6822.
[112] M. Karplus, J.A. McCammon, Molecular dynamics simulations of biomolecules, Nat.
Struct. Mol. Biol. 9 (2002) 646–652.
[113] W.F. van Gunsteren, J. Dolenc, A.E. Mark, Molecular simulation as an aid to exper-
imentalists, Curr. Opin. Struct. Biol. 18 (2008) 149–153.
[114] M. Velinova, D. Sengupta, A.V. Tadjer, S.J. Marrink, Sphere-to-rod transitions of
nonionic surfactant micelles in aqueous solution modeled by molecular dynamics
simulations, Langmuir 27 (2011) 14071–14077.
[115] W. Shinoda, R. DeVane, M.L. Klein, Computer simulation studies of self-assembling
macromolecules, Curr. Opin. Struct. Biol. 22 (2012) 175–186.
[116] P.V. Messina, J. Miguel Besada-Porto, J.M. Ruso, Self-assembly drugs: from micelles
to nanomedicine, Curr. Top. Med. Chem 14 (2014) 555–571.
[117] B. Aoun, V.K. Sharma, E. Pellegrini, S. Mitra, M. Johnson, R. Mukhopadhyay, Struc-
ture and dynamics of ionic micelles: MD simulation and neutron scattering
study, J. Phys. Chem. B. 119 (2015) 5079–5086.
[118] L. Vukovic, F.A. Khatib, S.P. Drake, A. Madriaga, K.S. Brandenburg, P. Král, et al.,
Structure and dynamics of highly PEG-ylated sterically stabilized micelles in aque-
ous media, J. Am. Chem. Soc. 133 (2011) 13481–13488.
[119] J. Gupta, C. Nunes, S. Vyas, S. Jonnalagadda, Prediction of solubility parameters and
miscibility of pharmaceutical compounds by molecular dynamics simulations, J.
Phys. Chem. B. 115 (2011) 2014–2023.
[120] S.M. Loverde, M.L. Klein, D.E. Discher, Nanoparticle shape improves delivery: ratio-
nal coarse grain molecular dynamics (rCG-MD) of taxol in worm-like PEG-PCL mi-
celles, Adv. Mater. 24 (2012) 3823–3830.
[121] L. Vuković, A. Madriaga, A. Kuzmis, A. Banerjee, A. Tang, K. Tao, et al., Solubilization
of therapeutic agents in micellar nanomedicines, Langmuir 29 (2013)
15747–15754.
[122] L. Huynh, C. Neale, R. Pomès, C. Allen, Systematic design of unimolecular star copol-
ymer micelles using molecular dynamics simulations, Soft Matter 6 (2010)
5491–5501.
[123] R. Vácha, F.J. Martinez-Veracoechea, D. Frenkel, Intracellular release of
endocytosed nanoparticles upon a change of ligand–receptor interaction, ACS
Nano 6 (2012) 10598–10605.
[124] W. Tian, Y.Q. Ma, Insights into the endosomal escape mechanism via investigation
of dendrimer–membrane interactions, Soft Matter 8 (2012) 6378–6384.
[125] N. Arai, K. Yasuoka, X.C. Zeng, A vesicle cell under collision with a Janus or homo-
geneous nanoparticle: translocation dynamics and late-stage morphology, Nano-
scale 5 (2013) 9089–9100.
[126] A.J. Makarucha, N. Todorova, I. Yarovsky, Nanomaterials in biological environment:
a review of computer modelling studies, Eur. Biophys. J. 40 (2011) 103–115.
[127] Y.C. Li, S. Rissanen, M. Stepniewski, O. Cramariuc, T. Róg, S. Mirza, et al., Study of
interaction between PEG carrier and three relevant drug molecules: piroxicam,
paclitaxel, and hematoporphyrin, J. Phys. Chem. B. 116 (2012) 7334–7341.
[128] F.J. Martinez-Veracoechea, D. Frenkel, Designing super selectivity in multivalent
nano-particle binding, Proc. Natl. Acad. Sci. U. S. A. 108 (2011) 10963–10968.
[129] S. Wang, E.E. Dormidontova, Nanoparticle design optimization for enhanced
targeting: Monte Carlo simulations, Biomacromolecules 11 (2010) 1785–1795.
[130] L. Liu, S. Parameswaran, A. Sharma, S.M. Grayson, H.S. Ashbaugh, S.W. Rick, Molec-
ular dynamics simulations of linear and cyclic amphiphilic polymers in aqueous
and organic environments, J. Phys. Chem. B. 118 (2014) 6491–6497.
[131] L. Lai, A.S. Barnard, Functionalized nanodiamonds for biological and medical appli-
cations, J. Nanosci. Nanotechnol. 15 (2015) 989–999.
[132] T. Panczyk, T.P. Warzocha, P.J. Camp, A magnetically controlled molecular
nanocontainer as a drug delivery system: the effects of carbon nanotube and mag-
netic nanoparticle parameters from monte carlo simulations, J. Phys. Chem. C 114
(2010) 21299–21308.
[133] T. Panczyk, A. Jagusiak, G. Pastorin, W.H. Ang, J. Narkiewicz-Michalek, Molecular
dynamics study of cisplatin release from carbon nanotubes capped by magnetic
nanoparticles, J. Phys. Chem. C 117 (2013) 17327–17336.
[134] H.M. Ding, Y.Q. Ma, Computer simulation of the role of protein corona in cellular
delivery of nanoparticles, Biomaterials 35 (2014) 8703–8710.
[135] G. Brancolini, D.B. Kokh, L. Calzolai, R.C. Wade, S. Corni, Docking of ubiquitin to gold
nanoparticles, ACS Nano 6 (2012) 9863–9878.
[136] D. Meneksedag-Erol, T. Tang, H. Uludağ, Probing the effect of miRNA on siRNA–PEI
polyplexes, J. Phys. Chem. B. 119 (2015) 5475–5486.
[137] A.F. Jorge, R.S. Dias, A.A. Pais, Enhanced condensation and facilitated release of DNA
using mixed cationic agents: a combined experimental and Monte Carlo study,
Biomacromolecules 13 (2012) 3151–3161.
[138] F. Tian, T. Yue, Y. Li, X. Zhang, Computer simulation studies on the interactions
between nanoparticles and cell membrane, Sci. China Chem. 57 (2014)
1662–1671.
[139] H.M. Ding, Y.Q. Ma, Theoretical and computational investigations of nanoparticle-
biomembrane interactions in cellular delivery, Small 11 (2015) 1055–1071.
[140] Y. Li, X. Zhang, D. Cao, Nanoparticle hardness controls the internalization pathway
for drug delivery, Nanoscale 7 (2015) 2758–2769.
[141] Y. Li, T. Yue, K. Yang, X. Zhang, Molecular modeling of the relationship between
nanoparticle shape anisotropy and endocytosis kinetics, Biomaterials 33 (2012)
4965–4973.
1705
[142] R. Vácha, F.J. Martinez-Veracoechea, D. Frenkel, Receptor-mediated endocytosis of
nanoparticles of various shapes, Nano Lett. 11 (2011) 5391–5395.
[143] X. Lin, Y. Li, N. Gu, Nanoparticle's size effect on its translocation across a lipid
bilayer: a molecular dynamics simulation, J. Comput. Theor. Nanosci. 7
(2010) 269–276.
[144] E.L. da Rocha, G.F. Caramori, C.R. Rambo, Nanoparticle translocation through a lipid
bilayer tuned by surface chemistry, Phys. Chem. Chem. Phys. 15 (2013)
2282–2290.
[145] R.C. Van Lehn, A. Alexander-Katz, Penetration of lipid bilayers by nanoparticles
with environmentally-responsive surfaces: simulations and theory, Soft Matter 7
(2011) 11392–11404.
[146] J. Lin, H. Zhang, Z. Chen, Y. Zheng, Penetration of lipid membranes by gold nano-
particles: insights into cellular uptake, cytotoxicity, and their relationship, ACS
Nano 4 (2010) 5421–5429.
[147] H.M. Ding, Y.Q. Ma, Role of physicochemical properties of coating ligands in
receptor-mediated endocytosis of nanoparticles, Biomaterials 33 (2012)
5798–5802.
[148] Y. Li, Computer investigations of influences of molar fraction and acyl chain length
of lipids on the nanoparticle–biomembrane interactions, RSC Adv. 5 (2015)
11049–11057.
[149] H.M. Ding, W. Tian, Y.Q. Ma, Designing nanoparticle translocation through mem-
branes by computer simulations, ACS Nano 6 (2012) 1230–1238.
[150] S. Wang, E.E. Dormidontova, Selectivity of ligand–receptor interactions between
nanoparticle and cell surfaces, Phys. Rev. Lett. 109 (2012) 238102.
[151] L. Zhang, M. Becton, X. Wang, Designing nanoparticle translocation through cell
membranes by varying amphiphilic polymer coatings, J. Phys. Chem. B. 119
(2015) 3786–3794.
[152] Y. Li, X. Zhang, D. Cao, A spontaneous penetration mechanism of patterned nano-
particles across a biomembrane, Soft Matter 10 (2014) 6844–6856.
[153] T. Yue, X. Zhang, Molecular understanding of receptor-mediated membrane re-
sponses to ligand-coated nanoparticles, Soft Matter 7 (2011) 9104–9112.
[154] L.F. Barraza, V.A. Jiménez, J.B. Alderete, Effect of PEGylation on the structure and
drug loading capacity of PAMAM-G4 dendrimers: a molecular modeling approach
on the complexation of 5-Fluorouracil with native and PEGylated PAMAM-G4,
Macromol. Chem. Phys. 216 (2015) 1689–1701.
[155] O.S. Lee, G.C. Schatz, Computational simulations of the interaction of lipid mem-
branes with DNA-functionalized gold nanoparticles, Biomedical Nanotechnolgy,
Springer 2011, pp. 283–296.
[156] Q. Mu, T. Hu, J. Yu, Molecular insight into the steric shielding effect of PEG on the
conjugated staphylokinase: biochemical characterization and molecular dynamics
simulation, PLoS One 8 (2013) (e68559).
[157] H. Lee, Molecular modeling of PEGylated peptides, dendrimers, and single-walled
carbon nanotubes for biomedical applications, Polymers 6 (2014) 776–798.
[158] A. Bunker, Molecular modeling as a tool to understand the role of poly (ethylene)
glycol in drug delivery, Computational Pharmaceutics: Application of Molecular
Modelling in Drug Delivery, John Wiley & Sons 2015, pp. 217–233.
[159] Y. Li, M. Kröger, W.K. Liu, Endocytosis of PEGylated nanoparticles accompanied by
structural and free energy changes of the grafted polyethylene glycol, Biomaterials
35 (2014) 8467–8478.
[160] K. Knop, R. Hoogenboom, D. Fischer, U.S. Schubert, Poly(ethylene glycol) in drug
delivery: pros and cons as well as potential alternatives, Angew. Chem. Int. Ed.
49 (2010) 6288–6308.
[161] J.K. Armstrong, G. Hempel, S. Koling, L.S. Chan, T. Fisher, H.J. Meiselman, et al., An-
tibody against poly(ethylene glycol) adversely affects PEG-asparaginase therapy in
acute lymphoblastic leukemia patients, Cancer 110 (2007) 103–111.
[162] L. Zhang, Z. Wang, Z. Lu, H. Shen, J. Huang, Q. Zhao, et al., PEGylated reduced
graphene oxide as a superior ssRNA delivery system, J. Mater. Chem. B. 1 (2013)
749–755.
[163] X. Sun, Z. Feng, L. Zhang, T. Hou, Y. Li, The selective interaction between silica nano-
particles and enzymes from molecular dynamics simulations, PLoS One 9 (2014)
(e107696).
[164] A. Adnan, R. Lam, H. Chen, J. Lee, D.J. Schaffer, A.S. Barnard, et al., Atomistic simula-
tion and measurement of pH dependent cancer therapeutic interactions with
nanodiamond carrier, Mol. Pharm. 8 (2011) 368–374.
[165] L. Lai, A.S. Barnard, Molecular and analytical modeling of nanodiamond for drug
delivery applications, Computational Pharmaceutics: Application of Molecular
Modelling in Drug Delivery, John Wiley & Sons 2015, pp. 169–196.
[166] M.L. Bello, A.M. Junior, B.A. Vieira, L.R.S. Dias, V.P. de Sousa, H.C. Castro, et al., Sodi-
um montmorillonite/amine-containing drugs complexes: new insights on interca-
lated drugs arrangement into layered carrier material, PLoS One 10 (2015)
(e0121110).
[167] V. Murthy, Z.P. Xu, S.C. Smith, Molecular modeling of layered double hydroxide
nanoparticles for drug delivery, Computational Pharmaceutics: Application of Mo-
lecular Modelling in Drug Delivery, John Wiley & Sons 2015, pp. 197–216.
[168] P. Cox, Atomistic modelling of drug delivery systems, Drug Design Strategies: Com-
putational Techniques and Applications, Royal Society of Chemistry 2012,
pp. 210–232.
[169] D.G. Fatouros, D. Douroumis, V. Nikolakis, S. Ntais, A.M. Moschovi, V. Trivedi, et al.,
In vitro and in silico investigations of drug delivery via zeolite BEA, J. Mater. Chem.
21 (2011) 7789–7794.
[170] M. Spanakis, N. Bouropoulos, D. Theodoropoulos, L. Sygellou, S. Ewart, A.M.
Moschovi, et al., Controlled release of 5-fluorouracil from microporous zeolites,
Nanomed. Nanotechnol. Biol. Med. 10 (2014) 197–205.
[171] M.C. Bernini, D. Fairen-Jimenez, M. Pasinetti, A.J. Ramirez-Pastor, R.Q. Snurr,
Screening of bio-compatible metal–organic frameworks as potential drug carriers
using Monte Carlo simulations, J. Mater. Chem. B. 2 (2014) 766–774.
1706 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
[172] S.T. Meek, J.A. Greathouse, M.D. Allendorf, Metal-organic frameworks: a
rapidly growing class of versatile nanoporous materials, Adv. Mater. 23
(2011) 249–267.
[173] G.M. Pavan, Modeling the interaction between dendrimers and nucleic acids: a
molecular perspective through hierarchical scales, ChemMedChem 9 (2014)
2623–2631.
[174] V. Jain, P.V. Bharatam, Pharmacoinformatic approaches to understand complexa-
tion of dendrimeric nanoparticles with drugs, Nanoscale 6 (2014) 2476–2501.
[175] D. Shcharbin, A. Shakhbazau, M. Bryszewska, Poly(amidoamine) dendrimer com-
plexes as a platform for gene delivery, Expert Opin. Drug Deliv. 10 (2013)
1687–1698.
[176] P. Posocco, E. Laurini, V. Dal Col, D. Marson, K. Karatasos, M. Fermeglia, et al., Tell
me something I do not know. Multiscale molecular modeling of dendrimer/
dendron organization and self-assembly in gene therapy, Curr. Med. Chem. 19
(2012) 5062–5087.
[177] D. Meneksedag-Erol, T. Tang, H. Uludağ, Molecular modeling of polynucleotide
complexes, Biomaterials 35 (2014) 7068–7076.
[178] M.R. Molla, P. Rangadurai, G.M. Pavan, S. Thayumanavan, Experimental and theo-
retical investigations in stimuli responsive dendrimer-based assemblies, Nanoscale
7 (2015) 3817–3837.
[179] E. Ficici, I. Andricioaei, S. Howorka, Dendrimers in nanoscale confinement: the in-
terplay between conformational change and nanopore entrance, Nano Lett. 15
(2015) 4822–4828.
[180] Y.L. Wang, Z.Y. Lu, A. Laaksonen, Specific binding structures of dendrimers on lipid
bilayer membranes, Phys. Chem. Chem. Phys. 14 (2012) 8348–8359.
[181] B. Nandy, P.K. Maiti, A. Bunker, Force biased molecular dynamics simulation study
of effect of dendrimer generation on interaction with DNA, J. Chem. Theory
Comput. 9 (2013) 722–729.
[182] G.M. Pavan, A. Danani, The influence of dendrons architecture on the “rigid” and
“flexible” behaviour in binding DNA—a modelling study, Phys. Chem. Chem.
Phys. 12 (2010) 13914–13917.
[183] G.M. Pavan, L. Albertazzi, A. Danani, Ability to adapt: different generations of
PAMAM dendrimers show different behaviors in binding siRNA, J. Phys. Chem. B.
114 (2010) 2667–2675.
[184] P. Posocco, S. Pricl, S. Jones, A. Barnard, D.K. Smith, Less is more — multiscale
modelling of self-assembling multivalency and its impact on DNA binding and
gene delivery, Chem. Sci. 1 (2010) 393–404.
[185] S.P. Jones, N.P. Gabrielson, C.H. Wong, H.F. Chow, D.W. Pack, P. Posocco, et al.,
Hydrophobically modified dendrons: developing structure–activity relationships
for DNA binding and gene transfection, Mol. Pharm. 8 (2011) 416–429.
[186] S.P. Jones, G.M. Pavan, A. Danani, S. Pricl, D.K. Smith, Quantifying the effect of sur-
face ligands on dendron–DNA interactions : insights into multivalency through a
combined experimental and theoretical approach, Chem. Eur. J. 16 (2010)
4519–4532.
[187] V. Percec, D.A. Wilson, P. Leowanawat, C.J. Wilson, A.D. Hughes, M.S. Kaucher, et al.,
Self-assembly of Janus dendrimers into uniform dendrimersomes and other com-
plex architectures, Science 328 (2010) 1009–1014.
[188] S. Zhang, H.J. Sun, A.D. Hughes, R.O. Moussodia, A. Bertin, Y. Chen, et al., Self-assembly
of amphiphilic Janus dendrimers into uniform onion-like dendrimersomes with pre-
dictable size and number of bilayers, Proc. Natl. Acad. Sci. U. S. A. 111 (2014)
9058–9063.
[189] S. Kavyani, S. Amjad-Iranagh, H. Modarress, Aqueous poly(amidoamine) dendri-
mer G3 and G4 generations with several interior cores at pHs 5 and 7: a molecular
dynamics simulation study, J. Phys. Chem. B. 118 (2014) 3257–3266.
[190] A. Barnard, P. Posocco, S. Pricl, M. Calderon, R. Haag, M.E. Hwang, et al., Degrad-
able self-assembling dendrons for gene delivery: experimental and theoretical
insights into the barriers to cellular uptake, J. Am. Chem. Soc. 133 (2011)
20288–20300.
[191] V. Carrasco-Sánchez, A. Vergara-Jaque, M. Zuñiga, J. Comer, A. John, F.M. Nachtigall,
et al., In situ and in silico evaluation of amine- and folate-terminated dendrimers as
nanocarriers of anesthetics, Eur. J. Med. Chem. 73 (2014) 250–257.
[192] C. Shi, D. Yuan, S. Nangia, G. Xu, K.S. Lam, J. Luo, A structure–property relationship
study of the well-defined telodendrimers to improve hemocompatibility of
nanocarriers for anticancer drug delivery, Langmuir 30 (2014) 6878–6888.
[193] R.M. Pearson, N. Patra, H.J. Hsu, S. Uddin, P. Král, S. Hong, Positively charged
dendron micelles display negligible cellular interactions, ACS Macro Lett. 2
(2012) 77–81.
[194] H. Lee, J.S. Choi, R.G. Larson, Molecular dynamics studies of the size and internal
structure of the PAMAM dendrimer grafted with arginine and histidine, Macro-
molecules 44 (2011) 8681–8686.
[195] H. Lee, R.G. Larson, Membrane pore formation induced by acetylated and polyeth-
ylene glycol-conjugated polyamidoamine dendrimers, J. Phys. Chem. C 115 (2011)
5316–5322.
[196] L. Yang, S.R.P. Rocha, PEGylated, NH2-terminated PAMAM dendrimers: A micro-
scopic view from atomistic computer simulations, Mol. Pharm. 11 (2014)
1459–1470.
[197] L. Albertazzi, F.M. Mickler, G.M. Pavan, F. Salomone, G. Bardi, M. Panniello, et al.,
Enhanced bioactivity of internally functionalized cationic dendrimers with PEG
cores, Biomacromolecules 13 (2012) 4089–4097.
[198] H. Lee, R.G. Larson, Effects of PEGylation on the size and internal structure of
dendrimers: self-penetration of long PEG chains into the dendrimer core, Macro-
molecules 44 (2011) 2291–2298.
[199] R. Bhattacharya, S. Kanchi, C. Roobala, A. Lakshminarayanan, O.H. Seeck, P.K. Maiti,
K.G. Ayappa, N. Jayaraman, J.K. Basu, A new microscopic insight into membrane
penetration and reorganization by PETIM dendrimers, Soft Matter 10 (2014)
7577–7587.
[200] R. Guo, J. Mao, L.T. Yan, Unique dynamical approach of fully wrapping dendrimer-
like soft nanoparticles by lipid bilayer membrane, ACS Nano 7 (2013)
10646–10653.
[201] X. He, Z. Qu, F. Xu, M. Lin, J. Wang, X. Shi, et al., Molecular analysis of interactions
between dendrimers and asymmetric membranes at different transport stages,
Soft Matter 10 (2014) 139–148.
[202] C.K. Tu, K. Chen, W.D. Tian, Y.Q. Ma, Computational investigations of a peptide-
modified dendrimer interacting with lipid membranes, Macromol. Rapid
Commun. 34 (2013) 1237–1242.
[203] Y.Q. Ma, pH-responsive dendrimers interacting with lipid membranes, Soft Matter
8 (2012) 2627–2632.
[204] L.Q. Xie, J.W. Feng, W.D. Tian, Y.Q. Ma, Generation-dependent gel-fluid phase tran-
sition of membrane caused by a PAMAM dendrimer, Macromol. Theory Simul. 23
(2014) 531–536.
[205] R.G. Bellini, A.P. Guimarães, M.A. Pacheco, D.M. Dias, V.R. Furtado, R.B. De
Alencastro, et al., Association of the anti-tuberculosis drug rifampicin with a
PAMAM dendrimer, J. Mol. Graph. Model. 60 (2015) 34–42.
[206] V. Jain, V. Maingi, P.K. Maiti, P.V. Bharatam, Molecular dynamics simulations of PPI
dendrimer–drug complexes, Soft Matter 9 (2013) 6482–6496.
[207] Y. Jiang, D. Zhang, Y. Zhang, Z. Deng, L. Zhang, The adsorption–desorption transi-
tion of double-stranded DNA interacting with an oppositely charged dendrimer in-
duced by multivalent anions, J. Chem. Phys. 140 (2014) 204912.
[208] X.F. Wen, J.L. Lan, Z.Q. Cai, P.H. Pi, S.P. Xu, L.J. Zhang, et al., Dissipative particle dy-
namics simulation on drug loading/release in polyester-PEG dendrimer, J. Nano-
particle Res. 16 (2014) 2403.
[209] V. Maingi, M.V.S. Kumar, P.K. Maiti, PAMAM dendrimer–drug interactions: effect of
pH on the binding and release pattern, J. Phys. Chem. B. 116 (2012) 4370–4376.
[210] F. Avila-Salas, C. Sandoval, J. Caballero, S. Guiñez-Molinos, L.S. Santos, R.E. Cachau,
et al., Study of interaction energies between the PAMAM dendrimer and nonsteroi-
dal anti-inflammatory drug using a distributed computational strategy and exper-
imental analysis by ESI-MS/MS, J. Phys. Chem. B. 116 (2012) 2031–2039.
[211] J. Lim, G.M. Pavan, O. Annunziata, E.E. Simanek, Experimental and computational
evidence for an inversion in guest capacity in high-heneration triazine dendrimer
hosts, J. Am. Chem. Soc. 134 (2012) 1942–1945.
[212] D. Ouyang, H. Zhang, H.S. Parekh, S.C. Smith, The effect of pH on PAMAM
dendrimer–siRNA complexation—endosomal considerations as determined by
molecular dynamics simulation, Biophys. Chem. 158 (2011) 126–133.
[213] B. Nandy, P.K. Maiti, DNA compaction by a dendrimer, J. Phys. Chem. B. 115 (2010)
217–230.
[214] D. Amado Torres, M. Garzoni, A.V. Subrahmanyam, G.M. Pavan, S. Thayumanavan,
Protein-triggered supramolecular disassembly: insights based on variations in li-
gand location in amphiphilic dendrons, J. Am. Chem. Soc. 136 (2014) 5385–5399.
[215] L.B. Jensen, G.M. Pavan, M.R. Kasimova, S. Rutherford, A. Danani, H.M. Nielsen, et al.,
Elucidating the molecular mechanism of PAMAM–siRNA dendriplex self-assembly:
effect of dendrimer charge density, Int. J. Pharm. 416 (2011) 410–418.
[216] K. Karatasos, P. Posocco, E. Laurini, S. Pricl, Poly (amidoamine)-based dendrimer/
siRNA complexation studied by computer simulations: effects of pH and genera-
tion on dendrimer structure and siRNA binding, Macromol. Biochem. 12 (2012)
225–240.
[217] G.M. Pavan, S. Monteagudo, J. Guerra, B. Carrion, V. Ocana, J. Rodriguez-Lopez, et al.,
Role of generation, architecture, pH and ionic strength on successful siRNA delivery
and transfection by hybrid PPV-PAMAM dendrimers, Curr. Med. Chem. 19 (2012)
4929–4941.
[218] G.M. Pavan, M.A. Mintzer, E.E. Simanek, O.M. Merkel, T. Kissel, A. Danani, Compu-
tational insights into the interactions between DNA and siRNA with “rigid” and
“flexible” triazine dendrimers, Biomacromolecules 11 (2010) 721–730.
[219] G.M. Pavan, P. Posocco, A. Tagliabue, M. Maly, A. Malek, A. Danani, et al., PAMAM
dendrimers for siRNA delivery: computational and experimental insights, Chem.
Eur. J. 16 (2010) 7781–7795.
[220] C. Shi, D. Guo, K. Xiao, X. Wang, L. Wang, J. Luo, A drug-specific nanocarrier design
for efficient anticancer therapy, Nat. Commun. 6 (2015) 7449.
[221] M. Kang, D. Lam, D.E. Discher, S.M. Loverde, Molecular modeling of block copoly-
mer self-assembly and micellar drug delivery, Computational Pharmaceutics: Ap-
plication of Molecular Modelling in Drug Delivery, John Wiley & Sons 2015,
pp. 53–80.
[222] A. Rösler, G.W.M. Vandermeulen, H.A. Klok, Advanced drug delivery devices via
self-assembly of amphiphilic block copolymers, Adv. Drug Deliv. Rev. 64 (2012)
270–279.
[223] C. Sun, T. Tang, Study on the role of polyethylenimine as gene delivery carrier using
molecular dynamics simulations, J. Adhes. Sci. Technol. 28 (2014) 399–416.
[224] S.M. Loverde, Computer simulation of polymer and biopolymer self-assembly for
drug delivery, Mol. Simul. 40 (2014) 794–801.
[225] D. Meneksedag-Erol, C. Sun, T. Tang, H. Uludag, Molecular dynamics simulations of
polyplexes and lipoplexes employed in gene delivery, Intracellular Delivery II,
Springer 2014, pp. 277–311.
[226] H. Guo, X. Qiu, J. Zhou, Self-assembled core–shell and Janus microphase sepa-
rated structures of polymer blends in aqueous solution, J. Chem. Phys. 139
(2013) 84907.
[227] C. Cai, L. Wang, J. Lin, X. Zhang, Morphology transformation of hybrid micelles self-
assembled from rod–coil block copolymer and nanoparticles, Langmuir 28 (2012)
4515–4524.
[228] H.Y. Chang, Y.L. Lin, Y.J. Sheng, H.K. Tsao, Structural characteristics and fusion path-
ways of onion-like multilayered polymersome formed by amphiphilic comb-like
graft copolymers, Macromolecules 46 (2013) 5644–5656.
[229] Y. Sheng, J. An, Y. Zhu, Self-assembly of ABA triblock copolymers under soft con-
finement, Chem. Phys. 452 (2015) 46–52.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
[230] H. Chen, E. Ruckenstein, Formation and degradation of multicomponent multicore
micelles: insights from dissipative particle dynamics simulations, Langmuir 29
(2013) 5428–5434.
[231] V. Taresco, L. Gontrani, F. Crisante, I. Francolini, A. Martinelli, L. D'Ilario, et al., Self-
assembly of catecholic moiety-containing cationic random acrylic copolymers, J.
Phys. Chem. B. 119 (2015) 8369–8379.
[232] S.Y. Nie, Y. Sun, W.J. Lin, W.S. Wu, X.D. Guo, Y. Qian, et al., Dissipative particle
dynamics studies of doxorubicin-loaded micelles assembled from four-arm star
triblock polymers 4AS-PCL-b-PDEAEMA-b-PPEGMA and their pH-release mecha-
nism, J. Phys. Chem. B. 117 (2013) 13688–13697.
[233] T. Wang, C. Chipot, X. Shao, W. Cai, Structural characterization of micelles formed
of cholesteryl-functionalized cyclodextrins, Langmuir 27 (2010) 91–97.
[234] L.X. Peng, A. Ivetac, A.S. Chaudhari, S. Van, G. Zhao, L. Yu, et al., Characterization of a
clinical polymer-drug conjugate using multiscale modeling, Biopolymers 93
(2010) 936–951.
[235] P. Pi, D. Qin, J. Lan, Z. Cai, X. Yuan, S. Xu, et al., Dissipative particle dynamics simu-
lation on the nanocomposites delivery system of quantum dots and poly (styrene-
b-ethylene oxide) copolymer, Ind. Eng. Chem. Res. 54 (2015) 6123–6134.
[236] J. Li, Y. Ouyang, X. Kong, J. Zhu, D. Lu, Z. Liu, A multi-scale molecular dynamics
simulation of PMAL facilitated delivery of siRNA, RSC Adv. 5 (2015)
68227–68233.
[237] G. Srinivas, R.V. Mohan, A.D. Kelkar, Polymer micelle assisted transport and deliv-
ery of model hydrophilic components inside a biological lipid vesicle: a coarse-
grain simulation study, J. Phys. Chem. B. 117 (2013) 12095–12104.
[238] H.M. Ding, Y.Q. Ma, Controlling cellular uptake of nanoparticles with pH-sensitive
polymers, Sci. Rep. 3 (2013) 2804.
[239] C. Sun, T. Tang, H. Uludag, A molecular dynamics simulation study on the effect of
lipid substitution on polyethylenimine mediated siRNA complexation, Biomate-
rials 34 (2013) 2822–2833.
[240] Z.X. Liao, S.F. Peng, Y.C. Ho, F.L. Mi, B. Maiti, H.W. Sung, Mechanistic study of
transfection of chitosan/DNA complexes coated by anionic poly(γ-glutamic
acid), Biomaterials 33 (2012) 3306–3315.
[241] S.F. Peng, M.T. Tseng, Y.C. Ho, M.C. Wei, Z.X. Liao, H.W. Sung, Mechanisms of cellu-
lar uptake and intracellular trafficking with chitosan/DNA/poly(γ-glutamic acid)
complexes as a gene delivery vector, Biomaterials 32 (2011) 239–248.
[242] M. Kepczynski, D. Jamróz, M. Wytrwal, J. Bednar, E. Rzad, M. Nowakowska, Interac-
tions of a hydrophobically modified polycation with zwitterionic lipid membranes,
Langmuir 28 (2011) 676–688.
[243] Y.L. Chiu, Y.C. Ho, Y.M. Chen, S.F. Peng, C.J. Ke, K.J. Chen, et al., The characteristics,
cellular uptake and intracellular trafficking of nanoparticles made of
hydrophobically-modified chitosan, J. Control. Release 146 (2010) 152–159.
[244] C. Sun, T. Tang, H. Uludağ, Probing the effects of lipid substitution on polycation
mediated DNA aggregation: a molecular dynamics simulations study,
Biomacromolecules 13 (2012) 2982–2988.
[245] S. Samanta, D. Roccatano, Interaction of curcumin with PEO–PPO–PEO block copol-
ymers: a molecular dynamics study, J. Phys. Chem. B. 117 (2013) 3250–3257.
[246] J. He, C. Chipot, X. Shao, W. Cai, Cyclodextrin-mediated recruitment and delivery of
amphotericin B, J. Phys. Chem. C 117 (2013) 11750–11756.
[247] P. Shan, J.W. Shen, D.H. Xu, L.Y. Shi, J. Gao, Y.W. Lan, et al., Molecular dynamics
study on the interaction between doxorubicin and hydrophobically modified chi-
tosan oligosaccharide, RSC Adv. 4 (2014) 23730–23739.
[248] M. Subashini, P.V. Devarajan, G.S. Sonavane, M. Doble, Molecular dynamics simula-
tion of drug uptake by polymer, J. Mol. Model. 17 (2011) 1141–1147.
[249] R. Anand, S. Ottani, F. Manoli, I. Manet, S. Monti, A close-up on doxorubicin binding
to γ-cyclodextrin: an elucidating spectroscopic, photophysical and conformational
study, RSC Adv. 2 (2012) 2346–2357.
[250] R. Namgung, Y.M. Lee, J. Kim, Y. Jang, B.H. Lee, I.S. Kim, et al., Poly-cyclodextrin and
poly-paclitaxel nano-assembly for anticancer therapy, Nat. Commun. 5 (2014)
3702.
[251] Z. Wang, J. Jiang, Dissipative particle dynamics simulation on paclitaxel loaded
PEO–PPO–PEO block copolymer micelles, J. Nanosci. Nanotechnol. 14 (2014)
2644–2647.
[252] Z. Wang, F. Wang, C. Su, Y. Zhang, Computer simulation of polymer delivery
system by dissipative particle dynamics, J. Comput. Theor. Nanosci. 10 (2013)
2323–2327.
[253] F. Razmimanesh, S. Amjad-Iranagh, H. Modarress, Molecular dynamics simulation
study of chitosan and gemcitabine as a drug delivery system, J. Mol. Model. 21
(2015) 165.
[254] S.Y. Nie, W.J. Lin, N. Yao, X.D. Guo, L.J. Zhang, Drug release from pH-sensitive poly-
meric micelles with different drug distributions: insight from coarse-grained sim-
ulations, ACS Appl. Mater. Interfaces 6 (2014) 17668–17678.
[255] Z. Luo, J. Jiang, pH-sensitive drug loading/releasing in amphiphilic copolymer PAE-
PEG: integrating molecular dynamics and dissipative particle dynamics simula-
tions, J. Control. Release 162 (2012) 185–193.
[256] J. Hao, Y. Cheng, R.J.K.U. Ranatunga, S. Senevirathne, M.C. Biewer, S.O. Nielsen, et al.,
A combined experimental and computational study of the substituent effect on mi-
cellar behavior of γ-substituted thermoresponsive amphiphilic poly (ε-
caprolactone), Macromolecules 46 (2013) 4829–4838.
[257] L.S. Zheng, Y.Q. Yang, X.D. Guo, Y. Sun, Y. Qian, L.J. Zhang, Mesoscopic simulations
on the aggregation behavior of pH-responsive polymeric micelles for drug deliv-
ery, J. Colloid Interface Sci. 363 (2011) 114–121.
[258] M.R. Rodríguez-Hidalgo, C. Soto-Figueroa, L. Vicente, Mesoscopic simulation of the
drug release mechanism on the polymeric vehicle P(ST-DVB) in an acid environ-
ment, Soft Matter 7 (2011) 8224–8230.
[259] R. Malik, J. Genzer, C.K. Hall, Proteinlike copolymers as encapsulating agents for
small-molecule solutes, Langmuir 31 (2015) 3518–3526.
1707
[260] S.K. Patel, A. Lavasanifar, P. Choi, Molecular dynamics study of the encapsulation
capability of a PCL-PEO based block copolymer for hydrophobic drugs with differ-
ent spatial distributions of hydrogen bond donors and acceptors, Biomaterials 31
(2010) 1780–1786.
[261] S.S. Thakur, H.S. Parekh, C.H. Schwable, Y. Gan, D. Ouyang, Solubilization of poorly
soluble drugs, Computational Pharmaceutics: Application of Molecular Modelling
in Drug Delivery, John Wiley & Sons 2015, pp. 31–51.
[262] S. Bagai, C. Sun, T. Tang, Potential of mean force of polyethylenimine-mediated
DNA attraction, J. Phys. Chem. B. 117 (2012) 49–56.
[263] H.S. Antila, M. Härkönen, M. Sammalkorpi, Chemistry specificity of DNA–
polycation complex salt response: a simulation study of DNA, polylysine and
polyethyleneimine, Phys. Chem. Chem. Phys. 17 (2015) 5279–5289.
[264] P. Pereira, A.F. Jorge, R. Martins, A.A. Pais, F. Sousa, A. Figueiras, Characterization of
polyplexes involving small RNA, J. Colloid Interface Sci. 387 (2012) 84–94.
[265] C. Sun, T. Tang, H. Uludag, Molecular dynamics simulations for complexation of
DNA with 2 kDa PEI reveal profound effect of PEI architecture on complexation,
J. Phys. Chem. B. 116 (2012) 2405–2413.
[266] D. Ouyang, H. Zhang, D. Herten, H.S. Parekh, S.C. Smith, Structure, dynamics and
energetics of siRNA-cationic vector complexation: a molecular dynamics study, J.
Phys. Chem. B. 114 (2010) 9220–9230.
[267] D. Ouyang, H. Zhang, H.S. Parekh, S.C. Smith, Structure and dynamics of multiple
cationic vectors — siRNA complexation by all-atomic molecular dynamics simula-
tions, J. Phys. Chem. B. 114 (2010) 9231–9237.
[268] A.F. Jorge, R.F.P. Pereira, S.C.C. Nunes, A.J.M. Valente, R.S. Dias, A.A.C.C. Pais,
Interpreting the rich behavior of ternary DNA-PEI-Fe(III) complexes,
Biomacromolecules 15 (2014) 478–491.
[269] B. Zhan, K. Shi, Z. Dong, W. Lv, S. Zhao, X. Han, et al., Coarse-grained simulation of
polycation/DNA-like complexes: role of neutral block, Mol. Pharm. 12 (2015)
2834–2844.
[270] M. Zhao, J. Zhou, C. Su, L. Niu, D. Liang, B. Li, Complexation behavior of oppositely
charged polyelectrolytes: effect of charge distribution, J. Chem. Phys. 142 (2015)
204902.
[271] J. Ziebarth, Y. Wang, Coarse-grained molecular dynamics simulations of DNA con-
densation by block copolymer and formation of core-corona structures, J. Phys.
Chem. B. 114 (2010) 6225–6232.
[272] Q. Luo, Y. Wang, H. Yang, C. Liu, Y. Ding, H. Xu, et al., Modeling the interaction of
interferon α-1b to bovine serum albumin as a drug delivery system, J. Phys.
Chem. B. 118 (2014) 8566–8574.
[273] R. Vijayaraj, S. Van Damme, P. Bultinck, V. Subramanian, Theoretical studies on the
transport mechanism of 5-fluorouracil through cyclic peptide based nanotubes,
Phys. Chem. Chem. Phys. 15 (2013) 1260–1270.
[274] H. Liu, J. Chen, Q. Shen, W. Fu, W. Wu, Molecular insights on the cyclic peptide
nanotube-mediated transportation of antitumor drug 5-fluorouracil, Mol. Pharm.
7 (2010) 1985–1994.
[275] J.Ł. Durzyńska, Ł. Przysiecka, R. Nawrot, J. Barylski, G. Nowicki, A. Warowicka, et al.,
Viral and other cell-penetrating peptides as vectors of therapeutic agents in med-
icine, J. Pharmacol. Exp. Ther. 354 (2015) 32–42.
[276] Y. Krishnan, F.C. Simmel, Nucleic acid based molecular devices, Angew. Chem. Int.
Ed. 50 (2011) 3124–3156.
[277] C.K. McLaughlin, G.D. Hamblin, H.F. Sleiman, Supramolecular DNA assembly, Chem.
Soc. Rev. 40 (2011) 5647–5656.
[278] J.I. Cutler, E. Auyeung, C.A. Mirkin, Spherical nucleic acids, J. Am. Chem. Soc. 134
(2012) 1376–1391.
[279] S.N. Barnaby, T.L. Sita, S.H. Petrosko, A.H. Stegh, C.A. Mirkin, Therapeutic applica-
tions of spherical nucleic acids, Nanotechnology-Based Precision Tools for the De-
tection and Treatment of Cancer, Springer 2015, pp. 23–50.
[280] K.A. Afonin, W.K. Kasprzak, E. Bindewald, M. Kireeva, M. Viard, M. Kashlev, B.A.
Shapiro, In silico design and enzymatic synthesis of functional RNA nanoparticles,
Acc. Chem. Res. 47 (2014) 1731–1741.
[281] S.R. Badu, R. Melnik, M. Paliy, S. Prabhakar, A. Sebetci, B.A. Shapiro, Modeling of
RNA nanotubes using molecular dynamics simulation, Eur. Biophys. J. 43 (2014)
555–564.
[282] S. Juul, F. Iacovelli, M. Falconi, S.L. Kragh, B. Christensen, R. Frøhlich, et al.,
Temperature-controlled encapsulation and release of an active enzyme in the cav-
ity of a self-assembled DNA nanocage, ACS Nano 7 (2013) 9724–9734.
[283] A.O. Elzoghby, W.M. Samy, N.A. Elgindy, Protein-based nanocarriers as promising
drug and gene delivery systems, J. Control. Release 161 (2012) 38–49.
[284] A.O. Elzoghby, W.M. Samy, N.A. Elgindy, Albumin-based nanoparticles as potential
controlled release drug delivery systems, J. Control. Release 157 (2012) 168–182.
[285] M. Pourmousa, M. Karttunen, Early stages of interactions of cell-penetrating pep-
tide penetratin with a DPPC bilayer, Chem. Phys. Lipids 169 (2013) 85–94.
[286] M. Pourmousa, J. Wong-Ekkabut, M. Patra, M. Karttunen, Molecular dynamic stud-
ies of transportan interacting with a DPPC lipid bilayer, J. Phys. Chem. B. 117
(2012) 230–241.
[287] X. He, M. Lin, B. Sha, S. Feng, X. Shi, Z. Qu, et al., Coarse-grained molecular dynamics
studies of the translocation mechanism of polyarginines across asymmetric mem-
brane under tension, Sci. Rep. 5 (2015) 12808.
[288] M. Islami, F. Mehrnejad, F. Doustdar, M. Alimohammadi, M. Khadem-Maaref, M.
Mir-Derikvand, et al., Study of orientation and penetration of LAH4 into lipid bilay-
er membranes: pH and composition dependence, Chem. Biol. Drug Des. 84 (2014)
242–252.
[289] Z.L. Li, H.M. Ding, Y.Q. Ma, Translocation of polyarginines and conjugated nanopar-
ticles across asymmetric membranes, Soft Matter 9 (2012) 1281–1286.
[290] R.S. Teixeira, T.F. Cova, S.M. Silva, R. Oliveira, M.J. Araújo, E.F. Marques, et al., Lysine-
based surfactants as chemical permeation enhancers for dermal delivery of local
anesthetics, Int. J. Pharm. 474 (2014) 212–222.
1708 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
[291] N. Todorova, C. Chiappini, M. Mager, B. Simona, I.I. Patel, M.M. Stevens, I.
Yarovsky, Surface presentation of functional peptides in solution determines
cell internalization efficiency of TAT conjugated nanoparticles, Nano Lett. 14
(2014) 5229–5237.
[292] Y. Li, D. Feng, X. Zhang, D. Cao, Design strategy of cell-penetrating copolymers for
high efficient drug delivery, Biomaterials 52 (2015) 171–179.
[293] A. Sanchez-Sanchez, S. Akbari, A.J. Moreno, F.L. Verso, A. Arbe, J. Colmenero, J.A.
Pomposo, Design and preparation of single-chain nanocarriers mimicking disor-
dered proteins for combined delivery of dermal bioactive cargos, Macromol.
Rapid Commun. 34 (2013) 1681–1686.
[294] L. Chen, T. Jiang, C. Cai, L. Wang, J. Lin, X. Cao, Polypeptide-based “smart” micelles
for dual-drug delivery: a combination study of experiments and simulations,
Adv. Healthcare Mater. 3 (2014) 1508–1517.
[295] E. Jabbari, X. Yang, S. Moeinzadeh, X. He, Drug release kinetics, cell uptake, and
tumor toxicity of hybrid VVVVVVKK peptide-assembled polylactide nanoparticles,
Eur. J. Pharm. Biopharm. 84 (2013) 49–62.
[296] X.D. Guo, L.J. Zhang, Z.M. Wu, Y. Qian, Dissipative particle dynamics studies on mi-
crostructure of pH-sensitive micelles for sustained drug delivery, Macromolecules
43 (2010) 7839–7844.
[297] X. Tian, F. Sun, X.R. Zhou, S.Z. Luo, L. Chen, Role of peptide self-assembly in antimi-
crobial peptides, J. Pept. Sci. 21 (2015) 530–539.
[298] I.W. Fu, C.B. Markegard, H.D. Nguyen, Solvent effects on kinetic mechanisms of self-
assembly by peptide amphiphiles via molecular dynamics simulations, Langmuir
31 (2014) 315–324.
[299] I.W. Fu, C.B. Markegard, B.K. Chu, H.D. Nguyen, The role of electrostatics and tem-
perature on morphological transitions of hydrogel nanostructures self-assembled
by peptide amphiphiles via molecular dynamics simulations, Adv. Healthcare
Mater. 2 (2013) 1388–1400.
[300] N. Thota, Z. Luo, Z. Hu, J. Jiang, Self-assembly of amphiphilic peptide (AF) 6H5K15:
coarse-grained molecular dynamics simulation, J. Phys. Chem. B. 117 (2013)
9690–9698.
[301] R. García-Fandiño, J.R. Granja, Effect of organochloride guest molecules on the sta-
bility of homo/hetero self-assembled α, γ-cyclic peptide structures: a computa-
tional study toward the control of nanotube length, J. Phys. Chem. C 117 (2013)
10143–10162.
[302] R. Bakry, R.M. Vallant, M. Najam-ul-Haq, M. Rainer, Z. Szabo, C.W. Huck, G.K. Bonn,
Medicinal applications of fullerenes, Int. J. Nanomedicine 2 (2007) 639–649.
[303] M. Martincic, G. Tobias, Filled carbon nanotubes in biomedical imaging and drug
delivery, Expert Opin. Drug Deliv. 12 (2015) 563–581.
[304] V.V. Chaban, T.I. Savchenko, S.M. Kovalenko, O.V. Prezhdo, Heat-driven release of a
drug molecule from carbon nanotubes: a molecular dynamics study, J. Phys. Chem.
B. 114 (2010) 13481–13486.
[305] N. Saikia, A.N. Jha, R.C. Deka, Dynamics of fullerene-mediated heat-driven release
of drug molecules from carbon nanotubes, J. Phys. Chem. Lett. 4 (2013)
4126–4132.
[306] U. Arsawang, O. Saengsawang, T. Rungrotmongkol, P. Sornmee, K. Wittayanarakul,
T. Remsungnen, et al., How do carbon nanotubes serve as carriers for gemcitabine
transport in a drug delivery system? J. Mol. Graph. & Model. 29 (2011) 591–596.
[307] Y. Li, T. Hou, Computational simulation of drug delivery at molecular level, Curr.
Med. Chem. 17 (2010) 4482–4491.
[308] M. Chehel Amirani, T. Tang, Binding of nucleobases with graphene and carbon
nanotube: a review of computational studies, J. Biomol. Struct. Dyn. 33 (2015)
1567–1597.
[309] M. Santosh, S. Panigrahi, D. Bhattacharyya, A.K. Sood, P.K. Maiti, Unzipping and
binding of small interfering RNA with single walled carbon nanotube: a platform
for small interfering RNA delivery, J. Chem. Phys. 136 (2012) 065106.
[310] B. Nandy, M. Santosh, P.K. Maiti, Interaction of nucleic acids with carbon nanotubes
and dendrimers, J. Biosci. 37 (2012) 457–474.
[311] B.D. Chen, C.L. Yang, J.S. Yang, M.S. Wang, X.G. Ma, Dynamic mechanism of HIV rep-
lication inhibitor peptide encapsulated into carbon nanotubes, Curr. Appl. Phys. 13
(2013) 1001–1007.
[312] J.W. Shen, T. Tang, X.H. Wei, W. Zheng, T.Y. Sun, Z. Zhang, L. Liang, Q. Wang, On the
loading mechanism of ssDNA into carbon nanotubes, RSC Adv. 5 (2015)
56896–56903.
[313] N. Wu, Q. Wang, B. Arash, Ejection of DNA molecules from carbon nanotubes, Car-
bon 50 (2012) 4945–4952.
[314] J. Li, L. Jiang, X. Zhu, Computational studies of the binding mechanisms of fullerenes
to human serum albumin, J. Mol. Model. 21 (2015) 177.
[315] J. Wong-Ekkabut, S. Baoukina, W. Triampo, I.M. Tang, D.P. Tieleman, L. Monticelli,
Computer simulation study of fullerene translocation through lipid membranes,
Nat. Nanotechnol. 3 (2008) 363–368.
[316] J. Barnoud, L. Urbini, L. Monticelli, C60 fullerene promotes lung monolayer collapse,
J. R. Soc. Interface 12 (2015) 20140931.
[317] N. Nisoh, M. Karttunen, L. Monticelli, J. Wong-Ekkabut, Lipid monolayer disruption
caused by aggregated carbon nanoparticles, RSC Adv. 5 (2015) 11676–11685.
[318] A.A. Skandani, R. Zeineldin, M. Al-Haik, Effect of chirality and length on the pene-
trability of single-walled carbon nanotubes into lipid bilayer cell membranes,
Langmuir 28 (2012) 7872–7879.
[319] H. Lee, Membrane penetration and curvature induced by single-walled carbon
nanotubes: the effect of diameter, length, and concentration, Phys. Chem. Chem.
Phys. 15 (2013) 16334–16340.
[320] S. Baoukina, L. Monticelli, D.P. Tieleman, Interaction of pristine and functionalized car-
bon nanotubes with lipid membranes, J. Phys. Chem. B. 117 (2013) 12113–12123.
[321] C.C. Chiu, W. Shinoda, R.H. DeVane, S.O. Nielsen, Effects of spherical fullerene nano-
particles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain
molecular dynamics approach, Soft Matter 8 (2012) 9610–9616.
[322] A. Jusufi, R.H. DeVane, W. Shinoda, M.L. Klein, Nanoscale carbon particles and the
stability of lipid bilayers, Soft Matter 7 (2011) 1139–1146.
[323] H. Lee, Interparticle dispersion, membrane curvature, and penetration induced by
single-walled carbon nanotubes wrapped with lipids and PEGylated lipids, J. Phys.
Chem. B. 117 (2013) 1337–1344.
[324] S. Kraszewski, A. Bianco, M. Tarek, C. Ramseyer, Insertion of short amino-
functionalized single-walled carbon nanotubes into phospholipid bilayer occurs
by passive diffusion, PLoS One 7 (2012) (e40703).
[325] S. Kraszewski, F. Picaud, I. Elhechmi, T. Gharbi, C. Ramseyer, How long a function-
alized carbon nanotube can passively penetrate a lipid membrane, Carbon 50
(2012) 5301–5308.
[326] H. Lee, Dispersion and bilayer interaction of single-walled carbon nanotubes mod-
ulated by covalent and noncovalent PEGylation, Mol. Simul. 41 (2014) 1254–1263.
[327] A. Di Crescenzo, M. Aschi, A. Fontana, Toward a better understanding of steric sta-
bilization when using block copolymers as stabilizers of single-walled carbon
nanotubes (SWCNTs) aqueous dispersions, Macromolecules 45 (2012)
8043–8050.
[328] A. Sridhar, B. Srikanth, A. Kumar, A.K. Dasmahapatra, Coarse-grain molecular
dynamics study of fullerene transport across a cell membrane, J. Chem. Phys. 143
(2015) 24907.
[329] E. Sarukhanyan, G. Milano, D. Roccatano, Coating mechanisms of single-walled car-
bon nanotube by linear polyether surfactants: insights from computer simulations,
J. Phys. Chem. C 118 (2014) 18069–18078.
[330] H. Lee, Molecular dynamics studies of PEGylated single-walled carbon nanotubes:
the effect of PEG size and grafting density, J. Phys. Chem. C 117 (2013)
26334–26341.
[331] H. Shrestha, R. Bala, S. Arora, Lipid-based drug delivery systems, J. Pharm. 2014
(2014) 801820.
[332] S. Mashaghi, T. Jadidi, G. Koenderink, A. Mashaghi, Lipid nanotechnology, Int. J. Mol.
Sci. 14 (2013) 4242–4282.
[333] A.L. Klibanov, K. Maruyama, V.P. Torchilin, L. Huang, Amphipathic
polyethyleneglycols effectively prolong the circulation time of liposomes, FEBS
Lett. 268 (1990) 235–237.
[334] M. Dzieciuch, S. Rissanen, N. Szydłowska, A. Bunker, M. Kumorek, D. Jamróz, et al.,
PEGylated liposomes as carriers of hydrophobic porphyrins, J. Phys. Chem. B. 119
(2015) 6646–6657.
[335] J. Lehtinen, A. Magarkar, M. Stepniewski, S. Hakola, M. Bergman, T. Róg, et al., Anal-
ysis of cause of failure of new targeting peptide in PEGylated liposome: molecular
modeling as rational design tool for nanomedicine, Eur. J. Pharm. Sci. 46 (2012)
121–130.
[336] A. Magarkar, T. Róg, A. Bunker, Molecular dynamics simulation of PEGylated mem-
branes with cholesterol: building toward the DOXIL formulation, J. Phys. Chem. C
118 (2014) 15541–15549.
[337] K. Laasonen, M.L. Klein, Molecular dynamics simulations of the structure and ion
diffusion in poly(ethylene oxide), J. Chem. Soc. Faraday Trans. 91 (1995)
2633–2638.
[338] F. Müller-Plathe, W.F. van Gunsteren, Computer simulation of a polymer electro-
lyte: lithium iodide in amorphous poly(ethylene oxide), J. Chem. Phys. 103
(1995) 4745–4756.
[339] C. Özdemir Dinç, G. Kibarer, A. Güner, Solubility profiles of poly(ethylene glycol)/
solvent systems. II. Comparison of thermodynamic parameters from viscosity mea-
surements, J. Appl. Polym. Sci. 117 (2010) 1100–1119.
[340] O. Borodin, G.D. Smith, R.L. Jaffe, Ab initio quantum chemistry and molecular dy-
namics simulations studies of LiPF6/poly(ethylene oxide) interactions, J. Comput.
Chem. 22 (2001) 641–654.
[341] M. Nowakowska, K. Nawalany, M. Kepczynski, Z. Krawczyk, Novel nanostructural
hybride materials for photodynamic theraphy, Macromol. Symp. 279 (2009)
132–137.
[342] I.F. Hakem, J. Lal, M.R. Bockstaller, Binding of monovalent ions to PEO in solution:
relevant parameters and structural transitions, Macromolecules 37 (2004)
8431–8440.
[343] A. Magarkar, E. Karakas, M. Stepniewski, T. Róg, A. Bunker, Molecular dynamics
simulation of PEGylated bilayer interacting with salt ions: a model of the liposome
surface in the bloodstream, J. Phys. Chem. B. 116 (2012) 4212–4219.
[344] M. Stepniewski, M. Pasenkiewicz-Gierula, T. Róg, R. Danne, A. Orlowski, M.
Karttunen, et al., Study of PEGylated lipid layers as a model for PEGylated liposome
surfaces: molecular dynamics simulation and Langmuir monolayer studies, Lang-
muir 27 (2011) 7788–7798.
[345] M. Pannuzzo, D.H. De Jong, A. Raudino, S.J. Marrink, Simulation of polyethylene
glycol and calcium-mediated membrane fusion, J. Chem. Phys. 140 (2014)
124905.
[346] A. Magarkar, T. Róg, A. Bunker, Molecular dynamics simulation of inverse-
phosphocholine lipids, J. Phys. Chem. C 118 (2014) 19444–19449.
[347] N.D. Winter, R.K.J. Murphy, T.V. O′ Halloran, G.C. Schatz, Development and model-
ing of arsenic-trioxide-loaded thermosensitive liposomes for anticancer drug
delivery, J. Liposome Res. 21 (2011) 106–115.
[348] E.K. Perttu, A.G. Kohli, F.C. Szoka, Inverse-phosphocholine lipids: a remix of a com-
mon phospholipid, J. Am. Chem. Soc. 134 (2012) 4485–4488.
[349] H. Lee, R.W. Pastor, Coarse-grained model for PEGylated lipids: effect of PEGylation
on the size and shape of self-assembled structures, J. Phys. Chem. B. 115 (2011)
7830–7837.
[350] J.C. Shillcock, Spontaneous vesicle self-assembly: A mesoscopic view of membrane
dynamics, Langmuir 28 (2011) 541–547.
[351] W. Shinoda, D.E. Discher, M.L. Klein, S.M. Loverde, Probing the structure of
PEGylated-lipid assemblies by coarse-grained molecular dynamics, Soft Matter 9
(2013) 11549–11556.
 M. Ramezanpour et al. / Biochimica et Biophysica Acta 1858 (2016) 1688–1709
[352] J.J. Janke, W.F.D. Bennett, D.P. Tieleman, Oleic acid phase behavior from molecular
dynamics simulations, Langmuir 30 (2014) 10661–10667.
[353] N. Dan, Nanostructured lipid carriers: effect of solid phase fraction and distribution
on the release of encapsulated materials, Langmuir 30 (2014) 13809–13814.
[354] N. Dan, Drug release through liposome pores, Colloids Surf. B 126 (2015) 80–86.
[355] C. Vitorino, J. Almeida, L.M. Gonçalves, A.J. Almeida, J.J. Sousa, A.A.C.C. Pais, Co-
encapsulating nanostructured lipid carriers for transdermal application: from
experimental design to the molecular detail, J. Control. Release 167 (2013)
301–314.
[356] J.P.M. Jämbeck, E.S.E. Eriksson, A. Laaksonen, A.P. Lyubartsev, L.A. Eriksson, Molec-
ular dynamics studies of liposomes as carriers for photosensitizing drugs: develop-
ment, validation, and simulations with a coarse-grained model, J. Chem. Theory
Comput. 10 (2014) 5–13.
[357] B. van Hoof, A.J. Markvoort, R.A. van Santen, P.A.J. Hilbers, Molecular simulation of
protein encapsulation in vesicle formation, J. Phys. Chem. B. 118 (2014)
3346–3354.
[358] C.D. Novina, P.A. Sharp, The RNAi revolution, Nature 430 (2004) 161–164.
[359] S.L. Wang, Optimizing drug delivery : Characterization of DLin-KC2-DMA/
distearoylphosphatidylserine by 31P and 2H NMR spectroscopy, Diss. Sci. Dep.
Mol. Biol. Biochem. (2013).
[360] D. Rozmanov, S. Baoukina, D.P. Tieleman, Density based visualization for molecular
simulation, Faraday Discuss. 169 (2014) 225–243.
[361] A. Martín-Molina, G. Luque-Caballero, J. Faraudo, M. Quesada-Pérez, J. Maldonado-
Valderrama, Adsorption of DNA onto anionic lipid surfaces, Adv. Colloid Interf. Sci.
206 (2014) 172–185.
[362] G. Ajnai, A. Chiu, T. Kan, C.C. Cheng, T.H. Tsai, J. Chang, Trends of gold nanoparticle-
based drug delivery system in cancer therapy, J. Exp. Clin. Med. 6 (2014) 172–178.
1709
[363] A.C. Yang, C.I. Weng, Structural and dynamic properties of water near monolayer-
protected gold clusters with various alkanethiol tail groups, J. Phys. Chem. C 114
(2010) 8697–8709.
[364] G. Milano, G. Santangelo, F. Ragone, L. Cavallo, A. Di Matteo, Gold nanoparticle/
polymer interfaces: all atom structures from molecular dynamics simulations, J.
Phys. Chem. C 115 (2011) 15154–15163.
[365] J. Yu, M.L. Becker, G.A. Carri, The influence of amino acid sequence and functional-
ity on the binding process of peptides onto gold surfaces, Langmuir 28 (2011)
1408–1417.
[366] K.H. Lee, F.M. Ytreberg, Effect of gold nanoparticle conjugation on peptide dynam-
ics and structure, Entropy 14 (2012) 630–641.
[367] R.C. Van Lehn, M. Ricci, P.H.J. Silva, P. Andreozzi, J. Reguera, K. Voïtchovsky, et al.,
Lipid tail protrusions mediate the insertion of nanoparticles into model cell mem-
branes, Nat. Commun. 5 (2014) 4482.
[368] R.C. Van Lehn, A. Alexander-Katz, Free energy change for insertion of charged,
monolayer-protected nanoparticles into lipid bilayers, Soft Matter 10 (2014)
648–658.
[369] R.C. Van Lehn, A. Alexander-Katz, Structure of mixed-monolayer-protected nano-
particles in aqueous salt solution from atomistic molecular dynamics simulations,
J. Phys. Chem. C 117 (2013) 20104–20115.
[370] R.C. Van Lehn, A. Alexander-Katz, Ligand-mediated short-range attraction drives
aggregation of charged monolayer-protected gold nanoparticles, Langmuir 29
(2013) 8788–8798.
[371] S.J. Marrink, A.H. de Vries, D.P. Tieleman, Lipids on the move: simulations of mem-
brane pores, domains, stalks and curves, Biochim. Biophys. Acta 1788 (2009)
149–168.