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Challenges in process control for continuous
processing for production of monoclonal antibody
products
Anurag S Rathore1, Saxena Nikita1, Garima Thakur1 and Navnath
Deore2
Continuous processing has been garnering much interest lately
for production of biopharmaceutical products. Purported
benefits include higher productivity (10-15X), significant
shrinkage in facility footprint as well as equipment cost, and
improved process control and consistency in product quality.
However, industrial implementation remains a non-trivial task
due to the significant complexities associated with controlling
continuous processes. Real time monitoring of critical quality
attributes followed by real time process control while desired,
may not be feasible for every attribute and for every unit
operation. This article presents a perspective on the challenges
that are faced while developing and implementing a robust and
adaptable automated control system for continuous
biopharmaceutical processes. Potential solutions are
presented together with gaps that have been identified.
Addresses
1
Department of Chemical Engineering, Indian Institute of Technology
Delhi, India
2
Tata Consultancy Services, India
Corresponding author: Rathore, Anurag S (asrathore@biotechcmz.com)
Current Opinion in Chemical Engineering 2021, 30:xx–yy
This review comes from a themed issue on Biotechnology and Bio-
process Eng; Biotechnology and Bioengineering
Edited by Doraiswami Ramkrishna and Jamey Young
https://doi.org/10.1016/j.coche.2021.100671
2211-3398/ã 2021 Elsevier Ltd. All rights reserved.
Current status of continuous processing
Motivated by the technological advancement in the field of
bioprocessing and biotherapeutics, pharmaceutical compa-
nies and contract manufacturing organizations are shifting
from batch to continuous processing to improve productiv-
ity, cope with growing demands, and reduce manufacturing
footprint. A recent market survey reported the approval and
production of 35 new monoclonal antibodies (mAbs) since
2013, with an increase in production from 7.2% to 18.3%
each year. The anticipated mAb production growth rate of
7%, 10% or 15% per year yields projected global sales of US$
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137-$220 billion by 2022 [1]. Development, scale-up, and
optimization of a bioprocess for commercial manufacturing
remain resource intensive tasks [2]. Based on the cost of
goods and sensitivity analysis, it has been estimated that the
overall capital cost for production of mAb per year for fed
batch process is three folds higher than for continuous
processing [3]. The continuous mode of operation has
the ability to handle upstream titre variations, to fulfil
product quality specifications and to produce the required
product in smallerunits, thereby making thesetupseasierto
create and maintain [4]. Development of advanced process
control strategies [5] along with model-based data driven
control is critical for automated operation of the continuous
train and for achieving high productivity. However, model-
based control needs mechanistic models, which thus far
remain too complex and computationally intensive for
industrial implementation. In addition, there remains a
gap in availability of commercial online/real time sensors
for direct measurement of critical quality attributes such as
glycosylation, charge variants, aggregates, or host cell impu-
rities so as to facilitate implementation of process analytical
technology (PAT, see glossary). Process non-linearities that
need to be effectively managed in continuous processing
include variable titers and flow rates along with a lack of
operational flexibility in most existing process systems,
thereby resulting in system conflicts during the process
scheduling. Achieving robust continuous operation
requires an improved level of automation to minimize
human intervention and appropriately handle a wide range
of product and process deviations. The appropriate struc-
ture of unit operations with combination of feed-forward/
feed-backward control strategies and suitable PAT tools
with proper automation must be evaluated, designed and
implemented from an end-to-end continuous perspective.
This paper aims to discuss challenges that are faced during
integration, automation and control of continuous processes
(Tables 1 and 2). Design and implementation of integrated
process control using a distributed control system has been
evaluated. This is crucial for realizing the benefits promised
by continuous processing, and to mitigate the risks associ-
ated with its added complexity and failure modes.
Modelling of bioprocess unit operations
Continuous biopharmaceutical manufacturing involves
integration of numerous upstream and downstream unit
operations into a single continuous process. Each unit
operation by itself is dynamic in nature with multivariable
Current Opinion in Chemical Engineering 2019, 30:100671
2 Biotechnology and Bioprocess Eng; Biotechnology and Bioengineering
Glossary
Process Analytical Technology (PAT): Defined by the US FDA as “a
mechanism to design, analyze, and control pharmaceutical
manufacturing processes through the measurement of Critical Process
Parameters (CPP) which affect Critical Quality Attributes (CQA)”.
Distributed Control System (DCS): Control system to supervise
continuous processes at manufacturing scale. It is a combination of
sensors, controllers and computers distributed throughout the facility.
Programmable Logic Controller (PLC): Controller to automate the
production line or process industrially. It receives, monitors and record
the real time data and perform specific action based on the pre-defined
programs.
Supervisory Control and Data Acquisition (SCADA): High level process
control and management architecture comprising of human-machine
interface, networked data communications and computers that interact
with the plant via PLCs and Controllers.
Quality-by-Design (QbD): Defined by the ICH Q8 guidelines as “a
systematic approach to development that begins with predefined
objectives and emphasizes product and process understanding”, with
an enhanced focus on designing quality in biotherapeutic products
through fundamental understanding and in-process analytics.
Quality-by-Testing (QbT): A methodology of ensuring product quality
by testing raw materials and the final product prior to packaging in each
batch, but without significant fundamental understanding or in-process
analytics.
Downstream Processing (DSP): A series of steps for recovery and
purification of the active biotherapeutic product from natural sources,
cell culture or fermentation broth, including but not limited to
clarification, chromatography, filtration, precipitation, and refolding.
Upstream processing (USP): Process steps related to production of the
product molecule including early cell isolation, cell banking, inoculation,
growth, and cultivation until final harvest and collection of the live cell
batch.
interactions of process parameters affecting product qual-
ity. In such a scenario, modelling of unit operations can be
quite useful and this has fuelled recent interest in mech-
anistic modelling. Empirical, mechanistic, as well as
hybrid models have been developed and implemented
in real time using on-line measurements of critical process
parameters and quality attributes [6,7,8,9,10]. Mecha-
nistic models are developed from an in-depth under-
standing of the unit operations and the underlying physi-
cal processes. Although predictive control systems based
on mechanistic models do exist for some individual unit
operations such as bioreactor [11,12], chromatography
[13,14] and ultrafiltration [15], plant-wide control strate-
gies derived purely from mechanistic models are yet to be
demonstrated. Data-driven statistical process control sys-
tems are useful at the plant level, but their implementa-
tion is limited by the diverse nature of the data, both in
type and time scale. Additionally, after data acquisition,
extensive efforts are required to analyse the data for
multivariate interactions. Techniques must be imple-
mented to reduce the dimensionality of the data to extract
the relevant information, such as hierarchical clustering,
multivariate least squares regression, batch evolution
modelling, artificial neural networks, or other prediction
and optimization algorithms [16,17]. However, a key
limitation is that the data driven models are inherently
dependent on the quality (varies due to the process
Current Opinion in Chemical Engineering 2019, 30:100671
randomness and variability) and quantity of data
(depends on the process operation time) available [18].
The accuracy of data driven models can be improved by
building hybrid models that combine mechanistic and
statistical approaches. Figure 1a and b summarize some of
the significant literature on development and implemen-
tation of model-based or data-driven control through
PAT.
Control of continuous processes
Control architecture for continuous processing must be
designed across a range of levels, with separate local and
plant wide control. For example, local control should
involve controlling glycosylation in the bioreactor, cell
debris clearance in the clarification step, HCP clearance
and product capture in the Protein A step, aggregate and
charge variant clearance in the polishing step, final con-
centration in the ultrafiltration step, and excipient con-
centrations in the diafiltration step.
In contrast, plant wide control should be for process
scheduling, management of surge tanks, and handling
of extreme deviations such as equipment breakdown or
product loss. The availability of the process models is an
added advantage for developing model-based control
strategies and thereby ensuring high process productivity.
The models must be developed at a range of levels,
including the smallest level (such as pressure monitoring
of depth filters and pH control of viral inactivation), single
unit operation level (such as column scheduling or pool-
ing in chromatography), multiple unit operation level
(such as surge tank flowrate matching with the subse-
quent unit operation), and plant wide level (such as surge
tank management across the continuous train to ensure
that none of them overflow or run dry, process scheduling
and handling of extreme deviations such as equipment
breakdown or product loss). The control loops must have
independent goals and be designed such that they can
operate at the same level in the control structure hierar-
chy without conflicts. This increases the overall flexibility
and robustness of the continuous train. As each unit
operation is generally designed for a specific purpose,
which is distinct from the other unit operations, it is
advised to develop control strategies independently. It
should be clear which CQA are impacted by a given unit
operation and thus control of that CQA should occur only
in the relevant control loop associated with that operation
to maintain process stability.
The proposed systematic control framework in Figure 2
has been designed taking all these considerations into
account. The system enables control based on real-time
process parameters collected from the equipment and
from the in-line/at-line sensors. This system also enables
integration with the PAT layer for developing model
based predictive control using multivariate data analysis
or empirical models. Regulatory frameworks to promote
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 Challenges in process control for continuous processing for production of monoclonal antibody products Rathore et al. 3

Table 1

Challenges faced during integration of analytical equipment

Analytical equipment Challenges

At-line high pressure liquid Multi-port valves are required to be integrated into the HPLC to draw samples of the required injection volume from the
chromatography (HPLC) process flow streams and flush the tubing with buffer in between sample collections. Careful positioning of sample
ports with in-line filters is required to prevent air or particles from entering the analytical columns.
Spectroscopic tools (FTIR, Flow cells with minimal hold-up volume are needed to take full advantage of the fast analytics facilitated by
NIR, MIR, Raman, spectroscopic tools, which can measure and quantify spectra on the time scale of a few seconds. However, these flow
fluorescence, multi- cells often have to be customized for biotherapeutic applications in terms of fixed/variable path length, back-pressure
wavelength UV) reduction, and sensitivity to vibrations. The spectrometer must be stable with minimal vibrations which can otherwise
lead to significant noise, especially with Raman spectroscopy. The spectrometer and flow cells/immersion probes
also need to be protected from air bubbles and temperature variations which can lead to spectral shifts. Multi-channel
spectrometers are useful for leveraging the expensive spectrometric detection device at multiple points in the
continuous train
In-line probes (pH, turbidity, Probes must be fully immersed in the flow stream and be resistant to calibration shifts, air bubbles, temperature
conductivity, pressure, changes and vibrations. The probes often do not have a human-machine interface and have to be directly connected
temperature, UV) to the overarching controller via a PLC or other input/output device using appropriate hardware handshaking.
At-line high pressure liquid Handshaking of the proprietary HPLC software with the overarching controller of the continuous train is required to
chromatography (HPLC) trigger the start, stop, and sampling intervals of the HPLC. Advanced synchronization can be required, for example if
the sample collection is at the outlet of a chromatography column and should only be triggered during elutions. Auto-
integration is required to obtain quantitative information from chromatograms without manual intervention, and these
algorithms need to be robust against potential baseline shifts, spikes in pressure or UV, and potentially large variations
in the attributes of the incoming sample. Data from auto-integrated chromatograms need to be shared with the
overarching controller in real time to facilitate control decisions or trigger alarms.
Spectroscopic tools (FTIR, Handshaking of proprietary spectrometry software with the overarching controller of the continuous train is required to
NIR, MIR, Raman, trigger spectral collection events. Automated multivariate data analytics models are required to obtain quantitative
fluorescence, multi- information from spectra in real time. The models need extensive calibration as they typically only work in a small
wavelength UV) operating range and need to be built to cover potential variations in process stream attributes without giving
erroneous data. Automated spectral quality checking and error detection algorithms are required to reduce noise.
Data from the MVDA algorithms needs to be shared with the overarching controller in real time.
In-line probes (pH, turbidity, Simple probes often do not come with proprietary software, so a complete data logging, data historian, and alarm
conductivity, pressure, system needs to be built to store the data trajectory and facilitate control decisions.
temperature, UV)

Table 2

Challenges faced during integration of process equipment

Unit operation Challenges

Bioreactor The stringent design space and process non-linearity poses a challenge in controller tuning. In addition, sensor calibration
and resolution for long duration operations is another issue.
Acoustic Wave The separation efficiency depends on load cell density which varies across batches and cell types. As AWS uses
Separator technology based on generation of standing 3D waves using low frequency acoustic forces, long duration operation
results in overheating of the equipment. Pausing the equipment for cooling down is not a feasible option owing to the
material sedimentation that often leads to hurdles in process scheduling.
Chromatography There is no gradient pump in the BioSMB to facilitate gradient elutions in polishing steps. Also, availability of seven pumps
is insufficient if performing multiple chromatography operations simultaneously.
Viral Inactivation Continuous flow at fixed flowrate is required to ensure equal residence time at low pH for all process material. Hardware
complexity increases in case of insufficient process material volume in the preceding unit operations. In such situations, to
prevent the extra hold time in coiled flow inverter reactor, standby buffer tank and pumps are required to drive the material
through the unit thereby increasing the risk of dilution of process stream.
Ultrafiltration and Flux- or TMP-based controllers are required for ensuring consistency over long continuous campaigns to handle
Diafiltration deviations arising from flux decline or variability in concentration of the incoming feed stream. The controller should be
tuned using a combination of pumps, sensors and control valves. Calibration of pumps is also a key concern as the
pumping of diafiltration buffer is conducted through six different ports simultaneously. In addition, combination of pumps
and valves is required to automate buffer flush and product recovery.
Dead-End Filtration Dead-end depth and sterile filtration are required at various points in the continuous train. A setup of filters connected in
parallel is used for switching the flow when one filter is clogged without pausing the process stream. In-line turbidity
sensors (for depth filtration) and pressure sensors (for sterile filtration) are required to be externally integrated for switching
based on turbidity/pressure breakthrough.
Surge Tanks Surge tanks are required at various points in the continuous train for flow-matching between different unit operations and
for added safety in case of unexpected deviations or equipment errors. The surge tank system must be built from the
ground up with appropriate sizing, material, temperature control and monitoring tools (weighing balances with real time
data provided to the DCS).

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4 Biotechnology and Bioprocess Eng; Biotechnology and Bioengineering

Figure 1

(a)

(b)

Current Opinion in Chemical Engineering

Implementation of PAT tools (primary y-axis) for multiple applications (secondary y- axis) in upstream mammalian cell culture (1a) and downstream
processing of biotherapeutics (1b) using different strategies (x-axis). For the details of the PAT-based control strategy, literature can be referred
with respect to the numbers on secondary y-axis. Each color is associated with a particular application [19–28,29,30–45,46,47–55,56,57,58,
59,60–64].

PAT implementation and continuous manufacturing for controller ensures data collection while maintaining
the innovation in development and manufacturing have integrity of each unit operation. In addition, keeping a
been provided by FDA and other regulatory agencies process data historian at a central location facilitates
[65,66]. Automating the process using a centralized analytics which involve more than one equipment and

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 Challenges in process control for continuous processing for production of monoclonal antibody products Rathore et al. 5

Figure 2

Current Opinion in Chemical Engineering

Potential control strategy solution showing control loops, CQA’s and CPP’s for continuous downstream processing.

allows easy implementation of advanced control algo-
rithms using additional software tools based on algorithms
in Python, MATLAB, R, and SIMCA. In the case illus-
trated here, Distributed Control System (DCS), Pro-
grammable Logic Controller (PLC), and Supervisory
Control and Data Acquisition (SCADA) are used to
integrate process equipment towards achieving synchro-
nised control of multiple unit operations. Figure 3
illustrates the control system network architecture for
integration of the unit operations, all of which are

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6 Biotechnology and Bioprocess Eng; Biotechnology and Bioengineering
Figure 3
Control system network architecture.
connected over ethernet protocol and interface with the
control system via a Python Snap7 interface and the key
inputs to DCS and key outputs from DCS are mentioned
in Table 4. A program created in the PLC would control
the scheduling, while SCADA is responsible for monitor-
ing and control of the operation, logging alarms, interfac-
ing with control algorithms written in other software, and
displaying the process trends and trajectories. FDA per-
spective on the adoption of control strategies for contin-
uous manufacturing and system integration revolves
around characterization of incoming material, system
dynamics and the way the perturbations propagate
through the system [67]. The state of control i.e., differ-
ent control levels, perturbation handling, process moni-
toring, fault detection and raw material control comprise
of the key elements [68]. In addition, application of
continuous manufacturing in various field is being
reviewed by FDA [69]. The risk-based and science-based
approaches are being promoted. These techniques are
aligned with quality by design paradigm [70]. In general,
the devised control strategies focus on regulating the
product quality during uncertainties by monitoring the
real time quality attributes (Level 1 control), monitoring
the end-product, raw material and process parameters
within the design space (Level 2) and monitoring the
material attributes and process parameters within a tightly
constrained design space (Level 3).
Current Opinion in Chemical Engineering 2019, 30:100671
Current Opinion in Chemical Engineering
Challenges faced during equipment
integration
A number of challenges arise when integrating the myriad
process and analytical equipment that typically exist in a
biopharmaceutical process [71,72,73]. The primary source
of these challenges is the fact that is that the equipment
are typically from different solution providers (analytical
and process equipment vendors) and almost always oper-
ate on a proprietary software, not open to alteration by the
user (Table 3). This is a result of absence of standard
integration protocols between various equipment vendors
and pre-configured functions of the equipment, along
with the absence of industry standard interfaces such
as open platform communication (OPC) for the lab-scale
equipment. Thus, for integrating the different equip-
ment, non-standard solutions such as overlaying a Python
layer using a calibrated coordinate system over the exist-
ing system software is required. Further, different equip-
ment have different IP addresses with no default gateway
configured, leading to challenges in integration on a
common network. Vendor support for integration is typi-
cally limited due to proprietary controls and proprietary
software linked to the unit operation hardware. In gen-
eral, equipment is protected and has custom- built user
interfaces, making it difficult to read data over standard
interface and implement direct control from the DCS.
Additional networking switches/firewalls are typically
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 Challenges in process control for continuous processing for production of monoclonal antibody products Rathore et al.
Table 3
Software challenges faced during integration of lab equipment
Process equipment Description
Bioreactor Single use bioreactor provided by GE
Healthcare Life Science ensures the
controlled environment for stable
growth of cell lines and proteins.
Acoustic Wave A novel filter-less technology provided
Separator by Pall Life Sciences for continuous
clarification on the basis of acousto-
phoretic separation.
BioSMB A multi-column continuous
chromatography technology provided
by Pall Life Sciences capable of
operating 16 columns simultaneously.
Researchers have integrated methods
for two types of chromatography (ex:
Protein A and CEX) such that a single
unit can be used for two different unit
operations in the continuous train.
In-Line Concentration Single-pass tangential flow filtration ILC No commercial software is available for
(ILC) and In-Line and ILD modules provided by Pall Life automated control of this unit operation.
Diafiltration (ILD) Science can achieve concentrations
from 2-10x and diafiltration of 5-10
diavolumes in a single pass. These are
connected in series and used for the
final formulation step in the continuous
train.
Viral Inactivation in A coiled tube with optimized mixing
Coiled Flow parameters used to achieve low pH hold
Inversion Reactor for viral inactivation in a continuous
(CFIR) manner by lowering the pH at the
entrance and allowing fixed residence
time.
Dead End Depth and Dead end filtration is required prior to
Sterile Filtration loading in the Protein A
chromatography columns (depth
filtration) and after viral inactivation
(sterile filtration). Continuous operation
is achieved by maintaining in-line
sensors and standby filters to which the
flow is switched when pressure or
turbidity breakthrough is detected.
required to integrate the equipment on one single net-
work of control system, as they have different IP
addresses and SubNet Masks. In the case of the BioSMB,
the vendor-provided software has multiple constraints
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7
Software challenges Potential solutions
Integrating analytical tools with the PLC based machine learning
existing interface is a challenge causing techniques can be implemented to
difficulty in implementation of model- overcome the challenge.
based control logics, continuous data
acquisition and real time analysis.
Real-time data logging to an external As OPC protocols are not provided by
excel file is supported. However, due to the vendor, an in-house coordinate-
unavailability of OPC, control can only based system can be developed in
be achieved through clicking in the Python to operate the instrument by
existing interface. The interface has layering over the existing interface. This
multiple tabs which require human layer can be in constant communication
intervention. with the DCS.
A human-machine interface is provided As OPC protocols are not provided by
with the equipment for both continuous vendor to read/write the instrument, an
method design and manual operation of in-house coordinate-based system can
pumps and valves. However, the be developed in Python to operate the
software lacks elements required for instrument by layering over the existing
sophisticated continuous automated interface. This layer can be in constant
control. For example, it does not allow communication with the DCS. This
real-time OPC based control of pumps allows control decisions for loading and
and valves, only for switching between elution chromatography steps on the
pre-set recipes which might not be basis of multiple factors including:
sufficient to handle unexpected process product breakthrough, surge tank level
deviations. There is no option for limits, and shifts in aggregate or charge
decision-making based on external variant content. Customized control
scripts or analyzers. Also, there are logic can also be written to schedule at-
limitations in the recipe design software. line HPLC injections, carry out
automated chromatogram integration,
and make pooling decisions based on
inbuilt empirical models.
Customized control logic can be written
to monitor pressure and conductivity
data from integrated in-line sensors and
carry out the following functions:
pressure monitoring, conductivity
monitoring, flux control to achieve
target concentration factor, TMP
control, flow-matching between ILC
and ILD, correct flowrate of formulation
buffer relative to the process stream,
and scheduling of flush, cleaning and
product recovery steps.
No commercial software is available for Customized control logic can be written
automated control of this unit operation. in the DCS to monitor and control pH at
inlet and outlet by integrating with acid
and base pumps and in-line pH sensors.
No commercial software is available for Customized control logic can be written
automated control of this unit operation. in the DCS to monitor the pressure and
turbidity sensors and integrate multi-
way valves to switch the flow path to a
new filter after pressure or turbidity
breakthrough. Customized logic can
also be written to carry out automated
water flush, buffer flush and product
recovery.
which severely limit the range of recipes or control actions
which could be developed, and an entire Python-based
layer has to be developed to by-pass the existing software
for implementation of PAT-based controls and integrated
Current Opinion in Chemical Engineering 2019, 30:100671
8 Biotechnology and Bioprocess Eng; Biotechnology and Bioengineering
Table 4
Key inputs to DCS and key outputs from the DCS
Unit operation Bioreactor AWS Capture
chromatography
Key inputs to Real time Turbidity Concentration
DCS aeration rate Breakthrough of first percentage
Real time column
agitation rate
Cell density
Key outputs Predicted Feed flow rate Valve positions
from DCS aeration rate Recirculation
Predicted flow rate
agitation rate Acoustic power
scheduling with the surge tanks before and after the
chromatography steps. Similar approach needs to be
undertaken for the AWS and ILC-ILD setups. Without
such customized control systems layered over the existing
unit operation hardware and software, it is not possible to
implement advanced scheduling strategies such as surge
tank level management in the case of deviations, or
advanced PAT tools such as NIR monitoring of mAb
and excipient concentrations. In addition, integrated
continuous manufacturing is a potential solution to
address the cost, flexibility, standardization, scaling speed
and quality related challenges of the hybrid biomanufac-
turing systems [71].
Concluding remarks
Continuous manufacturing in biopharmaceutical inte-
grates multiple unit operations and offers significant
advantages with respect to cost reduction, higher produc-
tivity and smaller footprint in comparison to batch pro-
cessing. However, the risk of product or process devia-
tions in a continuous set-up necessitates use of robust and
intelligent controllers that are capable of handling them
in an automated manner. Developing such integrated
controllers has several challenges with respect to devel-
oping model-based control strategies and interfacing
between the unit operation equipment and control sys-
tem. Once appropriate on-line sensors and PAT tools
have been developed and process control models and
loops have been designed, the biggest challenge is over-
coming the closed-source system software. This limits the
ability of the equipment to be interfaced with other
equipment. The optimal control system helps in sched-
uling, data archiving, plotting trends and carrying out
complex model-based analytics for control and prediction
in real time. The proposed control approach supports the
paradigm shift of manufacturing from conventional QbT-
based batch-wise, open-loop production to QbD-based
continuous, closed-loop production.
Acknowledgements
Authors would like to acknowledge funding support from Department of
Biotechnology, Ministry of Science and Technology through the Centre of
Current Opinion in Chemical Engineering 2019, 30:100671
Polishing chromatography Ultrafiltration – diafiltration
Charge variant/aggregate Pressure
Conductivity
Concentration
Elution pooling time Solenoid valve position, peristaltic
pump flow rate
Valve and pump Scheduling time
Excellence scheme (No. BT/COE/34/SP15097/2015). Authors would also
like to acknowledge technical support and funding from Pall Life Sciences
and Tata Consultancy Services.
References and recommended reading
Papers of particular interest, published within the period of review,
have been highlighted as:
 of special interest
 of outstanding interest
Declaration of Competing Interest
The authors report no declarations of interest.
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