Introduction

Biochemical engineering, also known as bioprocess engineering, is a field of study with roots
stemming from chemical engineering and biological engineering. It mainly deals with the design,
construction, and advancement of unit processes that involve biological organisms (such as
fermentation) or organic molecules (often enzymes) and has various applications in areas of
interest such as biofuels, food, pharmaceuticals, biotechnology, and water treatment processes.
The role of a biochemical engineer is to take findings developed by biologists and chemists in a
laboratory and translate that to a large-scale manufacturing process. They also have to design
bioreactors that can facilitate the growth of biological mass through the transformation or
degradation of material fed to the reactor.(Bioremediation of Pollutants, 2020). This is done
through special scientific software.

Literature Review

The mixture of technology and education opens up endless possibilities. Thus, the use of
technology brings about various delivery methods. It has access to a massive amount of
information, global interaction to enhance learning, and excellent examples through simulations
and models.(Arya, 2019). With the rise of technology, new and better software are now used in
the designing of bioreactors. One example of such software is MATLAB. MATLAB is a high-
level technical computing language and interactive environment for algorithm development, data
visualization, data analysis, and numeric computation. With MATLAB, scientists and engineers
can hybridize data from many data streams, including signal, image, text, and genetic, optimize
pharmaceutical production through process engineering, perform modeling and simulation for
drug discovery and development and create automatic output reports in Adobe Acrobat, or
Microsoft Word and PowerPoint file formats

Another recognized software in modelling biochemical processes is LabVIEW. It is a graphical

programming language designed for hardware automation. Programs in LabVIEW are called
virtual instruments (VIs) and integrate a graphical user interface (GUI) with the development of
code. A VI contains three components: a front panel, a block diagram, and a connector panel.
The front panel serves as the GUI which contains elements referred to as controls and indicators.
Controls such as buttons, sliders, and text boxes, allow the user to manipulate the value of data
used during code execution. Data values are displayed on the front panel with indicators such as
graphs, indicator lights, and gauges. Controls and indicators appear as terminals on the block
diagram where code development takes place. Block diagram structures, such as while loops,
control program execution and can reroute the data flowing through wires allowing for more
complex functionality. Due to LabVIEW’s native multitasking capabilities, execution of parallel
processes, such as data flowing through wires, occurs concurrently.

COMSOL Multiphysics software, an interactive environment for modeling and simulating

scientific and engineering problems, is a general-purpose software platform, based on advanced
numerical methods, for modeling and simulating physics-based problems. With COMSOL
Multiphysics, it is possible to account for coupled or multiphysics phenomena. With more than
30 add-on products to choose from, the simulation platform can be expanded with dedicated
physics interfaces and tools for biochemical applications. For example, COMSOL was applied
into the design of the passive vaccine storage device (PVSD) to safely transport vaccines to
every part of the world. During its design phase, the researchers tested the performance of
several PVSD prototypes in an environmental chamber with similar temperatures to those found
in Sub-Saharan Africa. To optimize the design of their PVSD system, prior to building
prototypes, the team used COMSOL Multiphysics and a variety of its add-on modules, including
the Heat Transfer Module and Molecular Flow Module.(Pambudi et al, 2020)

Another powerful software used in bioreactor design is ChemDraw. This is a drawing program
that allows users to sketch skeletal structures of chemical compounds, which can then be moved
into other programs, like MS Word, PowerPoint, and Adobe Illustrator. Users can also use it to
predict properties and spectra, convert chemical structures to IUPAC names, view 3D structures,
etc. ChemDraw is not limited to drawing chemical structures. Certain versions include
customizable bio-art ranging from enzymes and receptors to cartoons of entire organisms and
bench equipment. Templates in combination with chemical structures and reaction schemes can
be used to show how an experiment is performed or how a compound fits into an overall
experiment. One successful application of ChemCAD was in pervaporation as a process method
for concentrating formic acid produced from carbon dioxide. Azeotropic distillation simulations
for the formic acid (FA) – water (H2O) system using ChemCad 6.0 were used to determine the
energy requirement using steam costs in processing FA feed concentrations ranging from 5 to
30wt%. ( Kaczur et al,2020).
AutoCAD is a CAD (Computer Aided Design or Computer Aided Drafting) software application
for 2D and 3D design and drafting. It is developed and sold by Autodesk Inc., along with related
products like Revit, MEP, and 3ds Max Design. CAD software replaces the traditional drawing
board and makes design processes faster and smarter than ever before. (Bethany, 2017).In the
Nanoliter Volume Bioreactors for Cell Culturing, Autocad in combination with L-edit softwares
were used to design to types of microbioreactors, one having electrodes while the other was
designed without electrodes.This investigation was done to fulfil the desired functionalities such
as mixing, separation, flow control or setting the environment for biochemical reactions.
(Gencturk et al, 2021).

METAMOD, a BBC microcomputer-based software package for steady-state modelling and

control analysis of model metabolic pathways, is described, The package consists of two
programs. METADEF allows the user to define the pathway in terms of reactions, rate equations
and initial concentrations of metabolites. METACAL uses one of two algorithms to calculate the
steady-state concentrations and fluxes. One algorithm uses the current ratio of production and
consumption rates of variable metabolites to adjust iteratively their concentrations in such a way
that they converge towards the steady state. The other algorithm solves the roots of the system
equations by means of a quasi-Newtonian procedure. Control analysis allows the calculation of
elasticity, control and response coefficients, by means of finite difference approximation.
METAMOD is interactive and easy to use, and suitable for teaching and research purposes.
(Hofmeyr, 1986).

A very common software used in bioreactor design is Mathematica. It is a computational

software program based on symbolic mathematics that is used in scientific, engineering,
mathematical, and computing fields. Mathematica includes collections of curated data provided
for use in computations. It is integrated with Wolfram Alpha, an online service which provides
additional data, some of which is kept updated in real time. Some of the data sets include
astronomical, chemical, geopolitical, language, biomedical, and weather data.CplexA is a
Mathematica package that uses functional programming to efficiently compute probabilities and
average properties over such exponentially large number of states from the energetics of the
interactions. The package is particularly suited to study gene expression at complex promoters
controlled by multiple, local and distal, DNA binding sites for transcription factors.(Vilar and
Saiz, 2010).

John’s Macintosh Project software (JMP) links statistical data to graphics representing them, so
users can drill down or up to explore the data and various visual representations of it. Its primary
applications are for designed experiments and analyzing statistical data from industrial processes.
It is the next generation statistical software for interactive data analysis, visualization, modeling
and simulation. Key features include: Design of experiments (DOE) and robust process
optimization. Engineering analytics and predictive modeling.Since mixing in bioreactors is
known to be crucial for achieving efficient mass and heat transfer, both of which thereby impact
not only growth of cells but also product quality, the JMP software models the hydrodynamics
of an aerated stirred bioreactor for the production of biological mass via a cell culture.This is
achieved by estimating the volume averaged mass transfer coefficient under varying conditions
of the process parameters. (Sarkar et al, 2016).

OriginPro is a proprietary computer program for interactive scientific graphing and data analysis.
It is produced by OriginLab Corporation, and runs on Microsoft Windows. It has inspired several
platform-independent open-source clones and alternatives like LabPlot and SciDAVis. OriginPro
offers extended analysis tools for Peak Fitting, Surface Fitting, Statistics, Signal Processing and
Image Handling. Users can customize operations such as importing, graphing and analysis, all
from the GUI. Graphs, analysis results and reports update automatically when data or parameters
change.One application of OriginPro involves the development and characterization of a
parallelizable perfusion bioreactor for 3D cell culture.Here, a miniaturized, parallelizable
perfusion bioreactor system with two different bioreactor chambers was developed to allow the
cultivation of multiple independent samples under different conditions while ensuring
comprehensive control over the mechanical environment.
References

Pambudi, N.A., Sarifudin, A., Gandidi, I.M. and Romadhon, R., 2022. Vaccine cold chain
management and cold storage technology to address the challenges of vaccination programs.
Energy Reports, 8, pp.955-972.

Kaczur, J.J., McGlaughlin, L.J. and Lakkaraju, P.S., 2020. Investigating pervaporation as a
process method for concentrating formic acid produced from carbon dioxide. C, 6(2), p.42.

Gencturk, E., Mutlu, S. and Ulgen, K.O., 2021. Fabrication Protocol for Thermoplastic
Microfluidic Devices: Nanoliter Volume Bioreactors for Cell Culturing. In Bioreactors in Stem
Cell Biology: Methods and Protocols (pp. 27-38). New York, NY: Springer US.

Vilar, J.M. and Saiz, L., 2010. CplexA: a Mathematica package to study macromolecular-
assembly control of gene expression. Bioinformatics, 26(16), pp.2060-2061.

Sarkar, J., Shekhawat, L.K., Loomba, V. and Rathore, A.S., 2016. CFD of mixing of multi ‐phase
flow in a bioreactor using population balance model. Biotechnology Progress, 32(3), pp.613-628.