Bioprocess Engineering: Kinetics, Sustainability, and Reactor Design

939 Pages·2020·32.013 MB·English

by  Shijie Liu

Bioprocess Engineering
Kinetics, Sustainability, and Reactor Design
Third Edition
Shijie Liu
Professor
Chemical Engineering
SUNY ESF
Syracuse
NY, United States
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Chapter 1
What is bioprocess engineering?
Chapter outline
1.1 Biological cycle 1 1.10 Bioprocesses: regulatory constraints 12
1.2 Bioprocess engineering applications 2 1.11 The pillars of bioprocess kinetics and systems
1.3 Scales: living organism and manufacturing 3 engineering 13
1.4 Green chemistry 4 1.12 Summary 14
1.5 Sustainability 5 Problems 14
1.6 Biorefinery 5 References 14
1.7 Biotechnology and bioprocess engineering 8 Further readings 15
1.8 Mathematics, biology, and engineering 9
1.9 The story of penicillin: the dawn of bioprocess
engineering 9
1.1 Biological cycle
Fig. 1.1 illustrates the natural biological processes occurring on Earth. Living systems consist of plants, animals, and mi-
croorganisms. Sunlight is used by plants to convert CO and H O into carbohydrates and other organic matter, releasing O .
2 2 2
Animals consume plant matter, converting plant materials into animal cells, and using the chemical energy from oxidizing
plant matter into CO and H O (H O also serves as a key substrate for animals), finishing the cycle. Microorganisms further
2 2 2
convert dead animal and/or plant biomass into other form of organic substances fertilizing the growth of plants, releasing
CO and H O, and the cycle is repeated. Energy from the Sun is used to form molecules and organisms that we call life. Ma-
2 2
terials or matter participating in the biological cycle are renewable so long as the cycle is maintained. Bioprocess engineers
manipulate and make use of this cycle by designing processes to make desired products, either by training microorganisms,
plants, and animals, or via direct chemical conversions.
The reactor is the heart of any chemical and/or biochemical processes. With reactors, bioprocesses turn inexpensive sus-
tainably renewable chemicals such as carbohydrates, into valuable ones that humans need. As such, bioprocesses are chemi-
cal processes that use biological substrates and/or catalysts. While not limited to such, we tend to refer to bioprocesses as
(1) biologically converting inexpensive “chemicals” or materials into valuable chemicals or materials; and (2) manipulating
biological organisms to serve as “catalyst” for conversion or production of products that human need. Bioprocess engineers
are the only people technically trained to understand, design, and efficiently handle bioreactors. Bioprocess engineering
ensures that a favorable sustainable state or predictable outcome of a bioprocess is achieved. This is equivalent to saying
that bioprocess engineers are engineers with, differentiating from other engineers, training in biological sciences, especially
quantitative and analytical biological sciences, and green chemistry.
If one thinks of science as a dream, engineering is making the dream a reality. The maturing of Chemical Engineer-
ing to a major discipline and as one of the very few well-defined disciplines in the 1950s has led to the ease in the mass
production of commodity chemicals and completely changed the economics or value structure of materials and chemicals,
thanks to the vastly available what were then “waste” and “toxic” materials—fossil resources. Food and materials can be
manufactured from the cheap fossil materials. Our living standards improved significantly. Today, chemical reactors and
chemical processes are not built by trial-and-error, but by design. The performance of a chemical reactor can be predicted,
not just found to happen that way; the differences between large and small reactors are largely solved. Once a dream for
the visional pioneers, it can now be achieved at ease. Fossil chemical and energy sources have provided much of our needs
for advancing and maintaining the living standards of today. With the dwindling of fossil resources, we are facing yet an-
other value structure change. The dream has been shifted to realizing a society that is built upon renewable and sustainable
resources. Fossil sources will no longer be abundant for human use. Sustainability becomes the primary concern. Who is
going to make this dream come true?
Bioprocess Engineering. http://dx.doi.org/10.1016/B978-0-12-821012-3.00001-4
Copyright © 2020 Elsevier B.V. All rights reserved. 1
2 Bioprocess Engineering
FIGURE 1.1 The natural biological processes.
On a somewhat different scale, we can now manipulate life at its most basic level: the genetic. For thousands of years
people have practiced genetic engineering at the level of selection and breeding, or directed evolution. But now it can be
done in a purposeful, predetermined manner with the molecular-level manipulation of DNA, at a quantum leap level (as
compared with directed evolution) or by design. We now have tools to probe the mysteries of life in a way unimaginable
prior to the 1970s. With this intellectual revolution emerges new visions and new hopes: new medicines, semisynthetic
organs, abundant and nutritious foods, computers based on biological molecules rather than silicon chips, organisms to
degrade pollutants and clean up decades of unintentional damage to the environment, zero harmful chemical leakage to
the environment while producing a wide array of consumer products, and revolutionized industrial processes. Our aim of
comfortable living standards is ever higher.
Without hard work, these dreams will remain merely dreams. Engineers will play an essential role in converting these
visions into reality. Biosystems are very complex and beautifully constructed, but they must obey the rules of chemistry
and physics and they are susceptible to engineering analysis. Living cells are predictable, and processes to use them can be
methodically constructed on commercial scales. There lies a great task—analysis, design, and control of biosystems to the
greater benefit of a sustainable humanity. This is the job of the bioprocess engineer.
This text is organized such that you can learn bioprocess engineering from the principles. To limit the scope of the text, we
have left out the product purification technologies, while focusing on the production generation or biotransformations. We
attempt to bridge molecular level understandings to industrial applications. It is our hope that this will help you to strengthen
your desire and ability to participate in the intellectual revolution and to make an important contribution to the human society.
1.2 Bioprocess engineering applications
In a narrow sense, all human activities are centered around humans. In terms of human needs, bioprocess engineers deal
from the production and application of biomaterials, to health defense, biologics development, and production, including
gene therapy (manufacturing process), to the production of food and fuel as illustrated in Fig. 1.2. In all these applications,
fundamentally, molecular interaction and/or (bio-) transformation governs the production and/or protection processes.
A biologic drug is a product produced from a living organism or containing component(s) of living organisms. Biologics
include recombinant proteins, tissues, genes, allergens, cells, blood components, blood, and vaccines. Biologics are used to
treat numerous disease and conditions on humans. The transformation from chemicals to biologics, the functions or interac-
tions of a biologic with human body, pharmacology, and the design of the biologic are subject areas of bioprocess engineering.
Gene therapy is an experimental technique that uses genes to treat or prevent disease. This technique has the potential
to allow doctors to treat a disorder by inserting a gene into a patient’s cells instead of using drugs or surgery. Researchers
are testing several approaches to gene therapy, including:
Replacing a mutated gene that causes disease with a healthy copy of the gene.
l
Inactivating, or “knocking out,” a mutated gene that is functioning improperly.
l
Introducing a new gene into the body to help fight a disease.
l
Although gene therapy is a promising treatment option for a number of diseases (including inherited disorders, some types
of cancer, and certain viral infections), the technique remains risky and is still under study to make sure that it will be safe
and effective. Gene therapy is currently being tested only for diseases that have no other cures.
Cell therapy is the therapy in which cellular material is injected, grafted, or implanted into a patient; this generally
means intact, living cells. For example, T cells capable of fighting cancer cells via cell-mediated immunity may be injected
in the course of immunotherapy.
What is bioprocess engineering? Chapter | 1 3
FIGURE 1.2 The applications of bioprocess engineering centered around humanity needs.
Cell therapy originated in the 19th century when scientists experimented by injecting animal material in an attempt
to prevent and treat illness. Although such attempts produced no positive benefit, further research found in the mid 20th
century that human cells could be used to help prevent the human body rejecting transplanted organs, leading in time to
successful bone-marrow transplantation
Chimeric antigen receptor (CAR)-modified T cell therapy, for example, has proven to be effective for patients with B
cell hematological malignancies. Challenges remain in how to scale out the production of CAR T cells under current good
manufacturing procedure (cGMP) in an efficient, effective manner. Currently as a mostly autologous cell-based therapy,
the CAR-T cell manufacturing process represents a completely different manufacturing model from traditional biologics.
One of the challenges of this largely personalized medicine is the development of efficient technologies and cost-effective
clinical manufacturing platforms to support the later-stage clinical trials toward commercialization. Substantial efforts have
been placed on the upstream for gene transduction and cell expansion.
Apart from health defense and/or biologics, commodity products production is crucial for the human society. Food,
fuels, and materials fill in the basic needs.
1.3 Scales: living organism and manufacturing
Bioprocess engineering deals with a variable scale, from the molecular level at research to process operation in a factory
at manufacturing level. In health applications, this translates to medical research at the most fundamental level of enzyme/
protein to human health professionals at overall health. Fig. 1.3 shows side-side the comparison from a “traditional” chemi-
cal engineering view on the left to the “health” engineering on the right.
The function of a protein or an enzyme within human cells is important for the overall health of human. When or if
any changes to the protein or a foreign protein invades a human cell, the physiology will change, causing a domino effect/
change to far-reaching cells. Regulating the protein and enzyme functions can also be effected with ligands or chemicals.
The molecular interactions are key to the overall health of humans.
FIGURE 1.3 A comparison of the chemical engineering (left) with processes in a complex living organism: human body. The bottom is at the
microscopic scale where molecular interactions are examined, whereas at the top the factory as a whole is considered.
4 Bioprocess Engineering
1.4 Green chemistry
Green chemistry, also called sustainable chemistry, is a philosophy of chemical research and engineering that encourages
the design of products and processes that minimize the use and generation of hazardous substances while maximizing the
efficiency of the desired product generation. Whereas environmental chemistry is the chemistry of the natural environment,
and of pollutant chemicals in nature, green chemistry seeks to reduce and prevent pollution at its source. In 1990, the Pol-
lution Prevention Act was passed in the United States. This act helped create a modus operandi for dealing with pollution
in an original and innovative way. It aims to avoid problems before they happen.
Examples of green chemistry starts with the choice of solvent for a process—water, carbon dioxide, dry media, and
non-volatile (ionic) liquids, which are some of the excellent choices. These solvents are not harmful to the environment as
either emission can easily be avoided or they are ubiquous in nature.
Paul Anastas, then of the United States Environmental Protection Agency, and John C. Warner developed 12 principles
of green chemistry, which help to explain what the definition means in practice. The principles cover such concepts as—
(1) the design of processes to maximize the amount of (all) raw material that ends up in the product; (2) the use of safe,
environment-benign substances, including solvents, whenever possible; (3) the design of energy efficient processes; and (4)
the best form of waste disposal: not to create it in the first place. The 12 principles are:
1. It is better to prevent waste than to treat or clean up waste after it is formed.
2. Synthetic methods should be designed to maximize “atom efficiency.”
3. Wherever practicable, synthetic methodologies should be designed to use and generate substances that possess little or
no toxicity to human health and the environment.
4. Chemical products should be designed to preserve efficacy of function while reducing toxicity.
5. The use of auxiliary substances (e.g., solvents, separation agents, etc.) should be made unnecessary wherever possible
and innocuous when used.
6. Energy requirements should be recognized for their environmental and economic impacts and should be minimized.
Synthetic methods should be conducted at ambient temperature and pressure.
7. A raw material or feedstock should be renewable rather than depleting wherever technically and economically
practicable.
8. Reduce derivatives—Unnecessary derivatization (blocking group, protection/ deprotection, temporary modification)
should be avoided whenever possible.
9. Catalytic reagents (as selective as possible) are superior to stoichiometric reagents.
10. Chemical products should be designed so that at the end of their function they do not persist in the environment and
break down into innocuous degradation products.
11. Analytical methodologies need to be further developed to allow for real-time, in-process monitoring and control prior
to the formation of hazardous substances.
12. Substances and the form of a substance used in a chemical process should be chosen to minimize potential for chemi-
cal accidents, including releases, explosions, and fires.
One example of green chemistry achievements is the polylactic acid (or PLA). In 2002, Cargill Dow (now NatureWorks)
won the Greener Reaction Conditions Award for their improved polylactic acid polymerization process. Lactic acid is pro-
duced by fermenting corn and converted to lactide, the cyclic dimmer ester of lactic acid using an efficient, tin-catalyzed
cyclization. The L,L-lactide enantiomers is isolated by distillation and polymerized in the melt to make a crystallizable
polymer, which has use in many applications including textiles and apparel, cutlery, and food packaging. Wal-Mart has
announced that it is using/will use PLA for its produce packaging. The NatureWorks PLA process substitutes renewable
materials for petroleum feedstocks, does not require the use of hazardous organic solvents typical in other PLA processes,
and results in a high-quality polymer that is recyclable and compostable.
Understanding the concept of green chemistry holds a special position for bioprocess engineers. Processes we design
and operate must have minimal potential environmental impacts while optimized for maximum benefit. Basic steps for
green chemistry that are what bioprocess engineering do include:
1. Developing products and processes based on renewable resources, such as plant biomass;
2. Design processes that bypass dangerous/toxic-chemical intermediates;
3. Design processes that avoid dangerous/toxic solvent use;
4. Reducing chemical processing steps, but demands high efficiency;
5. Promoting biochemical processes to reduce chemical processing steps or toxic chemical utilization;
6. Design milder (closer to atmosphere temperature and pressure) processes and multiple product recovery routes;
What is bioprocess engineering? Chapter | 1 5
7. Bypassing chemical equilibrium with innovative reactor design, and biocatalysis, rather than adding intermediate steps.
8. Avoid production of unwanted products other than H O and CO .
2 2
1.5 Sustainability
Sustainability is the capacity to endure or maintain at the longest timescale permissible. In other words, sustainability is the
ability to maintain continuum. In ecology, the word describes how biological systems remain diverse and productive over
time. Long-lived and healthy wetlands and forests are examples of sustainable biological systems. For humans, sustainabil-
ity is the potential for long-term maintenance of well-being, which has environmental, economic, and social dimensions.
Healthy ecosystems and environments provide vital goods and services to humans and other organisms. Utilization and
release of substances at a rate that is harmonious with a steady state nature is the key for sustainability. This naturally leads
to a carrying capacity for each substance or species with which humans interact. The sustainable state can be influenced by
(process conditions or) how we interact with nature. There are two major ways of reducing negative human impact and en-
hancing ecosystem services. The first is environmental management; this approach is based largely on information gained
from earth science, environmental science, and conservation biology. The second approach is management of human con-
sumption of resources, which is based largely on information gained from economics. Practice of both of these major steps
can ensure a more favorable sustainable state to be evolved into.
Sustainability interfaces with economics through the social and ecological consequences of economic activity. Sus-
tainable economics involves ecological economics where social, cultural, health-related, and monetary/financial aspects
are integrated. Moving toward sustainability is also a social challenge that entails international and national law, urban
planning and transport, local and individual lifestyles and ethical consumerism. Ways of living more sustainably can take
many forms from reorganizing living conditions (e.g., ecovillages, eco-municipalities, and sustainable cities), reapprais-
ing economic sectors (permaculture, green building, sustainable agriculture), or work practices (sustainable architecture),
using science to develop new technologies (green technologies, renewable energy), to adjustments in individual lifestyles
that conserve natural resources. These exercises reduce our reliance or demand on disturbing the environment. To make all
these concepts come to light, bioprocess engineers will be at the forefront of developing and implementing the technologies
needed. On a grand scale, maintaining renewability or looking for a favorable predictable steady state on everything we
touch or interact is the key to sustainability (Fig. 1.4). This falls right in the arena of bioprocess engineering.
Are you ready for the challenge of designing processes that meets sustainability demands?
1.6 Biorefinery
On a grand scale, sustainability is the basis of nature. Enforcing sustainability at the time scale of humanity is an insurance
of our way of life to continue. Prior to the 1900s, agriculture and forestry were the predominant sources of raw materi-
als for energy, food and a wide range of everyday commodities, and the human civilization depended almost entirely on
renewable materials. Humanity was restricted by the sustainable supply inefficiently harvested from the biomass, which
drew energy from the sun. The industrial revolution has brought a leap in the human civilization. Mass production of goods
by machines dominates our daily life. The industrial revolution was brought to mature by the development of combustion
FIGURE 1.4 Change of sustainable state owing to human interruption.
6 Bioprocess Engineering
engines and subsequent development of fossil energy and chemical industry. Besides the more than doubling of useful bio-
mass production/harvest, mankind has increasingly tapped into the large fossil-energy reserves. At first the fossil chemicals
were regarded as waste and thus any use was welcomed. It soon became the cheapest chemical and energy sources for the
industrial revolution. As a result, our living standards have seen a leap. There is no turning back to the primitive way of life
in the past. However, fossil energy and chemical sources are depleting despite the cyclic price change of energy and com-
modity materials. There is a critical need to change the current industry and human civilization to a sustainable manner,
assuring that our way of life today continues on the path of improvement after the depletion of fossil sources. Our way of
life exists only if sustainability is maintained on a time scale no longer than our life span.
Biorefinery is concept in analogous to a petroleum refinery whereby a raw material feed (in this case plant ligocellulosic
biomass instead of petroleum) is refined to a potpourri of products (on demand). In a biorefinery, lignocellulosic biomass
is converted to chemicals, materials, and energy that runs on the human civilization, replacing the needs of petroleum,
coal, natural gas, and other non-renewable energy and chemical sources. Lignocellulosic biomass is renewable as shown
in Fig. 1.1, in that plant synthesizes chemicals by drawing energy from the sun and, carbon dioxide and water from the
environment, while releasing oxygen. Combustion of biomass releases energy, carbon dioxide, and water. Therefore, biore-
finery plays a key role in ensuring the cycle of biomass production and consumption included satisfying human needs for
energy and chemicals.
A biorefinery integrates a variety of conversion processes to produce multiple product streams such as transportation
liquid fuels, steam/heat, electricity, and chemicals from lignocellulosic biomass. Biorefinery has been identified as the most
promising route to the creation of a sustainable bio-based economy. Biorefinery is a collection of the essential technologies
to transform biological raw materials into a range of industrially useful intermediates. By producing multiple products,
a biorefinery maximizes the value derived from a lignocellulosic biomass feedstock. A biorefinery could produce one or
more low-volume, high-value chemical products together with a low-value, high-volume liquid transportation fuel, while
generating electricity and process heat for its own use and/or export.
Fig. 1.5 shows a schematic of various biorefinery processes. There are at least three steps in converting woody biomass:
pretreatment; cracking or rendering biomass to intermediate molecules; and conversion (of the intermediate molecules to
desired products). There are three major categories or approaches in pretreatment—systematical disassembling processes;
pyrolysis and gasification processes. In systematical disassembling processes, the lignocellulosic biomass is commonly
disassembled to individual components systematically for optimal conversions that followed. The basic approach is based
on a systematical disassembling and conversion to desired chemicals. This pretreatment method and the rout of conversion
FIGURE 1.5 A schematic of various biorefinery processes. (With permission from: Liu, S., 2015. A synergetic pretreatment technology for woody
biomass conversion. Appl. Ener. 144, 114–128).
What is bioprocess engineering? Chapter | 1 7
followed depend heavily on separation and/or physical fractionation of the intermediates as well as the final desired prod-
ucts. Pyrolysis applies heat and some oxygen (or none) to render the biomass to liquid, while gasification renders the bio-
mass to syngas. Biological conversions are preferred over chemical conversions due to their selectivity or green chemistry
concepts. However, owing to the complexity of the lignocellulosic biomass, a multitude of biological processes is required
for optimal operations. The biological reactions are also very slow and thus require larger facility foot prints. Especially
following the gasification, bioconversion is in the “primitive” stage of development.
Pyrolysis resembles more closely to the refinery whereby the products can be controlled in a more systematical man-
ner. It may be classified as systematical disassembling as well. However, there are restrictions on the type of products
the process can produce. Gasification as shown in Fig. 1.5 is at the extreme side of conversion technology, whereby the
lignocellulosic biomass is disassembled to the basic building block for hydrocarbons: H and CO, and then reassembled
2
to desired products as desired. The final products can be more easily tailored from syngas or CO + H . For example,
2
Fisher-Tropsch process can turn CO + H into higher alcohol, alkenes, and many other products. Syn gas (together with
2
air: mixture of N and O ) is also the starting point for ammonia synthesis, from which nitrogen fertilizers and many other
2 2
products are produced. However, all thermochemical processes suffer from selectivity. During the disassembling process,
“coke” or “carbon” is produced especially at high temperatures and thus reduces the conversion efficiency, if H and CO
2
are the desired intermediates. Thermal-chemical processes are generally considered less “green” than biological and other
sequential disassembling processes due to their severe operating conditions, poor selectivity or byproducts generation, and
thermodynamic restrictions.
The promise of a biorefinery to supply the products human needs is shown in Fig. 1.6 for the various examples of build-
ing blocks or platform chemicals that sugar (a specific example of glucose) can produce, besides the very basic building
blocks of CO and H . For example, glucose can be fermented to ethanol by yeast and bacteria anaerobically, and lactic acid
2
can be produced by lacto bacteria. As shown in Fig. 1.6, each arrow radiates from the glucose in the center represents a route
of biotransformation (or fermentation) by default, whereas chemical transformations are shown with labeled arrows. For
example, glucose can be dehydrated to 5-hydroxymethylfurfural catalyzed with an acid, which can be further decomposed
to levulinic acid by hydration. All these chemicals shown in Fig. 1.6 are examples of important platform (or intermediate)
chemicals, as well as commodity chemicals. For example, ethanol is well known for its use as a liquid transportation fuel.
FIGURE 1.6 The platform of chemicals derived from glucose (the molecule in the center of the diagram). Most of these chemicals are produced
via fermentation (or biotransformation), while a few of them are produced via chemical reaction (or chemical transformation) as indicated.