Bioprocess engineering kinetics, biosystems, sustainability, and reactor design by shijie liu

BIOPROCESS ENGINEERING KINETICS, BIOSYSTEMS, SUSTAINABILITY, AND REACTOR DESIGN SHIJIE LIU SUNY ESF Department of Paper and Bioprocess Engineering, Syracuse, NY 13210, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD PARIS • SAN DIEGO • SAN FRANCISCO • SYDNEY • TOKYO Elsevier Radarweg 29, PO Box 211, 1000 AE Amsterdam, The Netherlands The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK First edition 2013 Copyright Ó 2013 Elsevier B.V All rights reserved No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; email: permissions@elsevier.com Alternatively you can submit your request online by visiting the Elsevier web site at http://elsevier com/locate/permissions, and selecting Obtaining permission to use Elsevier material Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN: 978-0-444-59525-6 For information on all Elsevier publications visit our website at www.store.elsevier.com Printed and bound in Spain 12 13 14 15 16 10 Preface All I know is just what I read in the papers Will Rogers area of Biology and Chemical Engineering, to a discipline that covers the engineering and engineering science aspects of biotechnology, green chemistry, and biomass or renewable resources engineering As such, textbooks in the area are needed to cover the needs of educating the new generation of fine bioprocess engineers, not just by converting well-versed chemical engineers and engineering-savvy biologists to bioprocess engineers I hope that this textbook can fill this gap and brings the maturity of bioprocess engineering Yet, some of the materials in this text are deep in analyses that are suited for graduate work and/or research reference The key aspect that makes Bioprocess Engineering special is that Bioprocess Engineering as a discipline is centered around solving problems of transformation stemmed from cellular functions and biological and/ or chemical conversions concerning the sustainable use of renewable biomass The mechanism, rate, dynamic behavior, transformation performance and manipulations of bioprocess systems are the main topics of this text Chapter is an introduction of bioprocess engineering profession including green chemistry, sustainability considerations and regulatory constraints Chapter is an overview of biological basics or cell chemistry including cells, viruses, stem cell, amino acids, proteins, carbohydrates and various biomass components, and fermentation media In Chapter 3, a survey of chemical reaction analysis is introduced The basic knowledge of reaction rates, conversion, yield, stoichiometry and energy regularity The quote above is quite intriguing to me and reflective of this text Everything in this text can be found either directly or with “extrapolation” or “deduction” from the books and papers one can find to date The most influential books to this time are the “Biochemical Engineering Fundamentals” by J.E Bailey and D.F Ollis, “Elements of Chemical Reaction Engineering” by H.S Fogler, “The Engineering of Chemical Reactions” by L.D Schmidt, “Chemical Reaction Engineering” by O Levenspiel, “Bioprocess EngineeringdBasic Concepts” by M.L Shuler and F Kargi, and many others All these texts and others have formed part of this text In no intention this text is compiled to replace all these great textbooks of the time A mere rearrangement and/or compiling is made in this text to give you the reader an opportunity to understand some of the basic principles of chemical and biological transformations in bioprocess engineering The computer age has truly revolutionized the literature, beyond the literature revolution brought about by the mass production or availability of paper and distribution of books via library The explosion of the shear amount of literature, birth of interdisciplines and disciplines or subject areas in the past decades has been phenomenal Bioprocess Engineering is one that born of biotechnology and chemical engineering With the maturing of Bioprocess Engineering as a discipline, it evolves from an interdisciplinary subject ix x PREFACE for bioreactions are reviewed The concepts of approximate and coupled reactions are introduced, providing the basis of understanding for the metabolic pathway representations later in the book Mass and energy balances for reactor analyses, as well as the definitions of ideal reactors and commonly known bioreactors are introduced before an introduction to reactor system analyses The biological basics and chemical reaction basics are followed by the reactor analysis basics in Chapters and 5, including the effect of reaction kinetics, flow contact patterns and reactor system optimizations Gasification (of coal and biomass) is also introduced in Chapter How the ideal reactors are selected, what flow reactor to choose and what feed strategy to use are all covered in Chapter Chapters 6, 7, 8, 9, 10 and 11 are studies on bioprocess kinetics In Chapter 6, you will learn the collision theory for reaction kinetics and approximations commonly employed to arrive at simple reaction rate relations Kinetics of acid hydrolysis, of an important unit operation in biomass conversion, is introduced as a case study In Chapter 7, we turn to discuss the techniques for estimating kinetic parameters from experimental data, breaking away from the traditional straight line approaches developed before the computer age You can learn how to use modern tools to extract kinetic parameters reliably and quickly without complex manipulation of the data In Chapters and 9, we discuss the application of kinetic theory to catalytic systems Enzymes, enzymatic reactions and application of enzymes are examined in Chapter 8, while adsorption and solid catalysis are discussed in Chapter The derivation of simplified reaction rate relations, such as the MichaeliseMenten equation for enzymatic reaction and LHHW for solid catalysis, is demonstrated The applicability of these simple kinetic relations is discussed In Chapter 9, you will learn both ideal and non-ideal adsorption kinetics and adsorption isotherms Is multilayer adsorption the trademark for physisorption? The heterogeneous kinetic analysis theory is applied to reactions involving woody biomass where the solid phase is not catalytic in x9.5 Chapter 10 discusses the cellular genetics and metabolism The replication of genetic information, protein production, substrate uptake, and major metabolic pathways are discussed, hinting at the application of kinetic theory in complicated systems In Chapter 11, you will learn how cell grows: cellular material quantifications, batch growth pattern, cell maintenance and endogenous needs, medium and environmental conditions, and kinetic models Reactor analyses are also presented in Chapters and 11 In Chapters 12 and 13, we discuss the controlled cell cultivation Continuous culture and wastewater treatment are discussed in Chapter 12 Exponential growth is realized in continuous culturing An emphasis is placed on the reactor performance analyses, using mostly Monod growth model in examples, in both Chapters Chapter 13 introduces fed-batch operations and their analyses Fed batch can mimic exponential growth in a controlled manner as opposed to the batch operations where no control (on growth) is asserted besides environmental conditions Chapter 14 discusses the evolution and genetic engineering, with an emphasis on biotechnological applications You will learn how cells transform, how cells are manipulated, and what some of the applications of cellular transformation and recombinant cells are Chapter 15 introduces the sustainability perspectives Bioprocess engineering principles are applied to examine the sustainability of biomass economy and atmospheric CO2 Is geothermal energy a sustainable or renewable energy source? Chapter 16 PREFACE discusses the stability of catalysts: activity of chemical catalyst, genetic stability of cells and mixed cultures, as well as the stability of reactor systems Sustainability and stability of bioprocess operations are discussed A stable process is sustainable Multiple steady states, approach to steady state, conditions for stable operations and predatoreprey interactions are discussed Continuous culture is challenged by stability of cell biomass In ecological applications, sustainability of a bioprocess is desirable For industrial applications, the ability of the bioprocess system to return to the previous set point after a minor disturbance is an expectation In Chapter 17, the effect of xi mass transfer on the reactor performance, in particular with biocatalysis, is discussed Both external mass transfer, e.g suspended media, and internal mass transfer, e.g immobilized systems are discussed, as well as temperature effects The detailed numerical solutions can be avoided or greatly simplified by following directly from the examples It is recommended that examples be covered in classroom, rather than the reading material Chapter 18 discusses the reactor design and operation Reactor selection, mixing scheme, scale-up, and sterilization and aseptic operations are discussed Shijie Liu Nomenclature a a a ad a A A A A Ac ADP AMP ATP B B BOD BOD5 c C C C C CP CoA CHO COD CSTR d D Catalyst activity Specific surface or interfacial area, m2/m3 Thermodynamic activity Dimensionless dispersion coefficient Constant Chemical species Adenine Constant Heat transfer area, m2 Acetyl Adenosine diphosphate Adenosine monophosphate Adenosine triphosphate Chemical species Constant Biological oxygen demand Biological oxygen demand measured for days constant Chemical species Concentration, mol/L or kg/m3 Constant Cytosine Heat capacity, J/(mol$K), or kJ/(kg$K) Coenzyme A Chinese hamster ovary cell Chemical oxygen demand Continuously stirred tank reactor Diameter, m Diameter, m D D De DO DNA e E E EMP f f F F FAD FADH FDA FES g G G GRAS GMP GTP h H HC HMP J xiii Diffusivity, m2/s Dilution rate, sÀ1 Chirality or optical isomers: right-hand rule applies Concentration of dissolved oxygen, g/L Deoxyribonucleic acid electron Enzyme Energy, kJ/mol Embden-Meyerhof-Parnas Fractional conversion Fanning friction factor Flow rate, kg/s or kmol/s Farady constant Flavin adenine dinucleotide in oxidized form Flavin adenine dinucleotide in reduced form Food and Drug administration Fast equilibrium step (hypothesis) Gravitational acceleration, 9.80665 m2/s Gibbs free energy, kJ/mol Guanine Generally regarded as safe Good manufacture practice Guanosine triphosphate height or length Enthalpy, kJ/mol or kJ/kg Harvesting cost Hexose Monophosphate (pathway) Total transfer flux, kmol/s or kg/s xiv J k k K K KL L Lm _ m mS M MC MG MR MS MSS n N N NAD NADP OR OTR OUR p P P P P NOMENCLATURE Transfer flux, kmol/(m2$s) or kg/(m2$s) Kinetic rate constant Mass transfer coefficient, m/s Thermodynamic equilibrium constant Saturation constant, mol/L or kg/L Overall mass transfer coefficient (from gas to liquid) Length Chirality or optical isomers: left hand rule applies Amount of mass, kg Mass flow rate, kg/s Maintenance coefficient Molecular weight, Darton (D) or kg/kmol Molar (or mass) consumption rate Mass generation rate Mass removal rate Molar or Mass supply rate Multiple steady state Total matters in number of moles Mass transfer rate, kJ/(m2$s) or kg/(m2$s) Number of species Nicotinamide adenine dinucleotide Nicotinamide adenine dinucleotide phosphate Order of reaction Oxygen transfer rate Oxygen utilization rate Pressure Probability Pressure Product, or Product concentration, kg/m3, or g/L, or mol/L Power (of stirrer input) PX P0 P1 PCR PEP PFR PP PSSH P/O q Q _ Q r r R R R R Re RNA s S S S S S Sh SMG SMR t T T Productivity or production rate of biomass Probability of the vanishing of the entire population Probability of the entire population not vanishing Polymerase chain reaction Phosphoenol pyruvate Plug flow reactor Pentose phosphate (pathway) Pseudo-steady-state hypothesis ATP formation per oxygen consumption Thermal flux, J/s or W Volumetric flow rate, m3/s Thermal energy transfer rate into the system Radial direction Rate of reaction, mol/(m3$s) or kg/(L$s) Correlation coefficient Ideal gas constant, 8.314 J/ (mol$K) Product, or product concentration Recycle ratio Reynolds number Ribonucleic acid Selectivity Entropy Overall selectivity Substrate (or reactant) Substrate concentration, g/L Surface area, m2 Sherwood number Specific mass generation rate Specific mass removal rate Time, s Temperature, K Thymine xv NOMENCLATURE TCA u U U U U CoQn v V _ W _s W x x X X XSU XSU y y Y YF z z Z Z Tricarboxylic acid superficial velocity, m/s Average velocity or volumetric flux Internal energy Overall heat transfer coefficient, kJ/m2 Uracil Co-Enzyme ubiquinone Molar volume, m3/kmol Volume, m3 Rate of work input to the system Rate of shaft work done by the system Variable Axial direction Cell or biomass Cell biomass concentration, LÀ1, or g/L Biomass storage for managed forest Biomass storage for undisturbed unmanaged forest Mole fraction Variable Yields Yield factor, or ratio of stoichiometric coefficients Vertical direction Variable Collision frequency Valence of ionic species Greek Symbols a a b b Constant Chirality or optical isomers: two chiral centers with different hand gestures Heat of reaction parameter Constant b c g g gDR d D ε f h q m m mf n nf r s s s u u u Chirality or optical isomers: two chiral centers with the same hand gestures Fraction Thermodynamic activity coefficient Activation energy parameter Degree of reduction Thickness or distance Difference Void ratio Thiele modulus Effectiveness factor Fractional coverage (on available active sites) Specific rate of formation, or rate of reaction normalized by the catalyst or cell biomass concentration, sÀ1 or g$gÀ1$sÀ1 Specific biomass growth rate, sÀ1 or g$gÀ1$sÀ1 Dynamic viscosity of fluid, Pa$s Stoichiometric coefficient Kinematic viscosity of fluid or medium, m2/s Density, kg/m3 Active site Variance Space time, s Mass fraction Rotational speed Weighting factor Subscript ads app A b B c Adsorption Apparent Species A reverse reaction Batch Combustion xvi cat C C C C d d des D e e e eq eff f f f f F G H H i i i in I j m max net OPT NOMENCLATURE Catalyst Species C Cold stream Concentration based Calculated based on model Death Doubling Desorption Diffusion coefficient related Endogenous (growth needs) External (mass transfer) In effluent stream Equilibrium Effective Final or at end Fluid or medium Formation Forward reaction In feed stream Growth Heat of reaction Hot stream Reaction i Initial Impeller Inlet Inhibition Species j Maximum Maximum Net Optimum obs out p P P R R s S S S S S t T T U 0 + À N S Observed Outlet Particle Product Preparation Reaction; Reactor Reference; Reduced Solid Sterilization Saturation Substrate Surface Total species Tube, or reactor Tube Total Unloading Initial In feed Pre-exponential Plasmid-containing Plasmid-free maximum or at far field Total or sum Superscript * * 0 (Thermodynamic) Standard conditions Equilibrium Based on transitional state Catalyst mass based Variant 922 18 BIOREACTOR DESIGN AND OPERATION is no “back-mixing” of the reactant stream with product stream Reactants are loaded initially and the products are unloaded at the end of the reaction A batch reactor is characterized by no input into or output from the reactor during the course of the reaction, eliminating the potential of external contamination The substrate concentration remains highest inside the reactor, while the product concentration remains the lowest possible in the reactor The reactor operation is terminated when reaction is completed as desired A CSTR is characterized by a steady feed of substrate(s) into and effluent out of the reactor The substrate concentration can be controlled to a given value and is the lowest in the reactor The product concentration in the reactor is the highest The reactor operation is not to be terminated frequently (by design) A fed-batch reactor is a mode between batch and CSTR operation It can be designed to capture the qualities of a CSTR operation (and more), while maintaining the flexibility of a batch reactor operation The primary form of continuous culture is a steady-state CSTR or chemostat A chemostat ensures a time-invariant chemical environment for the cell cultivation The net-specific growth rate is equal to the dilution rate, which is determined by the flow rate to the chemostat Thus, the growth rate can be manipulated by the investigator This is a typical method of controlling the cell growth (and/or production formation rate) A constant dilution rate gives rise to a constant specific growth rate, which is equivalent to a fixed exponential growth rate Another benefit is the control of substrate concentration in the reactor at a given value, which can promote a desired product formation A cytostat (or turbidostat) adjusts flow rate to maintain a constant cell density (via turbidity) Cell density control via adjusting flow rate is not effective except at high flow rates A turbidostat operates well at high flow rates (near the washout point) and is useful in selecting cellular subpopulations that have adapted to a particular stress Continuous culturing is more productive than batch culturing The productivity of chemostat increases with increasing dilution rate to a maximum before sharply decreases near the washout limit There is a maximum cell biomass concentration near the washout limit The growth and/or product formation patterns can be different between batch and continuous cultivations In a batch system, lag phase is commonly observed which is absent in a continuous system On the other hand, Crabtree effect can be observed with changing flow rates in a continuous system, which is absent in a batch cultivation curve since the change occurs when the substrate is nearly completely consumed Bioreactors using suspended cells can be operated in many modes intermediate between a batch reactor and a single-stage chemostat Although a chemostat has potential productivity advantages for primary products, considerations of genetic instability, process flexibility, low quantities of product demand, and process reliability (such as biocontamination and biostability) have greatly limited the use of chemostat units The use of cell recycle with a CSTR increases volumetric productivity and has found use in large-volume, consistent production demand and low-product value processes (e.g waste treatment and fuel-grade ethanol production) Multistage continuous systems improve the potential usefulness of continuous processes for the production of secondary metabolites and for the use of genetically unstable cells The perfusion system is another option that is particularly attractive for animal cells 18.3 AERATION, AGITATION, AND HEAT TRANSFER 923 Batch operations are not controllable as all the substrate is added into the reactor at the start Fed-batch reactor is based on feeding of a growth-limiting nutrient substrate to a culture Cell growth and fermentation can be controlled by the feeding strategy The fedbatch strategy is typically used in bio-industrial processes to reach a high cell density in the bioreactor Mostly, the feed solution is highly concentrated to avoid dilution of the bioreactor In essence, fed-batch reactor is applied in such a fashion that a chemstat or CSTR is simulated with a seemingly batch operation The controlled addition of the nutrient directly affects the growth rate of the culture and allows avoiding overflow metabolism (formation of side metabolites, such as acetate for Escherichia coli, lactic acid in cell cultures, ethanol in Saccharomyces cerevisiae), oxygen limitation (anaerobiosis) Substrate limitation offers the possibility to control the reaction rates to avoid technological limitations connected to the cooling of the reactor and oxygen transfer Substrate limitation also allows the metabolic control, to avoid osmotic effects, catabolite repression, and overflow metabolism of side products Therefore, there are different operation strategies for fed-batch: 1) constant feed rate or constant growth/fermentation rate; 2) exponential feed rate or constant specific growth rate The exponential growth with fed-batch operation can be at any rate, up to the maximum rate in the exponential growth phase of a batch growth This is the case that closely resembles a chemostat operation Usually, maximum growth rate is not wanted for undesired by-product production which can be high at maximum growth 18.3 AERATION, AGITATION, AND HEAT TRANSFER For industrial-scale fermentors, oxygen supply and heat removal are key design limitations The severity of the oxygen requirement is a function of the organism The oxygen uptake ratio (OUR) can be written: OUR ¼ XmO2 (18.1) where mO2 dspecific uptake rate of oxygen and X is the biomass concentration Typical values of mO2 are shown in Table 18.4 OUR represents the consumption rate of oxygen, which is the demand from the cells OUR is balanced by the OTR when pseudo steady state is reached OTR is given by OTR ¼ KL a ðCà À CL Þ (18.2) Cà doxygen where solubility, CLdactual dissolved oxygen (DO), and KLa is the volumetric mass transfer coefficient The value of KLa can be estimated by: KL a ẳ kP0 =Vị0:4 vs ị0:5 u0:5 (18.3) where kdempirical constant, P0dpower requirement, Vdbioreactor volume, vSdsuperficial gas velocity, and udagitator rotation rate The value of P0 can be estimated from other correlations, such as !0:45 2 Pu uDi P0 ¼ k (18.4) Q0:56 924 18 BIOREACTOR DESIGN AND OPERATION TABLE 18.4 Typical Respiration Rates of Microbes and Cells in Culture mO2 , mmol-O2/(g-dw h) Organism Bacteria E coli 10e12 Azotobacter sp 30e90 Streptomyces sp 2e4 Yeast S cerevisiae Molds Penicillium sp 3e4 Aspergillus niger ca Plant cells Acer pseudoplatanus (sycamore) 0.3 Saccharum (sugar cane) 1e3 Animal cells HeLa 0.4  10À12 mol-O2/(h$cell) Diploid embryo WI-38 0.15  10À12 mol-O2/(h$cell) where Pu is the power requirement for ungassed vessel (i.e in the absence of aeration or airflow into the reactor) KLa is dependent on the media, salts, surfactants, pressure, and temperature making it difficult to predict KLa is however measurable Four approaches are generally used to measure KLa: unsteady state, steady state, dynamic, and sulfite test The reactor is filled with water or medium and sparged with nitrogen to remove oxygen The air is introduced and DO is monitored until the bioreactor is nearly saturated In the case of no consumption of oxygen in the reactor, mass balance of oxygen in the reactor leads to dCL ¼ KL aC CL ị dt (18.5a) CL ẳ C À ðCà À CL0 ÞexpðÀKL a$tÞ (18.5b) which can be integrated to yield The DO changes exponentially with time for unsteady-state accumulation of oxygen This is the theoretical basis for unsteady-state method of measuring the oxygen transfer coefficient It is the simplest and easiest one to implement 18.3 AERATION, AGITATION, AND HEAT TRANSFER 925 The sulfite method is conducted in the presence of Cu2ỵ, where sulfite (SO2 ) is oxidized ) in a zero order reaction The reaction is very rapid and consequently CL to sulfate (SO2À approaches zero The rate of sulfate formation is monitored and is proportional to O2 consumption (½ mol O2 consumed to produce mol of SO2À ) Mass balance of oxygen in the reactor leads to: dCSO2À ¼ KL a$C 0ị (18.6a) dt KL a ẳ dCSO2À 2Cà dt (18.6b) à where CSO2À is the concentration of sulfate (SO2À ) and C is a constant dependent on the medium composition, pressure, and temperature and can be measured separately The steady-state method uses a fermentor with active cells and may be the best method to determine KLa This method requires accurate measurement of O2 in all gas exit streams and reliable measurement of CL Mass balance on O2 in the gas allows rate of O2 uptake, OUR according to the following equation: KL a ¼ OUR Cà À CL (18.7) OUR can be estimated with off-line measurements of a sample in a respirometer, but information from the actual fermentor is ideal Cà is proportional to pO2 which depends on the total pressure and fraction of the gas that is O2 At sparger point, pO2 is significantly higher than at exit due to higher pressure and consumption in the bioreactor Knowledge of residence time distribution of gas bubbles is necessary to estimate a volume-averaged value of Cà The final method is the dynamic method This method is a simpler method that only requires the measurement of DO and can be used under actual fermentation conditions Mass balance on oxygen in the reactor leads to dCL ¼ OTR À OUR dt (18.8a) dCL ¼ KL aðCà À CL Þ À mO2 X dt (18.8b) or This method requires the air supply to be shut off for a short period (