M.Tech. BIOCHEMICAL ENGINEERING - Manipal University - one of the

M.Tech.

BIOCHEMICAL ENGINEERING

Department of Biotechnology,

Manipal Institute of Technology (MIT),

Manipal University,

Manipal

M. Tech. – Biochemical Engineering

FIRST SEMESTER SECOND SEMESTER

I

YEAR

Sub Code Subject Name L T P C Sub Code Subject Name L T P C

MAT 503

Mathematical and Numerical

Techniques in Chemical &

Biochemical Engineering 3 1 0 4 BIO 502

Bioreactor Design and

Analysis 3 1 0 4

BIO 505

Transport Phenomena in

Bioprocessing 3 1 0 4 BIO 516 Bioprocess Equipment Design 3 1 0 4

BIO 513

Advanced Biochemical

Engineering 3 1 0 4 BIO *** Program Elective I 4 0 0 4

BIO 515 Bioprocess dynamics and control 3 1 0 4 BIO *** Program Elective II 4 0 0 4

BIO 517

Advanced Downstream

Processing 3 1 0 4 BIO *** Program Elective III 4 0 0 4

HUM 501

Research Methodologies &

Technical Communication 1 2 3 2 xxx.xxx.x Open Elective 3 0 0 3

BIO 519

Upstream and Downstream

processing lab 0 0 6 2 BIO 518

Bioprocess dynamics and

control lab 0 0 6 2

BIO 544 Seminar 0 0 3 1

TOTAL 16 7 9 24 TOTAL 21 2 9 26

II

YEAR

BIO 699 Project Work 0 0 0 40

TOTAL 0 0 0 40

LIST OF PROGRAMME ELECTIVES

BIO 524 Biopharmaceuticals & Pharmaceutical Biotechnology

BIO 528 Solid waste management

BIO 530 Statistical Design and analysis of experiments in biotechnology

BIO 534 Immunotechnology

BIO 546 Biosensors

BIO 548 Bioprocess Modeling Analysis and Simulation

BIO 550 IPR issues in Biotechnology & Biosafety

BIO 552 Biological Thermodynamics

BIO 554 Multiphase Bioreactor design

BIO 556 Environmental Biotechnology

LIST OF OPEN ELECTIVES

BIO 540 Animal and Plant Biotechnology

BIO 542 Biofuels Engineering

M.Tech.

BIOCHEMICAL ENGINEERING

FIRST SEMESTER

MAT 503 MATHEMATICAL AND NUMERICAL [3 1 0 4]

TECHNIQUES IN CHEMICAL & BIOCHEMICAL ENGINEERING

Total No of periods: 48

Introduction, linear algebraic equations Eigenvalues and Eigenvectors of Matrices, sparse

Matrices -Tensors and their applications. [12]

Non linear algebraic equations function evaluation-least square curve fit-Newton inter-polation

formula-orthogonal polynomials and functions-ordinary differential equations initial value

problems and Boundary value problems - finite difference techniques. [12]

Orthogonal collocations on finite difference - Galerkin finite elements-shooting techniques

partial differential equations-finite difference technique (Method of lines) orthogonal collocation

on finite elements. [12]

The Galerkin finite Element technique-variational forms of PDE’s. Sturm-Louiville theory-

separation of variables and Fourier Transforms-Green’s function-uniqueness conditions for

linear and Nonlinear systems, steady state characteristics of Nonlinear Dynamical systems-

Linear stability and Limit cycles-secondary Bifurcations and chaos. [12]

Text / Reference Books:

1. Mathematical Methods in Chemical Engineering S.Pushpavanam, PHI, 1998.

2. Numerical methods for Engineer BySanthoshK.Gupta. Wiley Eastern Ltd. New Delhi.

3. Owen T. Hanna and Orville C. Sandall“Computations methods in Chemical Engineering”

PHI, 1998.

4. Davis, H.T. and Thomson K., Linear Algebra and Linear operators in Engineering with

applications of mathematica, Academic Press, 2000

BIO 505 TRANSPORT PHENOMENA IN BIOPROCESSING [3 1 0 4]


Introduction [03]

Introduction to Transport Phenomena – momentum, heat and mass transfer in bioprocessing

Momentum transfer [15]

Review of basic concepts – Conservation of Mass, Conservation of Energy, Momentum Balance

– Momentum Balance in a Circular Pipe, Flow Velocity Profile; Fermentation Broth Rheology –

Viscosity, Rheological Properties of Fermentation Broths, Factors affecting broth viscosity;

Mixing in a Bioreactor – Flow regimes with and without baffles, various types ofimpellers and

mixing equipment. Power Requirements for Mixing, Ungassed Newtonian Fluids, Gassed Fluids,

Improving Mixing in Fermenters, Effect of Rheological Properties on Mixing, Role of Shear in

Stirred Fermenters

Heat Transfer [15]

Review of basic concepts – Various modes of heat transfer, viz., conduction convection and

radiation. Design Equations for Heat Transfer Systems – Energy Balance, Calculation of Heat-

Transfer Coefficients.

Application of heat transfer in bioprocessing, Heat Management in Bioreactors, Relationship

between heat transfer, cell concentration and stirring conditions

Mass transfer [15]

Review of basic concepts – Diffusivity, theory of diffusion, analogy between mass, heat and

momentum transfer, role of diffusion in bioprocessing. Definition of binary mass transfer

coefficients, transfer coefficients at high mass transfer rates- boundary layer theory, penetration

theory.Convective mass transfer – Liquid-solid mass transfer, liquid-liquid mass transfer, gas

liquid mass transfer.

Oxygen transport to microbial cultures – Gas liquid mass transfer fundamentals, oxygen

requirement of microbial cultures.Oxygen requirements of microbial cultures oxygen mass

transfer fundamentals.oxygen transfer and oxygen demand. Oxygen transfer by aeration and

agitation.Determination of oxygen mass transfer coefficient by various methods including

dynamic gassing out and oxygen balance methods.

http://www.dcu.ie/~oshead/be322/Lectures/LectureH1.doc


1. Arthur T. Johnson, Biological Process Engineering: An Analogical Approach to Fluid

Flow, Heat Transfer, and Mass Transfer Applied to Biological Systems, John Wiley and

Sons, 1998.

2. Pauline M. Doran, Bioprocess Engineering Principles, Academic Press, 1995.

3. Blanch H.W and Douglas S. C, Biochemical Engineering, CRC Press, 1997.

4. Michael L Shuler andFikretKargi, Bioprocess Engineering: Basic Concepts,Prentice-Hall

of India Pvt Ltd, 2008.

BIO 513 ADVANCED BIOCHEMICAL ENGINEERING [3 1 0 4]


Microbial diversity and taxonomy, Prokaryotes and Eukaryotes, Types of Microorganisms;

Study of microscopes; general structural organization of bacteria and other microorganisms;

Uses of Microorganisms – Food, Pharmaceuticals, Industrial chemicals, Biopolymer, Biofuel,

Pesticide & Fertilizer [06]

Medium requirements for fermentation processes- Carbon, nitrogen, minerals, vitamins and other

complex nutrients; oxygen requirements; Criteria for good medium, Medium formulation for

optimal growth and product formation- examples of simple and complex media; Design and

usage of various commercial media for industrial fermentations, medium optimization methods

[06]

Strategies for isolation and preservation of microorganisms, Improvement of Industrial

Microorganisms, random mutagenesis, genetic engineering of strain improvement – Enzymes

used in genetic engineering, cloning vectors, cloning methodologies. [08]

Thermal death kinetics of microorganisms; Batch & Continuous heat -Sterilization of Liquid

media; Filter sterilization of liquid media, Design of Sterilization Equipments [06]

Proteins as enzymes; Classification of Enzymes; Mechanism of Enzyme Action; Michaelis-

Menten kinetics; Enzyme Inhibition Kinetics; Effect of pH and temperature, Enzyme

Immobilization – methods, mass transfer considerations, kinetics of immobilized enzyme

reactions [08]

Stoichiometry of Cell growth and product formation, elemental balances, degrees of reduction of

substrate and biomass, available electron balances, yield coefficients of biomass and product

formation, maintenance coefficients energetic analysis of microbial growth and product

formation, oxygen consumption and heat evolution in aerobic cultures, thermodynamic

efficiency of growth [06]

Phases of cell growth in batch cultures, Microbial Growth Kinetics – examples and derivation of

unstructured & structured kinetic models; Growth of Filamentous Organisms. Growth associated

(primary) and non-growth associated (secondary) product formation kinetics; LeudekingPiret

models; substrate and product inhibition on cell growth and product formation [08]

Text /Reference Books:

1. Michael Shuler and FikretKargi, Bioprocess Engineering: Basic Concepts, 2nd Edition,

Prentice Hall, Englewood Cliffs, NJ, 2002.

2. J. E. Bailey and D. F. Ollis, Biochemical Engineering Fundamentals, 2nd Edition, Mc-

Graw Hill, Inc., 1986.

3. Pauline Doran, Bioprocess engineering principles, 1st Edition, Academic Press, 1995.

4. Stanbury P.E., Whitaker A., Hall S.J, Principles of Fermentation Technology, 2nd

Edition, Pergamon Press, 1995.

5. Harvey W. Blanch, Douglas S. Clark, Biochemical Engineering, 2nd Edition, Marcel

Dekker, Inc, 1997.

BIO 515 BIOPROCESS DYNAMICS AND CONTROL [3 1 0 4]

Introduction, need for process control, design elements of a control system, Hardware for a

process control system [4]

Development of mathematical models, modeling considerations for process control purpose,

Degrees of control freedom [3]

Time Domain dynamics and Control classifications and definitions, Linearization and

Perturbationvariables, Responses of simple first and second order linear-time-invariant systems

[8]

Dynamic behaviour of First order and Second order systems, Solution using Simulink [3]

Laplace transformssolutions of linear differential equations using Laplace transforms [2]

Types controller actions, on-off control, PID control- dynamic behavior of feedback

controlled(PID) processes,Final control elements and characteristics. [6]

Stability Analysis of Feedback Systems-Notion of Stability, characteristic equation, Routh-

Hurwitzcriterion for stability, Root Locus Analysis, frequency response methods, PID

controllertuning. [6]

Advanced Control Systems- Cascade control, Over-ride Control, feed forward control, Ratio

control, Inverse response, Control system design concepts. [6]

Matrix Algebra, State-space methods, MIMO systems-interaction-RGA-Multivariable controller

tuningOver view of model predictive control [12]


1. Essentials of Process control, William L. Luyben and Michael L. Luyben, McGraw Hill

Inc, 1997

2. George Stephanopoulos Chemical Process Control-An Introduction to theory and

Practice, Prentice Hall International.

3. Process System Analysis and Control, Donald R. Coughanowr, McGraw Hill Science,

1991.

4. Wayne Bequette, “Process Control: Modeling design and simulation”, Prentice Hall

Publishing, 2003.

5. Dale E. Seborg, Duncan A. Mellichamp, Thomas F. Edgar and Francis J. Doyle, Process

Dynamics and control, John Wiley and sons, 2011.

6. Carlos A. Smith and Armando B. Corripio,”Principles and Practices of Automatic

Process Control”, John Wiley, 2005.

7. Process Control, Peter Harriott, Tata McGraw Hill Publishing Co. Ltd.

BIO 517 ADVANCED DOWNSTREAM PROCESSING[3 1 0 4]


Role of Downstream Processing in Biotechnology: [04]

Role and importance of downstream processing in biotechnological processes.Problems and

requirements of bioproduct purification.Economics and downstream processing in

Biotechnology. Cost cutting strategies, characterstics of biological mixtures, process design

criteria for various classes of bioproducts (high volume-low value products and low volume-

high value products), physicochemical basis of bio-separation processes.

Primary Separation and Recovery Processes: [04]

Cell disruption methods for intracellular products, removal of insolubles, biomass (and

particulate debris) separation techniques; flocculation and sedimentation, centrifugation and

filtration methods

Precipitation methods: [04]

Precipitation with salts, organic solvents & polymers

Extraction: [06]

Batch extractions, staged extractions-cross current, co current, counter current extractions.

Differential extractions, fractional extractions with a stationary phase, fractional extractions with

two moving phases.

Aqueous two-phase extraction: [06]

Reverse micelle extraction, supercritical fluid extraction, in-situ product removal/integrated

bioprocessing

Membrane-based separations (micro- & ultra-filtration): [06]

Theory; design & configuration of membrane separation equipment; applications; reverse

osmosis, dialysis, electro dialysis, Isoelectric focusing

Adsorption: [06]

Adsorption isotherms, industrial adsorbents, adsorption equipments for batch and continuous

operations (co current and counter current), adsorption in fixed beds.

Chromatography: [06]

Principles of chromatographic separation – gel filtration, reversed phase, hydrophobic

interaction, ion-exchange, expanded bed adsorption, bio affinity and IMAC, supercritical fluid

chromatography.

Case studies: [06]

Preparation of commercial enzymes: Continuous isolation of enzyme prolyl-t RNA synthetase

from mung bean, Intracellular foreign proteins from recombinant E.coli and extracellular

enzyme (protease) recovery; Purification of biosurfactants from fermentation broths.


1. Belter P.A, Cussler E and Wei Shan Hu, Bioseparation – Downstream Processing for

Biotechnology, Wiley Interscience, 1988.

2. Asenjo and Juan A. Asenjo,Separation Processes in Biotechnology, CRC Press, 1990.

3. Wankat P.C, Rate Controlled Separation, Kluwer Publishers, 1990.

4. Wang D.I.C, Cooney C.L, Demain A.L, Dunnil.P, Humphery A.E. and Lilly M.D.

Fermentation and Enzyme Technology, John Wiley and Sons, 1979.

HUM 501 RESEARCH METHODOLOGIES AND [1 2 3 2]

TECHNICAL COMMUNICATION


Mechanics of Research Methodology

Basic concepts: Types of research, Significance of research, Research framework, Case

study method, Experimental method, Sources of data, Data collection using

questionnaire, Interviewing, and experimentation.

Research formulation: Components, selection and formulation of a research problem,

Objectives of formulation, and Criteria of a good research problem.

Research hypothesis: Criterion for hypothesis construction, Nature of hypothesis, Need

for having a working hypothesis, Characteristics and Types of hypothesis, Procedure for

hypothesis testing.

Sampling Methods: Introduction to various sampling methods and their applications.

Data Analysis: Sources of data, Collection of data, Measurement and scaling technique,

and Different techniques of Data analysis.

Thesis Writing and Journal Publication

Writing thesis, Writing journal and conference papers, IEEE and Harvard styles of

referencing, Effective Presentation, Copyrights, and avoiding plagiarism.

Text / Reference Books

1. DrRanjit Kumar,Research Methodology: A Step-by-Step Guide for Beginners, SAGE, 2005.

2. Geoffrey R. Marczyk, David DeMatteo& David Festinger, Essentials of Research Design

and Methodology,John Wiley & Sons, 2004.

3. John W. Creswel , Research Design: Qualitative, Quantitative, and Mixed Methods

Approaches,SAGE, 2004

4. Suresh C. Sinha and Anil K. Dhiman, Research Methodology (2 Vols-Set),Vedam Books,

2006.

5. C. R. Kothari, Research Methodology: Methods and Techniques,New Age International

Publisher, 2008.

6. Donald R Cooper & Pamela S Schindler ,Business Research Methods,McGraw Hill

International, 2007.

7. R. Pannershelvam, Research Methodology,Prentice Hall, India, 2006

8. Manfred Max Bergman,Mixed Methods Research,SAGE Books, 2006.

9. Paul S. Gray, John B. Williamson, David A. Karp, John R. Dalphin, The Research

Imagination, Cambridge University press, 2007.

10. Cochrain& Cox, Experimental Designs, II Edn. Wiley Publishers, 2006.

BIO 519 Upstream and Downstream processing lab [0 0 6 2]

Experiments are based on Bioprocess Engineering, Microbiology, Molecular biology &rDNA

technology course works.

SECOND SEMESTER

BIO 502 BIOREACTOR DESIGN AND ANALYSIS [3 1 0 4]


Introduction and Review of Bio-reaction engineering concepts, Mass transfer effects in

heterogeneous reaction [04]

Stirred tank batch bioreactor: stirred batch bio reactor for enzymes, cell cultures [03]

Continuous Stirred Tank Bioreactor : Continuous operation of mixed reactor, enzyme

reactions in a mixed reactor, performance equation for M-M kinetics, substrate inhibition

kinetics and product inhibition kinetics, chemostat with cell cultures –steady state cell and

substrate concentrations and productivity as a function of dilution rate, CSTR with immobilized

enzymes, operation of CSTR in a constant feed rate policy-simulation for conversions with and

without diffusion limitations, chemostat in series, Graphical design [06]

Plug Flow and Packed Bed Bioreactor: Performance equation with Michelin-Menten kinetics,

substrate inhibition and product inhibition, plug flow reactor for immobilized enzymes,

operation of plug flow reactor in constant feed rate policy, simulation for conversion with and

without diffusion limitations [06]

Fed–batch reactor: Applications of fed reactor, Fed batch operation of mixed reactor, material

balance on cell and substrate [03]

Recycle system: Chemostat with recycle, Biological waste water treatment, Feed forward

control of the activated sludge process [04]

The Transient Behavior of Bioreactors: Stability analysis, Stability of the chemostat, Stability

of chemostat with substrate inhibition, Operating diagram, Transient responses of the chemostat,

control of the chemostat, Turbidostat operation, Nutristat operation [06]

Design of a fermenter: Basic function of a fermenter for microbial or animal cell culture, basic

bioreactor design criteria, overview of bioreactor types-stirred tank bioreactor, bubble column

bioreactor, air-lift reactor, propeller loop reactor, jet loop reactor, schematic overview of a

fermenter with control system, operating issues that affect reactor design, aeration and oxygen

mass transfer in bioreactor system [04]

Instrumentation and control: Methods of measuring process variables, measurement and

control of dissolved oxygen, pH and foam measurements [04]

Non-ideal flow: Non-ideal flow, RTD, E,C,F-curves, micro & Macro fluid, conversion

calculation for Macrofluid [08]


1. Blanch H.W and Douglas S. Clark, Biochemical Engineering, CRC Press, 1997.

2. Michael L Shuler andFikretKargi, Bioprocess Engineering: Basic Concepts, Prentice-Hall of

India Pvt Ltd, 2008.

3. Stanbury P.F., Whitaker A. and Hall S.J, Principles of Fermentation Technology.Elsevier

India Pvt Ltd, 2007.

4. Arthur T. Johnson, Biological Process Engineering: An Analogical Approach to Fluid Flow,

Heat Transfer, and Mass Transfer Applied to Biological Systems, John Wiley and Sons,

1998.

5. Pauline M. Doran, Bioprocess Engineering Principles. Academic Press, 1995.

6. Rao D.G., Introduction to Biochemical Engineering. Tata McGraw-Hill, 2005.

BIO 516 BIOPROCESS EQUIPMENT DESIGN [ 4 0 0 4 ]

Total No. periods: 48

Design of Pressure Vessels:

Codes and standards for pressure vessels, types of pressure vessels, material of construction,

selection of corrosion allowance and weld joint efficiency. Vessels for Biotechnology, piping

and valves for Biotechnology [10]

Design of fermenters:

Design criteria for fermentor, achievement &maintenance of aseptic conditions in fermentors,

Scale-up of fermenters, Design of chemostat, design of bubble column fermentor and air lift

fermentor [10]

Heat Exchangers:

Introduction, types of heat exchangers, codes and standards for heat exchangers,materials of

construction, baffles and tie rods, Design of shelland tube heat exchangers (U tube and fixed

tube) as per TEMAstandards [10]

Evaporator design:

Introduction, types of evaporators, types of feeding, design of triple effect evaporators [10]

Costing and Project Evaluation:

Cost estimation methods and economic evaluation of projects [8]

Text / Reference Books

1. “Process Equipment Design” by M.V. Joshi, McMillan India.

2. “Bioprocess Engineering-Systems, Equipment and Facilities” Edited by Bjorn K.Lydersen,

Nancy A D’elia and Kim L. Nelson. A Wiley Interscience Publication.

3. “Principles of Fermentation Technology” by PF STANBURY, S. Hall, A. Whitaker, 2nd

Edition,

Elsevier Science Publishers, 2003

4. Process equipment design” by L.E. Brownell and E. Young, John Wiley, New York,1963.

5. “Chemical Engineering Vol. 6” by J.M. Coulson, J.F. Richardson, and R.K. Sinott,Pergamon

Press.

6. Unfired Pressure Vessel Code BIS 2825

7. Code for Shell & Tube heat exchangers BIS 4503

8. Chemical Engineer’s Handbook by Perry.

BIO 524 BIOPHARMACEUTICALS AND PHARMACEUTICAL BIOTECHNOLOGY

Total No of Periods: 48 [4 0 0 4]

Pharmaceuticals, biologics and biopharmaceuticals [08]

Introduction to pharmaceutical products, Biopharmaceuticals and pharmaceutical biotechnology,

Biopharmaceuticals: current status and future, Pharmaco-Kinetics- absorption of drugs,

distribution of drugs, protein binding of drugs, Basic Issues in the Manufacture of

Macromoleucles, Traditional pharmaceuticals of biological origin-animal origin, plant origin,

microbial origin.

Pharmacokinetics [08]

Biotransformation of drugs, Preclinical Pharmacokinetics , Compartment modeling- one

compartment open model , two compartment open model, multi compartment model, non linear

kinetics, bioavailability and bioequivalence, excretion of drugs, pharmacokinetics – effects of

food and fasting.

The drug development and manufacturing process [08]

Drug discovery, Patenting- Patent types, The patent application, Patenting in biotechnology, Pre-

clinical trials, Clinical trials, The role and remit of regulatory authorities-The Food and Drug

Administration, The investigational new drug application, The new drug application, European

regulations, Guides to good manufacturing practice, Formulation and Delivery Issues of

Therapeutic Proteins, Biotechnology-Derived Drug Products: Formulation Development,

Stability Testing, Filling, and Packaging.

Pharmaceutical dosage forms: [16]

Dosage Forms and Basic Preparations, Excipients for Pharmaceutical Dosage Forms,

Compressed tablets, wet granulation, dry granulation or slugging, direct compression, tablet

formulation, coating, capsules, sustained action dosage form, parental, oral liquids, ointments,

recombinant blood products and therapeutic enzymes, hormones of therapeutic interest

Pharmaceutical products, Analysis and Control: laxatives – analgesics – non steroidal

contraceptives – external antiseptics – antacids and other, antibiotics – biological – hormones –

vitamins - preservation, analytical methods and test for various drugs and pharmaceuticals,

packaging techniques – quality control

Drug safety evaluation: [08]

Strategy and Phasing for Drug Safety Evaluation in the Discovery and Development of

Pharmaceuticals, Regulation of Human Pharmaceutical Safety, Acute Toxicity Testing in Drug

Safety Evaluation, Special Concerns for the Preclinical Evaluation of Biotechnology Products,

Immunotoxicology in Pharmaceutical Development, The Application of In Vitro Techniques in

Drug Safety Assessment, Pharmaceutical Quality Assurance


1. Heinrich Klefenz ,Industrial pharmaceutical biotechnology, John Wiley sons, 2002.

2. Susanna Wu-Pong, YongyutRojanasakul, and Joseph Robinson, Biopharmaceutical drug

and design and development, Humana Press, 2007.

3. Gary Walsh, Biopharmaceuticals: Biochemistry and Biotechnology (2e), John Wiley &

Sons, 2003.

4. Herbert A Kirst, Wu-KuangYeh; Milton J, Enzyme Technologies for pharmaceutical and

biotechnological applications, WILEY-VCH Verlag, 2003.

BIO 528 SOLID WASTE MANAGEMENT [4 0 0 4]

Total No. of Hours: 48

Introduction to solid waste management:

Waste generation in technological society, integrated solid waste management, operation of solid

state waste management systems. Legislative Trends and Impacts: major legislation, Government

agencies. [06]

Sources, Types and Composition of solid wastes:

Determination of the composition of municipal solid wastes in the field, Physical, chemical and

biological properties of MSW; transformations of solid waste; Properties and classification of

Hazardous wastes; transformations of Hazardous waste constituents found in MSW;

Management of hazardous wastes in MSW. [10]

Engineering Principles:

Solid waste generation and collection Rates,Collection of solid waste, Separation and Processing

and Transformation of solid waste, Transfer and Transport, Disposal of solid wastes and residual

matter: The landfill method, classification and types; Layout and preliminary design of landfills

[12]

Biological and chemical conversion technologies:

Biological principles, aerobic composting, low and high solids Anaerobic digestion,

development of anaerobic digestion processes and technologies for treatment of the organic

fraction of MSW; other biological transformation processes. Energy production from biological

conversion products, Fermentation and compost processes: Basic processes, feed stocks,

products, design parameters, reactor types, Application and economics, case histories. [14]

Solid waste management and planning issues: Meeting federal and state mandated diversion

goals:- source reduction and recycling, Implementation of solid waste management options;

planning, siting and permitting of waste management facilities [06]


1. Integrated solid waste management: Engineering principles and management issues by

George Tchobanoglous, 1993.

2. The solid waste handbook: A practical guide by William D Robinson, P.E., 1986.

BIO 530 STATISTICAL DESIGNS AND ANALYSIS OF EXPERIMENTS IN

BIOTECHNOLOGY [4 0 0 4]


Presentation & analysis of data: Errors in Data and calculations, presentation of experimental

data, data analysis, general procedures for plotting data, process flow diagrams [06]

Introduction to statistical design: Classical versus statistical approaches to experimentation,

diagnosing the experimental environment, good design requirements. Introduction to factorial

designs, definitions and principles, Basic Two-level factorial design experiments, 2k factorial

design [10]

Screening designs: Fractionating factorial designs, fractional factorial designs, Plackett-

Burmann screening designs [10]

Process Optimization experiments: Response surface methodology – concepts & methods,

design considerations, central composite designs and Box-Behnken response surface design [12]

Case studies: Optimizations of Media components, fermentation process and purification

process with specific case studies by using statistical software. [10]


1. Lawson J &Erjavec J, Modern Statistics for Engineering and Quality

Improvement(1e),Duxbury Press, 2001.

2. Montgomery Douglas C ,Design and analysis of experiments(6e), John Wiley, 2009.

3. Pauline Doran, Bioprocess Engineering Principles (1e), Academic Press, 1995.

BIO 534 IMMUNOTECHNOLOGY [4 0 0 4]


The Immune System: Introduction - innate and adaptive immunity. Lymphocytes - their origin

and differentiation; antigens - their structure and classification; complement and their biological

functions; types of immune responses; anatomy of immune response. [07]

Humoral Immunity: B-lymphocytes and their activation; structure and function of

immunoglobulins; immunoglobulin classes and subclasses. Genetic control of antibody

production.monoclonal antibodies and diagnosis. idiotypes and idiotypic antibodies. Major

histocompatibility complex. Blood Typing: AB, O & Rh. [07]

Cellular Immunology: Thymus derived lymphocytes (T cells) their classification. antigen

presenting cells (APC) -macrophages. dendritic cells. langerhans cells - their origin, activation

and functions; mechanisms of phagocytosis; identification of cell types of immune system;

immunosuppression. Immune tolerance. [07]

Antigen Antibody interactions: precipitation, agglutination, neutralization. Immunological and

antibody based assays: RIA, ELISA, Chemiluminescence, ELIspot, FACS, western blotting,

Immuno fluorescence, immuno precipitation, immuno diffusion, immunoelectrophoresis.

ImmunoHistochemistry and IHC methods.Immuno electron microscopy. [08]

Stem cells: Brief mention about stem cells and applications to immunology, Immunosuppressive

drugs. HLA and disease, mechanisms of immunity to tumor antigens. [06]

Autoimmunity: Auto antibodies in humans, pathogenic mechanisms, experimental models of

auto immune disease, treatment of auto immune disorders. [06]

Molecular Immunology: Preparation of vaccines, application of rDNA technology to

production of antibodies. Immunotherapy. [07]


1. RoittI ,Essential Immunology , Blackwell Scientific Publications, Oxford press ,1991.

2. Kuby J and WH Freeman, Immunology(6e), New York, 2007.

3. Benjarnini E. and Leskowitz s., Immunology A short course, Wiley Liss, NY, 1991.

4. Sambrook J et al ., Molecular cloning(Vol I, II and III)., Cold Spring Harbor laboratory

Press. New York, USA, (1989, 2000).

5. Gabriel Virella, Introduction to Medical Immunology (4e),Lippincott Williams & Wilkins

(1999).

BIO 546 BIOSENSORS [4 0 0 4]


Introduction: [08]

A historical perspective; Definition and Expanding Needs of Biosensors; Advantages and

limitations; Biosensor Economics; various components of biosensors

Types of Biosensors: [10]

Biocatalysts based biosensors, bio affinity based biosensors & microorganisms based biosensors,

biologically active material and analyte. Types of membranes used in biosensor constructions

Transducers in Biosensors: [08]

Various types of transducers; principles and applications; Bio-, chemi-, and

electrochemiluminescence for fiber-optic biosensors; Fluorescence-based fiber-optic biosensors

Kinetic modeling for biosensors: [10]

The purpose and practice of modeling; The flux equations, The flux diagram for the

membrane/enzyme/electrode, Deriving a complete kinetic model; Kinetic modeling in other

types of biosensors- Potentiometric enzyme electrodes, Optical and photometric biosensors,

Immunosensors

Application and Uses of Biosensors: [12]

Biosensors in medicine and health care, biosensors for agriculture and food; Low cost- biosensor

for industrial processes for online monitoring; biosensors for environmental monitoring.


1. Rajmohan Joshi, Biosensors(1e), Gyan Books, 2006

2. Cooper J.M. and Anthony E.G,Biosensors(2e), Oxford University Press, 2004.

3. Turner A.P.F, Karube.I and Wilson,G.S, Biosensors Fundamentals and applications,

Oxford Univ. Press, 1990

4. Sadana.A, Biosensors: Kinetics of Binding and Dissociation Using Fractals (1e),

Elsevier B.V, 1995

5. Ashok M and Kim Rogers, Enzyme & Microbial Biosensors: Techniques and

Protocols (Methods in Biotechnology)(1e), Humana Press, 1998.

6. Ashok M and Kim Rogers, Affinity Biosensors: Techniques and Protocols (Methods

in Biotechnology)(1e), Humana Press, 1998.

7. DamiaBarcelo, Biosensors for the Environmental Monitoring of Aquatic Systems:

Bioanalytical and Chemical Methods for Endocrine Disruptors(1e),Springer, 2009.

BIO 548 BIOPROCESS MODELING, ANALYSIS & SIMULATION [4 0 0 4]


Perspective on modeling of physical, chemical and biological phenomena, uses and limitations of

mathematical models in Bioprocess models- Basic classifications, fundamental features of

models. Several examples involving algebraic equations, ordinary differential equations,

difference equations partial differential equations, integral equations and integro-differential

equations. [12]

Elements of probability theory, stochastic models parameter estimation model forms for

parameter estimation. Parameter estimation using moments, design of experiments for parameter

estimation. Accuracy of parameter estimates. Design of experiments for model discrimination -

Regression and interpolation. [12]

Review of numerical techniques for the solution of bioprocess models. Non linear systems

analysis Phase – Plane analysis in classical bioreactor models, phase – plane plot for bioreactor

with monad kinetics. [08]

Introduction to nonlinear dynamics – A simple population growth model. More complex growth

models, chaotic behavior, cob web diagrams, stability of fixed point solutions. Introduction to

bifurcations behavior in single and two variable systems.Introduction to chaos.The Lorenz

equations. [08]

Introduction to population balance modeling in bioprocess engineering – The solution of

population balance equations. Budding of yeast population – Modeling of cells with dynamic

morphology – Modeling for biological populations with correlation between life spans of

siblings. Modeling of Industrial sterilization processes [08]


1. Wayne Bequette.B, Process dynamics modeling and analysis and simulation,.Prentice

Hall Inc, 2004.

2. John H. Seinfeld and Leon Lapidus., Mathematical Methods in Chemical Engg., (Vol. 3),

Process Modeling, Estimations and Identification. Prentice Hall, 1974.

3. Ramakrishna. D, Population Balances. Academic Press, 2000.

4. Shyam S. Sablani., Handbook of Food and Bioprocess Modeling Techniques. C R C

Press, 2006.

5. Volesky.B and J. Votruba., Modeling and Optimization of Fermentation Process

(Process Simulation and Modelling). Elsevier Science and Technology, 1992.

BIO 550 IPR ISSUES IN BIOTECHNOLOGY & BIOSAFETY [4 0 0 4]

Total Number of Periods: 48

Public acceptance issues for biotechnology: Case studies/experiences from developing and

developed countries. Biotechnology and hunger: Challenges for the Indian Biotechnological

research and industries. The Cartagena protocol on biosafety. Biosafety management: Key to the

environmentally responsible use of biotechnology. Ethical implications of biotechnological

products and techniques.Social and ethical implications of biological weapons. [08]

The legal and socioeconomic impacts of biotechnology, public education of the processes of

biotechnology involved in generating new forms of life for informed decision making – with

case studies. [06]

Biosafety regulations and National and International guidelines with regard to rDNA technology,

transgenic science, GM crops, etc. Experimental protocol approvals, levels of

containment.Guidelines for research in transgenic plants. Good manufacturing practice and Good

lab practice (GMO and GLP).

[08]

Environmental aspects of biotech application.Use of genetically modified organisms and their

release in environment. Special procedures for rDNA based product production. [06]

Intellectual property rights (IPR), WTO-GATT, TRIPS, international conventions patents and

methods of applications of patents. Plant breeder’s rights.Legal implications, Biodiversity and

farmers rights.Examples of patents in biotechnology.Special application of patent laws in

biotechnology. Licensing and cross licensing FlavrSavrTm-

Tomato as model case and case

studies. [12]

Beneficial applications and development of research, focus to the need of the poor. Identification

of directions for yield, effect in agriculture, aquaculture etc.Ethics and Biosafety aspects in

Bioremediation. [08]


1. Biotechnologies and Development, UNESCO Publications, 1988

2. A Biotechnologies in developing countries present and future, UNESCO Publishers, 1993

3. Singh. K, Intellectual property rights on Biotechnology, BCIL, New Delhi.

BIO 552 BIOLOGICAL THERMODYNAMICS [4 0 0 4]

Total no of periods: 48

Frontier of Biological Thermodynamics [09]

Energy conservation in living organism, Irreversibility and life, third law and biology, entropy

and protein stability, Energy, information processing and life, second law and evolution, Gibbs

free energy, Equilibrium concepts for biological thermodynamics.

Fundamental concepts of Thermodynamics [13]

System and Surroundings, First law of thermodynamics -Internal energy, enthalpy, Heat

capacity, applied examples from biochemistry. Second law – Entropy and universe, Concept of

heat engines, protein stability and calorimetric measurements, Fundamentals of Differential

scanning calorimeter and Isothermal calorimeter in biological property measurements, Third law

of thermodynamics, Maxwell equations, Gibbs-Duhem Equation and the Phase Rule, Legendre

Transforms.

Gibbs free energy and its Applications [13]

Gibbs free energy and equilibrium, Chemical potential, ionic solutions, Equilibrium constant,

standard state in biochemistry, Acid and bases, chemical coupling and redox reactions, Gibbs

free energy in photosynthesis, glycolysis citric acid cycle, Oxidative phosphorylation and ATP

hydrolysis, substrate cycling, Membrane transport, Enzyme substrate interaction, Haemoglobin,

Protien solubility, stability and dynamics.

Reaction Kinetics [13]

Rate of a reaction, rate constant and order of the reaction, effect of temperature, collision and

transition state theory, Electron transfer kinetics, Enzyme kinetics and inhibition, Reaction

mechanism of lysozyme, protein folding and pathological misfolding, polymerisation, muscle

contraction and the molecular motors.


1. Donald T. Haynie, Biological Thermodynamics, Cambridge press, 2008.

2. Robert A. Alberty, Thermodynamics of Biochemical Reactions, John willy publications,

2003.

BIO 554 MULTIPHASE BIOREACTOR DESIGN [4 0 0 4]

Total no of periods: 48

New Methodologies for Multiphase Bioreactors : Hydrodynamic and Mass Transfer

Characteristics of Multistage Slurry Reactors , Image Analysis and Multiphase Bioreactors:

image processing, biomass characterization, bioreactor imaging, , Data Acquisition, Modelling

and Control: components in bioprocess monitoring and control, measuring techniques for pH,

pressure, oxygen, carbon dioxide, biomass, classical modeling,basic modeling concepts, cell

models [06]

Design and Modeling of Immobilized Biocatalytic Reactors: Biocatalyst immobilization and

performance, immobilized enzyme reactors, modeling of immobilized biocatalyst reactors [06]

Advances in the Selection and Design of Two-Liquid Phase Biocatalytic Reactors: classification

of two-liquid phase biocatalytic processes, two liquid phase reactors: types of reactors, mass

transfer and reaction kinetics, reactor operation, downstream processing, process scale-up [06]

Enzymatic Membrane Reactors: The concept of a membrane bioreactor, enzyme retention,

substrate retention and product separation, membranes and modules, direct contact membrane

reactors, multiphase membrane reactors, applications of enzyme membrane reactors. [06]

Reversed MicellarBioreaction Systems: Reversed micellar principles, determinant factors for

biocatalysis in reversed micelles, reversed micellar bioreactors, characterization of micellar

membrane bioreactors [08]

Design of Liquid-Liquid-Solid Fluidised-Bed Bioreactors: Process lay-out and operation for

three-phase fluidized –bed bioreactor, loop reactors, performance of a conventional bioreactor

and a three-phase fluidized-bed bioreactor [08]

Bioreactor Design For Plant Cell Suspension Cultures: characterization of plant cells as

biocatalysts: morphology, broth rheology, oxygen requirement, shear sensitivity, performance in

suspension culture, bioreactor design and analysis for plant cells [08]


1. JoaquimM.S.Cabral. 2009. Multiphase Bioreactor design, Taylor & Francis.

2. Arthur T.Johnson. 1998. Biological Process Engineering. John Wiley & Sons

3. Pauline M. Doran. 1995. Bioprocess Engineering Principles. Academic Press.

4. Harvey W.Blanch and Douglas S. Clark. 1997. Biochemical Engineering CRC Press

BIO 556 ENVIRONMENTAL BIOTECHNOLOGY [4 0 0 4]


Fundamentals of Microorganisms: Microbial flora of soil, growth, ecological adaptations,

interactions among soil microorganisms, biogeochemical role of soil microorganisms. [04]

Degradation of Xenobiotic Compounds: Simple, aromatics, chlorinated, polyaromatic, petroleum

products pesticides and surfactants. [05]

Treatment of Industrial Wastes: Waste water characteristics, biological waste water treatment,

unit operations, design and modeling of activated -sludge process, mathematical modeling of

anaerobic-digester dynamics. Dairy, pulp, dye, leather and pharmaceuticals, solid waste

management. [06]

Biotechnology processes for oil recovery (microbial), toxic wastes treatment, petroleum wastes

treatment etc. [06]

Decontamination Engineering: Bioremediation processes, cleaner bioprocesses for waste

treatment for environmental pollution management. Ultra filtration systems for waste water

contaminant removal; industrial waste treatment opportunities for reverse osmosis and ultra

filtration. Bio-hazard Monitoring and Control - Risk assessment, hazard monitoring, remedial

measures, techniques and control strategies. [08]

Biofuels: Waste as an energy core, energy recovery systems for urban waste, technology

evaluation, concept of gasification of wastes with molten salt to produce low-BTU gas; pipeline

gas from solid wastes by syngas recycling process; conversion of feedlot wastes into pipeline

gas; fuels and chemicals from crops, production of oil from wood waste, fuels from wood waste,

methanol production from organic wastes. [08]

Applications: Renewable and non-renewable resources. Conventional fuels and their

environmental impacts. Animal oils. Modem fuels and their environmental impacts.

Biotechnological inputs in producing good quality natural fibres. Microbiological quality of food

and water.Treatment of municipal waste and industrial effluents.Degradation of Pesticides and

other toxic chemicals by Microorganisms Thuringiensis toxin as a natural pesticide.Biological

control of other insects swarming the agriculture fields.Enrichment of ores by

microorganisms.Biofertilizers Nitrogen fixing microorganisms enrich the soil with assimilable

nitrogen. Major contaminants of air, water and soil, Biomonitors of environment (Bioindicators),

Bioremediation using microbes, Phytoremediation, Treatment of distillery effluents, biofilms.

[11]


1. Foster C.F. and D.A. John Ware, Environmental Biotechnology, Ellis Horwood Limited,

1987.

2. Larry Anderson and David A, Fuels from waste , Tillman, Academic Press, 1997.

3. Enfors S.O and L. Hagstrom, Bioprocess Technology – Fundamentals and Applications,

RIT, Stockholm, 1992.

4. Young M.Y, Comprehensive Biotechnology(Vol 1-4),Pergamon Press, Oxford, 1985.

5. DeSilva E.D, Ratledge.C& A Sasson, Biotechnology, Economic and Social Aspect,

Camnridge University, Press Cambridge, 1992.

BIO 540 ANIMAL AND PLANT BIOTECHNOLOGY [3 0 0 3]

Total No. of Hours: 36

Plant Genome Organization [04]

Organization and features of mitochondrial, nuclear and choloroplast genome – Structural

features of gene families in plants, Totipotency, Regeneration of plants

Plant cell cultivation [06]

Biochemistry of major metabolic pathways, Autotrophic and heterotrophic growth, Plant growth

regulators and elicitors, Cell suspension culture development: methodology, kinetics of growth

and product formation, nutrient optimization, Plant products of industrial importance, Production

of secondary metabolites by plant suspension cultures, Hairy root cultures and their cultivation.

Techniques in raising transgencies and IPR [08]

Direct and indirect methods: Mechanical, Femptosyringe, electroporation, biolistic, Chemical:

Protoplast, Biological: Agrobacterium mediated plant transformation, chloroplast transformation,

in-planta transformation. Patent, Plant breeders rights, Implementation of IPR protection,

Emerging mechanisms for technology transfer, Enforcement laws and regulations

Animal Cell Organization and nutrient requirement [06]

Special features and organization of animal cells, Animal cell metabolism, Animal cell growth

characteristics, Principles of sterile techniques, Regulation and nutritional requirements for mass

cultivation of animal cell cultures.

Animal cell cultivation [06]

Substrate and product transport through mammalian cell, Animal cell growth kinetics and shear

force. Micro and Macro carrier attached growth, Cell culture in continuous, perfusion and

hollow-fiber reactor.

Techniques in animal biotechnology and IPR [06]

Hybridioma technology, Live stock improvement, Gene transfer methods in animals, Transgenic

animals, Applications of Cloning and xenotransplantation, Animal cell preservation, IPR in

Animal Biotechnology


1. Dixon R.A and Gonzales, Plant Cell Culture: A Practical Approach, IRL Press, 1995.

2. Lindsey. K and M.G.K. Jones, Plant Biotechnology in Agriculture, Prentice Hall, New

Jersey, 1990.

3. Biotol series, In vitro Cultivation of Plant cell, Butterworth Heinemann Ltd., 1994

4. Biotol series, In vitro Cultivation of Animal cell, Butterworth Heinemann Ltd. 1994.

5. Ranga .M.M, Animal Biotechnology(3e),Agrobios, 2007.

6. Bhojwani&Rajdhan, Animal and Plant Biotechnology, Elsevier, 1996.

BIO 542 BIOFUELS ENGINEERING [3 0 0 3]

Total no. of periods: 36

Introduction: [08]

Description of Biofuels; Energy Use & Efficiency; Biofuel Production; Alternative Energies;

Biochemical Pathways Review for Organoheterotrophic, Lithotrophic& Phototrophic

Metabolism; Importance of COD; Biofuel Feedstocks: Starch, Sugar, Lignocellulosic, Agro &

Industrial by-products.

Production of Bioethanol: [08]

Process Technology for Bioethanol production using Sugar; Starch and

LignocellulosicFeedstocks: Selection of micro-organisms and feedstock; Associated Unit

Operations; Determination of Bioethanol yield; Recovery of Bioethanol; Recent Advances;

Process Integration

Production of Biodiesel: [08]

Chemical, Thermodynamic & Reaction Kinetic Aspects of Biodiesel Production:

Transesterification and Supercritical Esterification, Saponification and Hydrolysis, Acid & Base

Catalysis; Sources of Oils; Methods of Biodiesel Production – General procedure and Large

scale production; Quality Control Aspects.

Production of Biohydrogen: [08]

Enzymes involved in H2 Production; Photobiological H2 Production: Biophotolysis and

Photofermentation; H2 Production by Fermentation: Biochemical Pathway, Batch Fermentation,

Factors affecting H2 production, Carbon sources, Process and Culture Parameters; Detection and

Quantification of H2

Microbial Fuel Cells: [08]

Biochemical Basis; Fuel Cell Design: Anode & Cathode Compartment, Microbial Cultures,

Redox Mediators, Exchange Membrane, Power Density; MFC Performance Methods: Substrate

& Biomass Measurements, Basic Power Calculations, MFC Performance: Power Density,

Single-Chamber vs Two-Chamber Designs, Wastewater Treatment Effectiveness; Future

Directions

Microbial Modeling of Biofuel Production: [08]

Microbial Growth Models: Unstructured, Single Limiting Nutrient Models, Inhibition Models,

Models for Multiple Limiting Substrates, Yield Parameters; Kinetic Rate Expressions;

Bioreactor Operation and Design for Biofuel Production: Batch, CSTR, CSTR with Cell

Recycle, Fed-Batch Systems, Plug Flow Systems; Modeling of Glucose Utilization and

Hydrogen Production; Batch and CSTR Fermentations and Simulations


1. Caye M. Drapcho, N.P. Nhuan and T. H. Walker, Biofuels Engineering Process

Technology , McGraw Hill Publishers, New York, 2008.

2. Jonathan R.M, Biofuels – Methods and Protocols (Methods in Molecular Biology Series),

Humana Press, New York, 2009.

3. Lisbeth Olsson (Ed.), Biofuels (Advances in Biochemical Engineering/Biotechnology

Series, Springer-Verlag Publishers, Berlin, 2007.

BIO 518 Bioprocess Dynamics and Control lab [0 0 6 2]

Experiments are based on Bioprocess Dynamics and Control, Bioprocess Modelling and

Simulation course works.

BIO 544 SEMINAR [0 0 3 1]

This course is designed for the students to develop skills in searching technical literature,

coordinating it and making a good presentation. Presentation of a good written report is also part

of exercise. The students will give the seminar on a topic assigned to them, on soft skills or

technical topics.

SECOND YEAR

BIO 699PROJECT WORK [0 0 0 40]

The students (individually) at the beginning of second year will be assigned project work to be

carried out in Industry/Institute under the supervision of a guide. The project should be

completed and submitted for evaluation at the end of the year.

Documents

M.Tech. BIOCHEMICAL ENGINEERING - Manipal University - one of the