Associate Professor



Dept of Chemical Engineering,                                                 

Indian Institute of Technology, Bombay                                    

Powai, Mumbai 400076 INDIA                                                          

Phone: +91 22 2576 7232                                                                  

Fax: +91 22  2572 6895  OR  +91 22  2572 3480


Email: pramodw{at}iitb.ac.ii




Academic Qualifications


Year                 Details of Degree

1995                Ph.D. in Chemical and Biochemical Engineering

The University of  Iowa, Iowa City, IA 52242 USA

Thesis Topic: Tailoring Enzyme Function in Organic Media

Thesis Supervisor:  Prof. Jonathan S. Dordick

Ph.D. research included tailoring enzymes via protein, solvent and catalyst engineering for biocatalytic applications under extreme conditions such as in the presence of organic solvents, at high temperatures, etc.


1991                Bachelor of Chemical Engineering (First Class with Distinction)

University Department of Chemical Technology,

University of Bombay, Matunga, Mumbai-400019



Awards received

·        INAE Young Engineer Award, 2005.

·        G. R. Manudhane Excellence in Research Award, IIT Bombay, 2005.

·        BOYSCAST fellowship (DST, Govt of India) to visit University of Delaware, USA (2004).

·        DAE Young Scientist Award (Dept. of Atomic Energy, Govt. of India) (1997).

·        AICTE Career Award for Young Teachers (1998).

·        Fellowship from the National Institute of Health (USA) through the Center for Biocatalysis and Bioprocessing. (The applicant was chosen out of 100+ applicants from the University of Iowa) (1993-1995).


Current Research Activities:


A)    Bioinformatics:  The wealth of biological data on genomics, proteomics, structure, etc., has a vast amount of knowledge hidden in it.  Our focus has been on deriving “new biological knowledge” from this data by applying data-mining and statistical tools.   Our research can be further classified in the following categories:

(i)                  Application of computational geometry and data-mining tools in structural biology: Pattern search in protein three dimensional structure database; Pharmacophore discovery by geometric techniques.

(ii)                Uncovering of regulatory networks via simulation of dynamic gene expression data. 

(iii)               Apply systems science approach & integrate the biological data available at different levels.  Development of virtual / in silico cells.   

B)    Physiologically Based Pharmacokinetic Modeling:  Physiologically based pharmacokinetic (PBPK) models describe how foreign substances (e.g. drugs and toxins) are processed in the body by absorption, distribution, metabolism, and excretion (ADME). The tremendous growth of computational power and biological knowledge create the context for innovative multi-scale modeling solutions that can substantially improve guidance in toxicology and drug development. In our modeling, we incorporate different scales ranging from the molecular level to the fluid flow level to the physiological system level. Our research consists of the following key sub-goals: (1) Molecular Level Models to predict physicochemical and biochemical characteristics of drug molecules; (2) Fluid Flow Models to account for variability due to blood perfusion in various sub-populations. (3) System Level Models and Integration: We plan to model whole-body physiological level phenomena and also account for the genetic variability in different subpopulation types (e.g. SNPs affecting transporters). The molecular level and fluid dynamics level information will be integrated into the physiological level model using systems and feedback control theory. 

C)    Fermentation Modeling, monitoring and control:  Our current work is based on experimental and theoretical analysis of rifamycin production using Amycolatopsis medittriane.  The work involves development of a kinetic model for growth, product formation and substrate uptake.  Model is being developed for fermentation in a complex media that offers multiple choices of carbon and nitrogen sources.  The model parameters are determined via a specially designed experimental plan.  Further, the model is being applied in model based optimization, monitoring and control of the fermentation process.  This is with academic as well as potential commercial interest in the production technology for rifamycin.  We have been applying several novel optimization techniques for optimal productivity at the flask as well as fermentor level.   A similar strategy is being applied to the fermentation of D-ribose using a transketolase deficient strain of B. subtilis.  The modeling and optimization strategy being developed is general and can be applied to any industrial fermentation process. 



Professional Experience (in reverse chronological order):

Sr. No


Position Held



Indian Institute of Technology, Bombay

Associate Professor

March 2003-Present


Indian Institute of Technology, Bombay

Assistant Professor

December 1997 to March 2003


Indian Institute of Technology, Kanpur

Assistant Professor

July 1996 to December 1997


EnzyMed Inc.

(2501 Crosspark Road,  Suite C150, Iowa City IA 52242, USA)


May 1995 to July 1996



Current Strength of Research Group (at IIT Bombay, India):

·        Ph.D. research scholars:  6

·        M. Tech. Dissertation students: 2

·        M.Sc. senior project students: 2

·        B. Tech. Senior project students: 2


Contribution in new course development:  A new course / elective on “Bioinformatics” was designed and offered to M.Tech. / Ph.D. students for the first time in IIT Bombay in Spring 2001 semester.  A similar course was offered as a six-day “continuing education program” for the working professionals from industry and academia in June 2001, which became extremely popular.  The Continuing Education Program in Bioinformatics has now been offered four times so far at IIT Bombay and has been oversubscribed each time.


Research Experience at EnzyMed Inc., USA  (2501 Crosspark Road,  Suite C150, Iowa City IA 52242, USA,  Duration: 13 months, May 1995-June 1996, Position Held:  Scientist)     EnzyMed, Inc. is a small scale drug discovery company, specializing in combinatorial chemistry.  The nature of the company’s business was to procure contracts for drug discovery from larger pharmaceutical companies to generate and screen (in vitro) combinatorial libraries.  I had helped the company to develop a niche in combinatorial biocatalysis.  Specifically, I have developed various experimental strategies for rapid generation of combinatorial libraries via enzymatic catalysis.




Courses taught:

1.      Bioinformatics (Graduate level) www.che.iitb.ac.in/faculty/pw/cl662.htm

2.      Modeling and simulation of bioprocesses (Graduate level)

3.      Biochemical engineering (Graduate level)

4.      Chemical Kinetics (Undergraduate level, 3rd year)

5.      Thermodynamics I (Undergraduate level, 2nd year).


Research papers in Refereed Journals.

1.              Bapat, P. M., Padiyar, N. U., Dave, N. N., Dash, S., Bhartiya, S., Wangikar P. P. (2006) Model based optimization of substrate feeding recipe for Rifamycin fermentation.  AICHE Journal, in press 

2.              Bapat, P. M., Das, D., Dave, N. N., Wangikar P. P. (2006) Phase shifts in the stoichiometry of rifamycin B fermentation and correlation with the trends in the parameters measured online.  Journal of Biotechnology, in press  DOI:10.1016/j.jbiotec.2006.06.014

3.              Joshi, S., Rana, S., Wangikar, P. P., Durani, S. (2006) Computational design of proteins stereochemically optimized in size, stability and folding speed”, Biopolymers, in press DOI: 10.1002/bip.20537

4.              Chandrasekaran, S., Bhartiya, S., Wangikar, P.P. (2006) “Substrate specificity of lipases in alkoxycarbonylation reaction: QSAR model development and experimental validation”, Biotechnol. Bioeng., in press.

5.              Bapat, P. M., Sohoni, S. V., Moses, T. A., Wangikar P. P. (2006) A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media.  Applied Microbiology and Biotechnology, in press

6.              Bapat, P. M., Bhartiya, S., Venkatesh, K. V., Wangikar P. P. (2006) A structured kinetic model to represent the utilization of multiple substrates in complex media during rifamycin B fermentation. Biotechnol. Bioeng., ., 93, 779-790. 

7.              Bapat, P. M., Nandy, S. K., Wangikar, P. P., and K.V. Venkatesh (2006) “Quantification of metabolically active biomass using Methylene Blue dye Reduction Test (MBRT): Measurement of CFU in about 200 s” Journal of Microbiological Methods, 65, 107-116

8.              Tendulkar, A. V., Sohoni, M. A., Ogunnaike, B. and Wangikar, P. P. (2005) “A geometric invariant-based framework for the analysis of protein conformational space” Bioinformatics, 21, 3622-3628

9.              Tendulkar, A. V., Joshi, A. A., Sohoni, M. A.,  and Wangikar, P. P. (2004) “Clustering of Protein Structural Fragments Reveals Modular Building Block Approach of Nature” J. Mol. Biol, 338, 611-629

10.           Bapat, P. M., Wangikar, P. P. (2004) “Optimization of rifamycin B fermentation in shake flasks via a machine-learning-based approach” Biotechnol. Bioeng., 86, 201-208

11.           Das, P., Ganesh, A., and Wangikar, P. P. (2004) “Influence of pretreatment for de-ashing of sugarcane bagasse on pyrolysis products”  Biomass Bioenergy, 445-457 

12.           Tendulkar, A. V., Wangikar, P.P., Sohoni, M. A., Samant, V. V., Mone, C. Y. (2003) “Parameterization and Classification of Protein Universe via Geometric Techniques”. J. Mol. Biol, 334, 157-172.

13.           Wangikar, P.P., Tendulkar, A. V., Ramya, S., Mali, D., Sarawagi, S. (2003) “Functional Sites in Protein Families uncovered via an Automated and Objective Graph Theoretic Approach”. J. Mol. Biol., 326, 955-978.

14.           Sureshkumar S. V., Phale P. S., Durani S., Wangikar, P. P. (2003) “ A Combined Sequence and Structure Analysis of the Fungal Laccase Family” Biotechnol. Bioeng., 83, 386-394. 

15.           Bapat, P. M., Kundu, S., Wangikar, P. P. (2003) “An optimized method for Aspergillus niger spore production on natural carrier substrates.” Biotechnol. Prog., 19, 1683-1688

16.           Chandrasekaran, S., Wangikar, P.P. (2003) “Method for Lipase-Catalyzed Carbonate Synthesis via One- and Two-Step Alkoxycarbonylation Reactions”, Biotechnol. Prog., 19, 332-337.

17.           Bhunia , A., Durani, S., Wangikar, P. P. (2001) “Horseradish Peroxidase Mediated Degradation of Dyes” Biotechnology and Bioengineering, 72, 562-567.

18.           Gandhi, N., Patil, N. S., Sawant, S., Joshi, J. B. Wangikar, P. P., Mukesh, D. (2001) “Lipase Catalyzed Esterification” Catalysis Reviews, 42 (4) 439-480.

19.           Wangikar, P. P., Michels, P.C., Clark, D.S. Dordick, J.S. (1997) “Structure and Function of Subtilisin BPN’ Solubilized in Organic Solvents” J. Am. Chem. Soc., 119, 70-76

20.           Wangikar, P. P., Carmichael, D., Clark, D.S., Dordick, J.S. (1996) “Active Site Titration of Serine Proteases in Organic Solvents” Biotechnology and Bioengineering, 50, 329-335

21.           Wangikar, P. P., Rich, J.O., Clark, D.S., Dordick, J.S. (1995) “Probing Enzymic Transition State Hydrophobicities” Biochemistry, 34, 12302-12310

22.           Xu, Z. -F., Affleck, R.A., Wangikar, P. P., Suzawa, V.S., Dordick, J.S., Clark, D.S. (1994) “Transition State Stabilization of Subtilisins in Organic  Media”, Biotechnology and Bioengineering, 43, 515-520

23.           Wangikar, P. P., Graycar, T.P., Estell, D.A., Clark, D.S., Dordick, J.S. (1993) “Protein and Solvent Engineering of Subtilisin  BPN’ in Nearly Anhydrous Organic Media” J. Am. Chem. Soc. 115, 12231-12237.

24.           Dordick, J. S., Xu, Z-F, Wangikar, P. P. (1992) “Enzyme Design for Non-aqueous Media” in Biocatalysis in Non-conventional Media, eds. J. Tramper et al, Elsevier Science Publishers.


Full length papers in refereed conference proceedings.

1.            Tendulkar, A.V., Ogunnaike, B. and Wangikar, P. P. Gaussian Mixture Modeling of a-Helix subclasses:  Structure and sequence variations. Accepted in Pac. Symp. Biocomput.. Grand Wailea, Wailea, Maui January 3-7, 2006

2.            Xuan Tien Doan, Rajgopalan Srinivasan,  Bapat, P. M., Wangikar P. P. “Dynamic PCA for phase identification of Rifamycin B fermentation in multi-substrate complex media”, accepted in Advanced Control of Chemical Processes (ADCHEM) Gramado, Brazil, April, 2-5, 2006.



List of Sponsored projects undertaken:

Sr. No

Sponsoring Agency (name of scheme, if any)

Project Title



Council of Scientific and Industrial Research:  New Millenium Initiative in Technology Leadership

Development of Portable and versatile Bioinformatics Software

20-7-2002 to 



Ministry of Human Resources Development (Thrust Areas Project)

Development of Bio-Informatic Platform for Organisation, Modelling and Stimulation of Gene Expression Data.

17-5-2002 to



Department of Science & Technology

Application of Plant Peroxidases & Laccases for removal of recalcitrant organic Chemicals and dyes from Industrial Wastewater

7-2-2000 to



All India Council for Technical Education

CAREER AWARD for Young Teachers

27-10-1998 to



IRCC, IIT Bombay, AICTE Incentive Project

Development of Multiphase Bioreactors for Contimuous Optical Resolution

24-6-1998 to



Board of Research in Nuclear Sciences (DAE Young Scientist Award)

Biocatalytic Synthesis of a Combinatorial Library of Carbanates for drug discovery

20-1-1998  to



IRCC, IIT Bombay

Seed Grant for Preliminary experiments to complete the Proof of Principle Study

2-4-1998  to


Consultation Assignments undertaken:


Sr. No

Company Name

Project Title

Start Date to End date


Ongoing Projects




Persistent Systems Pvt Ltd. Pune

To provide assistance in the area of Bioinformatics

5-2-2002  to May 2003


Lupin Ltd., Tarapore

Data-mining and pattern extraction from historic fermentation data for development of soft-sensors.

5-12-2002 to May 2003


Completed Projects




Orchid Chemicals & Pharm Ltd., Chennai

Development of Biotechnology Activity

20-4-2000 to 20-4-2001


Orchid Chemicals & Pharm Ltd., Chennai

Development of new processes for production of pharmaceuticals

22-3-1999 to 22-3-2000


Ramakrishna Vidyut Ayurvedic Pharmacy

Chemical Analysis of Mahabhringaraj Hair Oil

1-1-2001 to 30-6-2001


Spectrum Ethers Ltd.

Evaluation of Chemical Process

19-8-1999 to 20-9-1999



Continuing Education Programs (Workshops for working professionals) organized: http://www.che.iitb.ac.in/bioinformatics/shortcourse.htm



Topic of the workshop



No. of participants


Introduction to Statistical Design of Experiments.

3 days

April 25-27, 2005



Recent advances in fermentation and enzyme technology

3 days

March 9-11, 2000



Recent advances in fermentation and enzyme technology

4 days

Sept. 13-16,  2000




6 days

June   11-16, 2001



Bioinformatics (in-house course for Persistent Systems Pvt. Ltd., Pune)

2 days

Oct 19-20.   2001




6 days

Nov.  26- Dec. 1, 2001




6 days

May 6-11,  2002



Recent developments in fermentation and downstream processing

4 days

Oct. 14-17, 2003




6 days

November 17-22, 2003