Principal investigator

Prof. Costas D. Maranas

costas[at]psu.edu

Costas D. Maranas (b. 1967), Donald B. Broughton Professor, Department of Chemical Engineering, The Pennsylvania State University


BS, Chemical Engineering, Aristotle University, Greece, (1990)
MA, Chemical Engineering, Princeton University (1992)
Ph.D. in Chemical Engineering, Princeton University (1995)

Allan P. Colburn Award for Excellence in Publications by a Young Member of AIChE (2002), Outstanding Young Investigator Award of the Computing and Systems Technology AIChE Division (2006), S.V. Sotirchos Lectureship at 6th Panhellenic Chemical Engineering Conference (2007), Penn State Engineering Alumni Society (PSEAS) Outstanding Research Award (2012) Penn State Engineering Alumni Society (PSEAS) Premier Research Award (2016)

Editorial Boards for PLoS Computational Biology, BMC Systems Biology, IEEE Life Sciences, Biotechnology Journal and Metabolic Engineering

Fellow of the American Institute of Medical and Biological Engineering (AIMBE).

Reviewer for NSF, NIH and DOE.

Research interests: Computational protein, enzyme and antibody engineering; reconstruction, curation and analysis of metabolic networks; computational strain design and synthetic biology; metabolism of photosynthetic organisms; metabolism of obligatory anaerobes; modeling of microbial communities; optimization theory and algorithms.

Download CV (Dec. 2016)


Postdoctoral Scholars

Joshua Chan

sxc554[at]psu.edu

Ph.D., Biological Systems Engineering, Technical University of Denmark, Denmark


M.Phil., Computational Systems Biology, The Hong Kong Polytechnic University, Hong Kong, 2011
B.Sc., Mathematics and Physics, The University of Hong Kong, Hong Kong, 2008


Graduate Students

Matt Grisewood

mjg5185[at]psu.edu

MS, Chemical Engineering, Penn State, 2013


BS, Chemical Engineering, Penn State, 2011

Chiam Yu Ng

cun121[at]psu.edu

MS, Chemical and Biological Engineering, Korea University, South Korea, 2012


BE, Chemical and Biological Engineering, Korea University, South Korea, 2010

Saratram Gopalakrishnan

sxg375[at]psu.edu

B.E. Biotechnology, Manipal University, 2011


M.S.E. Chemical and Biomolecular Engineering, Johns Hopkins University, 2013

Ratul Chowdhury

rzc158[at]psu.edu

B.E., Chemical Engineering, Jadavpur University, India, 2013

Satyakam Dash

sud25[at]psu.edu

MS, Chemical and Biomolecular Engineering, Rice University, 2013.


MTech, Biotechnology and Biochemical Engineering, IIT Kharagpur, India, 2011.
BTech, Biotechnology and Biochemical Engineering, IIT Kharagpur, India, 2011.

Lin Wang

lqw5322[at]psu.edu

MS, Chemical Engineering, Carnegie Mellon University, 2015


BS, Southeast University, China, 2011

Charles Foster

cjf33[at]psu.edu

B.S. Chemical Engineering, Rutgers University, 2016

Debolina Sarkar

dxs498[at]psu.edu

B.E. Chemical Engineering, Birla Institute of Technology and Science, India, 2016


Group Alumni


Postdoctoral Scholars

Dr. Tong Li, 2013-2016. Email: tul12[at]psu.edu
PhD: University of Leuven, Belgium
Current position: Bioinformatics Scientist, BASF, San Diego.

Dr. Ali R. Zomorrodi, 2012-2013. Email: alirzomorrodi[at]gmail.com
PhD: Pennsylvania State University
Current position: Postdoctoral Research Associate, Bioinformatics Program & Biomedical Engineering Department, Boston University.

Dr. Patrick Suthers, 2005-2013. Email: suthers[at]engr.psu.edu
PhD: University of Wisconsin-Madison

Dr. YoungJung Chang, 2007-2008. Email: yjchang[at]andrew.cmu.edu
PhD: University of Illinois at Urbana-Champaign
Current position: Research Associate, Merck Sharp & Dohme Corp.

Dr. Evgeni Nikolaev, 2002-2005. Email: en46[at]cornell.edu
PhD: Lobachevsky Nizhegorod State University, Russia
Current position: Instructor of Mathematics, New Jersey State University (Rutgers).

Dr. Anshuman Gupta, 2002-2005. Email: anshumanxgupta[at]gmail.com
PhD: Pennsylvania State University
Current position: Vice President-Analytics, Indicus Analytics, India.

Dr. Kyle Camarda, 1998-2000. Email: camarda[at]ku.edu
PhD: University of Illinois at Urbana-Champaign
Current position: Associate Processor, Department of Chemical and Petroleum Engineering, University of Kansas.



PhD Theses Supervised

Dr. Margaret (Simons) Senftle, 2017. Email: msimons725[at]gmail.com
Thesis: "Development and Application of Metabolic Models for Determining the Effect of Genetic and Environmental Perturbations on Maize."
Current position:

Dr. Ali Khodayari, 2017. Email: ali.khodayari[at]gmail.com
Thesis: "Kinetic Modeling in Genome-scale Metabolic Models: Parameterization and Strain Design"
Current position: Research Scientist, Genomatica.

Dr. Akhil Kumar, 2017. Email: kmr.akhil[at]gmail.com
Thesis: "Elucidation and Synthetic Design of Biochemical Pathways Using novoStoic"
Current position: Applied Scientist, Amazon.

Dr. Thomas Mueller, 2016. Email: tmueller5293[at]gmail.com
Thesis: "Modeling Metabolism and Regulation to Facilitate Strain Characterization and Design"
Current position: Senior Associate, Axtria.

Dr. Anupam Chowdhury, 2016. Email: anupam.juchem[at]gmail.com
Thesis: "Developing optimization-based algorithms for rational engineering of microbial strains"
Current position: Scientist, Zymergen.

Dr. Rajib Saha, 2014. Email: rajibsaha11[at]gmail.com
Thesis: "Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms"
Current position: Assistant Professor, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln.

Dr. Robert Pantazes, 2014. Email: bob.pantazes[at]gmail.com
Thesis: "Computational methods for the de novo design of antibodies"
Current position: Assistant Professor, Department of Chemical Engineering, Auburn University.

Dr. Ali R. Zomorrodi, 2012. Email: alirzomorrodi[at]gmail.com
Thesis: "Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities"
Current position: Postdoctoral Research Associate, Bioinformatics Program & Biomedical Engineering Department, Boston University.

Dr. Sridhar Ranganathan, 2012. Email: sridhar.ranganathan[at]lifetech.com
Thesis: "Using computations to analyze and redesign metabolism"
Current position: Staff Scientist, Synthetic Biology, Life Technologies.

Dr. Francisco Vital-Lopez, 2011. Email: fvitallopez[at]bioanalysis.org
Thesis: "Development of hybrid intracellular/extracellular models of brain tumor progression and medication strategies"
Current position: Research scientist, Biotechnology High Performance Computing Software Applications Institute (BHSAI).

Dr. Prabhasa Ravikirthi, 2010. Email: prabhasarao@gmail.com
Thesis: "Construction of a genome-scale atom mapping model of E.coli for metabolic flux analysis"

Dr. Vinay Satish Kumar, 2010. Email: vinay[at]fb.com
Thesis: "Systems based optimization approaches to analyze and improve metabolic networks"
Current position: Data Scientist, Facebook.

Dr. Jonathan Chin, 2010. Email: jwc25[at]cornell.edu
Thesis: "Engineering and analysis of cofactor partitioning for NADPH-dependent xylitol production in Escherichia coli"
Current position: Scientist, Algenol Biofuels.

Dr. Hossein Fazelinia, 2009. Email: Hossein.Fazelinia[at]fccc.edu
Thesis: "Computational design and experimental characterization of proteins with novel functions"
Current position: Postdoctoral research fellow, Fox Chase Cancer Center.

Dr. Madhukar Dasika, 2007. Email: dasika[at]amyris.com
Thesis: "Systems engineering based approaches for biological network, inference, analysis and redesign"
Current position: Scientist, DuPont.

Dr. Manish Saraf, 2006. Email: manish.saraf[at]citi.com
Thesis: "Development of computational tools for the design and optimization of combinatorial protein libraries"
Current position: Vice President, Citigroup.

Dr. Gregory Moore, May 2005. Email: gmoore[at]xencor.com
Thesis: "Modeling and optimization in directed evolution protocols and protein engineering"
Current position: Senior Scientist, Protein Engineering, Xencor.

Dr. Priti Pharkya, December 2005. Email: ppharkya[at]genomatica.com
Thesis: "Optimization based redesign of microbial production systems"
Current position: Senior Research Scientist II, Genomatica.

Dr. Andreas Lehmann, December 2004. Email: Andreas.Lehmann[at]fccc.edu
Thesis: "Molecular design in chemical and biological systems"
Current position: Postdoctoral Associate, Fox Chase Cancer Center.

Dr. Anthony Burgard, 2004. Email: tony121psu[at]yahoo.com
Thesis: "Optimization-based frameworks for the analysis and redesign of metabolic networks"
Current position: Research General Engineer, National Energy Technology Laboratory.

Dr. Anshuman Gupta, August 2002. Email: anshumanxgupta[at]gmail.com
Thesis: "Supply chain management under uncertainty".
Current position: Vice President-Analytics, Indicus Analytics, India.

Dr. Shankar Vaidyaraman, August 2001. Email: shankar.vaidyaraman[at]zsassociates.com
Thesis: "Optimization based methodology for refrigeration system synthesis and molecular design"
Current position: Marketing Associate, Eli Lily and Company.


M.S. Student Theses/Projects Supervised

M. Mazharul Islam, 2014.
Thesis: "Dynamic multi-level and multi-objective metabolic modeling of microbial communities"
Current position: PhD Candidate (under the supervision of Dr. Armaou and Dr. Rioux) at Pennsylvania State University.

N. Gifford, 2014.
Thesis: "Computational Redesign of Acyl-acp Thioesterases for Increased Substrate Specificity"

M. Grisewood, 2013.
Thesis: "OptZyme: A Computational Tool for Altering Enzymatic Specificity"
Current position: Doctoral Student, Department of Chemical Engineering, Pennsylvania State University.

A. Kumar, 2013.
Thesis: "MetRxn: a knowledgebase of metabolites and reactions ining metabolic models and databases"
Current position: Doctoral student, Department of Bioinformatics and Genomics, Pennsylvania State University.

A. R. Zomorrodi, 2011.
Thesis: "Optimization-driven design of synthetic genetic circuits using biobricks"
Current position: Postdoctoral Research Associate, Bioinformatics Program & Biomedical Engineering Department, Boston University.

R. Saha, 2011.
Thesis: "Reconstruction of a genome-scale metabolic model of maize metabolism"
Current position: Assistant Professor, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln.

P. Ravikirthi, 2010.
Thesis: "Construction of a genome-scale atom mapping model of E.coli for metabolic flux analysis"
Current position: Bioinformatician, Positive Bioscience, India.

G. Khoury, 2010.
Thesis: "Computational design to switch protein cofactor specificity and create enzymatic activity"
Current position: Doctoral Student, Department of Chemical and Biological Engineering, Princeton University.

V. S. Kumar, 2008.
Thesis: "Optimization methods to compare strain design strategies in metabolic networks using different cellular objectives"
Current position: Data Scientist, Facebook.

S. Ranganathan, 2008.
Thesis: "Metabolic Engineering and Strain Design procedures for valuable chemical synthesis"
Current position: Staff Scientist, Synthetic Biology, Life Technologies.

M. Rogers, 2004.
Thesis: "Real options based planning of pharmaceutical product pipelines"
Current position: Business Development Manager, DuPont.

M. Kalp, 1999
Thesis: "Development of process design case studies for the capstone design course"
Current position: Project Engineer, Croda.

S. Petkov, August 1997
Thesis: "Analysis and optimization of chemical process systems under uncertainty"
Current position: Director Business Development, Huvepharma, Bulgaria.