Principal investigator

Prof. Costas D. Maranas


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.

Detailed CV (as of May 2021)

Short bio

Postdoctoral Scholars

John Irudaya Raj H


Ph.D., Chemical Engineering, Indian Institute of Technology Bombay, India, 2017.

B.Tech., Industrial Biotechnology, Anna University, India, 2010.

Patrick F. Suthers


PhD Chemical Engineering, University of Wisconsin–Madison, 2005

MS Chemical Engineering, University of Wisconsin–Madison, 2000
BS Chemical Engineering, Tennessee Technological University, 1997

Chen Chen


Ph.D, Chemistry, Wuhan University, China, 2011

B.S., Chemistry, Wuhan University, China, 2005

Wheaton L. Schroeder


Ph.D. Chemical Engineering, University of Nebraska - Lincoln, 2021

B.S. Chemical Engineering and Liberal Arts and Sciences (Mathematics), Iowa State University, 2015

Graduate Students

Hoang Dinh


M.S. Bioengineering, UC San Diego, 2017

B.S. Chemical Engineering, Penn State, 2015

Veda Sheersh Boorla


M.Tech and B.Tech
Chemical Engineering,
Indian Institute of Technology Kharagpur, 2019

Vikas Upadhyay


B.Tech Chemical Engineering,
Indian Institute of Technology Hyderabad, 2018

Mengqi Hu


B.S. Chemical Engineering, UC San Diego, 2017

Juliana Simas

Bachelor's in Biotechnology, University of Brasília, 2017

Master's in Computational Modeling, Laboratório Nacional de Computação Científica, 2020

Kevin Glass

B.S. Bioengineering: Biotechnology, University of California, San Diego, 2019

M.S. Bioengineering, University of California, San Diego, 2021

Group Alumni

Postdoctoral Scholars

Dr. Siu Hung Joshua Chan, 2015-2018. Email: joshua.chan[at]
PhD: Technical University of Denmark
Current position: Assistant Professor, Department of Chemical and Biological Engineering, Colorado State University

Dr. Hadi Nazem-Bokaee, 2014-2017. Email: Hadi.NazemBokaee[at]
PhD: Virginia Tech
Current position: Research Scientist in Computational & Systems Biology, CSIRO, Canberra

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

Dr. Ali R. Zomorrodi, 2012-2013. Email: azomorrodi[at]
PhD: Pennsylvania State University
Current position: Instructor in Pediatrics, faculty of Havard Medical School.

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

Dr. Evgeni Nikolaev, 2002-2005. Email: evgeni.nikolaev[at]
PhD: Lobachevsky Nizhegorod State University, Russia
Current position: Associate II Member in Clinical Investigations and Precision Therapeutics, Center for Quantitative Biology and Cancer Institute of New Jersey, Rutgers University

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

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

PhD Theses Supervised

Dr. Debolina Sarkar, 2021. Email: sarkardebolina27[at]
Thesis: "Integrating modeling of phototrophic metabolism leveraging multi-omics datasets"
Current position: Scientist I, IFF.

Dr. Charles Foster, 2021. Email: charlesfoster1766[at]
Thesis: "Leveraging the kinetics of metabolism and microbial growth for metabolic engineering and scientific discovery in Clostridia."
Current position: Scientist III, DSM.

Dr. Lin Wang, 2020. Email: wanglin44[at]
Thesis: "Computational methods for designing de novo metabolic pathways and genome-minimized chassis strains."
Current position: Bioinformatics Scientist II, Zymergen.

Dr. Ratul Chowdhury, 2019. Email: r.chowdhury.024[at]
Thesis: "Computational redesign of protein channels, enzymes, and antibodies."
Current position: Postdoctoral Researcher, Harvard Medical School.

Dr. Satyakam Dash, 2019. Email: sdash[at]
Thesis: "Metabolic modeling of Clostridia for biofuel production."
Current position: Scientist I, Zymergen.

Dr. Saratram Gopalakrishnan, 2019. Email: s1gopalakrishnan[at]
Thesis: "Nonlinear optimization techniques for genome-scale flux elucidation and kinetic parameterization."
Current position: Postdoctoral Researcher, UCSD.

Dr. Matthew Grisewood, 2018. Email: Matthew.Grisewood[at]
Thesis: "Development and Applications of Computational Enzyme Engineering Tools."
Current position: Senior scientist, Schrödinger.

Dr. Chiam Yu Ng, 2017. Email: ngchiamyu[at]
Thesis: "Computational Design and Optimization of Metabolic Pathways."
Current position: Solution Engineer, X.

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

Dr. Ali Khodayari, 2017. Email: akhodayari[at]
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]
Thesis: "Elucidation and Synthetic Design of Biochemical Pathways Using novoStoic"
Current position: Senior Data Scientist, Discovery Inc.

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

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

Dr. Rajib Saha, 2014. Email: rsaha2[at]
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: rjp0029[at]
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: azomorrodi[at]
Thesis: "Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities"
Current position: Instructor in Pediatrics, faculty of Havard Medical School.

Dr. Sridhar Ranganathan, 2012. Email: sridhar.ranganathan[at]
Thesis: "Using computations to analyze and redesign metabolism"
Current position: Cell Engineering Scientist, Thermo FIsher Scientific.

Dr. Francisco Vital-Lopez, 2011. Email: fvitallopez[at]
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. Vinay Satish Kumar, 2010. Email: vinay[at]
Thesis: "Systems based optimization approaches to analyze and improve metabolic networks"
Current position: Data Scientist, Facebook.

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

Dr. Hossein Fazelinia, 2009. Email: fazeliniah[at]
Thesis: "Computational design and experimental characterization of proteins with novel functions"
Current position: Research scientist, Children's Hospital of Philadelphia

Dr. Madhukar Dasika, 2007. Email: msd179[at]
Thesis: "Systems engineering based approaches for biological network, inference, analysis and redesign"
Current position: Data Scientist, Amgen.

Dr. Manish Saraf, 2006. Email: manish.saraf[at]
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]
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]
Thesis: "Optimization based redesign of microbial production systems"
Current position: Senior Research Scientist II, Genomatica.

Dr. Andreas Lehmann, December 2004. Email: andreas.lehmann[at]
Thesis: "Molecular design in chemical and biological systems"
Current position: Scientist at the Drug Discovery Group, Biogen.

Dr. Anthony Burgard, 2004. Email: Anthony.Burgard[at]
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]
Thesis: "Supply chain management under uncertainty".
Current position: Vice President-Analytics, Indicus Analytics, India.

Dr. Shankar Vaidyaraman, August 2001. Email: shankarraman_vaidyaraman[at]
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

Soodabeh Ghaffari, 2022. Email: soodabehghaffari[at]
Thesis: "Computational Redesign of Enzymes and Channel Proteins"

Mohammad Mazharul Islam, 2014. Email: mislam[at]
Thesis: "Dynamic multi-level and multi-objective metabolic modeling of microbial communities"
Current position: Research Associate (under the supervision of Dr. Jason Papin) at the University of Virgina.

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

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

George Khoury, 2010. Email: george.a.khoury[at]
Thesis: "Computational design to switch protein cofactor specificity and create enzymatic activity"
Current position: Aromatics & Utilities Business Team Leader, ExxonMobil.

Michael Rogers, 2004. Email: Michael.J.Rogers[at]
Thesis: "Real options based planning of pharmaceutical product pipelines"
Current position: Director Corporate Strategy, The Chemours Company.

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

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

Honor Undergraduate Student Theses/Projects Supervised

Matthew Allan, 2017. Email: mfallan[at]
Current position: PhD Candidate at MIT.

Stephen Spagnol, 2010. Email: SSpagnol[at]
Current position: Associate Principal Scientist at Merck.