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.

Detailed CV (as of May 2021)

Short bio


Postdoctoral Scholars

John Irudaya Raj H

jih11[at]psu.edu

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


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

Patrick F. Suthers

pfs13[at]psu.edu

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

czc325[at]psu.edu

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


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

Wheaton L. Schroeder

wls5190[at]psu.edu

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

hvd5034[at]psu.edu

M.S. Bioengineering, UC San Diego, 2017


B.S. Chemical Engineering, Penn State, 2015

Veda Sheersh Boorla

vqb5186[at]psu.edu

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

Vikas Upadhyay

vuu10[at]psu.edu

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

Mengqi Hu

mxh5936[at]psu.edu

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

Juliana Simas

jzs6897@psu.edu

Bachelor's in Biotechnology, University of Brasília, 2017


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

Kevin Glass

kmg6685@psu.edu

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]colostate.edu
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]csiro.au
PhD: Virginia Tech
Current position: Research Scientist in Computational & Systems Biology, CSIRO, Canberra

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

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

Dr. YoungJung Chang, 2007-2008. Email: yjchang[at]andrew.cmu.edu
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]gmail.com
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]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 Professor, Department of Chemical and Petroleum Engineering, University of Kansas.



PhD Theses Supervised

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

Dr. Charles Foster, 2021. Email: charlesfoster1766[at]gmail.com
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]gmail.com
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]gmail.com
Thesis: "Computational redesign of protein channels, enzymes, and antibodies."
Current position: Postdoctoral Researcher, Harvard Medical School.

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

Dr. Saratram Gopalakrishnan, 2019. Email: s1gopalakrishnan[at]ucsd.edu
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]schrodinger.com
Thesis: "Development and Applications of Computational Enzyme Engineering Tools."
Current position: Senior scientist, Schrödinger.

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

Dr. Margaret (Simons) Senftle, 2017. Email: Margaret.n.senftle[at]exxonmobil.com
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]genomatica.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: Senior Data Scientist, Discovery Inc.

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

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

Dr. Rajib Saha, 2014. Email: rsaha2[at]unl.edu
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]auburn.edu
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]mgh.harvard.edu
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]thermofisher.com
Thesis: "Using computations to analyze and redesign metabolism"
Current position: Cell Engineering Scientist, Thermo FIsher Scientific.

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. 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: Sr. Scientist, Algenol Biofuels.

Dr. Hossein Fazelinia, 2009. Email: fazeliniah[at]email.chop.edu
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]gmail.com
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]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]biogen.com
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]netl.doe.gov
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: shankarraman_vaidyaraman[at]lilly.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

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

Mohammad Mazharul Islam, 2014. Email: mislam[at]virginia.edu
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]exxonmobil.com
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]usa.dupont.com
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]mit.edu
Current position: PhD Candidate at MIT.

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