Publications of the Costas D. Maranas Research Group. Penn State Department of Chemical Engineering

Khodayari, A., Chowdhury, A., Maranas, C. D. (2014). "Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model", Frontiers in bioengineering and biotechnology, 2.
Simons M., Saha R., Amiour N., Kumar A., Guillard L., Clément G., Miquel M., Li Z., Mouille G., Lea P.J., Hirel B., Maranas C.D. (2014). "Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model", Plant Physiology, 1659-74, 166(3).
Mueller, T.J., Grisewood, M.J., Nazem-Bokaee, H., Gopalakrishnan, S., Ferry, J.G., Wood, T.K., Maranas, C.D. (2014). "Methane Oxidation by Anaerobic Archaea For Conversion to Liquid Fuels", J. Ind. Microbiol. Biotechnol.
Akhil Kumar and Costas D. Maranas (2014). "CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database", J. Chem. Inf. Model., 2014, 54 (12), pp 3417–3438.
Dash, S., Mueller, T. J., Venkataramanan, K. P., Papoutsakis, E. T., & Maranas, C. D. (2014). "Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model". Biotechnology for Biofuels, 7(1), 144.
Chowdhury A., A. R. Zomorrodi and C. D. Maranas (2014), "Bilevel optimization techniques in computational strain design". Computers and Chemical Engineering.
Simons, M., R. Saha, L. Guillard, G. Clément, P. Armengaud, R. Cañas, C.D. Maranas, P. Lea and B. Hirel (2014), "Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling", Journal of Experimental Botany.
Khodayari A., A.R. Zomorrodi, J.C. Liao and C.D. Maranas (2014), "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data". Metabolic engineering, 25C:50-62.
Saha, R.S., A. Chowdhury and C.D. Maranas (2014), "Recent advances in the reconstruction of metabolic models and integration of omics data", Current Opinion in Biotechnology, 29, 39-45.
Zomorrodi, A.R., M.M. Islam and C.D. Maranas (2014), "d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities", ACS Synthetic Biology, http://dx.doi.org/10.1021/sb4001307
Zomorrodi, A. R., and C.D. Maranas (2014), "Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits", European Journal of Operational Research, http://dx.doi.org/10.1016/j.ejor.2014.01.054
Chowdhury A., A.R. Zomorrodi and C.D. Maranas (2014), "k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design". PLoS Computational Biology, 10(2):e1003487. PMID: 24586136.
Tee,T.W., A. Chowdhury, C.D. Maranas and J.V. Shanks (2014) "Systems metabolic engineering design: Fatty acid production as an emerging case study", Biotechnology and Bioengineering. doi: 10.1002/bit.25205, PMID: 24481660.
Grisewood, M.J., N.P. Gifford, R.J. Pantazes, Y. Li, P.C. Cirino, M.J. Janik and C.D. Maranas (2013), "OptZyme: Computational Enzyme Redesign Using Transition State Analogues", PLoS ONE, 8(10):e75358, doi:10.1371/journal.pone.0075358, PMID: 24116038.
Mueller, T.J., B.M. Berla, H.B. Pakrasi, and C.D. Maranas (2013), "Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow", BMC Systems Biology, 7:142, doi:10.1186/1752-0509-7-142, PMID: 24369854.
Berla, B.M., Saha, R., Immethun, C.M., Maranas, C.D., Moon, T.S. and Pakrasi, H.B. (2013), "Synthetic biology of cyanobacteria: unique challenges and opportunities", Frontiers in Microbiology, 4, doi: 10.3389/fmicb.2013.00246, PMID: 24009604.
Zomorrodi, A.R., J.G. Lafontaine Rivera, J.C. Liao and C.D. Maranas (2013) "Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks", Biotechnology Journal, doi: 10.1002/biot.201200270, PMID: 23450699.
Pantazes, R.J. and C.D. Maranas (2013), "MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies", BMC Bioinformatics, 14 (168), doi:10.1186/1471-2105-14-168, PMID: 23718826.
Zomorrodi, A.R., P.F. Suthers, S. Ranganathan and C.D. Maranas (2012), "Mathematical optimization applications in metabolic networks", Metabolic Engineering, 14, 672–686, PMID: 23026121.
Saha, R., A.T. Verseput, B.M. Berla, T.J.Mueller, H.B. Pakrasi and C.D.Maranas (2012), "Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803," PLoS ONE, 7(10):e48285.PMID: 23133581.
Ranganathan, S., T.W. Tee, A. Chowdhury, A.R. Zomorrodi, J.M. Yoon, Y. Fu, J.V. Shanks, C.D. Maranas (2012), "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli", Metabolic Engineerirng, 14(6):687-704. PMID: 23036703.
Wang, N., K.A. Eckert, A.R. Zomorrodi, P. Xin, W. Pan, K.A. Eckert, J. Weisz, C.D. Maranas and G.A. Clawson (2012), "Decreased expression of HtrA1 in human breast epithelial cells triggers the epithelial-mesenchymal transition and activates the ATM damage response," PLoS One, 7(6):e39446, PMID: 22761798
Zomorrodi, A.R. and C.D. Maranas (2012), "OptCom: A multi-level optimization framework for the metabolic modeling and analysis of microbial communities," PLoS Computational Biology, 8(2):e1002363. PMID: 22319433
Kumar, A., P.F. Suthers and C.D. Maranas (2012), "MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases," BMC Bioinformatics, 13(6):e1002363. PMID: 22233419
Xu P., S. Ranganathan, Z.L. Fowler, C.D. Maranas and M.A.G. Koffas (2011), "Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA," Metabolic Engineering, 13(5):578-87. PMID: 21763447
Pantazes, R.J., M.J. Grisewood and C.D. Maranas (2011), "Recent advances in computational protein design," Current Opinion in Structural Biology, 6(21): 1-6. PMID: 21600758
Saha, R., P.F. Suthers and C.D. Maranas (2011), "Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism.," PLoS ONE, 6(7): e21784. PMID: 21755001
Satish Kumar, V., J.G. Ferry and C.D. Maranas (2011), "Metabolic reconstruction of the archaeon methanogen Methanosarcina acetivorans.," BMC Systems Biology, 5(1): 28. PMID: 21324125
Ravikirthi, P., P.F. Suthers and C.D. Maranas (2011), " Construction of an E. coli Genome-scale Atom Mapping Model for MFA Calculations,," Biotechnology & Bioengineering, 108(6): 1372-82. PMID: 21328316
Vital-Lopez, F.-G., A. Armaou, C.D. Maranas and M. Hutnik (2011), "Modeling the effect of chemotaxis in glioblastoma tumor progression.," AIChE Journal, 57(3): 778-792.
Zomorrodi, A.R. and C.D. Maranas (2010), "Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.," BMC Systems Biology, 4(1): 178. PMID: 21190580
Pantazes, R.J. and C.D. Maranas (2010), "OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding," Protein Engineering, Design & Selection, 23(11): 849-58. PMID: 20847101
Ranganathan, S. and C.D. Maranas (2010), "Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions," Biotechnology Journal, 5: 716-25. PMID: 20665644
Ranganathan, S., P.F. Suthers and C.D. Maranas (2010), "OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions," PLoS Computational Biology, 6(4): e1000744. PMID: 20419153
Suthers, P.F., Y. Chang and C.D. Maranas (2010), "Improved computational performance of MFA using elementary metabolite units and flux coupling," Metabolic Engineering, 12(2):123-8. PMID: 19837183
AbuOun, M., P.F. Suthers, G.I. Jones, B.R. Carter, M.P. Saunders, C.D. Maranas, M.J. Woodward and M.F. Anjun (2009), "Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain," Journal of Biological Chemistry, 284(43):29480-8. PMID: 19690172
Khoury, G.A., H. Fazelinia, J.W. Chin, R.J. Pantazes, P.C. Cirino and C.D. Maranas (2009), "Computational Design of Candida boidinii Xylose Reductase for Altered Cofactor Specificity," Protein Science, 18(10): 2125-38. PMID: 19693930
Suthers P.F., A. Zomorrodi and C.D. Maranas (2009), "Genome-scale Gene/Reaction Essentiality and Synthetic Lethality Analysis," Molecular Systems Biology, 5:301. PMID: 19690570
Satish Kumar, V. and C.D. Maranas (2009), "GrowMatch: An automated method for reconciling in silico/in vivo growth predictions," PLoS Computational Biology, 5(3): e1000308. PMID: 19282964
Suthers, P.F., M.S. Dasika, V. Satish Kumar, G. Denisov, J.I. Glass and C.D. Maranas (2009), "A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189," PLoS Computational Biology, 5(2): e1000285. PMID: 19214212
Lee, S., Y. Chang, D. Shin, J. Han, M. Seo, H. Fazelinia, C.D. Maranas and H. Kim (2009), "Designing the substrate specificity of D-hydantoinase using a rational approach," Enzyme and Microbial Technology, 44: 170.
Fazelinia H., P.C. Cirino and C.D. Maranas (2009), "OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold," Protein Science, 18(1): 180-95. PMID: 19177362
Chin, J.W., R. Khankal, C. Monroe, C.D. Maranas and P. Cirino (2009), "Analysis of NADPH supply during xylitol production by engineered Escherichia coli," Biotechnology and Bioengineering, 102: 209-20. PMID: 18698648
Chang, Y., P.F. Suthers and C.D. Maranas (2008), "Identification of optimal measurement sets for complete flux elucidation in MFA experiments," Biotechnology and Bioenginering, 100: 1039-49. PMID: 18553391
Dasika, M.S. and C.D. Maranas (2008), "OptCircuit: An optimization based method for computational design of genetic circuits," BMC Systerms Biology, 2: 24. PMID: 18315885
Gianchandani, E.P., M.A. Oberhardt, A.P. Burgard, C.D. Maranas and J.A. Papin, (2008), "Predicting biological system objectives de novo from internal state measurements," BMC Bioinformatics, 9: 43. PMID: 18218092
Vital-Lopez, F.G., A. Varshney, C.D. Maranas and A. Armaou (2008), "Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks," Computers & Chemical Engineering, 32: 2065-71.
Pantazes, R.J., M.C. Saraf and C.D. Maranas (2007), "Optimal protein library design using recombination or point mutations based on sequence-based scoring functions," Protein Engineering, Design & Selection, 20(8): 361-373. PMID: 17686879
Suthers, P.F, A.P. Burgard, M.S. Dasika, F. Nowroozi, S. Van Dien, J.D. Keasling and C.D. Maranas (2007), "Metabolic flux elucidation for large-scale models using ¹³C labeled isotopes," Metabolic Engineering, 9(5-6): 387-405. PMID: 17632026
Satish Kumar, V., M.S. Dasika and C.D. Maranas (2007), "Optimization based automated curation of metabolic reconstructions," BMC Bioinformatics, 8: 212. PMID: 17584497
Fazelinia, H., P.C. Cirino and C.D. Maranas (2007), "Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity," Biophysical Journal, 92(6): 2120-2130. PMID: 17208966
Christensen, C., A. Gupta, C.D. Maranas and R. Albert (2007), "Large-scale inference and graph theoretical analysis of gene-regulatory networks in B. subtilis," Physica A, 373, 796-810.
Vital-Lopez, F.G., C.D. Maranas and A. Armaou (2006), "A computational procedure for optimal engineering interventions using kinetic models of metabolism," Biotechnology Progress, 22(6): 1507-1517. PMID: 17137295
Dasika, M.S., A.P. Burgard and C.D. Maranas (2006), "A computational framework for the topological analysis and targeted disruption of signal transduction networks," Biophysical Journal, 91: 382-398.
Vital-Lopez, F.G., C.D. Maranas and A. Armaou (2006), "Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels," Proceedings of the 2006 American Control Conference, Minneapolis, MN.
Gupta, A., C.D. Maranas and R. Albert (2006), "Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites," Bioinformatics, 22: 209-214.
Saraf, M.C., G.L. Moore, N.M. Goodey, V.Y. Cao, S.J. Benkovic and C.D. Maranas (2006), "IPRO: An Iterative Computational Protein Library Redesign and Optimization Procedure," Biophysical Journal, 90: 4167-4180.
Pharkya, P. and C.D. Maranas (2006), "An Optimization Framework for Identifying Reaction Activation/Inhibition or Elimination Candidates for Overproduction in Microbial Systems," Metabolic Engineering, 8: 1-13.
Saraf, M.C., A. Gupta and C.D. Maranas (2005), "Design of combinatorial protein libraries of optimal size," Proteins, 60: 769-777.
Nikolaev, E.V., P. Pharkya, C. D. Maranas and A. Armaou (2005), "Optimal selection of enzyme levels using large-scale kinetic models," Proceedings of 16th International Federation of Automatic Control World Congress, Prague, Czech Republic, 6 pages.
Pharkya, P. and C.D. Maranas (2005), "A hierarchical framework for metabolic pathway discovery and strain design," FOSBE 2005 Proceedings: 141-144.
Fong, S.S., A.P. Burgard, C.D. Herring, E.M. Knight, F.R. Blattner, C.D. Maranas and B.O. Palsson (2005), "In silico design and adaptive evolution of Escherichia coli for production of lactic acid," Biotechnol Bioeng., 91: 643-648.
Nikolaev, E.V., A.P. Burgard and C.D. Maranas (2005), "Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions," Biophysical Journal 88: 37-49.
Rogers, M.J., M. Ding and C.D. Maranas (2005), " Valuation of Pharmaceutical R&D Licensing Deals Using a Real Options Based Approach," AIChE Journal, 51: 198-209.
Gupta, A., J.D. Varner and C.D. Maranas (2005), "Large-Scale Inference of the Transcriptional Regulation of Bacillus subtilis," Computers & Chemical Engineering, 29: 565-576.
Dasika, M.S., A. Gupta and C.D. Maranas (2005), "DEMSIM: A Discrete Event based Mechanistic Simulation Platform for Gene Expression and Regulation Dynamics," Journal of Theoretical Biology 232: 55-69.
Lehmann, A. and C.D. Maranas (2004), "Molecular Design Using Quantum Chemical Calculations for Property Estimation,"Ind. Eng. Chem. Res., 43: 3419-3432
Pharkya, P., A.P. Burgard and C.D. Maranas (2004), "OptStrain: A Computational Framework for Redesign of Microbial Production Systems," Genome Research, 14(11): 2367-76.
Dasika, M.S., A. Gupta and C.D. Maranas (2004), "A Mixed Integer Linear Programming Framework (MILP) for Inferring Time Delay in Gene Regulatory Networks," Pacific Symposium on Biocomputing
Saraf, M.C., A.R. Horswill, S.J. Benkovic and C.D. Maranas (2004), "FamClash: A method for ranking the activity of engineered enzymes," Proc. Natl. Acad. Sci. USA 101: 4142-4147. (See Commentary )
- Penn State press release
- ScienceDaily Magazine story
Rogers, M.J., M. Ding and C. D. Maranas (2004), "A Case Study on the Design of Pharmaceutical R&D Licensing Deals," FOCAPD Conference Proceedings, 475-479.
Moore, G.L. and C.D. Maranas (2004), "Computational Challenges in Combinatorial Library Design for Protein Engineering," AIChE Journal 50, 262-272.
Burgard, A.P.^#, E.V. Nikolaev ^#, C.H. Schilling and C.D. Maranas (2004), "Flux Coupling Analysis of Genome-scale Metabolic Reconstructions," Genome Research 14, 301-312. ^# These authors contributed equally to this work.
Gupta, A and C.D. Maranas (2004), "Real-Options-Based Planning Strategies under Uncertainty," Industrial & Engineering Chemistry Research 43, 3870-3878.
Saraf, M.C. and C.D. Maranas (2003), "Using a Residue Clash Map to Functionally Characterize Protein Recombination Hybrids," Protein Engineering 16(12), 1025-1034.
Pharkya, P., A.P. Burgard, and Maranas (2003), "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock," Biotechnology and Bioengineering 84, 887-899.
Moore, G.L. and C.D. Maranas (2003), "Modeling and Optimization of Directed Evolution Protocols." Enzyme Functionality: Design, Engineering, and Screening edited by A. Svendsen (pp. 185-212). New York, NY: Marcel Dekker, Inc.
Gupta, A. and C.D. Maranas (2003), "Managing demand uncertainty in supply chain planning," Computers and Chemical Engineering 27, 1219-1227.
Pharkya, P., E.V. Nikolaev and C.D. Maranas (2003), "Review of the BRENDA Database," Metabolic Engineering 5, 71-73.
Burgard, A.P., P. Pharkya and C.D. Maranas (2003), "OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization," Biotechnology and Bioengineering 84, 647-657.
Saraf, M.C., G.L. Moore and C.D. Maranas (2003), "Using multiple sequence correlation analysis to characterize functionally important protein regions," Protein Engineering 16, 397-406.
Moore, G.L. and C.D. Maranas (2003), "Identifying Residue-Residue Clashes in Protein Hybrids by Using a Second-order Mean-field Approach," Proc. Natl. Acad. Sci. USA 100, 5091-5096. (download archived supplemental information )
- Chemical & Engineering News
Burgard, A.P. and C.D. Maranas (2003), "Optimization-Based Framework for Inferring and Testing Hypothesized Metabolic Objective Functions," Biotechnology and Bioengineering 82, 670-677.
Gupta, A. and C.D. Maranas (2003), "Market-Based Pollution Abatement Strategies: Risk Management Using Emission Option Contracts," Industrial & Engineering Chemistry Research 42 802-810.
Maranas, C.D., G.L. Moore, A.P. Burgard and A. Gupta (2003), "Systems Engineering Challenges And Opportunities In Computational Biology," FOCAPO 2003 13-26.
Rogers, M.J., A. Gupta and C.D. Maranas (2003), "Risk Management in Real Options Based Pharmaceutical Portfolio Planning," FOCAPO 2003 241-244.
Rogers, M.J., A. Gupta and C.D. Maranas (2002), "Real Options Based Analysis of Optimal Pharmaceutical R&D Portfolios," Industrial & Engineering Chemistry Research 41, 6607-6620.
Moore, G.L. and C.D. Maranas (2002), "Predicting Out-of-Sequence Reassembly in DNA Shuffling," Journal of Theoretical Biology 219, 9-17.
Vaidyaraman, S. and C.D. Maranas (2002), "Synthesis of Mixed Refrigerant Cascade Cycles," Chemical Engineering Communications 189, 1057-1078.
Moore, G.L. and C.D. Maranas (2002), "eCodonOpt: A Systematic Computational Framework for Optimizing Codon Usage in Directed Evolution Experiments," Nucleic Acids Research 30, 2407-2416. (download Supplementary material)
Burgard, A.P. and C.D. Maranas (2002), "Review of the Biocatalysis/Biodegradation Database (UM-BBD)," Metabolic Engineering 4, 111-113.
Burgard, A.P., S. Vaidyaraman and C.D. Maranas (2001), "Minimal Reaction Sets for Escherichia Coli Metabolism under Different Growth Requirements and Uptake Environments," Biotechnology Progress 17, 791-797.
Burgard, A.P., G.L. Moore and C.D. Maranas (2001), "Review of the TEIRESIAS-based Tools of the IBM Bioinformatics and Pattern Discovery Group," Metabolic Engineering 3, 285-288.
Lutz, S., M. Ostermeier, G.L. Moore, C.D. Maranas and S.J. Benkovic (2001), "Creating multiple-crossover DNA libraries independent of sequence identity," Proc. Natl. Acad. Sci. USA 98, 11248-11253. (download supplemental Table 1, Figure 9, Figure 10)
Burgard, A.P. and C.D. Maranas (2001), "Review of Enzymes and Metabolic Pathways (EMP) database," Metabolic Engineering 3, 193-194.
Burgard, A.P. and C.D. Maranas (2001), "Probing the Performance Limits of the Escherichia coli Metabolic Network Subject to Gene Additions or Deletions," Biotechnology and Bioengineering 74, 364-375.
Gupta, A. and C.D. Maranas (2001), "Multiperiod Planning of Multisite Supply Chains Under Demand Uncertainty," European Symposium on Computer Aided Process Engineering 11, 871-882.
Maranas, C.D. (2001), "Optimization in Molecular Design and Bioinformatics," European Symposium on Computer Aided Process Engineering 11, 1157-1164.
Maranas, C.D. and A.P. Burgard (2001), "Review of EcoCyc and MetaCyc databases," Metabolic Engineering 3, 98-99.
Moore, G.L., C.D. Maranas, S. Lutz and S.J. Benkovic (2001), "Predicting Crossover Generation in DNA Shuffling," Proc. Natl. Acad. Sci. USA 98, 3226-3231. (download Supplementary material)
- Penn State press release
- Collegian newspaper story
- ScienceDaily Magazine story
- Bioresearch Online
Gupta, A., C.D. Maranas and C.M. McDonald (2000), "Midterm Supply Chain Planning Under Demand Uncertainty: Customer Demand Satisfaction and Inventory Management," Computers and Chemical Engineering 24, 2613-2621.
Gupta, A. and C.D. Maranas (2000), "A Two-Stage Modeling and Solution Framework for Multisite Midterm Planning under Demand Uncertainty," Industrial & Engineering Chemistry Research 39, 3799-3813.
Moore, G.L. and C.D. Maranas (2000), "Modeling DNA Mutation and Recombination for Directed Evolution Experiments," Journal of Theoretical Biology 205, 483-503.
Moore, G.L., C.D. Maranas, K.R. Gutshall and J.E. Brenchley (2000), "Modeling and Optimization of DNA Recombination," Computers and Chemical Engineering 24, 693-699.
Vaidyaraman, S. and C.D. Maranas (1999), "Simultaneous Refrigeration Cycle Synthesis and Refrigerant Selection," In proceedings of PRES'99, 2nd Conference on Process Integration, Modeling and Optimisation for Energy Saving and Pollution Reduction, May 31-June 2, Budapest, Hungary.
Camarda, K.V., B.W. Bonnell, C.D. Maranas and R. Nagarajan (1999), "Design of Surfactant Solutions with Optimal Macroscopic Properties," Computers and Chemical Engineering 23, Suppl., 467-470.
Gupta, A. and C.D. Maranas (1999), "A Hierarchical Lagrangean Relaxation Procedure for Solving Midterm Planning Problems," Industrial & Engineering Chemistry Research 38, 1937-1947.
Camarda, K.V. and C.D. Maranas (1999), "Optimization in Polymer Design using Connectivity Indices," Industrial & Engineering Chemistry Research 38, 1884-1892.
Vaidyaraman, S. and C.D. Maranas (1999), "Optimal Refrigeration Cycle Synthesis and Refrigerant Selection," AIChE Journal 45(5), 997-1017.
Raman, V.S. and C.D. Maranas (1998), "Optimization in product design with properties correlated with topological indices," Computers and Chemical Engineering 22(6), 747-763.
Petkov, S.B. and C.D. Maranas (1998), "Design of Multiproduct Batch Plants Under Demand Uncertainty with Staged Capacity Expansions," Computers and Chemical Engineering 22, Suppl., 789-792.
Petkov, S.B. and C.D. Maranas (1998), "Design of Single-Product Campaign Batch Plants under Demand Uncertainty," AIChE Journal 44(4), 896-911.
Petkov, S.B. and C.D. Maranas (1997), "Multiperiod Planning and Scheduling of Multipurpose Batch Plants Under Demand Uncertainty," Industrial & Engineering Chemistry Research 36(11), 4864-4881.
Petkov, S.B. and C.D. Maranas (1997), "Quantitative Assessment of Uncertainty in the Optimization of Metabolic Pathways," Biotechnology and Bioengineering 56(2), 145-161.
Maranas, C.D. (1997), "Optimization Accounting for Property Prediction Uncertainty in Polymer Design," Computers and Chemical Engineering 21, Suppl., 1019-1024.
Maranas, C.D. (1997), "Optimal Molecular Design Under Property Prediction Uncertainty," AIChE Journal 43(5), 1250-1264.
Androulakis, I.P., C.D. Maranas and C.A. Floudas (1997), "Prediction of Oligopeptide Conformations via Deterministic Global Optimization," Journal of Global Optimization 11, 1-34.
Maranas, C.D. and C.A. Floudas (1997), "Global Optimization in Generalized Geometric Programming," Computers and Chemical Engineering 21(4), 351-369.
Harding, S.T., C.D. Maranas, C.M. McDonald and C.A. Floudas (1997), "Locating All Homogeneous Azeotropes in Multicomponent Mixtures," Industrial & Engineering Chemistry Research 36(1), 160-178.
Maranas, C.D., I.P. Androulakis, C.A. Floudas, J.M. Mulvey and A.J. Berger (1997), "Solving Long-Term Financial Planning Problems via Global Optimization," Journal of Economics Dynamics and Control 21(8/9), 1405-1425.
Maranas, C.D. (1996), "Optimal Computer-Aided Molecular Design: Application to Polymer Design," Industrial & Engineering Chemistry Research 35(10), 3403-3414.
Adjiman, C.S., I.P. Androulakis, C.D. Maranas and C.A. Floudas (1996), "A Global Optimization Method, alphaBB, for Process Design," Computers and Chemical Engineering 20, Suppl. A, S419-S424.
Maranas, C.D, C.M. McDonald, S.T. Harding and C.A. Floudas (1996), "Locating All Azeotropes in Homogeneous Azeotropic Systems," Computers and Chemical Engineering 20, Suppl. A, S413-S418.
Maranas, C.D., I.P. Androulakis and C.A. Floudas (1995), "A Deterministic Global Optimization Approach for the Protein Folding Problem," Proc. of DIMACS Series in Discrete Mathematics and Theoretical Computer Science 23, 133-150.
Androulakis, I.P., C.D. Maranas and C.A. Floudas (1995), "alphaBB: A Global Optimization Method for General Constrained Nonconvex Problems," Journal of Global Optimization 7(4), 337-363.
Maranas, C.D. and C.A. Floudas (1995), "Finding All Solutions of Nonlinearly Constrained Systems of Equations," Journal of Global Optimization 7(2), 143-182.
Maranas, C.D., C.A. Floudas and P.N. Pardalos (1995), " New Results in the Packing of Equal Circles in a Square," Discrete Mathematics 142, 287-293.
Maranas, C.D. and C.A. Floudas (1994), "A Deterministic Global Optimization Approach for Molecular Structure Determination," Journal of Chemical Physics 100(2), 1247-1261.
Maranas, C.D. and C.A. Floudas (1994), "Global Minimum Potential Energy Conformations of Small Molecules," Journal of Global Optimization 4, 135-170.
Maranas, C.D. and C.A. Floudas, (1993), "A Global Optimization Method For Weber's Problem With Attraction And Repulsion," Proc. of Large Scale Optimization: State of the Art Conference (February 15-17, 1993, Florida University), Kluwer Academic Publishers B.V., 259-293.
Maranas, C.D. and C.A. Floudas (1993), "Global Optimization for Molecular Conformation Problems," Annals of Operations Research 42, 85-117.
Maranas, C.D. and C.A. Floudas (1992), "A Global Optimization Approach for Lennard-Jones Microclusters," Journal of Chemical Physics 97(10), 7667-7678.
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