Research Activities

The research program in the Computer-Aided Systems Laboratory is directed at obtaining a fundamental understanding of key issues in the areas of : (i) Product and Process Systems Engineering, and (ii) Bioinformatics and Computational Genomics, and as such they lie at the interface of chemical engineering, applied mathematics/operations research, computer science, computational chemistry and molecular biology. The unified thrust of our research is to address fundamental problems and application areas through detailed mathematical modeling at the microscopic, mesoscopic and/or macroscopic level, rigorous optimization theory and algorithms, and large-scale computations on high performance clusters.


Product and Process Design, Synthesis and Discovery

In this area, we aim at developing systematically new products and processes which meet the specified performance criteria of (i) minimum cost or maximum profit, (ii) energy efficiency, and (iii) good operability with respect to flexibility, controllability, reliability, safety, and environmental regulations. Our approach is based on a mixed-integer nonlinear optimization framework where discrete and continuous decisions are modeled explicitly. Current research work focuses on (a) simultaneous treatment of uncertainty and parameter estimation in nonideal separations; (b) new methods for addressing model uncertainty in product and process design and synthesis, and (c) new modeling and optimization approaches to address the topology of complex metabolic networks.

Selected References:

  • Rojnuckarin A., C.A. Floudas, H. Rabitz, and R.A. Yetter, "Optimal Control of a Plug Flow Reactor with a Complex Reaction Mechanism", Journal of Physical Chemistry, 97, 45, 11689-11695 (1993).
  • McDonald C.M. and C.A. Floudas (PostScript (1847K), PDF (610K)), "Global Optimization for the Phase and Chemical Equilibrium Problem : Application to the NRTL Equation", Computers and Chemical Engineering, 19, 11, pp. 1111-1141(1995).
  • McDonald C.M. and C.A. Floudas (PostScript (931K), PDF (488K)), "Decomposition Based and Branch and Bound Global Optimization Approaches for the Phase Equilibrium Problem", J. of Global Optimization, 5, 205-251 (1994).
  • McDonald C.M. and C.A. Floudas (PostScript (473K), PDF (351K)), "Global Optimization for the Phase Stability Problem", AIChE J., 41,7, 1798-1814(1995).
  • Hatzimanikatis V., C.A. Floudas, and J.E. Bailey, "Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization", AIChE J., 42, 1277-1292 (1996).
  • Hatzimanikatis V., C.A. Floudas, and J.E. Bailey, "Optimization of Regulatory Architectures in Metabolic Reaction Networks", Biotechnology and Bioengineering, 52, 485-500 (1996).
  • Rojnuckarin A., C.A. Floudas, H. Rabitz, and R.A. Yetter, "Methane Conversion to Ethylene and Acetylene : Optimal Control with Chlorine, Oxygen and Heat Flux", IE&C Fundamentals, 35, 683-696 (1996).
  • Schweiger C.A. and C.A. Floudas (PostScript (873K), PDF (412K)), "Interaction of Design and Control: Optimization with Dynamic Models", Optimal Control: Theory, Algorithms, and Applications, (W.W. Hager and P.M. Paradolos, Editors), Kluwer Academic Publishers, pp. 388-435, (1997).
  • McDonald C.M. and C.A. Floudas (PostScript (380K), PDF (376K)), "GLOPEQ: A New Computational Tool for the Phase and Chemical Equilibrium Problem", Computers and Chemical Engineering, 21, pp. 1-23, (1997).
  • Harding S.T., C.D. Maranas, C.M. McDonald, and C.A. Floudas (PostScript (389K), PDF (319K)), "Locating All Homogeneous Azeotropes in Multicomponent Mixtures", Industrial and Engineering Chemistry Research, 36, pp. 160-178, (1997).
  • Esposito W.R. and C.A. Floudas (PostScript (930K), PDF (463K)), "Global Optimization in Parameter Estimation of Nonlinear Algebraic Models via the Error-In-Variables Approach", Industrial and Engineering Chemistry Research, 37, pp.1841-1858, (1998).
  • Schweiger C.A. and C.A. Floudas (PostScript (1187K), PDF (569K)), "Optimization Framework for the Synthesis of Chemical Reactor Networks", Industrial and Engineering Chemistry Research, 38, pp.744-766, (1999).
  • Schweiger C.A. and C.A. Floudas (PostScript (1187K), PDF (569K)), "Optimization Framework for the Synthesis of Chemical Reactor Networks", Industrial and Engineering Chemistry Research, 38, pp.744-766, (1999).
  • Harding S.T., and C.A. Floudas "Phase Stability with Cubic Equations of State: A Global Optimization Approach", AIChE Journal, 46, 7, 1422-1440 (2000).
  • Harding S.T. and C.A. Floudas, "Locating Heterogeneous and Reactive Azeotropes", Industrial and Engineering Chemistry Research, 39, 6, 1576-1595 (2000).
  • Floudas C. A. and P. M. Pardalos, "Recent Developments in Global Optimization and Their Relevance to Process Design", In Proceedings of the Foundations of Computer Aided Process Design, FOCAPD'99, Malone M. F. and J. A. Trainham, Eds. (1999).
  • Faliks A., R.A. Yetter, C.A. Floudas, R. Hall, and H. Rabitz, "Optimal Control of Methane Conversion to Ethylene", Journal of Physical Chemistry A, 104, 10740-10746 (2000).
  • Faliks A., R.A. Yetter, C.A. Floudas, Y. Wei, and H. Rabitz, "Optimization of Living Polymerization Through Distributed Control of a Nitroxide Radical", POLYMER, 42, 2061-2065 (2001).
  • Faliks A., R.A. Yetter, C.A. Floudas, S.L. Bernasek, and M. Fransson and H. Rabitz, "Optimal Control of Catalytic Methanol Conversion to Formaldehyde", Journal of Physical Chemistry A, 105, 2099-2105 (2001).
  • Faliks A., R.A. Yetter, C.A. Floudas, Y. Wei, and H. Rabitz, "Optimization of Living Radical Polymerization Through Distributed Control of Energy", Macromolecular Chemistry and Physics, 202(13), 2797-2801 (2001).
  • Esposito W.R. and C.A. Floudas, "Deterministic Global Optimization in Isothermal Reactor Network Synthesis", Journal of Global Optimization, 22, 59-95 (2002).
  • Schweiger C.A. and C.A. Floudas, "The MINOPT Modeling Language", Invited Chapter in Modeling Languages, Ed. J. Kallrath, Kluwer Academic Publishers (2003).

Product and Process Operations: Scheduling and Planning

In this area, our primary objective in Scheduling and Planning is to investigate, refine, and apply effective combinatorial optimization models based on our novel continuous-time framework for short term scheduling of batch, semi-continuous and continuous processes. The thrust of our approach is to develop a unified framework that addresses intermediate due dates and demands, establishes the trade-offs in the design, synthesis and scheduling of multipurpose batch plants, and is directly applicable to large-scale manufacturing processes. Current research focuses on (a) new methods for short and medium-term scheduling of manufacturing processes, (b) short-term and medium-term scheduling under uncertainty in the processing times, product demands, and cost coefficients, and (c) new methods that reduce the integrality gap for combinatorial models in scheduling and planning.

Selected References:

  • Ierapetritou M.G. and C.A. Floudas (PostScript (862K), PDF (278K)), "Effective Continuous-Time Formulation for Short-Term Scheduling. 1. Multipurpose Batch Processes", Industrial and Engineering Chemistry Research, 37, pp.4341-4359, (1998).
  • Ierapetritou M.G. and C.A. Floudas (PostScript (960K), PDF (272K)), "Effective Continuous-Time Formulation for Short-Term Scheduling. 2. Continuous and Semicontinuous Processes", Industrial and Engineering Chemistry Research, 37, pp.4360-4374, (1998).
  • Ierapetritou M.G., T.S. Hene and C.A. Floudas "Continuous Time Formulation for Short Term Scheduling with Multiple Intermediate Due Dates", Industrial and Engineering Chemistry Research, 38, 9, 3446-3461 (1999).
  • Ierapetritou M.G. and C.A. Floudas, "Comments on An Improved RTN Continuous-Time Formulation for the Short-Term Scheduling of Multipurpose Batch Plants", Industrial and Engineering Chemistry Research, 40, 5040-5041 (2001).
  • Lin X. and C.A. Floudas, (PostScript (242K), PDF (135K)), "Design, Synthesis and Scheduling of Multipurpose Batch Plants via an Effective Continuous-Time Formulation", Computers and Chemical Engineering, 25, 665-674 (2001).
  • Lin X., C.A. Floudas, S. Modi, and N.M. Juhasz, (PostScript (12950K), PDF (6234K))), "Continuous-Time Optimization Approach for Medium-Range Production Scheduling of a Multiproduct Batch Plant", Industrial and Engineering Chemistry Research, 41, 3884-3906 (2002).
  • Lin X. and C.A. Floudas, "A Novel Continuous-Time Modeling and Optimization Framework for Well Platform Planning Problems", Optimization and Engineering, 4, 65-95 (2003).
  • Lin X. and E.D. Chajakis and C.A. Floudas, "Scheduling of Tanker Lightering via a Novel Continuous-Time Optimization Framework", Industrial and Engineering Chemistry Research, 42, 4441-4451 (2003).
  • Floudas C.A. and X. Lin, "Continuous-Time versus Discrete-Time Approaches for Scheduling of Chemical Processes: A Review", Computers and Chemical Engineering, submitted for publication (2003).
  • Floudas C.A. and X. Lin, "Mixed Integer Linear Programming in Process Scheduling: Modeling, Algorithms, and Applications", Annals of Operations Research, accepted for publication (2003).
  • Lin X. and E.D. Chajakis and C.A. Floudas, "Continuous-Time Scheduling of Tanker Lightering in Crude Oil Supply Chain" Proceedings of PSE-2003, 547-553 (2004).
  • Lin X., S.L. Janak, and C.A. Floudas, "A New Robust Optimization Approach for Scheduling under Uncertainty: I. Bounded Uncertainty", Computers and Chemical Engineering, in press (2004).
  • Lin X. and C.A. Floudas and J. Kallrath, "Global Solution Approach for a Nonconvex MINLP Problem in Product Portfolio Optimization", Journal of Global Optimization, submitted for publication (2003).
  • Janak S.L., X. Lin, and C.A. Floudas, "An Enhanced Continuous-Time Unit-Specific Event Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies", Industrial and Engineering Chemistry Research, accepted for publication (2004).

Discrete-Continuous Nonlinear Optimization

Modeling product and process synthesis problems, as well as fundamental problems in metabolic engineering and secondary structure prediction in protein folding results in mixed-integer linear and nonlinear optimization formulations. We have studied modeling and algorithmic issues in approaches based on the principles of Generalized Benders Decomposition, developed the framework MINOPT, and applied the resulting methodologies to the synthesis of separation systems, heat exchanger networks, reactor based systems, mass exchange networks, and analysis and synthesis of metabolic networks (see the graduate textbook Nonlinear Mixed-Integer Optimization by Floudas, 1995). Current emphasis is on investigating new methods for MINLP problems that are based on continuous representations.


Selected References:

Books, Monographs

  • Floudas C.A., "Nonlinear and Mixed-Integer Optimization : Fundamentals and Applications", Oxford University Press, (1995).
Refereed Journal and Proceedings Publications
  • Hatzimanikatis V., C.A. Floudas, and J.E. Bailey, "Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization", AIChE J., 42, 1277-1292 (1996).
  • Hatzimanikatis V., C.A. Floudas, and J.E. Bailey, "Optimization of Regulatory Architectures in Metabolic Reaction Networks", Biotechnology and Bioengineering, 52, 485-500 (1996).
  • Adjiman C.S. C.A. Schweiger and C.A. Floudas (PostScript (561K), PDF (291K)), "Nonlinear and Mixed-Integer Optimization in Chemical Process Network Systems", DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 40, pp. 429-452, (1998).
  • Adjiman C.S. C.A. Schweiger and C.A. Floudas (PostScript (957K), PDF (586K)), "Mixed-Integer Nonlinear Optimization in Process Synthesis", Handbook of Combinatorial Optimization, (Eds. D.-Z. Du and P.M. Pardalos), in press (1998).
  • Ierapetritou M.G., C.A. Floudas, S. Vasantharajan, and A.S. Cullick (PostScript (2731K), PDF (16986K)), "Optimal Location of Vertical Wells: A Decomposition Approach", AIChE Journal, 45, pp.844-859, (1998).
  • Schweiger C.A. and C.A. Floudas, (PostScript (306K), PDF (133K)), "Synthesis of Optimal Chemical Reactor Networks", Computers and Chemical Engineering, S47-50 (1999).
  • Adjiman C.S., I.P. Androulakis and C.A. Floudas (PostScript (1139K), PDF (576K)), "Global Optimization of Mixed Integer Nonlinear Problems", AIChE Journal, 46, 1769-1797 (2000).
  • Floudas C.A., "Mixed-Integer Nonlinear Optimization", Chapter in Handbook of Applied Optimization, Oxford University Press, M. Resende and P.M. Pardalos, (Eds.), 451 (2001).
  • Schweiger C.A. and C.A. Floudas, "The MINOPT Modeling Language", Invited Chapter in Modeling Languages, Ed. J. Kallrath, Kluwer Academic Publishers (2003).

Deterministic Global Optimization

A plethora of the most important problems in science and engineering, ranging from the atomistic domain to large-scale, process-level representations, are described mathematically by functions characterized by the existence of multiple minima and maxima, as well as first-, second-, and higher-order saddle points. The area of Global Optimization is concerned with theoretical, algorithmic and computational advances to address the computation and characterization of global minima and maxima, determine valid lower and upper bounds on the global minima and maxima, and address the enclosure of all solutions of nonlinear constrained systems of equations. The textbook Deterministic Global Optimization, (Floudas, 2000) povides a unified and insightful treatment of global optimization. Current research work focuses on theoretical and algorithmic studies of (a) novel deterministic global optimization methods for bilevel and multilevel nonlinear optimization models, (b) continuous approaches for mixed-integer nonlinear optimization problems, (c) new improved classes of convex underestimators for general nonlinear constrained problems, (d) hybrid deterministic global optimization methods, (e) new approaches for black/grey box models, and (f) large scale pooling and blending applications.


Selected References:

Books, Monographs

  • Floudas C.A. and P.M. Pardalos, "A Collection of Test Problems for Constrained Global Optimization Algorithms", Lecture Notes In Computer Science, Eds. G. Goos and J. Hartmanis, Vol. 455, Springer-Verlag (1990).
  • Floudas C.A. and P.M. Pardalos, Eds., "Recent Advances In Global Optimization", Princeton University Press (1992).
  • Floudas C.A. and P.M. Pardalos, Eds., "State of the Art In Global Optimization : Computational Methods and Applications", Kluwer Academic Publishers, (1996).
  • Floudas C.A., P.M. Pardalos, C.S. Adjiman, W.R. Esposito, Z. Gumus, S.T. Harding, J.L. Klepeis, C.A. Meyer, and C.A. Schweiger, "Handbook of Test Problems for Local and Global Optimization", Kluwer Academic Publishers, (1999).
  • Floudas C.A., "Deterministic Global Optimization: Theory, Methods and Applications", Kluwer Academic Publishers, (2000).
  • Floudas C.A. and P.M. Pardalos, Eds., "Encyclopedia of Optimization", Kluwer Academic Publishers, (2001).
  • Floudas C.A. and P.M. Pardalos, Eds., "Frontiers in Optimization", Kluwer Academic Publishers, (2003).
Chapters in Books
  • Floudas C.A. and V. Visweswaran (PostScript (427K), PDF (413K)), "Quadratic Optimization", Handbook of Global Optimization (R.Horst and P.M. Pardalos, Editors), Kluwer Academic Publishers, pp. 217-270 (1994).
  • Visweswaran V. and C.A. Floudas (PostScript (194K), PDF (163K)), "New Formulations and Branching Strategies for the GOP Algorithm", Global Optimization in Chemical Engineering, I.E. Grossmann, Editor, Kluwer Academic Publishers, Chapter 3, pp. 75-100 (1996).
  • Visweswaran V. and C.A. Floudas (PostScript (213K),PDF (204K)), "Computational Results for an Efficient Implementation of the GOP Algorithm and its Variants", Global Optimization in Chemical Engineering, I.E. Grossmann, Editor, Kluwer Academic Publishers, Chapter 4, pp. 111-153 (1996).
  • Floudas, C.A. (PostScript (603K), PDF (468K)), "Deterministic Global Optimization in Design, Control, and Computational Chemistry", IMA Proceedings: Large Scale Optimization with Applications. Part II: Optimal Design and Control, L.T. Biegler, A. Conn, L. Coleman, and F. Santosa, Eds., Springer-Verlag, Vol. 93, pp. 129-184 (1997).
Refereed Journal and Proceedings Publications
  • Floudas C.A. and V. Visweswaran (PostScript (340K), PDF (315K)), "A Global Optimization Algorithm (GOP) for Certain Classes of Nonconvex NLPs : I. Theory", Computers and Chemical Engineering, Vol. 14, No. 12, pp. 1397-1417(1990).
  • Visweswaran V. and C.A. Floudas (PostScript (304K), PDF (266K)), "A Global Optimization Algorithm (GOP) for Certain Classes of Nonconvex NLPs : II. Applications of Theory and Test Problems", Computers and Chemical Engineering, Vol. 14, No. 12, pp. 1417-1434(1990).
  • Floudas C.A. and V. Visweswaran (PostScript (240K), PDF (183K)), "A Primal-Relaxed Dual Global Optimization Approach", Journal of Optimization, Theory, and its Applications, Vol. 78, No. 2, pp. 187-225(1993).
  • Androulakis I.P., C.D. Maranas, and C.A. Floudas (PostScript (184K), PDF (154K)), "aBB : A Global Optimization Method for General Constrained Nonconvex Problems", Journal of Global Optimization, 7, 4, pp. 337-363(1995).
  • Adjiman C.S. and C.A. Floudas (PostScript (418K), PDF (250K)), "Rigorous Convex Underestimators for General Twice-Differentiable Problems", Journal of Global Optimization, 9, pp. 23-40, (1996).
  • Adjiman, C.S., S. Dallwig, C.A. Floudas, and A. Neumaier (PostScript (260K), PDF (437K)), "A Global Optimization Method, aBB, for General Twice-Differentiable Constrained NLPs - I. Theoretical Advances", Computers and Chemical Engineering, 22, pp. 1137-1158 (1998).
  • Adjiman C.S., S. Dallwig, C.A. Floudas, and A. Neumaier (PostScript (868K), PDF (437K)), "A Global Optimization Method, aBB, for General Twice-Differentiable Constrained NLPs - I. Theoretical Advances", Computers and Chemical Engineering, 22, pp. 1137-1158 (1998).
  • Floudas C.A. (PostScript (473K), PDF (198K)), "Recent Advances in Global Optimization for Process Synthesis, Design and Control: Enclosure of All Solutions", Computers and Chemical Engineering, S963-973 (1999).
  • Hertz D. and C. S. Adjiman and C. A. Floudas, "Two results on bounding the roots of interval polynomials", Computers and Chemical Engineering, 23, 1333-1339 (1999).
  • Adjiman C.S., I.P. Androulakis and C.A. Floudas (PostScript (1139K), PDF (576K)), "Global Optimization of Mixed Integer Nonlinear Problems", AIChE Journal, 46, 1769-1797 (2000).
  • Esposito W.R. and C.A. Floudas, "Deterministic Global Optimization in Optimal Control Problems", Journal of Global Optimization, 17, 97-126 (2000).
  • Esposito W.R. and C.A. Floudas, (PostScript (497K), PDF (453K)), "Global Optimization for the Parameter Estimation of Differential-Algebraic Systems", Industrial and Engineering Chemistry Research, 39, 5, 1291-1310 (2000).
  • Esposito W.R. and C.A. Floudas, (PostScript (398K), PDF (353K)), "Deterministic Global Optimization in Nonlinear Optimal Control Problems", Journal of Global Optimization, 17, 97-126 (2000).
  • Floudas C.A., "Global Optimization In Design and Control of Chemical Process Systems", Journal of Process Control, 10, 2-3, 125-134 (2000).
  • Gumus Z.H. and C.A. Floudas, ( PostScript(560K)), "Global Optimization of Nonlinear Bilevel Programming Problems", Journal of Global Optimization, 20, 1-31 (2001).
  • Floudas C.A., Z.H. Gumus, and M.G. Ierapetritou, ( PostScript(715K)), "Global Optimization in Design Under Uncertainty: Feasibility Test and Flexibility Index Problems", Industrial and Engineering Chemistry Research, 40, 4267-4282 (2001).
  • Adjiman C.S. and C.A. Floudas, "Deterministic Global Optimization of Processes: From Theory to Practice", Proceedings of Conference, France (2001).
  • Meyer C.A., C.A. Floudas, and A. Neumaier, "Global Optimization with Non-Factorable Constraints", Industrial and Engineering Chemistry Research, 25, 6413-6424 (2002).
  • Meyer C.A. and C.A. Floudas, "Convex Hull of Trilinear Monomials with Positive or Negative Domains: Facets of the Convex and Concave Envelopes", in Frontiers in Global Optimization, C.A. Floudas and P.M. Pardalos (Eds.), Kluwer Academic Publishers, 327-352 (2003).
  • Meyer C.A. and C.A. Floudas, "Convex Hull of Trilinear Monomials with Mixed Sign Domains", Journal of Global Optimization, in press (2003).
  • Akrotirianakis I.G. and C.A. Floudas, "A New Class of Improved Convex Underestimators for Twice Continuously Differentiable Constrained NLPs", Journal of Global Optimization, in press (2004).
  • Caratzoulas S. and C.A. Floudas, "A Trigonometric Convex Underestimator for the Base Functions in Fourier Space", Journal of Optimization, Theory and Its Applications, accepted for publication (2003).
  • Caratzoulas S. and C.A. Floudas, "A Trigonometric Convex Underestimator for the Base Functions in Fourier Space", Journal of Optimization, Theory and Its Applications, accepted for publication (2003).
  • Akrotirianakis I.G. and C.A. Floudas, "Computational Experience with a New Class of Convex Underestimators: Box Constrained NLP Problems", Journal of Global Optimization, in press (2004).
  • Gumus Z.H. and C.A. Floudas, "Global Optimization of Mixed-Integer Bilevel Programming Problems", Journal of Computational Management and Optimization, submitted for publication (2003).
  • Meyer C.A., and C.A. Floudas, "Convex underestimation of twice continuously differentiable functions by piecewise quadratic perturbation: Spline aBB underestimators", Journal of Global Optimization, accepted for publication (2004).

Bioinformatics and Computational Genomics

The overiding theme is to improve our fundamental understanding on the Sequence to Structure to Function roadmap. The genomics revolution has generated major challenges and opportunities for systems approaches in bioinformatics and computational genomics. The essential completion of several genome projects, including that of the human genome, provided a detailed map from the gene sequences to the protein sequences. The overwhelmingly large number of generated protein sequences makes protein structure prediction from the amino acid sequence of paramount importance. The elucidation of the protein structures provides information on the type of fold, the type of packing, the residues that are exposed to solvent, the residues that are buried to the core, the highly conserved residues, the candidate residues for mutations, as well as the shape and electrostatic properties of the fold. Such elements provide the basis for the development of approaches for the location of active sites, the determination of structural and functional motifs, the study of protein-protein, protein-ligand complexes and protein-DNA interactions, the design of new inhibitors, and drug discovery through target selection, lead discovery and optimization. Better understanding of the protein-ligand and protein-DNA interactions will provide important information on addressing key topology related questions in both the cellular metabolic and signal transduction networks. The thrust of our approach is the unique combination of detailed atomistic level modeling including state of the art solvation methods with rigorous deterministic global optimization methods, mixed-integer optimization, molecular dynamics, and free energy calculations. Current research focuses on (a) novel approaches for the ab initio secondary and tertiary structure prediction of polypeptides and proteins, (b) new methods for the tertiary structure refinement of proteins based on experimental data (e.g., NMR), (c) the dynamics of extended structures to beta sheet formation and the dynamics of protein folding, (d) a predictive framework for the protein-protein interactions and peptide docking problems, (e) novel optimization approaches for the de-novo protein design, and (f) the elucidation of the metabolic pathway mechanisms within yeast cells through a combination of micro DNA experiments and optimization theory.

Selected References:

  • Maranas C.D. and C.A. Floudas, "A Global Optimization Approach for Lennard-Jones Microclusters", Journal of Chemical Physics, Vol. 97, November 15, pp. 7667-7678 (1992).
  • Maranas C.D. and C.A. Floudas, "Global Minimum Potential Energy Conformations of Small Molecules", Journal of Global Optimization, Vol. 4, No. 2, pp. 135-170(1994).
  • Maranas C.D. and C.A. Floudas, "A Deterministic Global Optimization Approach for Molecular Structure Determination", Journal of Chemical Physics, Vol. 100, No. 2, pp. 1247-1261, 15 January (1994).
  • Hatzimanikatis V., C.A. Floudas, and J.E. Bailey, "Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization", AIChE J., 42, 1277-1292 (1996).
  • Hatzimanikatis V., C.A. Floudas, and J.E. Bailey, "Optimization of Regulatory Architectures in Metabolic Reaction Networks", Biotechnology and Bioengineering, 52, 485-500 (1996).
  • Androulakis, I.P., C.D. Maranas and C.A. Floudas, "Prediction of Oligopeptide Conformations via Deterministic Global Optimization", Journal of Global Optimization, 11, pp. 1-34, June (1997).
  • Androulakis I.P., N.N. Nayak, D.S. Monos, M.G. Ierapetritou, and C.A. Floudas (PostScript (11650K), PDF (5880K)), "A Predictive Method for Evaluation of Peptide Binding in Pocket-1 of HLA-DRB1 via Global Minimization of Energy Interactions", Proteins: Structure, Function, and Genetics, 29, 1, pp. 87-102, (1997).
  • Klepeis J.L., I. P. Androulakis, M. G. Ierapetritou, and C. A. Floudas (PostScript (6740K), PDF (3335K)), "Predicting Solvated Peptide Conformations via Global Minimization of Energetic Atom--to--Atom Interactions", Computers and Chemical Engineering, 22, pp. 765-788 (1998).
  • Floudas C.A., J.L. Klepeis and P.M. Pardalos (PostScript (508K), PDF (309K)), "Global Optimization Approaches in Protein Folding and Peptide Docking", DIMACS Series in Discrete Mathematics and Theoretical Computer Science, (Ed. F. Roberts), 47, 141-171 (1999).
  • Klepeis J.L. and C.A. Floudas (PostScript (13438K), PDF (13428K)), "A Comparative Study of Global Minimum Energy Conformations of Hydrated Peptides", Journal of Computational Chemistry, 20, pp.636-654, (1999).
  • Westerberg K.M. and C.A. Floudas (PostScript (2822K), PDF (10663K)), "Locating All Transition States and Studying Reaction Pathways of Potential Energy Surfaces", Journal of Chemical Physics, 110, pp.9259-9296, (1999).
  • Klepeis J.L. and C.A. Floudas (PostScript (1516K), PDF (5357K)), "Free Energy Calculations for Peptides via Deterministic Global Optimization", Journal of Chemical Physics, 110, pp.7491-7512, (1999).
  • Westerberg K.M. and C.A. Floudas, "Dynamics of Peptide Folding : Transition States and Reaction Pathways of Solvated and Unsolvated Tetra-Alanine", Journal of Global Optimization, 15, 261-297 (1999).
  • Klepeis J.L. and C.A. Floudas, "Deterministic Global Optimization and Torsion Angle Dynamics for Molecular Structure Prediction", Computers and Chemical Engineering, 24,1761-1766 (2000).
  • Klepeis J.L., H.D. Schafroth, K.M. Westerberg, and C.A. Floudas, (PostScript (19221K)), "Deterministic Global Optimization and Ab Initio Approaches for the Structure Prediction of Polypeptides, Dynamics of Protein Folding and Protein-Protein Interactions", Advances in Chemical Physics, 120, 265-457 (2002).
  • Klepeis J.L. and C.A. Floudas, (PostScript (1586K), PDF (7341K)), "Deterministic Global Optimization for Protein Structure Prediction", Chapter in Advances in Convex Analysis and Global Optimization, a Book in honor of C. Caratheodory, N. Hadjisavvas and P.M. Pardalos (Eds.), 31-74 (2001).
  • Klepeis J.L. and C.A. Floudas, (PostScript (823K), PDF (372K)), "Ab Initio Prediction of Helical Segments in Polypeptides", Journal of Computational Chemistry, 23, 1-22 (2002).
  • Klepeis J.L. and C.A. Floudas, "Prediction of Beta-Sheet Topology and Disulfide Bridges in Polypeptides", Journal of Computational Chemistry, 24, 191-208 (2003).
  • Klepeis J.L. and C.A. Floudas, "Ab Initio Tertiary Structure Prediction of Proteins", Journal of Global Optimization, 25, 113-140 (2003).
  • Klepeis J.L., M. Pieja, and C.A. Floudas, "A New Class of Hybrid Global Optimization Algorithms for Peptide Structure Prediction: Integrated Hybrids", Computer Physics Communications, 151, 121-140 (2003).
  • Klepeis J.L., M. Pieja, and C.A. Floudas, "A New Class of Hybrid Global Optimization Algorithms for Peptide Structure Prediction: Alternating Hybrids and Application fo Met-Enkephalin and Melittin", Biophysica Journal, 84, 869-882 (2003).
  • Klepeis J.L., C.A. Floudas, D. Morikis, C.G. Tsokos, E. Argyropoulos, L. Spruce, and J.D. Lambris, "Integrated Computational and Experimenal Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity", Journal of the American Chemical Society, 125(8), 8422-8423 (2003).
  • Floudas C.A., "Systems Approaches in Bioinformatics and Computational Genomics", Challenges for the Chemical Sciences in the 21th Century, Information and Communications Workshop, National Research Council of the National Academies, National Academies Press, 116-125 (2003).
  • Klepeis J.L. and C.A. Floudas, "ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence", Biophysical Journal, 85, 2119-2146 (2003).
  • Lin X., C.A. Floudas, Y. Wang, and J.R. Broach, "Theoretical and Computational Studies of the Glucose Signaling Pathways in Yeast Using Global Gene Expression Data", Biotechnology and Bioengineering, 84, 864-886 (2003).
  • Loose C., J.L. Klepeis, and C.A. Floudas, "A New Pairwise Folding Potential Based on Improved Decoy Generation and Side-Chain Packing", Proteins, 54, 303-314 (2004).
  • Klepeis J.L., C.A. Floudas, D. Morikis, and J.D. Lambris, "Design of Peptide Analogs with Improved Activity using a Novel de novo Protein Design Approach", Industrial and Engineering Chemistry Research, accepted for publication (2003).
  • Schafroth H.D. and C.A. Floudas, "Design of Peptide Binders for MHC and TCR Molecules via Mixed-Integer Optimization: An Innovative In Silico Approach", submitted for publication (2004).
  • Klepeis J.L. and C.A. Floudas, "Analysis and Prediction of Loop Segments in Protein Structures", Computers & Chemical Engineering, accepted for publication (2004).