Selected Publications through 2007 Christodoulos A. Floudas

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1 Selected Publications through 2007 Christodoulos A. Floudas For a complete listing of downloadable publications, click here A New Robust Optimization Approach for Scheduling under Uncertainty: II. Uncertainty with Known Probability Distribution. Comp. Chem. Eng., 31, 171, 2007 [with S.L. Janak and X. Lin]. Global Pairwise Sequence Alignment Through Mixed-Integer Linear Programming: A Template-Free Approach. Optim. Methods Softw, 22, 127, 2007 [with S.R. McAllister and R. Rajgaria]. Novel Formulations for the Sequence Selection Problem in de Novo Protein Design with Flexible Templates. Optim. Methods.Softw., 22, 51, 2007 [with H.K. Fung and M.S. Taylor]. A Template-Based Mixed-Integer Linear Programming Sequence Alignment Model. Chapter in Models and Algorithms for Global Optimization, Eds. A. Torn and J. Zilinskas, Springer, pp. 343, 2007 [with S.R. McAllister and R. Rajgaria]. Towards Optimal Techniques for Solving Global Optimization Problems: Symmetry-based Approach. Chapter in Models and Algorithms for Global Optimization, Eds. A. Torn and J. Zilinskas, Springer, 21, 2007 [with V. Kreinovich]. On the Functional Form of Convex Underestimators for Twice Continuously Differentiable Functions. Optimization Letters, 1, 187, 2007 [with V. Kreinovich]. A Mixed-Integer Optimization Framework for De Novo Peptide Identification. AIChE J., 53, 160, 2007 [with P.A. DiMaggio]. Improved Unit-specific Event-Based Continuous-Time Model for Short-Term Scheduling of continuous Processes: Rigorous Treatment of Storage Requirements. Ind. Eng. Chem. Res., 46, 1764, 2007 [with M.A. Shaik] De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization. Analytical Chemistry, 79, 1433, 2007 [with P.A. DiMaggio] Computational Methods in Protein Structure Prediction. Biotech. Bioeng., 97, 207, A Novel Clustering Approach and Prediction of Optimal Number of Clusters: Global Optimum Search with Enhanced Positioning. J. Global Optim., 39, 323, 2007 [with M.P. Tan and J.R. Broach] Systems Analysis, Optimization and Data Mining in Biomedicine Preface. Optim. Methods Softw., 22, 1, 2007 [with O.A. Prokepyev]

2 2006 "A Novel Approach for Alpha-Helical Topology Prediction in Globular Proteins: Generation of Interhelical Restraints. Proteins, 65, , 2006 [with S.R. McAllister, B.E. Mickus, J.L. Klepeis]. Advances in Protein Structure Prediction and De Novo Protein Design: A Review. Chem. Eng. Sci., 61, 966, 2006 [with H.K. Fung, S.R. McAllister, M. Mönnigmann and R. Rajgaria]. Mathematical Modeling and Optimization Methods for De Novo Protein Design. Systems Biology, Volume II: Networks, Models, and Applications. Eds. I. Rigoutsos and G. Stephanopoulos, Springer, pp 42-66, 2006 [with H.K. Fung]. Global Optimization of a Combinatorially Complex Generalized Pooling Problem. AIChE J., 52, 1027, 2006 [with C.A. Meyer]. Novel and Effective Integer Optimization Approach for the NSF Panel-Assignment Problem: A Multiresource and Preference-Constrained Generalized Assignment Problem. Ind. Eng. Chem. Res., 45, 258., 2006 [with S.L. Janak, M.S. Taylor, M. Burka and T.J. Mountziaris]. Structure Prediction of Alpha-Helical Proteins. Proceedings of the International Symposium on Mathematical and Computational Biology, BIOMAT V, Eds. R.P. Mondaini and R. Dilao, , 2006 [with S.R. McAllister]. Production Scheduling of a Large-Scale Industrial Batch Plant. I. Short-Term and Medium- Term Scheduling. Industrial Engineering Chemistry Research, 45, , 2006 [with S.L. Janak, J. Kallrath and N. Vormbrock]. Production Scheduling of a Large-Scale Industrial Batch Plant. II. Reactive Scheduling. Ind. Eng. Chem. Res., 45, 8253, 2006 [S.L. Janak, J. Kallrath and N. Vormbrock]. On the Functional Form of Convex Underestimators for Twice Continuously Differentiable Functions. Optim. Lett., 1, 1, 2006 [with V. Kreinovich] Continuous-Time Models for Short-Term Scheduling of Multipurpose Batch Plants: A Comparative Study. Ind. Eng. Chem. Res., 45, 6190, 2006 [with M.A. Shaik and S.L. Janak]. A Novel High Resolution C α -C α Distance Dependent Force Field Based on a High Quality Decoy Set. Proteins, 65, 726, 2006 [with R. Rajgaria and S.R. McAllister]. Rational Design of Shape Selective Separation and Catalysis: I. Concepts and Analysis. Chem. Eng. Sci., 61, 7933, 2006 [with C.E. Gounaris and J. Wei]. Rational Design of Shape Selective Separation and Catalysis: II. Mathematical Model and Computational Studies. Chem. Eng. Sci., 61, 7949, 2006 [with C.E. Gounaris and J. Wei] "Mixed Integer Linear Programming in Process Scheduling: Modeling, Algorithms, and Applications." Annals Oper. Res.,, 139, 131, 2005 [with X. Lin].

3 Global Optimization: Local Minima and Transition Points. J. Global Optim., 32, 409, 2005 [with H.Th. Jongen] Global Optimization of Mixed-Integer Bilevel Programming Problems. Comput. Manage. Sci., 2, 181, 2005 [with Z.H. Gümüs] Convex Envelopes for Edge-Concave Functions. Math. Prog., 103, 207, 2005 [with C.A. Meyer] "Ab Initio Prediction of the Three-Dimensional Structure of a De Novo Designed Protein: A Double-Blind Case Study." Proteins, 58, 560, 2005 [with J.L. Klepeis, Y.N. Wei and M.H. Hecht]. Convex Underestimation of Twice Continuously Differentiable Functions by Piecewise Quadratic Perturbation: Spline αbb Underestimatiors. J. Global Optim., 32, 221, 2005 [with C.A. Meyer]. Analysis and Prediction of Loop Segments in Protein Structures. Comp. Chem. Eng., 29, 423, 2005 [with J.L. Klepeis]. Global Optimization in the 21 st Century: Advances and Challenges. Comp. Chem. Eng., 29, 1185, 2005 [with I.G. Akrotirianakis, S. Caratzoulas, C.A. Meyer and J. Kallrath]. "Comments on "New General Continuous-Time State-Task Network Formulation for Short- Term Scheduling of Multipurpose Batch Plants" by Christos T. Maravelias and Ignacio E. Grossmann and on "Enhanced Continuous-Time Unit-Specific Event- Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies" by Stacy L. Janak, Xiaoxia Lin, and Christodoulos A. Floudas." Ind. Eng. Chem. Res., 44, , 2005 [with S.L. Janak]. Computational Comparison Studies of Quadratic Assignment Like Formulations for the In Silico Sequence Selection Problem in De Novo Protein Design. J. Comb. Optim., 10, 41, 2005 [with H.K. Fung, S. Rao, O. Prokopyev, P.M. Pardalos and F. Rendl]. Protein Loop Structure Prediction with Flexible Stem Geometries. Proteins, 61, 748, 2005 [with M. Mönnigmann]. Research Challenges, Opportunities and Synergism in Systems Engineering and Computational Biology. AIChE J., 51, 1872, Structure-Based Integrative Computational and Experimental Approach for the Optimization of Drug Design. Lecture Notes in Computer Science, 3515, 680, 2005 [with D. Morikis and J.D. Lambris] "Enhanced Continuous-Time Unit-Specific Event-Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies (Vol 43, Pg 2529, 2002)." Industrial & Engineering Chemistry Research, 44, , 2005 [with S.L. Janak and X.X. Lin]. Frontiers in Global Optimization. Kluwer Academic Publishers, 2004 [edited with P.M. Pardalos]. In Silico Protein Design: A Combinatorial and Global Optimization Approach. SIAM News, 37, 1, 2004 [with J.L. Klepeis]

4 "Computational Experience with a New Class of Convex Underestimators: Box-constrained NLP Problems." J Global Optim., 29, 249, 2004 [with I.G. Akrotirianakis]. "Trigonometric Convex Underestimator for the Base Functions in Fourier Space." J. Optim. Theory Appl., 124, 339, 2004 [with S. Caratzoulas]. Predicting Peptide Binding to MHC Pockets via Molecular Modeling, Implicit Solvation, and Global Optimization. Proteins, 54, 534, 2004 [with H.D. Schafroth]. Preface. J. Global Optim., 29, 247, 2004 [with P.M. Pardalos]. Improvement of the Anti-C3 Activity of Compstatin Using Rational and Combinatorial Approaches. Biochem. Soc. Trans., 32, 28, 2004 [with D. Morikis, A.M. Soulika, B. Mallik, J.L. Klepeis, and J.D. Lambris]. Trilinear Monomials with Mixed Sign Domains: Facets of the Convex and Concave Envelopes. J. Global Optim., 29, 125, 2004 [with C.A. Meyer]. A New Pairwise Folding Potential Based on Improved Decoy Generation and Side-Chain Packing. Proteins, 54, 303, 2004 [with C. Loose and J.L. Klepeis]. A New Robust Optimization Approach for Scheduling under Uncertainty: I. Bounded Uncertainty. Comp. Chem. Eng., 28, 1069, 2004 [with X.X. Lin and S.L. Janak]. Design of Peptide Analogues with Improves Activity Using a Novel de Novo Protein Design Approach. Ind. Eng. Chem. Res., 43, 3817, 2004 [with J.L. Klepeis, D. Morikis, C.G. Tsokos, and J.D. Lambris]. Enhanced Continuous-Time Unit-Specific Event-Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies. Ind. Eng. Chem. Res., 43, 2516, 2004 [with S.L. Janak and X.X. Lin]. Continuous-Time Versus Discrete-Time Approaches for Scheduling of Chemical Processes: A Review. Comp. Chem. Eng., 28, 2109, 2004 [with X.X. Lin] A New Class of Improved Convex Underestimators for Twice Continuously Differentiable Constrained NLPs. J. Global Optim., 30, 367, 2004 [with I.G. Akrotirianakis]. Methods of Ab Initio Prediction of Alpha Helices, Beta Sheets, and Polypeptide Tertiary Structures. U.S. Patent #6,832,162, December 14, 2004 [with J.L. Klepeis] A Novel Continuous-Time Modeling and Optimization Framework for Well Platform Planning Problems. Optim. Eng., 4, 65, 2003 [with X. Lin} Theoretical and Computational Studies of the Glucose Signaling Pathways in Yeast Using Global Gene Expression Data. Biotech. Bioengr., 84, 864, 2003 [with X.X. Lin, Y. Wang, and J.R. Broach]. Scheduling of Tanker Lightering via a Novel Continuous-Time Optimization Framework. Ind. Eng. Chem. Res., 42, 4441, 2003 [with X.X. Lin and E.D. Chajakis]. Hybrid Global Optimization Algorithms for Protein Structure Prediction: Alternating Hybrids. Biophys. J., 84, 869, 2003 [with J.L. Klepeis and M.J. Pieja].

5 A New Class of Hybrid Global Optimization Algorithms for Peptide Structure Prediction: Integrated Hybrids. Comp. Phys. Comm., 151, 121, 2003 [with J.L. Klepeis and M. Pieja]. Integrated Computational and Experimental Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity. J. Am. Chem. Soc., 125, 8422, 2003 [with J.L. Klepeis, D. Morikis, C.G. Tsokos, E. Argyropoulos, L. Spruce, and J.D. Lambris]. Prediction of Beta-Sheet Topology and Disulfide Bridges in Polypeptides. J. Comp. Chem., 24, 191, 2003 [with J.L. Klepeis]. ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence. Biophys. J., 85, 2119, 2003 [with J.L. Klepeis]. Ab Initio Tertiary Structure Prediction of Proteins. J. Global Optim., 25, 113, 2003 [with J.L. Klepeis] Deterministic Global Optimization in Isothermal Reactor Network Synthesis. J. Global Optim., 22, 59, 2002 [with W.R. Esposito]. Optimization of Polymer Synthesis Through Distributed Control of Polymerization Conditions. J. Appl. Poly. Sci., 85, 2922, 2002 [with A. Faliks, R.A. Yetter, Y. Wei, and H. Rabitz]. Continuous-Time Optimization Approach for Medium-Range Production Scheduling of a Multiproduct Batch Plant. Ind. Eng. Chem. Res., 41, 3884, 2002 [with X. Lin, S. Modi, and N.M. Juhasz]. ASTRO-FOLD: Ab Initio Secondary and Tertiary Structure Prediction in Protein Folding. In European Symposium on Computer Aided Process Engineering 12, Elsevier, 2002 [with J.L. Klepeis]. Predicting Peptide Binding to HLA Class II Molecules via Atomistic Level Modeling, Solvation Methods, and Deterministric Global Optimization. Tissue Antigens, 59, 25, 2002 [with H.D. Schafroth, D. Monos, and A. Constantinescou]. Global Optimization with Non-Factorable Constraints. Ind. Eng. Chem. Res., 25, 6413, 2002 [with C.A. Meyer and A. Neumaier] Encyclopedia of Optimization. Kluwer Academic Publishers, 2001 [edited with P.M. Pardalos]. Mixed-Integer Nonlinear Optimization. In Handbook of Applied Optimization, M. Resende and P.M. Pardalos, eds., Oxford University Press, 451, Deterministic Global Optimization and Its Applications. In Handbook of Applied Optimization, M. Resende and P.M. Pardalos, eds., 311, 2001.

6 Deterministic Global Optimization and Ab Initio Approaches for the Structure Prediction of Polypeptides, Dynamics of Protein Folding and Protein-Protein Interactions. Adv. Chem. Phys., 120, 266, 2001 [with J.L. Klepeis, H.D. Schafroth, and K.M. Westerberg]. Deterministic Global Optimization for Protein Structure Prediction. Book in Honor of C. Caratheodory, N. Hadjisavvas and P.M. Pardalos, eds., 31, 2001 [with J.L. Klepeis]. Global Optimization of Nonlinear Bilevel Programming Problems. J. Global Optim., 20, 1, 2001 [with Z.H. Gumus]. Global Optimization in Design Under Uncertainty: Feasibility Test and Flexibility Index Problems. Ind. Eng. Chem. Res., 40, 4267, 2001 [with Z.H. Gumus and M.G. Ierapetritou]. Design, Synthesis and Scheduling of Multipurpose Batch Plants via an Effective Continuous-Time Formulation. Comp. Chem. Eng., 25, 665, 2001 [with X. Lin]. Comments on Global Optimization for the Parameter Estimation of Differential Algebraic Systems. Ind. Eng. Chem. Res., 40, 490, 2001 [with W.R. Esposito]. Optimal Control of Methane Conversion to Ethylene. J. Phys. Chem. A, 104, 10740, 2001 [with A. Faliks, R.A. Yetter, R. Hall, and H. Rabitz]. Optimization of Living Polymerization Through Distributed Control of a Nitroxide Radical. Polymer, 42, 2061, 2001 [with A. Faliks, R.A. Yetter, Y.Wei, and H. Rabitz]. Optimal Control of Catalytic Methanol Conversion to Formaldehyde. J. Phys. Chem. A, 105, 2099, 2001 [with A. Faliks, R.A. Yetter, S.L. Bernasek, M. Fransson, and H. Rabitz]. Comments on An Improved RTN Continuous-Time Formulation for the Short-term Scheduling of Multipurpose Batch Plants. Ind. Eng. Chem. Res., 40, 5040, 2001 [with M.G. Ierapetritou]. Optimization of Living Radical Polymerization Through Distributed Control of Energy. Macromol. Chem. Phys., 202, 2797, 2001 [with A. Faliks, R.A. Yetter, Y. Wei, and H. Rabitz]. Ab Initio Prediction of Helical Segments in Polypeptides. J. Comput. Chem., 23, 245, 2001 [with J.L. Klepeis] Deterministic Global Optimization: Theory, Algorithms and Applications. Kluwer Academic Publishers, Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches. Kluwer Academic Publishers, 2000 [edited with P.M. Pardalos]. Global Optimization of Mixed Integer Nonlinear Problems. AIChE J., 46, 1769, 2000 [with C.S. Adjiman and I.P. Androulakis]. Phase Stability With Cubic Equations of State: A Global Optimization Approach. AIChE J., 46, 1422, 2000 [with S.T. Harding].

7 Locating Heterogeneous and Reactive Azeotropes. Ind. Eng. Chem. Res., 39, 1576, 2000 [with S.T. Harding]. Global Optimization in Parameter Estimation of Differential Algebraic Models. Ind. Eng. Chem. Res., 39, 1291, 2000 [with W.R. Esposito]. Deterministic Global Optimization in Optimal Control Problems. J. Global Optim., 17, 97, 2000 [with W.R. Esposito]. Deterministic Global Optimization and Torsion Angle Dynamics for Molecular Structure Prediction. Comp. Chem. Engr., 24, 1761, 2000 [with J.L. Klepeis]. Global Optimization in Design and Control of Chemical Process Systems. J. Process Control, 10, 125, Adaptive Feedback Control Flow Reactor. U.S. Patent #6,153,149, November 28, 2000 [with H.A. Rabitz and R.A. Yetter]. Earlier Books Handbook of Test Problems for Local and Global Optimization. Kluwer Academic Publishers, 1999 [with P.M. Pardalos, C.S. Adjiman, W.R. Esposito, Z. Gumus, S.T. Harding, J.L. Klepeis, C.A. Meyer, and C.A. Schweiger]. Nonlinear and Mixed-lnteger Optimization: Fundamentals and Applications. Oxford University Press, New York, NY., A Collection of Test Problems for Constrained Global Optimization Algorithms. Lecture Notes in Computer Science, Vol. 455, Springer-Verlag Publishers, 1990 [with P.M. Pardalos].