Publications

Books, Monographs

Journal Articles

1986

1. Floudas, C. A.; Ciric, A. R.; Grossmann, I. E. Automatic Synthesis of Optimum Heat Exchanger Network Configurations. AIChE Journal 1986, 32, 276.
2. Floudas, C. A.; Grossmann, I. E. Synthesis of Flexible Heat Exchanger Networks for Multiperiod Operation. Computers and Chemical Engineering 1986, 10 (2), 153-168.
3. Floudas, C. A.; Grossmann, I. E. Automatic Synthesis of Flexible Heat Exchanger Network Configurations for Multiperiod Operation. ASME Advanced Energy Systems 1986, AES-Vol. 2-1, 75-92.

1987

4. Floudas, C. A.; Grossmann, I. E. Automatic Synthesis of Multiperiod Heat Exchanger Network Configurations. Computers and Chemical Engineering 1987, 11 (2), 123-143.
5. Floudas, C. A.; Grossmann, I. E. Synthesis of Flexible Heat Exchanger Networks With Uncertain Flowrates and Temperatures. Computers and Chemical Engineering 1987, 11 (4), 319-336.
6. Grossmann, I. E.; Floudas, C. A. Active Constraint Strategy for Flexibility Analysis of Chemical Processes. Computers and Chemical Engineering 1987, 11 (6), 675-693.
7. Floudas, C. A. Separation Synthesis of Multicomponent Feed Streams into Multicomponent Product Streams. AIChE Journal 1987, 33 (4), 540-551.

1988

8. Paules, G. E. IV; Floudas, C. A. Synthesis of Flexible Distillation Sequences for Multiperiod Operation. Computers and Chemical Engineering 1988, 12 (4), 267-280.
9. Floudas, C. A.; Paules IV, G. E. A Mixed-Integer Nonlinear Programming Formulation for the Synthesis of Heat-Integrated Distillation Sequences. Computers and Chemical Engineering 1988, 12 (6), 531-546.
10. Floudas, C. A.; Anastasiadis, S. H. Synthesis of General Distillation Sequences with Several Multicomponent Feeds and Products. Chemical Engineering Science 1988, 43 (9), 2407-2419.

1989

11. Paules, G. E. IV; Floudas, C. A. APROS: Algorithmic Development Methodology For Discrete-Continuous Optimization Problems. Operations Research Journal 1989, 37 (6), 902-915.
12. Ciric, A. R.; Floudas, C. A. A Retrofit Approach of Heat Exchanger Networks. Computers and Chemical Engineering 1989, 13 (6), 703-715.
13. Georgiou, A.; Floudas, C. A. An Optimization Model for the Generic Rank Determination of Structural Matrices. International Journal of Control 1989, 49 (5), 1633-1644.
14. Georgiou, A.; Floudas, C. A. Structural Analysis and Synthesis of Feasible Control Systems - Theory and Applications. Chemical Engineering Research and Design 1989, 67, 600-618.
15. Floudas, C. A.; Aggarwal, A.; Ciric, A. R. Global Optimum Search for Nonconvex NLP and MINLP Problems. Computers and Chemical Engineering 1989, 13 (10), 1117-1132.
16. Floudas, C. A.; Ciric, A. R. Strategies for Overcoming Uncertainties In Heat Exchanger Network Synthesis. Computers and Chemical Engineering 1989, 13 (10), 1133-1152.

1990

17. Ciric, A. R.; Floudas, C. A. A Mixed-Integer Nonlinear Programming Model For Retrofitting Heat Exchanger Networks. Industrial & Engineering Chemistry Research 1990, 29, 239-251.
18. Ciric, A. R.; Floudas, C. A. Application of the Simultaneous Match-Network Optimization Approach to the Pseudo-Pinch Problem. Computers and Chemical Engineering 1990, 14 (3), 241-250.
19. Kokossis, A. C.; Floudas, C. A. Optimization of Complex Reactor Networks: I-Isothermal Operation. Chemical Engineering Science 1990, 43 (3), 595-614.
20. Georgiou, A.; Floudas, C. A. Structural Properties of Large Scale Systems. International Journal of Control 1990, 51 (1), 169-187.
21. Aggarwal, A.; Floudas, C. A. Synthesis of General Separation Sequences - Nonsharp Separations. Computers and Chemical Engineering 1990, 14 (6), 631-653.
22. Floudas, C. A.; Aggarwal, A. A Decomposition Approach for Global Optimum Search In The Pooling Problem. Operations Research Journal On Computing 1990, 2 (3), 225-234.
23. Ciric, A. R.; Floudas, C. A. A Comprehensive Optimization Model For The Retrofit Of Heat Recovery Networks. Journal of Heat Recovery Systems and CHP 1990, 10 (4), 407-422.
24. Aggarwal, A.; Floudas, C. A. A Decomposition Approach for Global Optimum Search in QP, NLP and MINLP problems. Annals of Operations Research, Special Volume On Computational methods In Global Optimization 1990, 25,.
25. Psarris, P.; Floudas, C. A. Improving Dynamic Operability in MIMO Systems with Time Delays. Chemical Engineering Science 1990, 45 (12), 3505-3524.
26. Floudas, C. A.; Visweswaran, V. A Global Optimization Algorithm (GOP) for Certain Classes of Nonconvex NLPs : I. Theory. Computers and Chemical Engineering 1990, 14 (12), 1397-1417.
27. Visweswaran, V.; Floudas, C. A. A Global Optimization Algorithm (GOP) for Certain Classes of Nonconvex NLPs : II. Applications of Theory and Test Problems. Computers and Chemical Engineering 1990, 14 (12), 1417-1434.

1991

28. Kokossis, A. C.; Floudas, C. A. Synthesis of Isothermal Reactor-Separator-Recycle Systems. Chemical Engineering Science 1991, 46 (5/6), 1361-1383.
29. Ciric, A. R.; Floudas, C. A. Heat Exchanger Network Synthesis Without Decomposition. Computers and Chemical Engineering 1991, 15 (6), 385-396.
30. Psarris, P.; Floudas, C. A. Dynamic Operability of MIMO Systems with Time Delays and Transmission Zeroes. I. Assessment. Chemical Engineering Science 1991, 46 (10), 2691-2707.
31. Psarris, P.; Floudas, C. A. Dynamic Operability of MIMO Systems with Time Delays and Transmission Zeroes. II. Enhancement. Chemical Engineering Science 1991, 46 (10), 2709-2728.

1992

32. Paules, G. E. IV; Floudas, C. A. Stochastic Programming In Process Synthesis : A two-Stage Model with MINLP Recourse for Multiperiod Heat-Integrated Distillation Sequences. Computers and Chemical Engineering 1992, 16 (3), 189-210.
33. Aggarwal, A.; Floudas, C. A. Synthesis of Heat Integrated Nonsharp Distillation Sequences. Computers and Chemical Engineering 1992, 16 (2), 89-108.
34. Visweswaran, V.; Floudas, C. A. Unconstrained and Constrained Global Optimization of Polynomial Functions in One Variable. Journal of Global Optimization 1992, 2 (1), 73-99.
35. Maranas, C. D.; Floudas, C. A. A Global Optimization Approach for Lennard-Jones Microclusters. Journal of Chemical Physics 1992, 97 (10), 7667-7678.

1993

36. Floudas, C. A.; Visweswaran, V. A Primal-Relaxed Dual Global Optimization Approach. Journal of Optimization 1993, Theory (and its Applications), 187-225.
37. Visweswaran, V.; Floudas, C. A. New Properties and Computational Improvement of the GOP Algorithm For Problems With Quadratic Objective Function and Constraints. Journal of Global Optimization 1993, 3 (4), 439-462.
38. Maranas, C. D.; Floudas, C. A. Global Optimization for Molecular Conformation Problems. Annals of Operations Research 1993, 42, 85-117.
39. Kokossis, A. C.; Floudas, C. A. Stability Issues in Process Synthesis. Computers and Chemical Engineering 1993, 18, S93-S97.
40. Ierapetritou, M.; Pistikopoulos, E. N.; Floudas, C. A. Operational Planning Under Uncertainty. Computers and Chemical Engineering 1993, 18, S553-S557.
41. Liu, W. B.; Floudas, C. A. A Remark on the GOP Algorithm for Global Optimization. Journal of Global Optimization 1993, 3 (4), 519-521.
42. Rojnuckarin, A.; Floudas, C. A.; Rabitz, H.; Yetter, R. A. Optimal Control of a Plug Flow Reactor with a Complex Reaction Mechanism. Journal of Physical Chemistry 1993, 97 (45), 11689-11695.

1994

43. Maranas, C. D.; Floudas, C. A. Global Minimum Potential Energy Conformations of Small Molecules. Journal of Global Optimization 1994, 4 (2), 135-170.
44. Kokossis, A. C.; Floudas, C. A. Optimization of Complex Reactor Networks-II: Nonisothermal Operation. Chemical Engineering Science 1994, 49 (7), 1037-1051.
45. Kokossis, A. C.; Floudas, C. A. Stability in Optimal Design: Synthesis of Complex Reactor Networks. AIChE J. 1994, 40 (5), 849-861.
46. Maranas, C. D.; Floudas, C. A. A Deterministic Global Optimization Approach for Molecular Structure Determination. Journal of Chemical Physics 1994, 100 (2), 15 January.
47. Luyben, M. L.; Floudas, C. A. A Multiobjective Optimization Approach for Analyzing the Interaction of Design and Control, Part 1: Theoretical Framework and Binary Distillation Synthesis. Computers and Chemical Engineering 1994, 18 (10), 933-969.
48. Luyben, M. L.; Floudas, C. A. A Multiobjective Optimization Approach for Analyzing the Interaction of Design and Control, Part 2: Reactor-Separator-Recycle System. Computers and Chemical Engineering 1994, 18 (10), 971-994.
49. Papalexandri, K. P.; Pistikopoulos, E. N.; Floudas, C. A. Mass Exchange Networks for Waste Minimization: A Simultaneous Approach. Chemical Engineering Research and Design 1994, 72, 279-294.
50. McDonald, C. M.; Floudas, C. A. Decomposition Based and Branch and Bound Global Optimization Approaches for the Phase Equilibrium Problem. J. of Global Optimization 1994, 5, 205-251.

1995

51. Maranas, C. D.; Floudas, C. A.; Pardalos, P. M. New Results in the Packing of Equal Circles in a Square. Discrete Mathematics 1995, 142, 287-293.
52. Liu, W. B.; Floudas, C. A. Convergence of the GOP Algorithm for a Large Class of Smooth Optimization Problems. Journal of Global Optimization 1995, 6, 207.
53. McDonald, C. M.; Floudas, C. A. Global Optimization for the Phase and Chemical Equilibrium Problem: Application to the NRTL Equation. Computers and Chemical Engineering 1995, 19 (11), 1111-1141.
54. Psarris, P.; Floudas, C. A. Robust Stability Analysis of Systems with Real Parametric Uncertainty : A Global Optimization Approach. International J. of Robust and Nonlinear Control 1995, 6, 699-717.
55. McDonald, C. M.; Floudas, C. A. Global Optimization for the Phase Stability Problem. AIChE J. 1995, 41 (7), 1798-1814.
56. McDonald, C. M.; Floudas, C. A. Global Optimization and Analysis for the Gibbs Free Energy Function for the UNIFAC, Wilson, and ASOG Equations. Industrial & Engineering Chemistry Research 1995, 34, 1674-1687.
57. Androulakis, I. P.; Maranas, C. D.; Floudas, C. A. αBB: A Global Optimization Method for General Constrained Nonconvex Problems. Journal of Global Optimization 1995, 7 (4), 337-363.
58. Maranas, C. D.; Floudas, C. A. Finding All Solutions of Nonlinearly Constrained Systems of Equations. Journal of Global Optimization 1995, 7 (2), 143-182.

1996

59. Liu, W. B.; Floudas, C. A. A Generalized Primal-Relaxed Dual Approach for Global Optimization. Journal of Optimization Theory and its Applications 1996, 90, 417-434.
60. Rojnuckarin, A.; Floudas, C. A.; Rabitz, H.; Yetter, R. A. Methane Conversion to Ethylene and Acetylene : Optimal Control with Chlorine, Oxygen and Heat Flux. IE&C Fundamentals 1996, 35, 683-696.
61. Hatzimanikatis, V.; Floudas, C. A.; Bailey, J. E. Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization. AIChE J. 1996, 42, 1277-1292.
62. Maranas, C. D.; McDonald, C. M.; Harding, S. T.; Floudas, C. A. Locating All Azeotropes in Homogeneous Azeotropic Systems. Computers and Chemical Engineering 1996, 20, S413-418.
63. Adjiman, C. S.; Androulakis, I. P.; Maranas, C. D.; Floudas, C. A. A Global Optimization Method αBB for Process Design. Computers and Chemical Engineering 1996, 20, S419-424.
64. Hatzimanikatis, V.; Floudas, C. A.; Bailey, J. E. Optimization of Regulatory Architectures in Metabolic Reaction Networks. Biotechnology and Bioengineering 1996, 52, 485-500.
65. Adjiman, C. S.; Floudas, C. A. Rigorous Convex Underestimators for General Twice-Differentiable Problems. Journal of Global Optimization 1996, 9, 23-40.
66. Ierapetritou, M. G.; Pistikopoulos, E. N.; Floudas, C. A. Operational Planning Under Uncertainty. Computers and Chemical Engineering 1996, 20, 1499-1516.

1997

67. Maranas, C. D.; Androulakis, I. P.; Floudas, C. A.; Berger, A. J.; Mulvey, J. M. Solving Stochastic Control Problems in Finance via Global Optimization. Journal of Economics, Dynamics and Control 1997, 21, 1405-1425.
68. Maranas, C. D.; Floudas, C. A. Global Optimization in Generalized Geometric Programming. Computers and Chemical Engineering 1997, 21, 351-370.
69. McDonald, C. M.; Floudas, C. A. GLOPEQ: A New Computational Tool for the Phase and Chemical Equilibrium Problem. Computers and Chemical Engineering 1997, 21, 1-23.
70. Androulakis, I. P.; Maranas, C. D.; Floudas, C. A. Prediction of Oligopeptide Conformations via Deterministic Global Optimization. Journal of Global Optimization 1997, 11, 1-34.
71. Vassiliadis, V. S.; Floudas, C. A. The Modified Barrier Function Approach for Large-Scale Optimization. Computers and Chemical Engineering 1997, 21, 855-874.
72. Harding, S. T.; Maranas, C. D.; McDonald, C. M.; Floudas, C. A. Locating All Homogeneous Azeotropes in Multicomponent Mixtures. Industrial & Engineering Chemistry Research 1997, 36, 160-178.
73. Harding, S. T.; Floudas, C. A. Global Optimization in Multiproduct and Multipurpose Batch Design Under Uncertainty. Industrial & Engineering Chemistry Research 1997, 36, 1644-1664.
74. Androulakis, I. P.; Nayak, N. N.; Monos, D. S.; Ierapetritou, M. G.; Floudas, C. A. 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 1997, 29 (1), 87-102.
75. Adjiman, C. S.; Androulakis, I. P.; Floudas, C. A. Global Optimization of MINLP Problems in Process Synthesis and Design. Computers and Chemical Engineering 1997, 21, S445-S450.

1998

76. Klepeis, J. L.; Androulakis, I. P.; Ierapetritou, M. G.; Floudas, C. A. Predicting Solvated Peptide Conformations via Global Minimization of Energetic Atom-to-Atom Interactions. Computers and Chemical Engineering 1998, 22, 765-788.
77. Adjiman, C. S.; Dallwig, S.; Floudas, C. A.; Neumaier, A. A Global Optimization Method, αBB, for General Twice-Differentiable Constrained NLPs - I. Theoretical Advances. Computers and Chemical Engineering 1998, 22, 1137-1158.
78. Adjiman, C. S.; Androulakis, I. P.; Floudas, C. A. A Global Optimization Method, αBB, for General Twice-Differentiable Constrained NLPs - II. Implementation and Computational Results. Computers and Chemical Engineering 1998, 22, 1159-1179.
79. Klepeis, J. L.; Ierapetritou, M. G.; Floudas, C. A. Protein Folding and Peptide Docking: A Molecular Modeling and Global Optimization Approach. Computers and Chemical Engineering 1998, 22, S3-S10.
80. Esposito, W. R.; Floudas, C. A. Parameter Estimation in Nonlinear Algebraic Models via Global Optimization. Computers and Chemical Engineering 1998, 22, S213-S220.
81. Ierapetritou, M. G.; Floudas, C. A. Short-term Scheduling: New Mathematical Models vs. Algorithmic Improvements. Computers and Chemical Engineering 1998, 22, S419-S426.
82. Esposito, W. R.; Floudas, C. A. Global Optimization in Parameter Estimation of Nonlinear Algebraic Models via the Error-In-Variables Approach. Industrial & Engineering Chemistry Research 1998, 37, 1841-1858.
83. Ierapetritou, M. G.; Floudas, C. A. Effective Continuous-Time Formulation for Short-Term Scheduling. 1. Multipurpose Batch Processes. Industrial & Engineering Chemistry Research 1998, 37, 4341-4359.
84. Ierapetritou, M. G.; Floudas, C. A. Effective Continuous-Time Formulation for Short-Term Scheduling. 2. Continuous and Semicontinuous Processes. Industrial & Engineering Chemistry Research 1998, 37, 4360-4374.

1999

85. Schweiger, C. A.; Floudas, C. A. Optimization Framework for the Synthesis of Chemical Reactor Networks. Industrial & Engineering Chemistry Research 1999, 38, 744-766.
86. Klepeis, J. L.; Floudas, C. A. A Comparative Study of Global Minimum Energy Conformations of Hydrated Peptides. Journal of Computational Chemistry 1999, 20, 636-654.
87. Westerberg, K. M.; Floudas, C. A. Locating All Transition States and Studying Reaction Pathways of Potential Energy Surfaces. Journal of Chemical Physics 1999, 110, 9259-9296.
88. Klepeis, J. L.; Floudas, C. A. Free Energy Calculations for Peptides via Deterministic Global Optimization. Journal of Chemical Physics 1999, 110, 7491-7512.
89. Ierapetritou, M. G.; Floudas, C. A.; Vasantharajan, S.; Cullick, A. S. Optimal Location of Vertical Wells: A Decomposition Approach. AIChE Journal 1999, 45, 844-859.
90. Ierapetritou, M. G.; Hene, T. S.; Floudas, C. A. Effective Continuous-Time Formulation for Short Term Scheduling. 3. Multiple Intermediate Due Dates. Industrial & Engineering Chemistry Research 1999, 38 (9), 3446-3461.
91. Klepeis, J. L.; Floudas, C. A.; Morikis, D.; Lambris, J. D. Predicting Peptide Structures Using NMR Data and Deterministic Global Optimization. Journal of Computational Chemistry 1999, 20 (13), 1354-1370.
92. Schweiger, C. A.; Floudas, C. A. Synthesis of Optimal Chemical Reactor Networks. Computers and Chemical Engineering 1999, S47-50.
93. Ierapetritou, M. G.; Hene, T. S.; Floudas, C. A. Short-Term Scheduling of Batch Plants with Multiple Intermediate Due Dates. Computers and Chemical Engineering 1999, 23, S515-518.
94. Floudas, C. A. Recent Advances in Global Optimization for Process Synthesis, Design and Control: Enclosure of All Solutions. Computers and Chemical Engineering 1999, S963-973.
95. Hertz, D.; Adjiman, C. S.; Floudas, C. A. Two results on bounding the roots of interval polynomials. Computers and Chemical Engineering 1999, 23, 1333-1339.
96. Westerberg, K. M.; Floudas, C. A. Dynamics of Peptide Folding: Transition States and Reaction Pathways of Solvated and Unsolvated Tetra-Alanine. Journal of Global Optimization 1999, 15, 261-297.

2000

97. Adjiman, C. S.; Androulakis, I. P.; Floudas, C. A. Global Optimization of Mixed Integer Nonlinear Problems. AIChE Journal 2000, 46, 1769-1797.
98. Harding, S. T.; Floudas, C. A. Phase Stability with Cubic Equations of State: A Global Optimization Approach. AIChE Journal 2000, 46 (7), 1422-1440.
99. Harding, S. T.; Floudas, C. A. Locating Heterogeneous and Reactive Azeotropes. Industrial & Engineering Chemistry Research 2000, 39 (6), 1576-1595.
100. Esposito, W. R.; Floudas, C. A. Global Optimization for the Parameter Estimation of Differential-Algebraic Systems. Industrial & Engineering Chemistry Research 2000, 39 (5), 1291-1310.
101. Esposito, W. R.; Floudas, C. A. Deterministic Global Optimization in Nonlinear Optimal Control Problems. Journal of Global Optimization 2000, 17, 97-126.
102. Klepeis, J. L.; Floudas, C. A. Deterministic Global Optimization and Torsion Angle Dynamics for Molecular Structure Prediction. Computers and Chemical Engineering 2000, 24, 1761-1766.
103. Floudas, C. A. Global Optimization In Design and Control of Chemical Process Systems. Journal of Process Control 2000, 10 (2-3), 125-134.
104. Faliks, A.; Yetter, R. A.; Floudas, C. A.; Hall, R.; Rabitz, H. Optimal Control of Methane Conversion to Ethylene. Journal of Physical Chemistry A 2000, 104, 10740-10746.

2001

105. Gümüş, Z. H.; Floudas, C. A. Global Optimization of Nonlinear Bilevel Programming Problems. Journal of Global Optimization 2001, 20, 1-31.
106. Floudas, C. A.; Gümüş, Z. H.; Ierapetritou, M. G. Global Optimization in Design Under Uncertainty: Feasibility Test and Flexibility Index Problems. Industrial & Engineering Chemistry Research 2001, 40, 4267-4282.
107. Lin, X.; Floudas, C. A. Design, Synthesis and Scheduling of Multipurpose Batch Plants via an Effective Continuous-Time Formulation. Computers and Chemical Engineering 2001, 25, 665-674.
108. Esposito, W. R.; Floudas, C. A. Rebuttal to Comments on “Global Optimization for the Parameter Estimation of Differential Algebraic System”. Industrial & Engineering Chemistry Research 2001, 40, 490-491.
109. Faliks, A.; Yetter, R. A.; Floudas, C. A.; Wei, Y.; Rabitz, H. Optimization of Living Polymerization Through Distributed Control of a Nitroxide Radical. POLYMER 2001, 42, 2061-2065.
110. Faliks, A.; Yetter, R. A.; Floudas, C. A.; Bernasek, S. L.; Fransson, M.; Rabitz, H. Optimal Control of Catalytic Methanol Conversion to Formaldehyde. Journal of Physical Chemistry A 2001, 105, 2099-2105.
111. Ierapetritou, M. G.; Floudas, C. A. Comments on “An Improved RTN Continuous-Time Formulation for the Short-Term Scheduling of Multipurpose Batch Plants”. Industrial & Engineering Chemistry Research 2001, 40, 5040-5041.
112. Faliks, A.; Yetter, R. A.; Floudas, C. A.; Wei, Y.; Rabitz, H. Optimization of Living Radical Polymerization Through Distributed Control of Energy. Macromolecular Chemistry and Physics 2001, 202 (13), 2797-2801.

2002

113. Klepeis, J. L.; Schafroth, H. D.; Westerberg, K. M.; Floudas, C. A. 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 2002, 120, 265-457.
114. Esposito, W. R.; Floudas, C. A. Deterministic Global Optimization in Isothermal Reactor Network Synthesis. Journal of Global Optimization 2002, 22, 59-95.
115. Klepeis, J. L.; Floudas, C. A. Ab Initio Prediction of Helical Segments in Polypeptides. Journal of Computational Chemistry 2002, 23, 245-266.
116. Lin, X.; Floudas, C. A.; Modi, S.; Juhasz, N. M. Continuous-Time Optimization Approach for Medium-Range Production Scheduling of a Multiproduct Batch Plant. Industrial & Engineering Chemistry Research 2002, 41, 3884-3906.
117. Meyer, C. A.; Floudas, C. A.; Neumaier, A. Global Optimization with Non-Factorable Constraints. Industrial & Engineering Chemistry Research 2002, 41, 6413-6424.
118. Faliks, A.; Yetter, R. A.; Floudas, C. A.; Wei, Y.; Rabitz, H. Optimization of Polymer Synthesis Through Distributed Control of Polymerization Conditions. Journal of Applied Polymer Science 2002, 85 (14), 2922-2928.

2003

119. Lin, X.; Floudas, C. A. A Novel Continuous-Time Modeling and Optimization Framework for Well Platform Planning Problems. Optimization and Engineering 2003, 4, 65-95.
120. Klepeis, J. L.; Floudas, C. A. Prediction of Beta-Sheet Topology and Disulfide Bridges in Polypeptides. Journal of Computational Chemistry 2003, 24, 191-208.
121. Klepeis, J. L.; Floudas, C. A. Ab Initio Tertiary Structure Prediction of Proteins. Journal of Global Optimization 2003, 25, 113-140.
122. Lin, X.; Chajakis, E. D.; Floudas, C. A. Scheduling of Tanker Lightering via a Novel Continuous-Time Optimization Framework. Industrial & Engineering Chemistry Research 2003, 42, 4441-4451.
123. Klepeis, J. L.; Pieja, M.; Floudas, C. A. A New Class of Hybrid Global Optimization Algorithms for Peptide Structure Prediction: Integrated Hybrids. Computer Physics Communications 2003, 151, 121-140.
124. Klepeis, J. L.; Pieja, M.; Floudas, C. A. A New Class of Hybrid Global Optimization Algorithms for Peptide Structure Prediction: Alternating Hybrids and Application fo Met-Enkephalin and Melittin. Biophysical Journal 2003, 84, 869-882.
125. Klepeis, J. L.; Floudas, C. A.; Morikis, D.; Tsokos, C. G.; Argyropoulos, E.; Spruce, L.; Lambris, J. D. Integrated Computational and Experimenal Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity. Journal of the American Chemical Society 2003, 125 (28), 8422-8423.
126. Klepeis, J. L.; Floudas, C. A. 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 2003, 85, 2119-2146.
127. Lin, X.; Floudas, C. A.; Wang, Y.; Broach, J. R. Theoretical and Computational Studies of the Glucose Signaling Pathways in Yeast Using Global Gene Expression Data. Biotechnology and Bioengineering 2003, 84, 864-886.

2004

128. Meyer, C. A.; Floudas, C. A. Convex Hull of Trilinear Monomials with Mixed Sign Domains. Journal of Global Optimization 2004, 29 (2), 125-155.
129. Floudas, C. A.; Lin, X. Continuous-Time versus Discrete-Time Approaches for Scheduling of Chemical Processes: A Review. Computers and Chemical Engineering 2004, 28 (11), 2109-2129.
130. Akrotirianakis, I. G.; Floudas, C. A. A New Class of Improved Convex Underestimators for Twice Continuously Differentiable Constrained NLPs. Journal of Global Optimization 2004, 30 (4), 367-390.
131. Caratzoulas, S.; Floudas, C. A. Trigonometric Convex Underestimator for the Base Functions in Fourier Space. Journal of Optimization Theory and Applications 2004, 124 (2), 339-362.
132. Lin, X.; Janak, S. L.; Floudas, C. A. A New Robust Optimization Approach for Scheduling under Uncertainty: I. Bounded Uncertainty. Computers and Chemical Engineering 2004, 28, 1069-1085.
133. Loose, C.; Klepeis, J. L.; Floudas, C. A. A New Pairwise Folding Potential Based on Improved Decoy Generation and Side-Chain Packing. Proteins 2004, 54, 303-314.
134. Klepeis, J. L.; Floudas, C. A.; Morikis, D.; Lambris, J. D. Design of Peptide Analogs with Improved Activity using a Novel de novo Protein Design Approach. Industrial & Engineering Chemistry Research 2004, 43, 3817-3826.
135. Schafroth, H. D.; Floudas, C. A. Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization. Proteins 2004, 54, 534-556.
136. Akrotirianakis, I. G.; Floudas, C. A. Computational Experience with a New Class of Convex Underestimators: Box Constrained NLP Problems. Journal of Global Optimization 2004, 29 (3), 249-264.
137. Morikis, D.; Soulika, A. M.; Mallik, B.; Klepeis, J. L.; Floudas, C. A.; Lambris, J. D. Improvement of the anti-C3 activity of complement using rational and combinatorial approaches. Biochemical Society Transactions 2004, 32, 28-32.
138. Janak, S. L.; Lin, X.; Floudas, C. A. Enhanced Continuous-Time Unit-Specific Event Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies. Industrial & Engineering Chemistry Research 2004, 43, 2516-2533.

2005

139. Floudas, C. A.; Lin, X. Mixed Integer Linear Programming in Process Scheduling: Modeling, Algorithms, and Applications. Annals of Operations Research 2005, 139 (1), 131-162.
140. Lin, X.; Floudas, C. A.; Kallrath, J. Global Solution Approach for a Nonconvex MINLP Problem in Product Portfolio Optimization. Journal of Global Optimization 2005, 32, 417-431.
141. Floudas, C. A.; Th. Jongen, H. Global Optimization: Local Minima and Transition Points. Journal of Global Optimization 2005, 32, 409-415.
142. Gümüş, Z. H.; Floudas, C. A. Global Optimization of Mixed-Integer Bilevel Programming Problems. Journal of Computational Management and Optimization 2005, 2 (3), 181-212.
143. Klepeis, J. L.; Wei, Y.; Hecht, M. H.; Floudas, C. A. Ab Initio Prediction of the 3-Dimensional Structure of a De Novo Designed Protein: A Double Blind Case Study. Proteins 2005, 58, 560-570.
144. Meyer, C. A.; Floudas, C. A. Convex underestimation of twice continuously differentiable functions by piecewise quadratic perturbation: Spline αBB underestimators. Journal of Global Optimization 2005, 32 (2), 221-258.
145. Klepeis, J. L.; Floudas, C. A. Analysis and Prediction of Loop Segments in Protein Structures. Computers and Chemical Engineering 2005, 29, 423-436.
146. Meyer, C. A.; Floudas, C. A. Convex Envelopes for Edge-Concave Functions. Mathematical Programming 2005, 103 (2), 207-224.
147. Floudas, C. A.; Akrotirianakis, I. G.; Caratzoulas, S.; Meyer, C. A.; Kallrath, J. Global Optimization in the 21st Century: Advances and Challenges. Computers and Chemical Engineering 2005, 29 (6), 1185-1202.
148. Floudas, C. A.; Fung, H. K.; McAllister, S. R.; Monnigmann, M.; Rajgaria, R. Advances in Protein Structure Prediction and De Novo Protein Design: A Review. Chemical Engineering Science 2005, 61, 966-988.
149. Floudas, C. A.; Janak, S. L. Comments on “New General Continuous-Time State Task Network Formulation for Short-Term Scheduling of Multipurpose Batch Plants” and on “Enhanced Continuous Time Unit Specific Event Based Formulation for Short Term Scheduling of Multipurpose Batch Processes”. Industrial & Engineering Chemistry Research 2005, 44, 1985-1986.
150. Fung, H. K.; Rao, S.; Floudas, C. A.; Prokopyev, O.; Pardalos, P. M.; Rendl, F. Computational Comparison Studies of Quadratic Assignment Like Formulations for the In Silico Sequence Selection Problem in De Novo Protein Design. Journal of Combinatorial Optimization 2005, 10, 41-60.
151. Monnigmann, M.; Floudas, C. A. Protein Loop Structure Prediction with Flexible Stem Geometries. Proteins 2005, 61, 748-762.
152. Floudas, C. A. Research Challenges, Opportunities and Synergism in Systems Engineering and Computational Biology. AIChE Journal 2005, 51 (7), 1872-1884.
153. Morikis, D.; Floudas, C. A.; Lambris, J. D. Structure-based integrative computational and experimental approach for the optimization of drug design. Lecture Notes in Computer Science 2005, 3515, 680-688.

2006

154. Meyer, C.; Floudas, C. A. Global Optimization of a Combinatorially Complex Generalized Pooling Problem. AIChE Journal 2006, 52 (3), 1027-1037.
155. Janak, S. L.; Taylor, M.; Floudas, C. A.; Burka, M.; Mountziaris, T. J. A Novel and Effective Integer Optimization Approach for the NSF Panel Assignment Problem: A Mutli-Resource and Preference-Constrained Generalized Assignment Problem. Industrial & Engineering Chemistry Research 2006, 45 (1), 258-265.
156. Janak, S. L.; Floudas, C. A.; Kallrath, J.; Vormbrock, N. Production Scheduling of a Large-Scale Industrial Batch Plant. I. Short-Term and Medium-Term Scheduling. Industrial & Engineering Chemistry Research 2006, 45 (25), 8234-8252.
157. Janak, S. L.; Floudas, C. A.; Kallrath, J.; Vormbrock, N. Production Scheduling of a Large-Scale Industrial Batch Plant. II. Reactive Scheduling. Industrial & Engineering Chemistry Research 2006, 45 (25), 8253-8269.
158. McAllister, S. R.; Mickus, B. E.; Klepeis, J. L.; Floudas, C. A. A Novel Approach for Alpha-Helical Topology Prediction in Globular Proteins: Generation of Interhelical Restraints. Proteins 2006, 65, 930-952.
159. Shaik, M. A.; Janak, S. L.; Floudas, C. A. Continuous-Time Models for Short-Term Scheduling of Multipurpose Batch Plants: A Comparative Study. Industrial & Engineering Chemistry Research 2006, 45 (18), 6190-6209.
160. Rajgaria, R.; McAllister, S. R.; Floudas, C. A. A Novel High Resolution Cα-Cα Distance Dependent Force Field Based on a High Quality Decoy Set. Proteins 2006, 65 (3), 726-741.
161. Gounaris, C. E.; Floudas, C. A.; Wei, J. Rational Design of Shape Selective Separation and Catalysis: I. Concepts and Analysis. Chemical Engineering Science 2006, 61 (24), 7933-7948.
162. Gounaris, C. E.; Wei, J.; Floudas, C. A. Rational Design of Shape Selective Separation and Catalysis: II. Mathematical Model and Computational Studies. Chemical Engineering Science 2006, 61 (24), 7949-7962.

2007

163. Floudas, C. A.; Kreinovich, V. On the Functional Form of Convex Underestimators for Twice Continuously Differentiable Functions. Optimization Letters 2007, 1 (2), 187-192.
164. Janak, S. L.; Lin, X.; Floudas, C. A. A New Robust Optimization Approach for Scheduling under Uncertainty: II. Uncertainty with Known Probability Distribution. Computers and Chemical Engineering 2007, 31, 171-195.
165. McAllister, S. R.; Rajgaria, R.; Floudas, C. A. Global Pairwise Sequence Alignment Through Mixed-Integer Linear Programming: A Template-Free Approach. Optimization Methods and Software 2007, 22 (1), 127-144.
166. Fung, H. K.; Taylor, M. S.; Floudas, C. A. Novel Formulations for the Sequence Selection Problem in de Novo Protein Design with Flexible Templates. Optimization Methods and Software 2007, 22 (1), 51-71.
167. DiMaggio, P. A.; Floudas, C. A. A mixed-integer optimization framework for de novo peptide identification. AIChE Journal 2007, 53 (1), 160-173.
168. Shaik, M. A.; Floudas, C. A. An Improved Unit-Specific-Event based Continuous-Time Model for Short-Term Scheduling of Continuous Processes: Rigorous Treatment of Storage Requirements. Industrial & Engineering Chemistry Research 2007, 46, 1764-1779.
169. Floudas, C. A.; Stein, O. The Adaptive Convexification Algorithm: A Feasible Point Method for Semi-Infinite Programming. SIAM Journal of Optimization 2007, 18 (4), 1187-1208.
170. Tan, M. P.; Broach, J. R.; Floudas, C. A. A Novel Clustering Approach and Prediction of Optimal Number of Clusters: Global Optimum Search with Enhanced Positioning. J. Global Optimization 2007, 39, 323-346.
171. Tan, M. P.; Broach, J. R.; Floudas, C. A. Evaluation of Normalization and Pre-Clustering Issues in a Novel Clustering Approach: Global Optimum Search with Enhanced Positioning. Journal of Bioinformatics and Computational Biology 2007, 5 (4), 895-913.
172. DiMaggio, P. A.; Floudas, C. A. De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization. Analytical Chemistry 2007, 79, 1433-1466.
173. Floudas, C. A. Computational Methods in Protein Structure Prediction. Biotechnology and Bioengineering 2007, 97, 207-213.

2008

174. McAllister, S. R.; Rajgaria, R.; Floudas, C. A. A Path Selection Approach to Global Pairwise Sequence Alignment using Integer Linear Optimization. Optimization 2008, 57, 101-111.
175. Janak, S. L.; Floudas, C. A. Improving Unit-Specific Event Based Continuous-Time Approaches for Batch Processes: Integrality Gap and Task Splitting. Computers and Chemical Engineering 2008, 32 (4-5), 913-955.
176. Li, H.-L.; Tsai, J.-F.; Floudas, C. A. Convex Underestimation for Posynomial Functions of Positive Variables. Optimization Letters 2008, 2 (3), 333-340.
177. Shaik, M. A.; Floudas, C. A. Unit-Specific-Event based Continuous-Time Approach for Short-Term Scheduling of Batch Plants using RTN Framework. Computers and Chemical Engineering 2008, 32, 260-274.
178. Rajgaria, R.; McAllister, S. R.; Floudas, C. A. Distance Dependent Centroid to Centroid Force Fields using High Resolution Decoys. Proteins 2008, 70, 950-970.
179. Gounaris, C. E.; Floudas, C. A. Tight Convex Underestimators for C2-Continuous Problems: I. Univariate Functions. J. Global Optimization 2008, 42, 51-67.
180. Gounaris, C. E.; Floudas, C. A. Tight Convex Underestimators for C2-Continuous Problems: II. Multivariate Functions. J. Global Optimization 2008, 42, 69-89.
181. Fung, H. K.; Welsh, W. J.; Floudas, C. A. Computational De Novo Peptide and Protein Design: Rigid Templates versus Flexible Templates. Industrial & Engineering Chemistry Research 2008, 47, 993-1001.
182. Fung, H. K.; Floudas, C. A; Taylor, M. S.; Zhang, L.; Morikis, D. Towards Full Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2. Biophysical J. 2008, 94, 584-599.
183. Gounaris, C. E.; Floudas, C. A. Convexity of Products of Univariate Functions and Convexification Transformations for Geometric Programming. J. Opt. Theory and App. 2008, 138 (1), 407-427.
184. DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Biclustering via Optimal Re-ordering of Data Matrices in Systems Biology: Rigorous Methods and Comparative Studies. BMC Bioinformatics 2008, 9, 458.
185. McAllister, S. R.; DiMaggio, P. A; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Descriptor-Free Molecular Discovery in Large Libraries by Adaptive Substituent Reordering. Bioorganic and Medicinal Chemistry Letters 2008, 18 (22), 5967-5970.
186. Yoon, S. G.; Park, S. B.; Park, S.; Lee, J.; Verderame, P. M.; Floudas, C. A. Synergy in Mergers of Petrochemical Companies within a Complex Considering Purchasing and Selling Advantage with Process Integration. Industrial & Engineering Chemistry Research 2008, 47 (15), 5556-5567.
187. Taylor, M. S.; Fung, H. K.; Rajgaria, R.; Filizola, M.; Weinstein, H.; Floudas, C. A. Mutations Affecting the Oligomerization Interface of G-Protein Coupled Receptors Revealed by a Novel De Novo Protein Design Framework. Biophysical J. 2008, 94, 2470-2481.
188. DiMaggio, P. A.; Floudas, C. A.; Lu, B.; Yates, J. R. A Hybrid Method for Peptide Identification using Integer Linear Optimization, Local Database Search, and QTOF or OrbiTrap Tandem Mass Spectrometry. J. Proteome Res. 2008, 7, 1584-1593.
189. DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Optimal Methods for Re-ordering Data Matrices in Systems Biology and Drug Discovery Applications. Biophysical Reviews and Letters 2008, 3, 19-42.
190. Tan, M. P.; Smith, E. R.; Broach, J. R.; Floudas, C. A. Microarray Data Mining: A Novel Optimization-Based Approach to Uncover Biologically Coherent Structures. BMC Bioinformatics 2008, 9, 268-283.
191. Verderame, P. M.; Floudas, C. A. Integrated Operational Planning and Medium-Term Scheduling of a Large-Scale Industrial Batch Plants. Industrial & Engineering Chemistry Research 2008, 47, 4845-4860.
192. McAllister, S. R.; Floudas, C. A. Alpha-Helical Topology Prediction and Generation of Distance Restraints in Membrane Proteins. Biophysical Journal 2008, 95 (11), 5281-5295.

2009

193. Shaik, M. A.; Floudas, C. A.; Kallrath, J.; Pitz, H. J. Production Scheduling of a Large-Scale Industrial Continuous Plant: Short-Term and Medium-Term Scheduling. Computers and Chemical Engineering 2009, 33 (3), 670-686.
194. McAllister, S. R.; DiMaggio, P. A.; Floudas, C. A. Mathematical Modeling and Efficient Optimization Methods for the Distance-Dependent Rearrangement Clustering Problem. J. of Global Optimization 2009, 45, 111-129.
195. McAllister, S. R.; Floudas, C. A. Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space. Optimization Methods and Software 2009, 24 (4-5), 837-855.
196. Verderame, P. M.; Floudas, C. A. Operational Planing Framework for Multisite Production and Distribution Networks. Computers & Chemical Engineering 2009, 33 (5), 1036-1050.
197. Floudas, C. A.; Gounaris, C. E. A Review of Recent Advances In Global Optimization. J. of Global Optimization 2009, 45, 3-38.
198. Rajgaria, R.; McAllister, S. R.; Floudas, C. A. Towards Accurate Residue-Residue Contact Prediction for Alpha Helical Proteins via Integer Linear Optimization. Proteins 2009, 74 (4), 929-947.
199. Shaik, M. A.; Floudas, C. A. Novel Unified Modeling Approach for Short-term Scheduling. Industrial & Engineering Chemistry Research 2009, 48, 2947-2964.
200. Misener, R.; Gounaris, C. E.; Floudas, C. A. Global Optimization of Gas Lifting Operations: A Comparative Study of Piecewise Linear Formulations. Industrial & Engineering Chemistry Research 2009, 48 (13), 6098-6104.
201. Yoon, S. G.; Park, S.; Lee, J.; Floudas, C. A.; Verderame, P. Selecting the optimal target company based on synergy calculation for the vertical merger in a petrochemical complex. Industrial & Engineering Chemistry Research 2009, 48 (3), 1511-1521.
202. Gounaris, C. E.; Misener, R.; Floudas, C. A. Computational comparison of piecewise-linear relaxations for pooling problems. Industrial & Engineering Chemistry Research 2009, 48 (12), 5742-5766.
203. Verderame, P. M.; Floudas, C. A. Operational planning of large scale industrial batch plants under demand due date and amount uncertainty: I. Robust optimization framework. Industrial & Engineering Chemistry Research 2009, 48 (15), 7214-7231.
204. Ranjan, R.; Thust, S.; Gounaris, C. E.; Woo, M.; Floudas, C. A.; Keitz, M. V.; Valentas, K. J.; Wei, J.; Tsapatsis, M. Adsorption of fermentation inhibitors from lignocellulosic biomass hydrolyzates for improved ethanol yield and value-added product recovery. Microporous Mesoporous Materials 2009, 122 (1-3), 143-148.
205. Young, N. L.; DiMaggio, P. A.; Plazas-Mayorca, M. D.; Baliban, R. C.; Floudas, C. A.; Garcia, B. A. High-throughput characterization of combinatorial histone codes. Molecular & Cellular Proteomics 2009, 8 (10), 2266-2284.
206. Wei, J.; Floudas, C. A.; Gounaris, C. E. Search engines for shape selectivity. Catalysis Letters 2009, 133 (1-2), 234-241.
207. DiMaggio, P. A.; Young, N. L.; Baliban, R. C.; Garcia, B. A.; Floudas, C. A. A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry. Molecular & Cellular Proteomics 2009, 8 (11), 2527-2543.
208. Misener, R.; Floudas, C. A. Advances for the pooling problem: Modeling, global optimization and computational studies. Appl. Comput. Math. 2009, 8, 3-22.
209. Subramani, A.; DiMaggio, P. A.; Floudas, C. A. Selecting high quality protein structures from diverse conformational ensembles. Biophysical J. 2009, 97, 1728-1736.
210. Sun, J.; Abdeljabbar, D. M.; Clarke, N.; Bellows, M. L.; Floudas, C. A.; Link, A. J. Reconstitution and Engineering of Apoptotic Protein Interactions on the Bacterial Cell Surface. J. Molecular Biology 2009, 394, 297-305.
211. Yoon, S. G.; Park, S.; Lee, J.; Verderame, P.; Floudas, C. A. Evaluation of synergy effect in the horizontal merger of companies in a petrochemical complex. Industrial & Engineering Chemistry Research 2009, 48 (24), 11017-11033.

2010

212. Birgin, E. G.; Floudas, C. A.; Martinez, J. M. Global Minimization using an Augmented Lagrangian Method with Variable Lower-Level Constraints. Mathematical Programming, Ser. A 2010, 125, 139-162.
213. DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. A network flow model for biclustering via optimal re-ordering of data matrices. J. of Global Optimization 2010, 47 (3), 343-354.
214. McAllister, S. R.; Floudas, C. A. An Improved Hybrid Global Optimization Method for Protein Tertiary Structure Prediction. Computational Optimization and Applications 2010, 45, 377-413.
215. Bellows, M. L.; Fung, H. K.; Taylor, M. S.; Floudas, C. A.; Lopez de Victoria, A.; Morikis, D. New Compstatin Variants Through Two De Novo Protein Design Frameworks. Biophysical Journal 2010, 98 (10), 2337-2346.
216. Lu, H.-C.; Li, H.-L.; Gounaris, C. E.; Floudas, C. A. Convex Relaxation for Solving Posynomial Programs. Journal of Global Optimization 2010, 46, 147-154.
217. DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Enhancing Molecular Discovery Using Descriptor-Free Rearrangement Clustering Techniques for Sparse Data Sets. AIChE J. 2010, 56 (2), 405-418.
218. Baliban, R. C.; DiMaggio, P. A.; Young, N. L.; Plazas-Mayorca, M. D.; Garcia, B. A.; Floudas, C. A. A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Molecular and Cellular Proteomics 2010, 9 (5), 764-779.
219. Gounaris, C. E.; Wei, J.; Floudas, C. A. Rational design of shape selective separations and catalysis: Lattice relaxation, locally optimal conformations and effective aperture size. AIChE J. 2010, 56 (3), 611-632.
220. Rajgaria, R.; Wei, Y.; Floudas, C. A. Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3d structure prediction method ASTRO-FOLD. Proteins 2010, 78, 1825-1846.
221. Misener, R.; Floudas, C. A. Piecewise-linear approximations of multidimensional functions. Journal of Optimization Theory and its Applications 2010, 145, 120-147.
222. Verderame, P. M.; Floudas, C. A. Operational planning of large scale industrial batch plants under demand due date and amount uncertainty: II. Conditional value at risk framework. Industrial & Engineering Chemistry Research 2010, 49 (1), 260-275.
223. Misener, R.; Gounaris, C. E.; Floudas, C. A. Mathematical modeling and global optimization of large scale extended pooling problems with the EPA complex emissions contraints. Computers and Chemical Engineering 2010, 34, 1432-1456.
224. Li, J.; Susarla, N.; Karimi, I. A.; Shaik, M. A.; Floudas, C. A. An analysis of some unit-specific event-based models for the short term scheduling of non-continuous processes. Industrial & Engineering Chemistry Research 2010, 49, 633-647.
225. Bellows, M. L.; Floudas, C. A. Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7 and histone demethylases. Current Drug Targets 2010, 11 (3), 264-278.
226. Li, J.; Floudas, C. A. Optimal event point determination for short term scheduling of multipurpose batch plants via unit-specific event-based continuous-time approaches. Industrial & Engineering Chemistry Research 2010, 49, 7446-7469.
227. Verderame, P. M.; Floudas, C. A. Integration of operational planning and medium-term scheduling for large-scale industrial batch plants under demand and processing time uncertainty. Industrial & Engineering Chemistry Research 2010, 49, 4948-4965.
228. Verderame, P. M.; Elia, J. A.; Li, J.; Floudas, C. A. Planning and scheduling under uncertainty: A review across multiple sectors. Industrial & Engineering Chemistry Research 2010, 49, 3993-4017.
229. Misener, R.; Floudas, C. A. Global optimization of large-scale generalized pooling problems: Quadratically constrained MINLP models. Industrial & Engineering Chemistry Research 2010, 49, 5424-5438.
230. Young, N. L.; Plazas-Mayorca, M. D.; DiMaggio, P. A.; Flaniken, I. Z.; J., B. A; Mishra, N.; LeRoy, G.; Floudas, C. A.; Garcia, B. A. Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a. J. American Society for Mass Spectrometry 2010, 21, 960-970.
231. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Toward novel hybrid biomass, coal, and natural gas processes for satisfying current transportation fuel demands, 1: Process alternatives, gasification modeling, process simulation, and economic analysis. Industrial & Engineering Chemistry Research 2010, 49, 7343-7370.
232. Elia, J. A.; Baliban, R, C.; Floudas, C. A. Toward novel hybrid biomass, coal, and natural gas processes for satisfying current transportation fuel demands, 2: Simultaneous heat and power integration. Industrial & Engineering Chemistry Research 2010, 49, 7371-7388.
233. Tamamis, P.; Morikis, D.; Floudas, C. A.; Archontis, G. Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins 2010, 78 (12), 2655-2667.
234. DiMaggio, P. A.; Subramani, A.; Judson, R. S.; Floudas, C. A. A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix clustering and logistic regression. Toxicological Sciences 2010, 118 (1), 251-265.
235. Verderame, P.; Floudas, C. A. Multisite planning under demand and transportation time uncertainty: Robust optimization and conditional value at risk frameworks. Industrial & Engineering Chemistry Research 2010, 50 (9), 4959-4982.
236. Bellows, M. L.; Taylor, M. S.; Cole, P. A.; Shen, L.; Siliciano, R. F.; Fung, H. K.; Floudas, C. A. Discovery of entry inhibitors for HIV-1 via a novel de novo protein design framework. Biophysical J. 2010, 99, 3445-3453.

2011

237. Pan, S. J.; Cheung, W. L.; Fung, H. K.; Floudas, C. A.; Link, A. J. Computational design of the lasso peptide antibiotic microcin J25. Protein Engineering, Design & Selection 2011, 24, 275-282.
238. Elia, J. A.; Baliban, R. C.; Xiao, X.; Floudas, C. A. Optimal energy supply network determination and life cycle analysis for hybrid coal, biomass and natural gas to liquid (CBGTL) plants using carbon-based hydrogen production. Computers and Chemical Engineering 2011, 35, 1399-1430.
239. Wei, Y.; Floudas, C. A. Enhanced inter-helical residue contact prediction in transmembrane proteins. Chemical Engineering Science 2011, 66, 4356-4369.
240. Lopez de Victoria, A.; Gorham Jr., R. D.; Bellows-Peterson, M. L.; Ling, J.; D., Lo D; Floudas, C. A.; Morikis, D. A new generation of potent complement inhibitors of the compstatin family. Chemical Biology and Drug Design 2011, 77, 431-440.
241. Misener, R.; Thompson, J. P.; Floudas, C. A. APOGEE: Global Optimization of Standard, Generalized, and Extended Pooling Problems via Linear and Logarithmic Partitioning Schemes. Comput. Chem. Eng. 2011, 35, 876-892.
242. Gounaris, C. E.; Rajendran, K.; Kevrekidis, I. G. ,; Floudas, C. A. Generation of Networks with Prescribed Degree-Dependent Clustering. Optim. Lett. 2011, 5, 435-451.
243. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Optimization framework for the simultaneous process synthesis, heat and power integration of a thermochemical hybrid biomass, coal, and natural gas facility. Computers and Chemical Engineering 2011, 35, 1647-1690.
244. Khoury, G. A.; Baliban, R. C.; Floudas, C. A. Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Scientific Reports 2011, 1 (90), 1-5.
245. First, E. L.; Gounaris, C. E.; Wei, J.; Floudas, C. A. Computational characterization of zeolite porous networks: an automated approach. Physical Chemistry Chemical Physics 2011, 13, 17339-17358.
246. Li, Z.; Ding, R.; Floudas, C. A. A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear Optimization and Robust Mixed Integer Linear Optimization. Industrial & Engineering Chemistry Research 2011, 50, 10567-10603.
247. Torrente, M. P.; Zee, B. M.; Young, N. L.; Baliban, R. C.; LeRoy, G.; Floudas, C. A.; Hake, S. B.; Garcia, B. A. Proteomic Interrogation of Human Chromatin. PLoS ONE 2011, 6 (9), e24747.
248. Tamamis, P.; Pierou, P.; Mytidou, C.; Floudas, C. A.; Morikis, D.; Archontis, G. Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin. Proteins: Structure, Function, and Bioinformatics 2011, 79 (11), 3166-3179.

2012

249. First, E. L.; Gounaris, C. E.; Floudas, C. A. Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization. Journal of Chemical Information and Modeling 2012, 52 (1), 84-92.
250. Li, J.; Misener, R.; Floudas, C. A. Continuous-time modeling and global optimization approach for scheduling of crude oil operations. AIChE Journal 2012, 58 (1), 205-226.
251. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Simultaneous process synthesis, heat, power, and water integration of thermochemical hybrid biomass, coal, and natural gas facilities. Computers & Chemical Engineering 2012, 37, 297-327.
252. Baliban, R. C.; Sakellari, D.; Li, Z.; DiMaggio, P. A.; Garcia, B. A.; Floudas, C. A. Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. Journal of Clinical Periodontology 2012, 39 (3), 203-212.
253. Wei, Y.; Thompson, J.; Floudas, C. A. CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science 2012, 468 (2139), 831-850.
254. Subramani, A.; Floudas, C. A. β-sheet Topology Prediction with High Precision and Recall for β and Mixed α/β Proteins. PLoS ONE 2012, 7 (3), e32461.
255. Floudas, C. A.; Elia, J. A.; Baliban, R. C. Hybrid and single feedstock energy processes for liquid transportation fuels: A critical review. Computers & Chemical Engineering 2012, 41 (6), 24-51.
256. Tang, Q.; Li, J.; Floudas, C. A.; Deng, M.; Yan, Y.; Xi, Z.; Chen, P.; Kong, J. Optimization framework for process scheduling of operation-dependent automobile assembly lines. Optimization Letters 2012, 6 (4), 797-824.
257. Tamamis, P.; López de Victoria, A.; Gorham, R. D.; Bellows-Peterson, M. L.; Pierou, P.; Floudas, C. A.; Morikis, D.; Archontis, G. Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs. Chemical Biology & Drug Design 2012, 79 (5), 703-718.
258. Subramani, A.; Wei, Y.; Floudas, C. A. ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction. AIChE Journal 2012, 58 (5), 1619-1637.
259. Li, J.; Verderame, P. M.; Floudas, C. A. Operational Planning of Large-Scale Continuous Processes: Deterministic Planning Model and Robust Optimization for Demand Amount and Due Date Uncertainty. Industrial & Engineering Chemistry Research 2012, 51 (11), 4347-4362.
260. Bellows-Peterson, M. L.; Fung, Ho Ki; Floudas, C. A.; Kieslich, C. A.; Zhang, Li; Morikis, D.; Wareham, K. J.; Monk, P. N.; Hawksworth, O. A.; Woodruff, T. M. De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation. Journal of Medicinal Chemistry 2012, 55 (9), 4159-4168.
261. Li, Z.; Tang, Q.; Floudas, C. A. A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: II. Probabilistic Guarantees on Constraint Satisfaction. Industrial & Engineering Chemistry Research 2012, 51 (19), 6769-6788.
262. Elia, J. A.; Baliban, R. C.; Floudas, C. A. Nationwide energy supply chain analysis for hybrid feedstock processes with significant CO2 emissions reduction. AIChE Journal 2012, 58 (7), 2142-2154.
263. Baliban, R. C; Elia, J. A; Misener, R.; Floudas, C. A Global optimization of a MINLP process synthesis model for thermochemical based conversion of hybrid coal, biomass, and natural gas to liquid fuels. Computers & Chemical Engineering 2012, 42, 64-86.
264. Li, J.; Xiao, X.; Tang, Q.; Floudas, C. A. Production Scheduling of a Large-Scale Steelmaking Continuous Casting Process via Unit-Specific Event-Based Continuous-Time Models: Short-Term and Medium-Term Scheduling. Industrial & Engineering Chemistry Research 2012, 51 (21), 7300-7319.
265. Subramani, A.; Floudas, C. A. Structure Prediction of Loops with Fixed and Flexible Stems. The Journal of Physical Chemistry B 2012, 116 (23), 6670-6682.
266. Skjäl, A.; Westerlund, T.; Misener, R.; Floudas, C. A. A Generalization of the Classical αBB Convex Underestimation via Diagonal and Nondiagonal Quadratic Terms. Journal of Optimization Theory and Applications 2012, 154 (2), 462-490.
267. Li, J.; Misener, R.; Floudas, C. A. Scheduling of crude oil operations under demand uncertainty: A robust optimization framework coupled with global optimization. AIChE Journal 2012, 58 (8), 2373-2396.
268. Baliban, R. C.; DiMaggio, P. A.; Plazas-Mayorca, M. D.; Garcia, B. A.; Floudas, C. A. PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization. Journal of Proteome Research 2012, 11 (9), 4615-4629.
269. Misener, R.; Floudas, C. A. Global optimization of mixed-integer models with quadratic and signomial functions: a review. Applied and Computational Mathematics 2012, 11, 317-336.
270. Baliban, R. C.; Elia, J. A.; Weekman, V.; Floudas, C. A. Process synthesis of hybrid coal, biomass, and natural gas to liquids via Fischer–Tropsch synthesis, ZSM-5 catalytic conversion, methanol synthesis, methanol-to-gasoline, and methanol-to-olefins/distillate technologies. Computers & Chemical Engineering 2012, 47 (12), 29-56.
271. Misener, R.; Floudas, C. A. Global optimization of mixed-integer quadratically-constrained quadratic programs (MIQCQP) through piecewise-linear and edge-concave relaxations. Mathematical Programming 2012, 136, 155-182.
272. Hasan, M. M. F.; Baliban, R. C.; Elia, J. A.; Floudas, C. A. Modeling, Simulation, and Optimization of Postcombustion CO2 Capture for Variable Feed Concentration and Flow Rate. 1. Chemical Absorption and Membrane Processes. Industrial & Engineering Chemistry Research 2012, 51 (48), 15642-15664.
273. Hasan, M. M. F.; Baliban, R. C.; Elia, J. A.; Floudas, C. A. Modeling, Simulation, and Optimization of Postcombustion CO2 Capture for Variable Feed Concentration and Flow Rate. 2. Pressure Swing Adsorption and Vacuum Swing Adsorption Processes. Industrial & Engineering Chemistry Research 2012, 51 (48), 15665-15682.

2013

274. First, E. L.; Floudas, C. A. MOFomics: Computational pore characterization of metal–organic frameworks. Microporous and Mesoporous Materials 2013, 165, 32-39.
275. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Biomass to liquid transportation fuels (BTL) systems: process synthesis and global optimization framework. Energy Environ. Sci. 2013, 6 (1), 267-287.
276. Baliban, R. C.; Sakellari, D.; Li, Z.; Guzman, Y. A.; Garcia, B. A.; Floudas, C. A. Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization. Journal of Clinical Periodontology 2013, 40 (2), 131-139.
277. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Novel Natural Gas to Liquids Processes: Process Synthesis and Global Optimization Strategies. AIChE Journal 2013, 59 (2), 505-531.
278. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Biomass and Natural Gas to Liquid Transportation Fuels: Process Synthesis, Global Optimization, and Topology Analysis. Industrial & Engineering Chemistry Research 2013, 52 (9), 3381-3406.
279. First, E. L.; Gounaris, C. E.; Floudas, C. A. Predictive Framework for Shape-Selective Separations in Three-Dimensional Zeolites and Metal–Organic Frameworks. Langmuir 2013, 29 (18), 5599-5608.
280. Smadbeck, J.; Peterson, M. B.; Khoury, G. A.; Taylor, M. A.; Floudas, C. A. Protein WISDOM: a Workbench for In Silico De novo Design of BioMolecules. Journal of Visualized Experiments 2013, e50476, 1-25.
281. Gounaris, C. E.; Wiesemann, W.; Floudas, C. A. The Robust Capacitated Vehicle Routing Problem Under Demand Uncertainty. Operations Research 2013, 61, 677-693.
282. Baliban, R. C.; Elia, J. A.; Floudas, C. A.; Gurau, B.; Weingarten, M. B.; Klotz, S. D. Hardwood Biomass to Gasoline, Diesel, and Jet Fuel: 1. Process Synthesis and Global Optimization of a Thermochemical Refinery. Energy & Fuels 2013, 27 (8), 4302-4324.
283. Elia, J. A.; Baliban, R. C.; Floudas, C. A.; Gurau, B.; Weingarten, M. B.; Klotz, S. D. Hardwood Biomass to Gasoline, Diesel, and Jet Fuel: 2. Supply Chain Optimization Framework for a Network of Thermochemical Refineries. Energy & Fuels 2013, 27 (8), 4325-4352.
284. Baliban, R. C.; Elia, J. A.; Floudas, C. A.; Xiao, X.; Zhang, Z.; Li, J.; Cao, H.; Ma, J.; Qiao, Y.; Hu, X. Thermochemical Conversion of Duckweed Biomass to Gasoline, Diesel, and Jet Fuel: Process Synthesis and Global Optimization. Industrial & Engineering Chemistry Research 2013, 52 (33), 11436-11450.
285. Misener, R.; Floudas, C. A. GloMIQO: Global mixed-integer quadratic optimizer. Journal of Global Optimization 2013, 57 (1), 3-50.
286. Tamamis, P.; Floudas, C. A. Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop. Biophysical Journal 2013, 105 (6), 1502-1514.
287. Gorham Jr., R. D.; Forest, D. L; Tamamis, P.; Victoria, A. L. d; Kraszni, M.; Kieslich, C. A; Banna, C. D; Bellows-Peterson, M. L; Larive, C. K; Floudas, C. A; Archontis, G.; Johnson, L. V; Morikis, D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Experimental Eye Research 2013, 116, 96-108.
288. Hasan, M. M. F.; First, E. L.; Floudas, C. A. Cost-effective CO2 capture based on in silico screening of zeolites and process optimization. Phys. Chem. Chem. Phys. 2013, 15 (40), 17601-17618.
289. Gounaris, C. E; First, E. L; Floudas, C. A Estimation of diffusion anisotropy in microporous crystalline materials and optimization of crystal orientation in membranes. The Journal of Chemical Physics 2013, 139 (12), 124703.
290. Khoury, G. A.; Thompson, J. P.; Smadbeck, J.; Kieslich, C. A.; Floudas, C. A. Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. Journal of Chemical Theory and Computation 2013, 9 (12), 5653-5674.

2014

291. Khoury, G. A.; Smadbeck, J.; Kieslich, C. A.; Floudas, C. A. Protein folding and de novo protein design for biotechnological applications. Trends in Biotechnology 2014, 32 (2), 99-109.
292. Smadbeck, J.; Peterson, M. B.; Zee, B. M.; Garapaty, S.; Mago, A.; Lee, C.; Giannis, A.; Trojer, P.; A., Garcia. B.; Floudas, C. A. De Novo Peptide Design and Experimental Validation of Histone Methyltransferase Inhibitors. PLoS ONE 2014, 9 (2), e90095.
293. Guzman, Y. A; Sakellari, D.; Arsenakis, M.; Floudas, C. A Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review. Expert Review of Proteomics 2014, 11 (1), 31-41.
294. Khoury, G. A.; Tamamis, P.; Pinnaduwage, N.; Smadbeck, J.; Kieslich, C. A.; Floudas, C. A. Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines. Proteins: Structure, Function, and Bioinformatics 2014, 82 (5), 794-814.
295. First, E. L.; Hasan, M. M. F.; Floudas, C. A. Discovery of novel zeolites for natural gas purification through combined material screening and process optimization. AIChE Journal 2014, 60 (5), 1767-1785.
296. Elia, J. A.; Baliban, R. C.; Floudas, C. A. Nationwide, Regional, and Statewide Energy Supply Chain Optimization for Natural Gas to Liquid Transportation Fuel (GTL) Systems. Industrial & Engineering Chemistry Research 2014, 53 (13), 5366-5397.
297. Tamamis, P.; Floudas, C. A. Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop. PLoS ONE 2014, 9 (4), e95767.
298. Tamamis, P.; Floudas, C. A. Elucidating a Key Component of Cancer Metastasis: CXCL12 (SDF-1α) Binding to CXCR4. Journal of Chemical Information and Modeling 2014, 54 (4), 1174-1188.
299. Hasan, M. M. F.; Boukouvala, F.; First, E. L.; Floudas, C. A. Nationwide, Regional, and Statewide CO2 Capture, Utilization, and Sequestration Supply Chain Network Optimization. Industrial & Engineering Chemistry Research 2014, 53 (18), 7489-7506.
300. Elia, J. A.; Floudas, C. A. Energy Supply Chain Optimization of Hybrid Feedstock Processes: A Review. Annual Review of Chemical and Biomolecular Engineering 2014, 5 (1), 147-179.
301. Ye, Y.; Li, J.; Li, Z.; Tang, Q.; Xiao, X.; Floudas, C. A. Robust optimization and stochastic programming approaches for medium-term production scheduling of a large-scale steelmaking continuous casting process under demand uncertainty. Computers & Chemical Engineering 2014, 66, 165-185.
302. Misener, R.; Floudas, C. A. A Framework for Globally Optimizing Mixed-Integer Signomial Programs. Journal of Optimization Theory and Applications 2014, 161 (3), 905-932.
303. Misener, R.; Floudas, ChristodoulosA. ANTIGONE: Algorithms for coNTinuous / Integer Global Optimization of Nonlinear Equations. Journal of Global Optimization 2014, 59 (2-3), 503-526.
304. Tamamis, P.; Floudas, C. A Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5. Scientific Reports 2014, 4 (5447), 1-9.
305. Smadbeck, J.; Chan, K. H.; Khoury, G. A.; Xue, Bo; Robinson, R. C.; Hauser, C. A. E.; Floudas, C. A. De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides. PLoS Comput Biol 2014, 10 (7), e1003718.
306. Khoury, G. A.; Liwo, A.; Khatib, F.; Zhou, H.; Chopra, G.; Bacardit, J.; Bortot, L. O.; Faccioli, R. A.; Deng, X.; He, Yi; Krupa, P.; Li, J.; Mozolewska, M. A.; Sieradzan, A. K.; Smadbeck, J.; Wirecki, T.; Cooper, S.; Flatten, J.; Xu, K.; Baker, D.; Cheng, J.; Delbem, A. C. B.; Floudas, C. A.; Keasar, C.; Levitt, M.; Popović, Z.; Scheraga, H. A.; Skolnick, J.; Crivelli, S. N.; Players, F. WeFold: A coopetition for protein structure prediction. Proteins: Structure, Function, and Bioinformatics 2014, 82 (9), 1850-1868.
307. Li, Z.; Floudas, C. A. A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: III. Improving the Quality of Robust Solutions. Industrial & Engineering Chemistry Research 2014, 53 (33), 13112-13124.
308. Li, Z.; Floudas, C. A. Optimal scenario reduction framework based on distance of uncertainty distribution and output performance: I. Single reduction via mixed integer linear optimization. Computers & Chemical Engineering 2014, 70 (0), 50-66.
309. Niziolek, A. M; Onel, O.; Elia, J. A.; Baliban, R. C.; Xiao, X.; Floudas, C. A Coal and Biomass to Liquid Transportation Fuels: Process Synthesis and Global Optimization Strategies. Industrial & Engineering Chemistry Research 2014, 53 (44), 17002-17025.
310. Onel, O.; Niziolek, A. M.; Hasan, M. M. F.; Floudas, C. A. Municipal solid waste to liquid transportation fuels - Part I: Mathematical modeling of a municipal solid waste gasifier. Computers & Chemical Engineering 2014, 71 (0), 636-647.
311. Khoury, G. A; Bhatia, N.; Floudas, C. A Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models. Computers & Chemical Engineering 2014, 71 (0), 745-752.
312. Khoury, G. A.; Smadbeck, J.; Tamamis, P.; Vandris, A. C.; Kieslich, C. A.; Floudas, C. A. Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family. ACS Synthetic Biology 2014, 3 (12), 855-869.
313. Halai, R.; Bellows-Peterson, M. L; Branchett, W.; Smadbeck, J.; Kieslich, C. A; Croker, D. E; Cooper, M. A; Morikis, D.; Woodruff, T. M; Floudas, C. A; Monk, P. N Derivation of ligands for the complement C3a receptor from the C-terminus of C5a. European journal of pharmacology 2014, 745, 176-181.

2015

314. Elia, J. A; Li, Ji; Floudas, C. A Strategic planning optimization for natural gas to liquid transportation fuel (GTL) systems. Computers & Chemical Engineering 2015, 72 (0), 109-125.
315. Misener, R.; Smadbeck, J. B.; Floudas, C. A. Dynamically generated cutting planes for mixed-integer quadratically constrained quadratic programs and their incorporation into GloMIQO 2. Optimization Methods and Software 2015, 30 (1), 215-249.
316. Onel, O.; Niziolek, A. M.; Elia, J. A.; Baliban, R. C.; Floudas, C. A. Biomass and Natural Gas to Liquid Transportation Fuels and Olefins (BGTL+C2_C4): Process Synthesis and Global Optimization. Industrial & Engineering Chemistry Research 2015, 54 (1), 359-385.
317. Niziolek, A. M; Onel, O.; Hasan, M. M. F.; Floudas, C. A Municipal solid waste to liquid transportation fuels - Part II: Process synthesis and global optimization strategies. Computers & Chemical Engineering 2015, 74 (0), 184-203.
318. Niziolek, A. M.; Onel, O.; Elia, J. A.; Baliban, R. C.; Floudas, C. A. Coproduction of liquid transportation fuels and C6_C8 aromatics from biomass and natural gas. AIChE Journal 2015, 61 (3), 831-856.

Chapters in Books

1. Visweswaran, V.; Floudas, C. A. Global Optimization of Problems with Polynomial Functions In One Variable. In Recent Advances In Global Optimization; Floudas, C. A., Pardalos, P. M., Eds.; Princeton Series in Computer Science; Princeton University Press: Princeton, NJ, 1992; pp 165-200.
2. Maranas, C. D.; Floudas, C. A. A Global Optimization Method for Weber’s Problem with Attraction and Repulsion. In Large Scale Optimization: State of the Art; Hager, W. W., Hearn, D. W., Pardalos, P. M, Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1993; pp 259-293.
3. Floudas, C. A.; Visweswaran, V. Quadratic Optimization. In Handbook of Global Optimization; Horst, R., Pardalos, P. M., Eds.; Kluwer Academic Publishers, 1994; pp 217-270.
4. Maranas, C. D.; Androulakis, I. P.; Floudas, C. A. A Deterministic Global Optimization Approach for the Protein Folding Problem. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding; Pardalos, P. M., Shalloway, D., Xue, G., Eds.; DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 23; American Mathematical Society, 1995; pp 133-150.
5. Visweswaran, V.; Floudas, C. A. New Formulations and Branching Strategies for the GOP Algorithm. In Global Optimization in Chemical Engineering; Grossmann, I. E., Ed.; Kluwer Academic Publishers, 1996; Chapter 3, pp 75-100.
6. Visweswaran, V.; Floudas, C. A. Computational Results for an Efficient Implementation of the GOP Algorithm and its Variants. In Global Optimization in Chemical Engineering; Grossman, I. E., Ed.; Kluwer Academic Publishers, 1996; Chapter 4, pp 111-153.
7. Androulakis, I. P.; Visweswaran, V.; Floudas, C. A. Distributed Decomposition based Approaches in Global Optimization. In State of the Art in Global Optimization : Computational Methods and Applications; Floudas, C. A., Pardalos, P. M., Eds.; Book Series on Nonconvex Optimization and Its Applications; Kluwer Academic Publishers, 1996.
8. Visweswaran, V.; Floudas, C. A.; Ierapetritou, M. G.; Pistikopoulos, E. N. A Decomposition based Global Optimization Approach for Solving Bilevel Linear and Nonlinear Quadratic Programs. In State of the Art in Global Optimization: Computational Methods and Applications; Floudas, C. A., Pardalos, P. M., Eds.; Book Series on Nonconvex Optimization and Its Applications; Kluwer Academic Publishers, 1996.
9. Floudas, C. A. Deterministic Global Optimization in Design, Control, and Computational Chemistry. In Large-Scale Optimization with Applications; Biegler, L. T., Conn, A. R., Coleman, T. F., Santosa, F. N., Eds.; The IMA Volumes in Mathematics and its Applications, Vol. 93, Part II: Optimal Design and Control; Springer-Verlag: New York, 1997; pp 129-184.
10. Schweiger, C. A.; Floudas, C. A. Interaction of Design and Control: Optimization with Dynamic Models. In Optimal Control: Theory, Algorithms, and Applications; Hager, W. W., Pardalos, P. M., Eds.; Kluwer Academic Publishers, 1997; pp 388-435.
11. Floudas, C. A.; Zlobec, S. Optimality and Duality in Parametric Convex Lexicographic Programming. In Multilevel Optimization: Algorithms and Applications; Migdalas, A., Pardalos, P. M., Varbrand, P., Eds.; Kluwer Academic Publishers, 1998; pp 359-379.
12. Androulakis, I. P.; Floudas, C. A. Distributed Branch and Bound Algorithms for Global Optimization. In Parallel Processing of Discrete Problems; Pardalos, P. M., Ed.; IMA Volumes in Mathematics and its Applications, Vol. 106; Springer-Verlag, 1998; pp 1-36.
13. Adjiman, C. S.; Schweiger, C. A.; Floudas, C. A. Mixed-Integer Nonlinear Optimization in Process Synthesis. In Handbook of Combinatorial Optimization; Du, D.-Z., Pardalos, P. M., Eds.; Springer, 1998.
14. Adjiman, C. S.; Schweiger, C. A.; Floudas, C. A. Nonlinear and Mixed-Integer Optimization in Chemical Process Network Systems. In Network Design: Connectivity and Facilities Location; Pardalos, P. M., Du, D.-Z., Eds.; DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 40; American Mathematical Society, 1998; pp 429-452.
15. Floudas, C. A.; Klepeis, J. L.; Pardalos, P. M. Global Optimization Approaches in Protein Folding and Peptide Docking. In Mathematical Support for Molecular Biology; Farach-Colton, M., Roberts, F. S., Vingron, M., Waterman, M., Eds.; DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 47; American Mathematical Society, 1999; pp 141-171.
16. Ierapetritou, M. G.; Androulakis, I. P.; Monos, D. S.; Floudas, C. A. Structure Prediction of Binding Sites of MHC Class II Molecules based on the Crystal of HLA-DRB1 and Global Optimization. In Optimization in Computational Chemistry and Molecular Biology; Floudas, C. A., Pardalos, P. M., Eds.; Kluwer Academic Publishers, 2000; pp 157-190.
17. Klepeis, J. L.; Floudas, C. A. Methodology for Elucidating the Folding Dynamics of Peptides : Met-Enkephalin Case Study. In Optimization in Computational Chemistry and Molecular Biology; Floudas, C. A., Pardalos, P. M., Eds.; Kluwer Academic Publishers, 2000; pp 19-46.
18. Floudas, C. A. Mixed-Integer Nonlinear Optimization. In Handbook of Applied Optimization; Resende, M., Pardalos, P. M., Eds.; Oxford University Press, 2001; p 451.
19. Floudas, C. A. Deterministic Global Optimization and Its Applications. In Handbook of Applied Optimization; Resende, M., Pardalos, P. M., Eds.; Oxford University Press, 2001; p 311.
20. Klepeis, J. L.; Floudas, C. A. Deterministic Global Optimization for Protein Structure Prediction. In Advances in Convex Analysis and Global Optimization, a Book in Honor of C. Caratheodory; Hadjisavvas, N., Pardalos, P. M., Eds.; 2001; pp 31-74.
21. Meyer, C. A.; Floudas, C. A. Convex Hull of Trilinear Monomials with Positive or Negative Domains: Facets of the Convex and Concave Envelopes. In Frontiers in Global Optimization; Floudas, C. A., Pardalos, P. M., Eds.; Kluwer Academic Publishers, 2003; pp 327-352.
22. Schweiger, C. A.; Floudas, C. A. The MINOPT Modeling Language. In Modeling Languages; Kallrath, J., Ed.; Kluwer Academic Publishers, 2003.
23. McAllister, S. R.; Floudas, C. A. Structure Prediction of Alpha-Helical Proteins. In BIOMAT 2005: International Symposium on Mathematical and Computational Biology; Mondaini, R. P., Dilão, R., Eds.; Springer, 2006; pp 265-288.
24. Floudas, C. A.; Fung, H. K. Mathematical Modeling and Optimization Methods for De Novo Protein Design. In Systems Biology; Rigoutsos, I., Stephanopoulos, G., Eds.; Oxford University Press, 2007; pp 42-66.
25. McAllister, S. R.; Rajgaria, R.; Floudas, C. A. A Template-based Mixed-Integer Linear Programming Sequence Alignment Model. In Models and Algorithms for Global Optimization; Torn, A., Zilinskas, J., Eds.; Springer-Verlag, 2007; pp 343-360.
26. Floudas, C. A.; Kreinovich, V. Towards Optimal techniques for Solving Global Optimization Problems: Symmetry-based Approach. In Models and Algorithms for Global Optimization; Torn, A., Zilinskas, J., Eds.; Springer-Verlag, 2007; pp 21-42.
27. Floudas, C. A; Fung, H. K.; Morikis, D.; Taylor, M. S.; Zhang, L. Overcoming the Key Challenges in De Novo Protein Design: Enhancing Computational Efficiency and Incorporating True Backbone Flexibility. In BIOMAT 2006: International Symposium on Mathematical and Computational Biology; Mondaini, R. P., Ed.; Springer, 2007; pp 133-183.
28. DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Optimal Methods for Re-ordering Matrices in Systems Biology and Drug Discovery Applications. In BIOMAT 2007: International Symposium on Mathematical and Computational Biology; Mondaini, R., Ed.; Springer, 2008; pp 133-183.
29. Tan, M. P.; Floudas, C. A. A Novel Clustering Approach: Global Optimum Search with Enhanced Positioning. In Clustering Challenges in Biological Networks; Butenko, S., Chaovalitwongse, W. A., Pardalos, P. M., Eds.; 2009; pp 307-332.
30. Floudas, C. A.; Gounaris, C. E. An Overview of Advances in Global Optimization during 2003-2008. In Fields Workshop on Global Optimization; Pardalos, P. M., Coleman, T. F., Eds.; Fields Communications Series, Vol. 55; 2009; pp 105-154.
31. Bellows, M. L.; Fung, H. K.; Floudas., C. A. Recent Advances In De Novo Protein Design. In Process Systems Engineering Vol. 6 Molecular Systems Engineering; Adjiman, C. S., Galindo, A., Eds.; Wiley-VCH, 2010; pp 207-232.
32. Guzman, Y. A; Hasan, M. M. F.; Floudas, C. A Computational Comparison of Convex Underestimators for Use in a Branch-and-Bound Global Optimization Framework. Optimization in Science and Engineering; Springer, 2014; pp 229-246.

Conference Proceedings

1. Luyben, M. L.; Floudas, C. A. Interaction between Design and Control in a Reactor Separator Recycle system. Proceedings of Process Systems Engineering, PSE ‘94; 199; pp 893-898.
2. Floudas, C. A.; Grossmann, I. E. A New Approach For Evaluating Flexibility In Chemical Process Design. Proceedings of Process Systems Engineering, PSE ‘85, Cambridge, England; 1985; pp 619-631.
3. Floudas, C. A.; Grossmann, I. E.; Wood, R. Automatic Synthesis and Optimization of Heat Exchanger Networks. Proceedings of Chemical Engineering Conference, CHEMECA; 1986; Paper 5a.
4. Floudas, C. A.; Grossmann, I. E. Synthesis of Flexible Heat Exchanger Networks. Proceedings of Chemical Engineering Fundamentals: The Use of Computers in Chemical Engineering, CEF ‘87; 1987; pp 711-717.
5. Paules, G. E. IV; Floudas, C. A. Design of Multiperiod Distillation Sequences. Proceedings of the First International Conference on Foundations of Computer-Aided Process Operati, FOCAPO ‘87; Reklaitis, G. V., Spriggs, H. D., Eds.; Elsevier Science Ltd, 1987; pp 647-653.
6. Georgiou, A.; Floudas, C. A. Determination of Generic Rank of Structural Matrices. Proceedings of the 22nd Conference on Information Sciences and Systems, Princeton University; 1988; pp 585-590.
7. Ciric, A. R.; Floudas, C. A. Optimization Model for Retrofitting Heat Exchanger Networks. I.Ch.E. Symposium Series No. 109; 1988; pp 61-75.
8. Floudas, C. A. Multicomponent Multi-feed Multi-product Synthesis of Distillation Sequences. I.Ch.E. Symposium Series No. 109; 1988; pp 137-159.
9. Floudas, C. A.; Ciric, A. R. Global Optimum Issues on Heat Exchanger Network Synthesis. Proceedings of Process Systems Engineering, PSE ‘88; 1988; pp 104-110.
10. Ciric, A. R.; Floudas, C. A. Retrofitting Heat Exchanger Networks: A Two-stage Approach. Design Theory 1988; Newsome, S. L., Spillers, W. R., Finger, S., Eds.; Springer-Verlag, 1989; pp 265-286.
11. Floudas, C. A.; Aggarwal, A.; Ciric, A. R. Global Optimum Search In Non-convex Design Problems. Proceedings of the NSF Engineering Design Research Conference, UMASS, Amherst; 1989; pp 435-451.
12. Georgiou, A.; Floudas, C. A. Simultaneous Process Synthesis and Control: Minimization of Disturbance Propagation In Heat Recovery Systems. In Foundations of Computer-Aided Process Design, Proceedings of the Third International Conference on Foundations of Computer-Aided Process Design, Snowmass Village, Colorado, July 10-14, 1989; Siirola, J. J., Grossmann, I. E., Stephanopoulos, G., Eds.; Elsevier, 1990; pp 435-450.
13. Ciric, A. R.; Floudas, C. A. A MINLP Model For Retrofitting Heat Exchanger Networks. Proceedings of the NSF Design and Manufacturing Systems Conference, Arizona State University; 1990.
14. Aggarwal, A.; Floudas, C. A. Optimal Synthesis of Nonsharp Separation Sequences. In Computer Applications in Chemical Engineering, Proceedings of the European Symposium on Computer Applications in Chemical Engineering, ComChem ‘90, The Hague, The Netherlands, May 7-9, 1990; Bussemaker, H. Th., Iedema, P. D., Eds.; Elsevier: Amsterdam, 1990; pp 243-248.
15. Psarris, P.; Floudas, C. A. A General Framework for the Enhancement of Dynamic Operability in MIMO Systems with Time Delays. Proceedings of the 23rd Conference on Information Sciences and Systems, Princeton University; 1990.
16. Visweswaran, V.; Floudas, C. A. A Global Optimization Algorithm (GOP) For Certain Classes of Nonconvex NLPs - III. New Properties For Improved Computational Performance. Proceedings of Process Systems Engineering, PSE ‘91; 1991; pp I.6.1-I.6.17.
17. Psarris, P.; Floudas, C. A. Interaction of Process Design and Control: Dynamic Operability in Multivariable Time Delay Systems. Proceedings of Process Systems Engineering, PSE ‘91; 1991; pp II.8.1-II.8.17.
18. Luyben, M. L.; Floudas, C. A. A Multi-objective Optimization Approach for the Interaction of Design and Control. Proceedings of the IFAC Meeting on Design and Control; 1992; pp 101-107.
19. Papalexandri, K. P.; Pistikopoulos, E. N.; Floudas, C. A. Synthesis of Mass Exchanger Networks for Waste Minimization: An MINLP Approach. Proceedings of ESCAPE-4; 1994; pp 351-358.
20. McDonald, C. M.; Floudas, C. A. Global Optimization for the phase equilibrium problem using the NRTL equation. Proceedings of ESCAPE-4; 1994; pp 273-280.
21. Luyben, M. L.; Floudas, C. A. Interaction between Design and Control in Heat-Integrated Distillation Synthesis. Proceedings of IFAC, IPDC ‘94; 1994; pp 76-82.
22. Barmish, B. R.; Floudas, C. A.; Hollot, C. V.; Tempo, R. A Global Linear Programming Solution to Some Open Robustness Problems Including Matrix Polytope Stability. Proceedings of the ACC ‘95 Conference; 1995.
23. Floudas, C. A.; Grossmann, I. E. Algorithmic approaches to process synthesis: Logic and global optimization. Proceedings of the Fourth International Conference on Foundations of Computer-Aided Process Design, Snowmass, Colorado, July 10-14, 1994; 1995; pp 198-221.
24. Floudas, C. A. Global Optimization In Design and Control of Chemical Process Systems. Proceedings of DYCOPS-5 on Dynamics and Control of Process Systems; 1998; pp 167-178.
25. Schweiger, C. A.; Floudas, C. A. Process Synthesis, Design and Control: A Mixed Integer Optimal Control Framework. Proceedings of DYCOPS-5 on Dynamics and Control of Process Systems; 1998; pp 189-194.
26. Floudas, C. A.; Pardalos, P. M. Recent Developments in Global Optimization and Their Relevance to Process Design. Proceedings of Foundations of Computer Aided Process Design, FOCAPD ‘99; Malone, M. F., Trainham, J. A., Eds.; 1999.
27. Esposito, W. R.; Floudas, C. A. Global Optimization of Nonconvex Problems with Differential-Algebraic Constraints. Proceedings of the European Symposium on Computer Aided Process Engineering, ESCAPE-10; Pierucci, S., Ed.; Elsevier, 2000; pp 73-78.
28. Lin, X.; Floudas, C. A. Design, Synthesis and Scheduling of Multipurpose Batch Plants via an Effective Continuous-time Formulation. Proceedings of the European Symposium on Computer Aided Process Engineering, ESCAPE-10; Pierucci, S., Ed.; Elsevier, 2000; pp 1159-1164.
29. Gümüş, Z. H.; Floudas, C. A. Nonlinear Bilevel Programming: A Deterministic Global Optimization Framework. Proceedings of the European Symposium on Computer Aided Process Engineering, ESCAPE-11; Elsevier, 2001.
30. Klepeis, J. L.; Floudas, C. A. ASTRO-FOLD: Ab Initio Secondary and Tertiary Structure Prediction in Protein Folding. Proceedings of the European Symposium on Computer Aided Process Engineering, ESCAPE-12; Elsevier, 2002.
31. Schafroth, H. D.; Monos, D.; Constantinescou, A.; Floudas, C. A. Predicting Peptide Binding to HLA Class II Molecules via Atomistic Level Modeling, Solvation Methods, and Deterministic Global Optimization. In HLA 2002: Immunobiology of the Human MHC, Proceedings of the 13th International Histocompatibility Workshop and Conference, Seattle, WA, May 12-22, 2002; Hansen, J. A., Ed.; IHWC Press, 2002.
32. Floudas, C. A. Systems Approaches in Bioinformatics and Computational Genomics. In Information and Communications: Challenges for the Chemical Sciences in the 21st Century, Proceedings of the Workshop on Information and Communications, Washington, D.C., Oct 31-Nov 2, 2002; National Research Council, National Academies Press: Washington, D.C., 2003; pp 116-125.
33. Lin, X.; Chajakis, E. D.; Floudas, C. A. Continuous-Time Scheduling of Tanker Lightering in Crude Oil Supply Chain. Proceedings of Process Systems Engineering, PSE ‘03; 2004; pp 547-553.
34. Floudas, C. A.; Klepeis, J. L.; Lambris, J. D.; Morikis, D. De novo protein design: An interplay of global optimization, mixed-integer optimization, and experiments. Proceedings of FOCAPD ‘2004; Floudas, C. A., Agrawal, A., Eds.; 2004; pp 133-146.
35. Floudas, C. A.; Akrotirianakis, I. G.; Caratzoulas, S.; Meyer, C. A.; Kallrath, J. Global Optimization in the 21st Century. Proceedings of the European Symposium on Computer-Aided Process Engineering, ESCAPE-14; Barbosa-Povoa, A., Matos, A., Eds.; Elsevier B.V., 2004; pp 23-51.
36. McAllister, S. R.; Floudas, C. A. Alpha Helical Topology and Tertiary Structure Prediction in Globular Proteins. Proceedings of the 46th IEEE Conference on Decision and Control; 2007; pp 4551-4556.
37. Tan, M. P.; Broach, J. R.; Floudas, C. A. A Novel Clustering Approach: Global Optimum Search with Enhanced Positioning. Proceedings of the 17th European Symposium on Computer Aided Process Engineering - ESCAPE17; Pleşu, V., Agachi, P. S., Eds.; Elsevier B.V., 2007;, Computer Aided Chemical Engineering pp 983-988.
38. Misener, R.; Gounaris, C. E.; Floudas, C. A. Advances in global optimization for standard, generalized, and extended pooling problems with the EPA complex emissions model constraints. In Design for Energy and the Environment, Proceedings of FOCAPD ‘09; Halwagi, M. M., Linninger, A. A., Eds.; 2009; pp 1053-1071.
39. Baliban, R. C.; Elia, J. A.; Floudas, C. A. Towards novel hybrid biomass and coal processes for satisfying transportation fuel demands. Proceedings of the 2nd Annual Gas Processing Symposium, 2010; Eljack, F. T., Reklaitis, G. V., El-Halwagi, M. M., Eds.; Elsevier, 2010.
40. Misener, R.; Gounaris, C. E.; Floudas, C. A. Global optimization and parametric analysis of large-scale extended pooling problems. Proceedings of the 20th European Symposium on Computer Aided Process Engineering - ESCAPE20; Pierucci, S., Buzzi Ferraris, G., Eds.; Elsevier B.V., 2010.

Patents

1. Rabitz, H. A.; Floudas, C. A.; Yetter, R. A. Adaptive Feedback Control Flow Reactor. U.S. Patent 6,153,149. Nov 28, 2000.
2. Klepeis, J. L.; Floudas, C. A. Methods of Ab Initio Prediction of Alpha Helices, Beta Sheets, and Polypeptide Tertiary Structures. U.S. Patent 6,832,162. Dec 14, 2004.
3. Lambris, J. D.; Morikis, D.; Floudas, C. A. Compstatin Analogs Identified by Computer Modeling and Optimization. U.S. Pat. Appl. Sept 2002. (University of Pennsylvania, Princeton University, UC Riverside)
4. Klepeis, J. L.; Floudas, C. A. In Silico Protein Discovery. U.S. Pat. Appl. May 2003. (Princeton University)
5. Janak, S.; Taylor, M. S.; Floudas, C. A.; Burka, M.; Mountziaris, T. A Novel and Effective Integer Optimization Approach for the NSF Panel Assignment Problem: A Mutli-Resource and Preference-Constrained Generalized Assignment Problem. U.S. Pat. Appl. Sept 2005.
6. Gounaris, C. E.; Floudas, C.A.; Wei, J. Rational Design of Shape Selective Separation and Catalysis. U.S. Pat. Appl. Dec 2006.

Doctoral Theses

1. Paules, G. E. IV Synthesis and Analysis of Flexible and Complex Heat-Integrated Distillation Sequences. Ph.D. Thesis, Princeton University, Princeton, NJ, June 1990.
2. Ciric, A. R. Global Optimum and Retrofit Issues in Heat Exchanger Network and Utility System Synthesis. Ph.D. Thesis, Princeton University, Princeton, NJ, June 1990.
3. Aggarwal, A. Synthesis and Analysis of General Distillation Sequences. Ph.D. Thesis, Princeton University, Princeton, NJ, October 1990.
4. Kokossis, A. C. Synthesis and Optimization of Reactor Networks and Reactor-Separator-Recycle Systems. Ph.D. Thesis, Princeton University, Princeton, NJ, May 1992.
5. Psarris, P. The Impact of Process Design and Model Uncertainty in the Dynamic Performance of Multivariable Time Delay Systems. Ph.D. Thesis, Princeton University, Princeton, NJ, October 1992.
6. Luyben, M. L. Analyzing the Interaction Between Process Design and Process Control. Ph.D. Thesis, Princeton University, Princeton, NJ, June 1993.
7. Visweswaran, V. Global Optimization of Nonconvex Nonlinear Problems. Ph.D. Thesis, Princeton University, Princeton, NJ, May 1995.
8. McDonald, C. M. Global Optimization for the Phase and Chemical Equilibrium Problem. Ph.D. Thesis, Princeton University, Princeton, NJ, May 1995.
9. Maranas, C. D. Global Optimization in Computational Chemistry and Process Systems Engineering. Ph.D. Thesis, Princeton University, Princeton, NJ, May 1995.
10. Adjiman, C. S. J. Global Optimization Techniques for Process Systems Engineering. Ph.D. Thesis, Princeton University, Princeton, NJ, June 1998.
11. Schweiger, C. A. Process Synthesis, Design, and Control: Optimization with Dynamic Models and Discrete Decisions. Ph.D. Thesis, Princeton University, Princeton, NJ, June 1999.
12. Harding, S. T. Analysis and Design of Nonideal Distillation Processes. Ph.D. Thesis, Princeton University, Princeton, NJ, December 2000.
13. Esposito, W. R. Jr. Global Optimization in the Estimation, Control, and Synthesis of Chemical Processes. Ph.D. Thesis, Princeton University, Princeton, NJ, April 2001.
14. Klepeis, J. L. Global Optimization in Protein Folding. Ph.D. Thesis, Princeton University, Princeton, NJ, April 2002.
15. Schafroth, H. D. Prediction of Peptide Binding to MHC Molecules via Molecular Modeling and Global Optimization. Ph.D. Thesis, Princeton University, Princeton, NJ, February 2003.
16. Lin, X. Scheduling, Planning, and Design of Chemical Processing Systems: Continuous-Time Approaches. Ph.D. Thesis, Princeton University, Princeton, NJ, April 2003.
17. Gümüş, Z. H. Global Optimization for Bilevel Programming Problems and Applications. Ph.D. Thesis, Princeton University, Princeton, NJ, April 2003.
18. Meyer, C. A. Convex Relaxations and Convex Envelopes for Deterministic Global Optimization. Ph.D. Thesis, Princeton University, Princeton, NJ, February 2004.
19. Janak, S. L. Scheduling of Multiproduct and Multipurpose Batch Plants. Ph.D. Thesis, Princeton University, Princeton, NJ, January 2007.
20. McAllister, S. R. Mathematical Optimization and Algorithmic Development for Protein Structure Prediction. Ph.D. Thesis, Princeton University, Princeton, NJ, February 2008.
21. Fung, H. K. Computational De Novo Protein Design with Flexible Templates. Ph.D. Thesis, Princeton University, Princeton, NJ, October 2008.
22. Gounaris, C. E. Advances in Global Optimization and the Rational Design of Shape Selective Separations. Ph.D. Thesis, Princeton University, Princeton, NJ, October 2008.
23. Tan, M. P. Novel Optimization-based Methods of Studying Cellular Signaling Pathways. Ph.D. Thesis, Princeton University, Princeton, NJ, January 2009.
24. Rajgaria, R. High Resolution Force Fields and Residue Contact Prediction Models for Protein Structure Prediction. Ph.D. Thesis, Princeton University, Princeton, NJ, May 2009.
25. DiMaggio, P. A. In Silico Methods for Discovery in Proteomics, Systems Biology, and Drug Discovery. Ph.D. Thesis, Princeton University, Princeton, NJ, January 2010.
26. Verderame, P. M. Planning and Scheduling of Batch Processes Under Uncertainty. Ph.D. Thesis, Princeton University, Princeton, NJ, March 2011.
27. Peterson, M. B. Targeting Disease with a New De Novo Protein Design Framework for Dug Discovery. Ph.D. Thesis, Princeton University, Princeton, NJ, September 2011.
28. Subramani, A. Advances in Computational Protein Structure Prediction. Ph.D. Thesis, Princeton University, Princeton, NJ, October 2011.
29. Misener, R. Novel Global Optimization Methods: Theoretical and Computational Studies on Pooling Problems with Environmental Constraints. Ph.D. Thesis, Princeton University, Princeton, NJ, September 2012.
30. Baliban, R. C. High-throughput methods for in silico discovery of peptides, proteins, and post-translational modifications in proteomics. Ph.D. Thesis, Princeton University, Princeton, NJ, September 2012.