Special Issue Preface pubs.acs.org/JPCB
Publications of William C. Swope (1) Swope, W. C.; Schaefer III, H. F. Model Organometallic Systems. The Interaction of 2S Beryllium (1+) Ion, 1S Beryllium, and 3P Beryllium Atoms with Acetylene and Ethylene. J. Am. Chem. Soc. 1976, 98, 7962−7967. (2) Swope, W. C.; Schaefer III, H. F. Model Studies of πBonded Organometallic Systems Mn-C2H2 and MnC2H4. Mol. Phys. 1977, 34, 1037−1048. (3) Dykstra, C. E.; Gaylord, A. S.; Gwinn, W. D.; Swope, W. C.; Schaefer III, H. F. The Uncoupled Symmetric Stretching Frequency of H3+. J. Chem. Phys. 1978, 68, 3951−3952. (4) Lucchese, R. R.; Brooks, B. R.; Meadows, J. H.; Swope, W. C.; others. BERKELEY: An “Open Ended” Configuration Interaction (CI) Program Designed for Minicomputers. J. Comput. Phys. 1978, 26, 243−251. (5) Dykstra, C. E.; Swope, W. C. The H3+ Potential Surface. J. Chem. Phys. 1979, 70, 1−3. (6) Harris, R. A.; Swope, W. C. A Harmonic Oscillator Model for the Magnetic Properties of a Closed-Shell System: II. The Magnetic Shielding. Mol. Phys. 1979, 38, 287−298. (7) Swope, W. C. Selected Topics on the Electronic Structure of Small Molecules (Functions of N Fermion Particles and Electric and Magnetic Properties of Small Molecules) [Ph.D. Thesis]. 1979. (8) Swope, W. C.; Lee, Y.-P.; Schaefer III, H. F. Diatomic Sulfur: Low Lying Bound Molecular Electronic States of S2. J. Chem. Phys. 1979, 70, 947−953. (9) Swope, W. C.; Lee, Y.-P.; Schaefer III, H. F. Sulfur Oxide: Low-Lying Bound Molecular Electronic States of SO. J. Chem. Phys. 1979, 71, 3761−3769. (10) Swope, W.; Schaefer III, H.; Yarkony, D. A Genealogical Electronic Coupling Procedure Incorporating the Hartree−Fock Interacting Space and Suitable for Degenerate Point Groups. Application to Excited States of BH3. J. Chem. Phys. 1980, 73, 407−415. (11) Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. A Computer Simulation Method for the Calculation of Equilibrium Constants for the Formation of Physical Clusters of Molecules: Application to Small Water Clusters. J. Chem. Phys. 1982, 76, 637−649. (12) Andrea, T. A.; Swope, W. C.; Andersen, H. C. The Role of Long Ranged Forces in Determining the Structure and Properties of Liquid Water. J. Chem. Phys. 1983, 79, 4576. (13) Swope, W. C.; Andersen, H. C. A Molecular Dynamics Method for Calculating the Solubility of Gases in Liquids and the Hydrophobic Hydration of Inert-Gas Atoms in Aqueous Solution. J. Phys. Chem. 1984, 88, 6548−6556. (14) Swope, W. C.; Andersen, H. C. 106-Particle MolecularDynamics Study of Homogeneous Nucleation of Crystals in a Supercooled Atomic Liquid. Phys. Rev. B 1990, 41, 7042. (15) Ferguson, D. M.; Pearlman, D. A.; Swope, W. C.; Kollman, P. A. Free Energy Perturbation Calculations © 2014 William C. Swope
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Involving Potential Function Changes. J. Comput. Chem. 1992, 13, 362−370. Olson, R. W.; Swope, W. C. Laser Drilling with Focused Gaussian Beams. J. Appl. Phys. 1992, 72, 3686−3696. Swope, W. C.; Ferguson, D. M. Alternative Expressions for Energies and Forces due to Angle Bending and Torsional Energy. J. Comput. Chem. 1992, 13, 585−594. Swope, W. C.; Andersen, H. C. Thermodynamics, Statistical Thermodynamics, and Computer Simulation of Crystals with Vacancies and Interstitials. Phys. Rev. A 1992, 46, 4539. Spellmeyer, D. C.; Swope, W. C. The Effect of Workstation Technology on Methods in Drug Design and Discovery. Perspect. Drug Discovery Des. 1993, 1, 359−370. Swope, W. C.; Andersen, H. C. A Computer Simulation Method for the Calculation of Chemical Potentials of Liquids and Solids Using the Bicanonical Ensemble. J. Chem. Phys. 1995, 102, 2851−2863. Bagchi, K.; Andersen, H. C.; Swope, W. Computer Simulation Study of the Melting Transition in Two Dimensions. Phys. Rev. Lett. 1996, 76, 255. Bagchi, K.; Andersen, H. C.; Swope, W. Observation of a Two-Stage Melting Transition in Two Dimensions. Phys. Rev. E 1996, 53, 3794. Haas, L. M.; Kodali, P.; Rice, J. E.; Schwarz, P. M.; Swope, W. C. Integrating Life Sciences Data-with a Little Garlic. In Bio-Informatics and Biomedical Engineering, 2000. Proceedings. IEEE International Symposium on; IEEE, 2000; pp. 5−12. Allen, F.; Almasi, G.; Andreoni, W.; Beece, D.; Berne, B. J.; Bright, A.; Brunheroto, J.; Cascaval, C.; Castanos, J.; Coteus, P.; Crumley, P.; Curioni, A.; Denneau, D.; Donath, W.; Eleftheriou, M.; Fitch, B.; Fleischer, B.; Georgiou, C. J.; Germain, R.; Giampapa, M.; Gresh, D.; Gupta, M.; Haring, R.; Ho, H.; Hochschild, P.; Hummel, S.; Jonas, T.; Lieber, D.; Martyna, G.; Maturu, K.; Moreira, J.; Newns, D.; Newton, M.; Philhower, R.; Picunko, P.; Pitera, J.; Pitman, M.; Rand, R.; Royyuru, A.; Salapura, V.; Sanomiya, A.; Shah, R.; Sham, Y.; Singh, S.; Snir, M.; Suits, F.; Swetz, R.; Swope, W. C.; Vishnumurthy, N.; Ward, T. J. C.; Warren, H.; Zhou, R. Blue Gene: A Vision for Protein Science Using a Petaflop Supercomputer. IBM Syst. J. 2001, 40, 310−327. Haas, L. M.; Schwarz, P. M.; Kodali, P.; Kotlar, E.; Rice, J. E.; Swope, W. C. DiscoveryLink: A System for Integrated Access to Life Sciences Data Sources. IBM Syst. J. 2001, 40, 489−511. Pitman, M. C.; Huber, W. K.; Horn, H.; Krämer, A.; Rice, J. E.; Swope, W. C. FLASHFLOOD: A 3D FieldBased Similarity Search and Alignment Method for
Special Issue: William C. Swope Festschrift Published: June 19, 2014 6365
dx.doi.org/10.1021/jp5024394 | J. Phys. Chem. B 2014, 118, 6365−6367
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Special Issue Preface
Flexible Molecules. J. Comput.-Aided Mol. Des. 2001, 15, 587−612. Swope, W. C.; Coffin, J. M.; Robson, B. Deep Computing for the Life Sciences-Preface. IBM J. Res. Dev. 2001, 45, 363−365. Swope, W. C. Deep Computing for the Life Sciences. IBM Syst. J. 2001, 40, 248−262. Bays, A. R.; Haas, L. M.; Horn, H. W.; Rice, J. E.; Schwarz, P. M.; Swope, W. C. Method and System for Organizing an Annotation Structure and for Querying Data and Annotations; US Patent 6,519,603, 2003. Fitch, B. G.; Germain, R. S.; Mendell, M.; Pitera, J.; Pitman, M.; Rayshubskiy, A.; Sham, Y.; Suits, F.; Swope, W.; Ward, T. C.; Zhestkov, Y; Zhou, R. Blue Matter, an Application Framework for Molecular Simulation on Blue Gene. J. Parallel Distrib. Comput. 2003, 63, 759− 773. Pitera, J. W.; Swope, W. Understanding Folding and Design: Replica-Exchange Simulations of “Trp-Cage” Miniproteins. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7587−7592. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins. J. Chem. Phys. 2003, 119, 5740−5761. Chodera, J. D.; Dill, K. A.; Swope, W. C.; Pitera, J. W. Constructing Master Equation Models of Peptide Dynamics from Molecular Dynamics Simulations. I. Simple Solvated Systems. 2004. Cragun, B.; Rice, J.; Schwarz, P.; Swope, W.; Tran, H.; others. Heterogeneous Indexing for Annotation Systems; WO Patent 2,004,114,148, 2004. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an Improved Four-Site Water Model for Biomolecular Simulations: TIP4P-Ew. J. Chem. Phys. 2004, 120, 9665− 9678. Swope, W. C.; Pitera, J. W.; Suits, F. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory. J. Phys. Chem. B 2004, 108, 6571−6581. Swope, W. C.; Pitera, J. W.; Suits, F.; Pitman, M.; Eleftheriou, M.; Fitch, B. G.; Germain, R. S.; Rayshubski, A.; Ward, T. C.; Zhestkov, Y.; Zhou, R. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide. J. Phys. Chem. B 2004, 108, 6582−6594. Yang, W. Y.; Pitera, J. W.; Swope, W. C.; Gruebele, M. Heterogeneous Folding of the Trpzip Hairpin: Full Atom Simulation and Experiment. J. Mol. Biol. 2004, 336, 241− 251. Enenkel, R. F.; Fitch, B. G.; Germain, R. S.; Gustavson, F. G.; Martin, A.; Mendell, M.; Pitera, J. W.; Pitman, M.; Rayshubskiy, A.; Suits, F.; Swope, W; Ward, T. J. C. Custom Math Functions for Molecular Dynamics. IBM J. Res. Dev. 2005, 49, 465−474. Horn, H. W.; Swope, W. C.; Pitera, J. W. Characterization of the TIP4P-Ew Water Model: Vapor Pressure and Boiling Point. J. Chem. Phys. 2005, 123, 194504. Suits, F.; Pitman, M.; Pitera, J. W.; Swope, W. C.; Germain, R. S. Overview of Molecular Dynamics
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Techniques and Early Scientific Results from the Blue Gene Project. IBM J. Res. Dev. 2005, 49, 475−487. Bays, A. R.; Haas, L. M.; Horn, H. W.; Rice, J. E.; Schwarz, P. M.; Swope, W. C. System for Organizing an Annotation Structure and for Querying Data and Annotations; US Patent 7,013,307, 2006. Chodera, J. D.; Swope, W. C.; Pitera, J. W.; Dill, K. A. Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations. Multiscale Model. Simul. 2006, 5, 1214−1226. Chong, L. T.; Swope, W. C.; Pitera, J. W.; Pande, V. S. Kinetic Computational Alanine Scanning: Application to p53 Oligomerization. J. Mol. Biol. 2006, 357, 1039−1049. Fitch, B. G.; Rayshubskiy, A.; Eleftheriou, M.; Ward, T. C.; Giampapa, M.; Zhestkov, Y.; Pitman, M. C.; Suits, F.; Grossfield, A.; Pitera, J.; Swope, W.; Zhou, R.; Feller, S.; Germain, R. S. Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L. In Computational Science− ICCS 2006; Springer, 2006; pp. 846−854. Larios, E.; Pitera, J. W.; Swope, W. C.; Gruebele, M. Correlation of Early Orientational Ordering of Engineered λ6−85 Structure with Kinetics and Thermodynamics. Chem. Phys. 2006, 323, 45−53. Pitera, J. W.; Haque, I.; Swope, W. C. Absence of Reptation in the High-Temperature Folding of the trpzip2 β-Hairpin Peptide. J. Chem. Phys. 2006, 124, 141102. Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics. J. Chem. Phys. 2007, 126, 155101. Srinivas, G.; Swope, W. C.; Pitera, J. W. Interfacial Fluctuations of Block Copolymers: A Coarse-Grain Molecular Dynamics Simulation Study. J. Phys. Chem. B 2007, 111, 13734−13742. Chuma, A.; Horn, H. W.; Swope, W. C.; Pratt, R. C.; Zhang, L.; Lohmeijer, B. G.; Wade, C. G.; Waymouth, R. M.; Hedrick, J. L.; Rice, J. E. The Reaction Mechanism for the Organocatalytic Ring-Opening Polymerization of L-Lactide Using a Guanidine-Based Catalyst: HydrogenBonded or Covalently Bound? J. Am. Chem. Soc. 2008, 130, 6749−6754. Fitch, B. G.; Rayshubskiy, A.; Eleftheriou, M.; Ward, T.; Giampapa, M.; Pitman, M. C.; Pitera, J.; Swope, W. C.; Germain, R. S. Blue Matter: Scaling of N-Body Simulations to One Atom per Node. IBM J. Res. Dev. 2008, 52, 145−158. Fitch, G. G.; Rayshubskiy, A.; Eleftheriou, M.; Ward, T.; Giampapa, M.; Pitman, M. C.; Pitera, J.; Swope, W. C.; Germain, R. S. Blue Matter: Scaling of N-Body Simulations to One Atom per Node. Curr. Top. Membr. 2008, 60, 159−180. Pitera, J. W.; Swope, W. C.; Abraham, F. F. Observation of Noncooperative Folding Thermodynamics in Simulations of 1BBL. Biophys. J. 2008, 94, 4837−4846. Chong, L. T.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Comparison of Computational Approaches for Predicting the Effects of Missense Mutations on p53 Function. J. Mol. Graphics Modell. 2009, 27, 978−982. Swope, W. C.; Horn, H. W.; Rice, J. E. Accounting for Polarization Cost When Using Fixed Charge Force dx.doi.org/10.1021/jp5024394 | J. Phys. Chem. B 2014, 118, 6365−6367
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Fields. I. Method for Computing Energy. J. Phys. Chem. B 2010, 114, 8621−8630. Swope, W. C.; Horn, H. W.; Rice, J. E. Accounting for Polarization Cost When Using Fixed Charge Force Fields. II. Method and Application for Computing Effect of Polarization Cost on Free Energy of Hydration. J. Phys. Chem. B 2010, 114, 8631−8645. Chodera, J. D.; Elms, P. J.; Swope, W. C.; Prinz, J.-H.; Marqusee, S.; Bustamante, C.; Noé, F.; Pande, V. S. A Robust Approach to Estimating Rates from TimeCorrelation Functions. ArXiv Prepr. ArXiv11082304 2011. Chodera, J. D.; Swope, W. C.; Noé, F.; Prinz, J.-H.; Shirts, M. R.; Pande, V. S. Dynamical Reweighting: Improved Estimates of Dynamical Properties from Simulations at Multiple Temperatures. J. Chem. Phys. 2011, 134, 244107. Pitman, M. C.; Fitch, B. G.; Horn, H. W.; Huber, W.; Rice, J. E.; Swope, W. C.; others. Field-Based Similarity Search System and Method; US Patent 8,014,990, 2011. Prigozhin, M. B.; Sarkar, K.; Law, D.; Swope, W. C.; Gruebele, M.; Pitera, J. Reducing Lambda Repressor to the Core. J. Phys. Chem. B 2011, 115, 2090−2096. Prinz, J.-H.; Chodera, J. D.; Pande, V. S.; Swope, W. C.; Smith, J. C.; Noé, F. Optimal Use of Data in Parallel Tempering Simulations for the Construction of DiscreteState Markov Models of Biomolecular Dynamics. J. Chem. Phys. 2011, 134, 244108. Appel, E. A.; Lee, V. Y.; Nguyen, T. T.; McNeil, M.; Nederberg, F.; Hedrick, J. L.; Swope, W. C.; Rice, J. E.; Miller, R. D.; Sly, J. Toward Biodegradable Nanogel Star Polymers via Organocatalytic ROP. Chem. Commun. 2012, 48, 6163−6165. Fitch, B. G.; Horn, H. W.; Huber, W.; Pitman, M. C.; Rice, J. E.; Swope, W. C. Field-Based Similarity Search System and Method; US Patent 8,306,755, 2012. Mobley, D. L.; Liu, S.; Cerutti, D. S.; Swope, W. C.; Rice, J. E. Alchemical Prediction of Hydration Free Energies for SAMPL. J. Comput.-Aided Mol. Des. 2012, 26, 551− 562. Swope, W. C.; Carr, A. C.; Parker, A. J.; Sly, J.; Miller, R. D.; Rice, J. E. Molecular Dynamics Simulations of Star Polymeric Molecules with Diblock Arms, a Comparative Study. J. Chem. Theory Comput. 2012, 8, 3733−3749. Vosmeer, C. R.; Rustenburg, A. S.; Rice, J. E.; Horn, H. W.; Swope, W. C.; Geerke, D. P. QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation. J. Chem. Theory Comput. 2012, 8, 3839−3853. Cerutti, D. S.; Rice, J. E.; Swope, W. C.; Case, D. A. Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization. J. Phys. Chem. B 2013, 117, 2328−2338. Pitman, M. C.; Fitch, B. G.; Horn, H. W.; Huber, W.; Rice, J. E.; Swope, W. C. Field-Based Similarity Search System and Method; US Patent 20,130,036,120, 2013.
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