Among the greatest challenges for molecular simulation are the limited time and spatial scales that can be afforded using the current computer technology and simulation algorithms, especially when applied to complex biochemical problems. The goals of our research are to greatly expand the territory accessible to molecular simulation by circumventing these constraints and to develop an atom-based approach that can be used as a practical tool to provide important molecular-level information for long time-scale events of chemical, biological, and environmental interest. This research direction is fueled by our recent development of an aggregation-volume-bias Monte Carlo based technique that led to a series of successful studies of rare vapor-liquid nucleation events. Given that nucleation can be viewed as a common theme between the long time-scale events involved in phase transitions and those occurring in a broad range of biochemical systems (such as self-assembly and folding) due to the strong resemblance of their thermodynamic and kinetic characteristics, we see an opportunity to extend the methodology developed here to a wide range of challenging long time-scale problems. Some of this work has been featured as cover-pages of both June 14, 2007 and January 28, 2008 issues of Physical Chemistry Chemical Physics, and both June 18, 2009 and September 2, 2010 issues of Journal of Physical Chemistry C.
T.D. Loeffler, D.E. Henderson, and B. Chen. Vapor-liquid nucleation in two dimensions: An intriguing sign switch of the errors of the classical nucleation theory. J. Chem. Phys., 2012, submitted for publication.
S.J. Keasler, H. Kim, and B. Chen. Sign preference in ion-induced nucleation: Contributions to the free energy barrier. J. Chem. Phys., 2012, accepted for publication.
S.J. Keasler, H. Kim, and B. Chen. Ion-induced nucleation: Importance of ionic polarizability. J. Phys. Chem. A, 2010, 114, 4595-4600.
R.B. Nellas, S.J. Keasler, J.I. Siepmann, and B. Chen. Exploring the discrepancies between experiment, theory, and simulation for the homogeneous gas-to-liquid nucleation of 1-pentanol. J. Chem. Phys., 2010, 132, 164517.
M.J. McGrath, J.N. Ghogomu, T.T. Narcisse, J.I. Siepmann, B. Chen, I. Napari, and H. Vahkamäki. Vapor–liquid nucleation of argon: Exploration of various intermolecular potentials. J. Chem. Phys., 2010, 133, 084106.
C.D. Wick, B. Chen, and K.T. Valsaraj. Computational investigation of the influence of surfactants on the air-water interfacial behavior of polycyclic aromatic hydrocarbons. J. Phys. Chem. C, 2010, 114, 14520-14527.
J. Gao, R. Ding, Y. Liu, B. Chen, X. Cui, and J.I. Siepmann. Web-based visualization and analysis of atmospheric nucleation processes. International Journal of u- and e- Service, Science and Technology , 2009, 2, art. 3.
S.M. Kathmann, G.K. Schenter, B.C. Garrett, B. Chen, and J.I. Siepmann. Thermodynamics and Kinetics of Nanoclusters Controlling Gas-to-Particle Nucleation. J. Phys. Chem. C, 2009, 113, 10354-10370.
B. Chen, R.B. Nellas, and S.J. Keasler. Fractal aggregates in protein crystal nucleation. J. Phys. Chem. B, 2008, 112, 4725-4730.
R.B. Nellas, S.J. Keasler, and B. Chen. Molecular content and structure of aqueous organic nanodroplets from the vapor-liquid nucleation study of the water/n-nonane/1-alcohol series. J. Phys. Chem. A, 2008, 112, 2930-2939
R.B. Nellas and B. Chen. Towards understanding the nucleation mechanism for multi-component systems: An atomistic simulation of the ternary nucleation of water/n-nonane/1-butanol. Phys. Chem. Chem. Phys., 2008, 10, 506-514
B. Chen, H. Kim, S.J. Keasler, and R.B. Nellas. An aggregation-volume-bias Monte Carlo investigation on the condensation of a Lennard-Jones vapor and crystal nucleation in cluster systems: An in-depth evaluation of the classical nucleation theory. J. Phys. Chem. B, 2008, 112, 4067-4078
R.B. Nellas, B. Chen, and J.I. Siepmann. Dumbbells and Onions in Ternary Nucleation. Phys. Chem. Chem. Phys., 2007, 9, 2779-2781
B. Chen and J.I. Siepmann. Microscopic structure and solvation in dry and wet octanol. Journal of Physical Chemistry B, 2006, 110, 3555-3563
Ling Zhang, Jake L. Rafferty, J.Ilja Siepmann, Bin Chen and Mark R. Schure. Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations. J. Chromatogr. A, 2006, 1126, 219-231
S.J. Keasler, R.B. Nellas, and B. Chen. Water mediated attraction between repulsive ions - A cluster-based simulation approach. J. Chem. Phys., 2006, 125, 144520
J.Q. Wei, H.W. Zhu, Y.H. Li, B. Chen, Y. Jia, K.L. Wang, Z.C. Wang, W.J. Liu, J.B. Luo, M.X. Zheng, D.H. Wu, Y.Q. Zhu, and B.Q. Wei. Ultrathin single-layered membranes from double-walled carbon nanotubes. Adv. Mater., 2006, 18, 1695-1700
Ricky B. Nellas, Matthew E. McKenzie, and Bin Chen. Probing the nucleation mechanism for the binary n-nonane/1-alcohol series with atomistic simulations. J. Phys. Chem. B, 2006, 110, ASAP article
M.E. McKenzie and B. Chen. Unravelling the peculiar nucleation mechanisms for non-ideal binary mixtures with atomistic simulations. J. Phys. Chem. B, 2006, 110, 3511-3516
Y.A. Mantz, B. Chen, and G.J. Martyna. Structural correlation and motifs in liquid water at selected temperatures: Ab initio and empirical model predictions. Journal of Physical Chemistry B, 2006, 110, 3540-3554
I.-F.W. Kuo, C.J. Mundy, B.L. Eggimann, M.J. McGrath, J.I. Siepmann, B. Chen, J. Vieceli, and D.J. Tobias. Structure and dynamics of the aqueous liquid-vapor interface: A comprehensive particle-based simulation study. Journal of Physical Chemistry B, 2006, 110, 3738-3746
I. Ivanov, B. Chen, S. Raugei, and M.L. Klein. Relative pKa values from first principles molecular dynamics: The case of histidine deprotonation. Journal of Physical Chemistry B, 2006, 110, 6365-6371
Y.A. Mantz, B. Chen, and G.J. Martyna. Temperature-dependent water structure: Ab initio and empirical model predictions. Chem. Phys. Lett., 2005, 405, 294-299
B. Chen, J.I. Siepmann, and M.L. Klein. Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volume-bias Monte Carlo investigation for fixed-charge and polarizable models. J. Phys. Chem. A, 2005, 109, 1137-1145
X.S. Zhao, B. Chen, S. Karaborni, and J.I. Siepmann. Vapor-liquid and vapor-solid phase equilibria for united-atom benzene models and their triple points: The importance of quadrupolar interactions. J. Phys. Chem. B, 2005, 109, 5368-5374
R.J. Doerksen, B. Chen, D. Liu, G. Tew, W.F. DeGrado, and M.L. Klein. Controlling the conformation of arylamides: Computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers. Chem. Eur. J., 2004, 10, 5008-5016
I.-F.W. Kuo, C.J. Mundy, M.J. McGrath, J.I. Siepmann, J. VandeVondele, M. Sprik, J. Hutter, B. Chen, M.L. Klein, F. Mohamed, M. Krack, and M. Parrinello. Liquid water from first principle: Validation of different sampling approaches. J. Phys. Chem. B, 2004, 108, 12990-12998
D. Liu, S. Choi, B. Chen, R.J. Doerksen, D.J. Clements, J.D. Winkler, M.L. Klein, and W.F. DeGrado. Nontoxic membrane-active antimicrobial arylamide oligomers. Ang. Chem. Int. Ed., 2004, 43, 1158-1162
B. Chen, I. Ivanov, M.L. Klein, and M. Parrinello. Hydrogen bonding in water. Phys. Rev. Lett., 2003, 91, 215503
B. Chen, J. I. Siepmann, and M. L. Klein. Simulating the nucleation of water/ethanol and water/n-nonane mixtures: Mutual enhancement and two-pathway nucleation. J. Am. Chem. Soc., 2003, 125, 3113-3118
B. Chen, J.I. Siepmann, S. Karaborni, and M.L. Klein. Vapor-liquid and vapor-solid phase equilibria of fullerenes: The role of the potential shape on the triple point. J. Phys. Chem. B, 2003, 107, 12320-12323
R.J. Doerksen, B. Chen, J. Yuan, J.D. Winkler, and M. L. Klein. Novel conformationally-constrained beta-peptides characterized by 1H NMR chemical shifts. Chem. Comm., 2003, 20, 2534-2535
R.J. Doerksen, B. Chen, and M.L. Klein. Intramolecular hydrogen bonds: Ab initio Car-Parrinello simulations of arylamide torsion. Chem. Phys. Lett., 2003, 380, 150-157
G. Tew, D. Liu, B. Chen, R.J. Doerksen, J. Kaplan, P.J. Carroll, M.L. Klein, and W.F. DeGrado. De novo design of biomimetic antimicrobial polymers. Proc. Natl. Acad. Sci., 2002, 99, 5110-5114
B. Chen, I. Ivanov, J.M. Park, M. Parrinello, and M.L. Klein. Solvation structure and mobility mechanism of OH-: A Car-Parrinello molecular dynamics investigation of alkaline solutions. J. Phys. Chem. B, 2002, 106, 12006-12016
B. Chen, J.I. Siepmann, K.J. Oh, and M.L. Klein. Simulating vapor-liquid nucleation of n-alkanes. J. Chem. Phys., 2002, 116, 4317-4329
B. Chen, J.M. Park, I. Ivanov, G. Tabacchi, M.L. Klein, and M. Parrinello. First principles study of aqueous hydroxide solutions. J. Am. Chem. Soc., 2002, 124, 8534-8535
B. Chen, J.I. Siepmann, and M.L. Klein. Vapor-liquid interfacial properties of mutually saturated water/1-butanol solutions. J. Am. Chem. Soc., 2002, 124, 12232-12237
B. Chen, J.J. Potoff, and J.I. Siepmann. Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of primary, secondary and tertiary alcohols. J. Phys. Chem. B, 2001, 105, 3093--3104
B. Chen, J.I. Siepmann, K.J. Oh, and M.L. Klein. Aggregation-volume-bias Monte Carlo simulations of vapor-liquid nucleation barriers for Lennard-Jonesium. J. Chem. Phys., 2001, 115, 10903-10913
B. Chen, J.I. Siepmann, and M.L. Klein. Direct Gibbs ensemble Monte Carlo simulations for solid-vapor phase equilibria: Applications to Lennard-Jonesium and carbon dioxide. J. Phys. Chem. B, 2001, 105, 9840-9848
B. Chen and J.I. Siepmann. Improving the efficiency of the aggregation-volume-bias Monte Carlo algorithm. J. Phys. Chem. B, 2001, 105, 11275-11282
B. Chen, J.J. Potoff, and J.I. Siepmann. Adiabatic nuclear and electronic sampling Monte Carlo simulations in the Gibbs ensemble: Application to polarizable force fields for water. J. Phys. Chem. B, 2000, 104, 2378-2390
B. Chen and J.I. Siepmann. A novel Monte Carlo algorithm for simulating strongly associating fluids: Applications to water, hydrogen fluoride, and acetic acid. J. Phys. Chem. B, 2000, 104, 8725-8734
B. Chen, J. Xing, and J.I. Siepmann. Development of polarizable water force fields for phase equilibrium calculations. J. Phys. Chem. B, 2000, 104, 2415-2423
B. Chen and J.I. Siepmann. Partitioning of alkane and alcohol solutes between water and (dry or wet) 1-octanol. J. Am. Chem. Soc., 2000, 122, 6464-6467