Bin Chen

Bin Chen

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Bachelor's Degree(s): Peking University, 1996
PhD: University of Minnesota, 2001
PostDoc: University of Pennsylvania, 2001-2003

 

Area of Interest

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.

Selected Publications

T.D. Loeffler, A. Sepehri, and B. Chen, ‘An improved Monte Carlo scheme for efficient particle transfer in heterogeneous systems in the grand canonical ensemble: Application to vapor-liquid nucleation’, J. Chem. Theory Comput., accepted for publication (2015).

R. Kumar, C. Knight, C.D. Wick, and B. Chen, ‘Bringing reactivity to the aggregation-volume-bias Monte Carlo based simulation framework: Water nucleation induced by a reactive proton’, J. Phys. Chem. B 119, 9068-9075 (2015).

A. Sepehri, T.D. Loeffler, and B. Chen, ‘Improving the efficiency of configurational-bias Monte Carlo: A density-guided method for generating bending angle trials for linear and branched molecules’, J. Chem. Phys. 141, 074102 (2014).

H. Kim, S.J. Keasler, and B. Chen, ‘A nucleation-based approach to the study of hydrophobic interactions under confinement: Enhanced hydrophobic interactions driven by energetic contributions’, J. Phys. Chem. B 118, 6875-6884 (2014).

T.D. Loeffler and B. Chen, ‘Surface induced nucleation of a Lennard-Jones system on an implicit surface at sub-freezing temperatures: A comparison with the classical nucleation theory’, J. Chem. Phys. 139, 234707 (2013).

T.D. Loeffler, D.E. Henderson, and B. Chen, ‘Vapor-liquid nucleation in two dimensions: On the intriguing sign switch of the errors of the classical nucleation theory’, J. Chem. Phys. 137, 194304 (2012).

S.J. Keasler, H. Kim, and B. Chen, ‘Sign preference in ion-induced nucleation: Contributions to the free energy barrier’, J. Chem. Phys. 137, 174308 (2012).

S.J. Keasler, H. Kim, and B. Chen, ‘Ion-induced nucleation: Importance of ionic polarizability’, J. Phys. Chem. A 114, 4595-4600 (2010).

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. 132, 164517 (2010).

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. 133, 084106 (2010).

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 114, 14520-14527 (2010).

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 2, art. 3 (2009).

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 113, 10354-10370 (2009).

B. Chen, R.B. Nellas, and S.J. Keasler, ‘Fractal aggregates in protein crystal nucleation’, J. Phys. Chem. B 112, 4725-4730 (2008). 

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 112, 2930-2939 (2008).

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. 10, 506-514 (2008).

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 112, 4067-4078 (2008).

R.B. Nellas, B. Chen, and J.I. Siepmann, ‘Dumbbells and Onions in Ternary Nucleation’, Phys. Chem. Chem. Phys. 9, 2779-2781 (2007).

B. Chen and J.I. Siepmann, ‘Microscopic structure and solvation in dry and wet octanol’, J. Phys. Chem. B 110, 3555-3563 (2006).

L. Zhang, J.L. Rafferty, J.I. Siepmann, B. Chen and M.R. Schure, ‘Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations’, J. Chromatogr. A 1126, 219-231 (2006).

S.J. Keasler, R.B. Nellas, and B. Chen, ‘Water mediated attraction between repulsive ions - A cluster-based simulation approach’, J. Chem. Phys. 125, 144520 (2006).

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. 18, 1695-1700 (2006).

R.B. Nellas, M.E. McKenzie, and B. Chen, ‘Probing the nucleation mechanism for the binary n-nonane/1-alcohol series with atomistic simulations’, J. Phys. Chem. B 110, 18619-18628 (2006).

M.E. McKenzie and B. Chen, ‘Unravelling the peculiar nucleation mechanisms for non-ideal binary mixtures with atomistic simulations’, J. Phys. Chem. B 110, 3511-3516 (2006).

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’, J. Phys. Chem. B 110, 3540-3554 (2006).

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’, J. Phys. Chem. B 110, 3738-3746 (2006).

I. Ivanov, B. Chen, S. Raugei, and M.L. Klein, ‘Relative pKa values from first principles molecular dynamics: The case of histidine deprotonation’, J. Phys. Chem. B 110, 6365-6371 (2006).

Y.A. Mantz, B. Chen, and G.J. Martyna, ‘Temperature-dependent water structure: Ab initio and empirical model predictions’, Chem. Phys. Lett. 405, 294-299 (2005).

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 109, 1137-1145 (2005).

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 109, 5368-5374 (2005).

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. 10, 5008-5016 (2004).

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 108, 12990-12998 (2004).

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. 43, 1158-1162 (2004).

B. Chen, I. Ivanov, M.L. Klein, and M. Parrinello, ‘Hydrogen bonding in water’, Phys. Rev. Lett. 91, 215503 (2003).

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. 125, 3113-3118 (2003).

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 107, 12320-12323 (2003).

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. 20, 2534-2535 (2003).

R.J. Doerksen, B. Chen, and M.L. Klein, ‘Intramolecular hydrogen bonds: Ab initio Car-Parrinello simulations of arylamide torsion’, Chem. Phys. Lett. 380, 150-157 (2003).

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. 99, 5110-5114 (2002).

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 106, 12006-12016 (2002).

B. Chen, J.I. Siepmann, K.J. Oh, and M.L. Klein, ‘Simulating vapor-liquid nucleation of n-alkanes’, J. Chem. Phys. 116, 4317-4329 (2002).

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. 124, 8534-8535 (2002).

B. Chen, J.I. Siepmann, and M.L. Klein, ‘Vapor-liquid interfacial properties of mutually saturated water/1-butanol solutions’, J. Am. Chem. Soc. 124, 12232-12237 (2002).

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 105, 3093-3104 (2001).

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. 115, 10903-10913 (2001).

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 105, 9840-9848 (2001).

B. Chen and J.I. Siepmann, ‘Improving the efficiency of the aggregation-volume-bias Monte Carlo algorithm’, J. Phys. Chem. B 105, 11275-11282 (2001).

J.M. Stubbs, B. Chen, J.J. Potoff, and J.I. Siepmann, ‘Monte Carlo calculations for the phase equilibria of alkanes, alcohols, water, and their mixtures’, Fluid Phase Equilib. 183/184, 301-309 (2001).

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 104, 2378-2390 (2000).

B. Chen, J. Xing, and J.I. Siepmann, ‘Development of polarizable water force fields for phase equilibrium calculations’, J. Phys. Chem. B 104, 2391-2401 (2000).

M.G. Martin, B. Chen, and J.I. Siepmann, ‘Molecular structure and phase diagram of n-heptane in supercritical ethane: A Gibbs ensemble Monte Carlo study’, J. Phys. Chem. B 104, 2415-2423 (2000).

B. Chen and J.I. Siepmann, ‘Partitioning of alkane and alcohol solutes between water and (dry or wet) 1-octanol’, J. Am. Chem. Soc. 122, 6464-6467 (2000).

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 104, 8725-8734 (2000).

M.G. Martin, N.D. Zhuravlev, B. Chen, P.W. Carr, and J.I. Siepmann, ‘Origins of the solvent chain-length dependence of Gibbs free energies of transfer’, J. Phys. Chem. B 103, 2977-2980 (1999).

B. Chen and J.I. Siepmann, ‘Transferable potentials for phase equilibria. 3. Explicit-hydrogen description of n-alkanes’, J. Phys. Chem. B 103, 5370-5379 (1999).

B. Chen and J.I. Siepmann, ‘Monte Carlo algorithms for simulating systems with adiabatic separation of electronic and nuclear degrees of freedom’, Theo. Chem. Acc. 103, 87-104 (1999).

M.G. Martin, B. Chen, and J.I. Siepmann, ‘A novel Monte Carlo algorithm for polarizable force fields: Application to a fluctuating charge model for water’, J. Chem. Phys. 108, 3383-3385 (1998).

B. Chen, M.G. Martin, and J.I. Siepmann, ‘Thermodynamic properties of the Williams, OPLSAA and MMFF94 all-atom force fields for normal alkanes’, J. Phys. Chem. B 102, 2578-2586 (1998).