Bin Chen
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, ‘’, J. Phys. Chem. B 119, 9068-9075 (2015).
A. Sepehri, T.D. Loeffler, and B. Chen, ‘’, J. Chem. Phys. 141, 074102 (2014).
H. Kim, S.J. Keasler, and B. Chen, ‘’, J. Phys. Chem. B 118, 6875-6884 (2014).
T.D. Loeffler and B. Chen, ’, J. Chem. Phys. 139, 234707 (2013).
T.D. Loeffler, D.E. Henderson, and B. Chen, ’, J. Chem. Phys. 137, 194304 (2012).
S.J. Keasler, H. Kim, and B. Chen, ‘’, J. Chem. Phys. 137, 174308 (2012).
S.J. Keasler, H. Kim, and B. Chen, ‘’, 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, ‘’, J. Chem. Phys. 133, 084106 (2010).
C.D. Wick, B. Chen, and K.T. Valsaraj, ’, 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, ‘’, 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, ’, 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, ‘’, 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,, 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, ‘’, Chem. Phys. Lett. 405, 294-299 (2005).
B. Chen, J.I. Siepmann, and M.L. Klein, ‘’, 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, ‘’, 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, ‘’, Chem. Comm. 20, 2534-2535 (2003).
R.J. Doerksen, B. Chen, and M.L. Klein, ‘, 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, ‘’, 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, ‘’, 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, ‘’, 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, ‘’, J. Phys. Chem. B 104, 2391-2401 (2000).
M.G. Martin, B. Chen, and J.I. Siepmann, ‘’, J. Phys. Chem. B 104, 2415-2423 (2000).
B. Chen and J.I. Siepmann, ‘’, J. Am. Chem. Soc. 122, 6464-6467 (2000).
B. Chen and J.I. Siepmann, ‘’, J. Phys. Chem. B 104, 8725-8734 (2000).
M.G. Martin, N.D. Zhuravlev, B. Chen, P.W. Carr, and J.I. Siepmann, ‘’, J. Phys. Chem. B 103, 2977-2980 (1999).
B. Chen and J.I. Siepmann, ’, J. Phys. Chem. B 103, 5370-5379 (1999).
B. Chen and J.I. Siepmann, ‘’, Theo. Chem. Acc. 103, 87-104 (1999).
M.G. Martin, B. Chen, and J.I. Siepmann, ‘’, J. Chem. Phys. 108, 3383-3385 (1998).
B. Chen, M.G. Martin, and J.I. Siepmann, ‘’, J. Phys. Chem. B 102, 2578-2586 (1998).