L. Y. Chen's Refereed publications

List 1 at NIH NCBI (up to date)

List 2 at PubMed

(past publications or preprints)

Thermodynamic integration in 3n dimensions without biases or alchemy for protein interactions, Chen LY. (2017) preprint in BioRxiv doi: 10.1101/150870

Affinity and path of binding xylopyranose unto E. coli xylose permease, Wambo TO, Chen LY, Phelix C, Perry G. (2017) BBRC DOI:10.1016/j.bbrc.2017.10.053

Elongation affinity, activation barrier, and stability of Abeta42 oligomers/fibrils in physiological saline, Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. (2017) BBRC DOI:10.1016/j.bbrc.2017.04.084

Computing Osmotic Permeabilities of Aquaporins AQP4, AQP5, and GlpF from Near-Equilibrium Simulations, Wambo TO, Rodriguez RA, Chen LY. (2017) BBA Biomem. DOI: 10.1016/j.bbamem.2017.04.022 . preprint in BioRxiv doi: 10.1101/102343

Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Villarreal OD, Yu L, Rodriguez RA, Chen LY. Biochemical and biophysical research communications. 2017; 483(1):203-208. DOI:10.1016/j.bbrc.2016.12.165

Molecular dynamics study of human carbonic anhydrase II in complex with Zn2 + and acetazolamide on the basis of all-atom force field simulations, Wambo TO, Chen LY, McHardy SF, Tsin AT. (2016) Biophysical Chemistry, DOI:10.1016/j.bpc.2016.05.006

1,3-Propanediol binds inside the water-conducting pore of aquaporin 4: Does this efficacious inhibitor have sufficient potency? Yu L, Villarreal OD, Chen LL, Chen LY, Journal of Systems and Integrative Neuroscience (2016) 2(1): 91-98. DOI: 10.1576/JSIN.1000117

1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins, Yu L, Rodriguez RA, Chen LL, Chen LY, Perry G, McHardy SF, Yeh CH. Protein Sci. (Journal of the Protein Society) (2016) 25(2): 433-441. DOI:10.1002/pro.2832

Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way to Reversibly Concentrate Functionalized Nanoparticles, Villarreal OD, Chen LY, Whetten RL, Demeler B. J. Phys. Chem. B (2015) DOI: 10.1021/acs.jpcb.5b09864

Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics, Rodriguez RA, Yu L, Chen LY. J Chem Theory Comput. (2015) DOI: 10.1021/acs.jctc.5b00340.

Hybrid steered molecular dynamics approach to computing the absolute binding free-energy of ligand-protein complexes---A brute force approach that is fast and accurate, L. Y. Chen, J. Chem. Theory Comput. (2015) DOI:10.1021/ct501162f.

Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin, L. Y. Chen, Biophysical Chemistry (2015) DOI: 10.1016/j.bpc.2015.01.004. Free PMC Article: PMC4339505 (Preprint: arXiv.org >Quantitative Biology > Subcellular Processes)

Computing membrane-AQP5-phosphatidylserine binding affinities, L. Y. Chen, Molecular Membrane Biology (2015) DOI: 10.3109/09687688.2015.1006275.

Ligandâmodulated interactions between charged monolayerâprotected Au144(SR)60 gold nanoparticles in physiological saline, DOI:10.1039/C4CP05137H O. D. Villarreal, L. Y. Chen, R. L. Whetten, and M. J. Yacaman, Phys. Chem. Chem. Phys. (2015).

Does Plasmodium falciparum have an Achilles's heel? L. Y. Chen, Malaria Chemotherapy, Control, and Elimination

Interaction between functionalized gold nanoparticles in physiological saline, S. A. Alsharif, L. Y. Chen, A. Tlahuice-Flores, R. L. Whetten, and M. J. Yacaman, Phys. Chem. Chem. Phys., DOI:10.1039/C3CP54503B (2014). PDF here SI here.

Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF, L. Y. Chen, BBA Biomembranes 1828, 1786 (2013). DOI: 10.1016/j.bbamem.2013.03.008.

Glycerol inhibits water permeation through Plasmodium falciparum aquaporin, L. Y. Chen, Journal of Structural Biology 181, 71-76 (2013) DOI:10.1016/j.jsb.2012.10.007.

In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid, Y. B. Zhang and L. Y. Chen, Biophysical Chemistry 171, 24-30 (2013) DOI: 10.1016/j.bpc.2012.09.004.

Mercury inhibits the L170C mutant of Aquaporin Z by making waters clog the water channel, Y. B. Zhang, Y. B. Cui, and L. Y. Chen, Biophysical Chemistry, 160, 69 (2012) DOI: 10.1016/j.bpc.2011.07.006.

Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z, G. Hu, L. Y. Chen, and J. Wang, Journal of Molecular Modeling, 18, 3731 (2012). DOI: 10.1007/s00894-012-1379-2.

Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles, Robert Renthal, Lorenzo Brancaleon, Isaac Pena, Frances Silva, and Liao Y. Chen, Biophysical Chemistry 159, 321 (2011) DOI:10.1016/j.bpc.2011.08.005.

Diffusion in periodic potentials with path integral hyperdynamics, T. Ikonen, M. D. Khandkar, L. Y. Chen, S. C. Ying, and T. Ala Nissila, Phys. Rev. E 84, 026703 (2011) . DOI: 10.1103/PhysRevE.84.026703.

Exploring the free-energy landscapes of biological systems with steered molecular dynamics, L. Y. Chen, Phys. Chem. Chem. Phys. 13, 6176 (2011) (PDF here). DOI: 10.1039/c0cp02799e.

Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation, G. Hu, Q. Zhang, and L. Y. Chen, Journal of Molecular Modeling 17, 1919-1926 (2011) DOI: 10.1007/s00894-010-0892-4.

In silico experiments of single-chain antibody fragment against drugs of abuse, G. D. Hu and L. Y. Chen, Biophysical Chemistry 153, 97 (2010) DOI:10.1016/j.bpc.2010.10.008.

Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations, L. Y. Chen, Biophysical Chemistry, 151, 178 (2010), DOI: 10.1016/j.bpc.2010.05.014.

Determination of equilibrium free-energy from non-equilibrium work measurements, L. Y. Chen, D. A. Bastien, and H. E. Espejel, Phys. Chem. Chem. Phys., 12, 6579 (2010), DOI:10.1039/B926889H.

Response to "Comments on 'On the Crooks fluctuation theorem and the Jarzynski equality' and "Non-equilibrium fluctuation-dissipation theorem of Brownian dynamics'", L. Y. Chen, Journal of Chemical Physics, 130, 107102 (2009).

Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics, L. Y. Chen, Journal of Chemical Physics, 129, 144113 (2008). doi: http://dx.doi.org/10.1063/1.2992153

On the Crooks fluctuation theorem and the Jarzynski equality, L. Y. Chen, Journal of Chemical Physics, 129, 091101 (2008).

Study of Lennard-Jones clusters: Effects of anharmonicities far from saddle points, L. Y. Chen and N. J. M. Horing, International Journal of High Speed Electronics and Systems, 18, 119 (2008).

An exact formulation of hyper-dynamics simulations with applications to enthalpic and entropic barriers, L. Y. Chen and N. J. M. Horing, Journal of Chemical Physics, 126, 224103 (2007).

Dielectric Response of a Planar Periodic Array of Polarizable Wires Parallel to an Interface with a Nonlocal Dynamic Plasma-like Medium, N. J. M. Horing, L. Y. Chen, and H. L. Cui, Physics Letters A, 361, 164 (2007). http://dx.doi.org/10.1016/j.physleta.2006.09.037

Inverse Dielectric Function of a Lateral Quantum Wire Superlattice Parallel to the Interface of a Plasma-Like Semiconductor, N. J. M. Horing and L. Y. Chen, Physical Review B 74, 195336 (2006).

Factorization of the constants of the motion, P. L. Nash and L. Y. Chen, Canadian Journal of Physics, 84, 717 (2006).

Transition rate prefactors for systems of many degrees of freedom, L. Y. Chen and N. J. M. Horing, Journal of Chemical Physics, 124, 164102 (2006).

Efficient transition path sampling for systems with multiple reaction pathways, L. Y. Chen, P. L. Nash, and N. J. M. Horing, Journal of Chemical Physics, 123, 094104 (2005).

Transient Brownian motion in response to a sudden temperature change, L. Y. Chen, International Journal of Modern Physics B 18, 02524 (2004).

Path integral approach to Brownian motion driven with an ac driving force, L. Y. Chen and P. L. Nash, Journal of Chemical Physics, 121, 3984 (2004).

Transient response of a Brownian particle with general damping, L. Y. Chen and P. L. Nash, Journal of Chemical Physics, 120, 3348 (2004).

Sampling transition path with a one point boundary scheme, L. Y. Chen and P. L. Nash, Journal of Chemical Physics, 119, 12749 (2003).

Magnetoimage effects in the van der Waals interaction of an atom and a bounded, dynamic, nonlocal plasmalike medium, N. J. M. Horing and L. Y. Chen, Physical Review A 66, 042905 (2002).

Brownian motion in a two dimensional potential: A new numerical solution method, L. Y. Chen, Int. J. Mod. Phys. B 16, 3643 (2002) .

Search for transition paths and evaluation of rate constants through accelerated Langevin dynamics, L. Y. Chen, S. C. Ying, and T. Ala-Nissila, Physical Review E 65, 42101 (2002).

Selective activation dynamics: A minimal path approach, L. Y. Chen, P. L. Nash, and S. C. Ying, in NATO Series: Collective surface diffusion coefficients under non-equilibrium conditions, eds. M. C. Tringides and Z. Chvoj, Kluwer, Dordrecht (2001).

Kramers problem revisited: A minimal path approximation to the Langevin equation, L. Y. Chen, Modern Physics Letters B 14, 975(2000).

Solution of the Langevin equation for rare event rates using a path-integral formalism, L. Y. Chen and S. C. Ying, Physical Review B60,16965 (1999). http://dx.doi.org/10.1103/PhysRevB.60.16965

Chaotic behavior in a dynamic system related to the stationary path of the path-integral for a Brownian particle in a double-well potential, L. Y. Chen, Modern Physics Letters B12, 1075 (1998).

Experimental and theoretical investigation of the microscopic vibrational and diffusional dynamics of sodium atoms on a Cu(001) surface, A. P. Graham, F. Hofmann, J. P. Toennies, L. Y. Chen, and S. C. Ying, Physical Review B56, 10567 (1997). http://dx.doi.org/10.1103/PhysRevB.56.10567

Determination of the Na/Cu(001) potential energy surface from Helium scattering studies of the surface dynamics, A. P. Graham, F. Hofmann, J. P. Toennies, L. Y. Chen, and S. C. Ying, Physical Review Letters 78, 3900 (1997). http://dx.doi.org/10.1103/PhysRevLett.78.3900

Efficient finite difference solutions to the time-dependent Schrodinger equation, P. L. Nash and L. Y. Chen, Journal of Computational Physics 130, 266 (1997).

Landauer approach to time-dependent transport, L. Y. Chen and P. L. Nash, Modern Physics Letters B11, 35 (1997).

Surface diffusion in the low friction limit: Occurrence of long jumps, L. Y. Chen, M. R. Baldan, and S. C. Ying, Physical Review B54, 8856 (1996). http://dx.doi.org/10.1103/PhysRevB.54.8856

Nonequilibrium Statistical Mechanics in mesoscopic systems, L. Y. Chen and P. L. Nash, in Thermal Field Theories and their Applications, Eds. Y. X. Gui, F. C. Khanna, and Z. B. Su, World Scientific (1996).

Diffusion of light adatoms on solid surfaces (brief review), L. Y. Chen and S. C. Ying, Modern Physics Letters B9, 307 (1995).

Shot noise suppression in quantum point contact systems, L. Y. Chen and S. C. Ying, Modern Physics Letters B9, 573 (1995).

Theory of surface diffusion: crossover from classical to quantum regime, L. Y. Chen and S. C. Ying, Physical Review Letters 73, 700 (1994). http://dx.doi.org/10.1103/PhysRevLett.73.700

Dynamics of adatoms on solid surfaces, L. Y. Chen and S. C. Ying, Physical Review B49, 13838 (1994). http://dx.doi.org/10.1103/PhysRevB.49.13838

Frequency response of mesoscopic conductors: a time dependent Landauer approach, L. Y. Chen and S. C. Ying, Journal of Physics: Condensed Matter 6, 5061 (1994).

Diffusive and frustrated translational modes of adsorbates on solid surfaces (brief review), L. Y. Chen and S. C. Ying, Modern Physics Letters B8, 843 (1994).

Diffusion and Vibration of adatoms on a solid surface, L. Y. Chen and S. C. Ying, Physical Review Letters 71, 4361 (1993). http://dx.doi.org/10.1103/PhysRevLett.71.4361

Vibrational lineshape and diffusion constant of adsorbed atoms, L. Y. Chen and S. C. Ying, Journal of Electronic Spectroscopy 64, 797 (1993).

Dynamic properties of sequential resonant tunneling systems, L. Y. Chen, Modern Physics Letters B 7, 1677 (1993).

Charge accumulation and frequency characteristics of sequential tunneling, L. Y. Chen, Physical Review B48, 4914 (1993). http://dx.doi.org/10.1103/PhysRevB.48.4914

Coherent vs sequential tunneling distinguished in the I-V characteristics of 3D double-barrier resonant-tunneling structures, L. Y. Chen and C. S. Ting, Modern Physics Letters B6, 1811 (1992).

Nonequilibrium Green's function approach to transport characteristics of resonant-tunneling double-barrier junctions, L. Y. Chen and C. S. Ting, International Journal Modern Physics B6, 1099 (1992).

Impurity resisitivity under thermalized condition, C. S. Ting, and L. Y. Chen, International Journal Modern Physics B6, 1079 (1992).

Noise characteristics of sequential tunneling of double-barrier systems, L. Y. Chen and C. S. Ting, Physical Review B46, 4714 (1992). http://dx.doi.org/10.1103/PhysRevB.46.4714

Coulomb staircase in the I-V characteristic of ultra-small double-barrier resonant-tunneling structures, L. Y. Chen and C. S. Ting, Physical Review B (Rapid Comm.) 44, 5916 (1991). http://dx.doi.org/10.1103/PhysRevB.44.5916

Quantum Effect on Shot Noise Suppression in Transport through Microstructures, L. Y. Chen, G. Levine, J. Yang, and C. S. Ting, Modern Physics Letters B5, 315 (1991).

Theoretical investigation of noise characteristics of a double barrier resonant tunneling system, L. Y. Chen and C. S. Ting, Physical Review B (Rapid Comm.) 43, 4534 (1991). http://dx.doi.org/10.1103/PhysRevB.43.4534

Dynamic Properties of Double Barrier Resonant Tunneling Structures, L. Y. Chen and C. S. Ting, Physical Review B43, 2097 (1991). http://dx.doi.org/10.1103/PhysRevB.43.2097

Closed Time Path Green's Function and Its Application in Transport Theory, Z. B. Su, L. Yu, and L. Y. Chen, in Thermal Field Theories and Their Applications, eds. H. Ezawa, T. Arimitsu and Y. Hashimoto, Elsevier, North Holland (1991).

L. Y. Chen, G. Levine, J. Yang and C. S. Ting, Compel-the International Journal for Computation and Mathematics in Electrical and Electronic Engineering 10 (4), 539-545 (1991).

Frequency response of double barrier resonant tunneling systems biased in the the negative differential resistance region (brief review), L. Y. Chen and C. S. Ting, Modern Physics Letters B 4, 1077 (1990).

ac conductance of a double barrier resonant tunneling system under a dc bias voltage, L. Y. Chen and C. S. Ting, Physical Review Letters 64, 3159 (1990). http://dx.doi.org/10.1103/PhysRevLett.64.3159

Consistent derivation of impurity resistivity from the force balance equation, L. Y. Chen, C. S. Ting, and N. J. M. Horing, Physical Review B42, 1129 (1990). http://dx.doi.org/10.1103/PhysRevB.42.1129

Path integral approach to transient transport of a double barrier resonant tunneling system, L. Y. Chen and C. S. Ting, Physical Review B41, 8533 (1990). http://dx.doi.org/10.1103/PhysRevB.41.8533

Adiabatic resistivity from the force balance equation, L. Y. Chen, C. S. Ting, and N. J. M. Horing, Solid State Commun. 73, 437 (1990).

Equivalence of quantum Boltzmann equation and Kubo formula for dc conductivity, L. Y. Chen and Z. B. Su, International Journal of Modern Physics B4, 293 (1990).

Quantum Boltzmann equation and Kubo formula for electronic transport in solids, L. Y. Chen and Z. B. Su, Physical Review B40, 9309 (1989). http://dx.doi.org/10.1103/PhysRevB.40.9309

Chu, X. L., Chen, L. Y., and Velarde, M. G. (1989). Two-Component Benard Steady Convection with Surface Adsorption. NATO ASI Series, 174, 343-356.

Effect of inelastic scattering on impurity resistivity, L. Y. Chen, C. S. Ting and N. J. M. Horing, Physical Review B40, 3756(1989). http://dx.doi.org/10.1103/PhysRevB.40.3756

Consistent treatment for single electron in thermal crystal with an applied electric field, Z. B. Su, L. Y. Chen, and C. S. Ting, Physical Review B38, 3866 (1988). http://dx.doi.org/10.1103/PhysRevB.38.3866

Consistent path integral study for a single electron in a thermal crystal with an applied electric field, Z. B. Su, L. Y. Chen, and C. S. Ting, Physical Review Letters 60, 2323 (1988). http://dx.doi.org/10.1103/PhysRevLett.60.2323

Influence functional and closed time path Green's function, Z. B. Su, L. Y. Chen, X. T. Yu and K. C. Chou, Physical Review B37, 9810 (1988). http://dx.doi.org/10.1103/PhysRevB.37.9810

Nonperturbative balance equation for the nonequilibrium electron-impurity-phonon system in an applied high electric field, Z. B. Su, L. Y. Chen and J. L. Birman, Physical Review B35, 9744 (1987). http://dx.doi.org/10.1103/PhysRevB.35.9744

Benard convective instability of a two-component fluid system with surface chemical reaction, L. Y. Chen and X. L. Chu, Commun. Theor. Phys. (Beijing), 8, 179 (1987).

Hydrodynamic stability of two-component fluid heated from below with surface adsorption, X. L. Chu and L. Y. Chen, Commun. Theor. Phys. (Beijing), 8, 167 (1987).

Stability of two-component Benard fluid with surface adsorption accumulation, X. L. Chu and L. Y. Chen, Commun. Theor. Phys. (Beijing), 6, 237 (1986).

Convective Instability of a Two-Component Fluid-Fluid System, L. Y. Chen and X. L. Chu, Commun. Theor. Phys. (Beijing), 6, 81 (1986).

Stability and Spontaneous Motion II, L. Y. Chen, J. Xingyang Normal College, 2,44(1986) (in Chinese).

Stability and Spontaneous Motion I, L. Y. Chen, J. Xinyang Normal College, 1, 53 (1985) (in Chinese).

Conference talks and seminar presentations

Invited Talk, Telluride Science Research Center Workshop on Reaction Coordinates and Order Parameters, July 2014.

Invited Talk, Telluride Science Research Center Workshop on Reaction Coordinates and Order Parameters, June 2012.

Contributed Talk, American Physical Society March Meeting, Dallas, 2011.

Invited Talk, Telluride Science Research Center Workshop on Reaction Coordinates and Order Parameters, June 2010.

Invited Seminar Talk, Brown University, May 13, 2010.

Invited Talk, 1st POSTECH workshop on Self-Organization in Biological Systems, Pohang, Korea, January 2010.

Invited Talk, Telluride Science Research Center Workshop on Reaction Coordinates and Order Parameters, June 2008.

Invited Talk, Telluride Science Research Center Workshop on Energy Landscape, Telluride, CO 2007.

Invited Talk, American Chemical Society Fall Meeting, San Franscico, CA 2006.

One contributed talk and one poster presentation, American Physical Society March Meeting, Austin, TX 2003.

Invited Seminar Talk, Brown University, December 6, 2001.

Invited Lectures, Helsinki University of Technology and Helsinki Institute of Physics Graduate Summer School, 2001.

Invited Talk, NATO Advanced Research Workshop on Surface Diffusion, Prague, Czech, October 2000.

Invited Talk, CECAM (European Centre of Atomic and Molecular Computations) Workshop on Surface Diffusion, Lyon, France, May 1999.

Invited Seminar, Department of Physics, Helsinki University of Technology, Helsinki, Finland, 1999.

Contributed Talk, MRS Fall Symposium K, Boston, 1998.

Invited Lectures, The Helsinki Institute of Physics Graduate Workshop on Surface Diffusion and Dynamics, Helsinki, Finland, 1997.

Invited Talk, The 4th International Workshop on Thermal Field Theories and Their Applications, Dalian, China, 1995.

Contributed Talk, The 19th International Union of Pure and Applied Physics Conference on Statistical Physics, Xiamen, China, 1995.

Contributed Talk, American Physical Society March Meeting, San Jose, CA 1995.

Invited Condensed Matter Physics Seminar at SUNY Stony Brook, NY, March 1994.

Surface Science Seminar at Brown University, Providence, RI, December 1993.

Boston University Surface Physics Conference, Boston, MA, July 1993.

Contributed Talk, American Physical Society March Meeting, Seatle, WA 1993.

Invited Talk, The 7th International Conference on the Numerical Analysis of Semiconductor Devices and Integrated Circuits, Copper Mountain, CO, April 1991.

Contributed Talk, The 7th International Conference on the Numerical Analysis of Semiconductor Devices and Integrated Circuits, Copper Mountain, CO, April 1991.

Two contributed Talks, American Physical Society March Meeting, Cincinnati, OH 1991.

Physics Seminar at Texas Center for Superconductivity, University of Houston, Houston, TX, Februray 1991.

Two contributed Talks, American Physical Society March Meeting, Los Angelos, CA 1990.

Contributed Talk, American Physical Society March Meeting, St Louis, MO 1989.

Contributed Talk, The 3rd Asia-Pacific Physics Conference, Hong Kong, 1988.

Contributed Talk, The 4th National Conference on Condensed Matter and Statistical Physics, Xiamen, China, 1987.