Xiaolin Cheng Adjunct Professor

Dr. Xiaolin Cheng is a staff scientist at the Center for Molecular Biophysics of the Oak Ridge National Laboratory. He is also an adjunct professor in the Department of  Biochemistry & Cellular and Molecular Biology at the University of Tennessee, Knoxville. Xiaolin received his B.S. from Nanjing University, China, and his Ph.D. in Computational Chemistry from the State University of New York at Stony Brook, where he worked with Prof. Carlos Simmerling on application of enhanced sampling approaches to biomolecular simulations. He subsequently joined Prof. Andy McCammon's group at University of California, San Diego as a postdoctoral research associate, mainly working on nicotinic acetylcholine receptor simulation, and methodological development for fast and scalable continuum electrostatic calculation. Xiaolin moved to ORNL in early 2008.

Research Interest:

• Fast and scalable continuum electrostatic calculation
  We develop numerical techniques for faster and more scalable solution of the linearized Poisson-Boltzmann equation using the boundary integral method, and incorporate the continuum electrostatic forces into Brownian and molecular dynamics simulations
• Assembly of cellulase complex on the cellulose surface
  We investigate how the catalytic, binding and linker domains of the cellulase assemble on the cellulose surface using Brownian and molecular dynamics dynamics simulations.
• Enhanced sampling methods for petascale computing
  We port and adapt state-of-the-art enhanced sampling methods to scalable molecular dynamics simulation programs, such as LAMMPS; we also develop strategies to accelerate convergence of sampling for 'ensemble' molecular dynamics simulation on petascale capability computers.
• Understanding allosteric mechanisms in nAChR
  Our work in this area has been focused on understanding the gating motion in nAChR at the atomic level, that is, how the conformational changes triggered by neurotransmitter binding are transmitted to the remote transmembrane pore region.

Publications:

• Lu B, Cheng X, Huang J and McCammon JA. An improved Poisson-Boltzmann solver using an adaptive fast multipole method. Journal of Chemical Theory and Computation, 2009, in press.
• Cheng X, Ivanov I, Wang HL, Sine SM, and McCammon JA. Molecular Dynamics Simulations of a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor. Biophysical Journal, 2009, 96(11).
• Wang H, Toghraee R, David Papke D, Cheng X, McCammon JA, Umberto Ravaioli U and Sine SM. Ion Conduction through the Nicotinic Acetylcholine Receptor. Biophysical Journal, 2009, 96(10).
• Amaro RE, Cheng X, Ivanov I, Xu D, and McCammon JA. Characterizing Loop Dynamics and Substrate Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations. Journal of the American Chemical Society, 2009, 131(13), 4702-4709.
• Cheng Y, Cheng X, Radić Z and McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chemico-Biological Interactions, 2008, 175(1-3), 196-199
• Wang H, Cheng X, Taylor P, McCammon JA and Sine SM. Single cation transport through nicotinic receptor governed by dynamics, electrostatics and hydrophobicity of the channel. PLoS Comp. Biol. 2008, 4(2):e41
• Lu B, Cheng X, and McCammon JA Computation of macromolecular electrostatics: an integral equation solver accelerated by a new version of fast multiple method. J. Comput. Phys. 2007, 226,1348-1366
  
• Cheng X, Ivanov I, Wang H, Sine SM, and McCammon JA. Global collective motions of the α7 nicotinic acetylcholine receptor: implications for the gating mechanism Biophys. J. 2007, 93, 1–13
• Ivanov I, Cheng X, Sine SM and McCammon JA. Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family J. Am. Chem. Soc. 2007, 129(26), 8217-8224
• Cheng Y, Cheng X, Radic Z, and McCammon JA. Acetylcholinesterase: Mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses. J. Am. Chem. Soc. 2007, 129, 6562-6570
• Lu B*, Cheng X*, Huang J and McCammon JA. An order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci USA 2006, 103, 19314 *joint first author
  
• Cheng X, Wang HL, Grant B, Sine SM and McCammon JA. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comp. Biol. 2006, 2(9): e134
• Rafi S, Cui G, Song K, Cheng X, Tonge P and Simmerling C. Insight through MM-PBSA calculations into the binding affinity of triclosan and three analogs for FabI, the E. Coli enoyl reductase. J. Med. Chem. 2006, 49, 4574-80.
  
• Cheng X, Lu B, Grant B, Law R and McCammon JA. Channel opening motion of a7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J. Mol. Biol. 2006, 355, 310-24.
• Lu B, Cheng X, Hou T and McCammon JA. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. J. Chem. Phys. 2005, 123, 084904
  
• Cheng X, Kelso C, Hornak V, de Los Santos C, Grollman AP and Simmerling C. Dynamic behavior of DNA base pairs containing 8-oxoguanine. J. Am. Chem. Soc. 2005, 127, 13906-18
  
• Cheng X, Cui G, Hornak V and Simmerling C. A modified replica exchange method for local structure refinement simulations. J. Phys. Chem. B 2005, 109, 8220-8230
  
• Cheng X, Hornak V and Simmerling C. Improved conformational sampling through an efficient combination of mean-field simulation approaches. J. Phys. Chem. B 2004, 108, 426-437