Xiaolin Cheng

photo of Xiaolin Cheng
Professional Website

Xiaolin Cheng, PhD

Professor
Medicinal Chemistry and Pharmacognosy
5041 Pelotonia Research Center
cheng.1302@osu.edu
(614) 292-3198

Professional Interests

Dr. Cheng’s laboratory aims to develop an interdisciplinary research program centered on Computer Aided Drug Design and Discovery. Closely collaborating with experimental chemists and biologists, our group utilizes a myriad of computational modeling & simulation, and data analytics techniques to understand molecular basis of drug action and to rationally design new drug molecules. Our group also has long-standing interests in: a) developing and applying multiscale computational techniques to investigate the structure, dynamics and function of complex biomolecular (and cellular ) systems; and b) bridge large-scale molecular simulation with systems biology (cellular metabolism and signaling networks) towards a new drug discovery paradigm.

Publications

  • The Cytotoxic Cardiac Glycoside (−)-Cryptanoside A from the Stems of Cryptolepis dubia and Its Molecular Targets, Journal of Natural Products. 2023 Jun | journal-article. doi: 10.1021/acs.jnatprod.3c00094.
  • Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures, Journal of Chemical Information and Modeling. 2023 Feb | journal-article. doi: 10.1021/acs.jcim.2c01441.
  • Voltage controlled shutter regulates channel size and motion direction of protein aperture as durable nano-electric rectifier-----An opinion in biomimetic nanoaperture, Biomaterials. 2022 Dec | journal-article. doi: 10.1016/j.biomaterials.2022.121863.
  • Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein, The Journal of Physical Chemistry B. 2022 Nov | journal-article. doi: 10.1021/acs.jpcb.2c04641.
  • Design of peptide inhibitors targeting β-catenin using generative deep learning and molecular dynamics simulations, . 2022 Sep | preprint. doi: 10.21203/rs.3.rs-2019700/v1.
  • Facilitative lysosomal transport of bile acids alleviates ER stress in mouse hematopoietic precursors, Nature Communications. 2021 Dec | journal-article. doi: 10.1038/s41467-021-21451-6.
  • In Vitro and In Vivo Inhibition of MATE1 by Tyrosine Kinase Inhibitors, Pharmaceutics. 2021 Nov | journal-article. doi: 10.3390/pharmaceutics13122004.
  • Development of Murine Leukemia Virus Integrase-Derived Peptides That Bind Brd4 Extra-Terminal Domain as Candidates for Suppression of Acute Myeloid Leukemia, ACS Pharmacology & Translational Science. 2021 Oct | journal-article. doi: 10.1021/acsptsci.1c00159.
  • Interaction of (+)-Strebloside and Its Derivatives with Na+/K+-ATPase and Other Targets, Molecules. 2021 Sep | journal-article. doi: 10.3390/molecules26185675.
  • Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects, Journal of Biological Chemistry. 2021 Sep | journal-article. doi: 10.1016/j.jbc.2021.101007.
  • Mechanistic Insights into the Allosteric Inhibition of Androgen Receptors by Binding Function 3 Antagonists from an Integrated Molecular Modeling Study, Journal of Chemical Information and Modeling. 2021 Jul | journal-article. doi: 10.1021/acs.jcim.1c00124.
  • Reply to: Insufficient evidence for ageing in protein dynamics, Nature Physics. 2021 Jul | journal-article. doi: 10.1038/s41567-021-01270-8.
  • Structural Insights into the Interactions of Digoxin and Na+/K+-ATPase and Other Targets for the Inhibition of Cancer Cell Proliferation, Molecules. 2021 Jun | journal-article. doi: 10.3390/molecules26123672.
  • Activated nanoscale actin-binding domain motion in the catenin–cadherin complex revealed by neutron spin echo spectroscopy, Proceedings of the National Academy of Sciences. 2021 Mar | journal-article. doi: 10.1073/pnas.2025012118.
  • Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor, Biochemistry. 2021 Mar | journal-article. doi: 10.1021/acs.biochem.0c00935.
  • Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy, Nature Microbiology. 2021 Mar | journal-article. doi: 10.1038/s41564-020-00843-2.
  • Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems, Current Topics in Medicinal Chemistry. 2021 Jan | journal-article. doi: 10.2174/1568026620666201126162945.
  • Computational investigation of the binding of a designed peptide to λ light chain amyloid fibril, Physical Chemistry Chemical Physics. 2021 Jan | journal-article. doi: 10.1039/d1cp01825f.
  • Accelerating structure-based design of rapid uncharged reactivators of organophosphate-inhibited human acetylcholinesterase by joint X-ray/neutron mechanistic studies, Proceedings of The 2nd International Online Conference on Crystals. 2020 Nov | conference-paper. doi: 10.3390/iocc_2020-08037.
  • Lines of communication within and between catalytic subunits of human acetylcholinesterase revealed by cryo- and room-temperature X-ray crystallography and by Small Angle X-ray Scattering (SAXS), Proceedings of The 2nd International Online Conference on Crystals. 2020 Nov | conference-paper. doi: 10.3390/iocc_2020-07323.
  • A computational study of effects on membrane recruitment of the polar linkers in Vitamin E derivatives, Biochimica et Biophysica Acta (BBA) - General Subjects. 2020 Oct | journal-article. doi: 10.1016/j.bbagen.2020.129655.
  • Direct structural evidence supporting a revolving mechanism in DNA packaging motors, Biophysics Reports. 2020 Oct | journal-article. doi: 10.1007/s41048-020-00115-w.
  • The structures of polyunsaturated lipid bilayers by joint refinement of neutron and X-ray scattering data, Chemistry and Physics of Lipids. 2020 Jul | journal-article. doi: 10.1016/j.chemphyslip.2020.104892.
  • SCNrank: spectral clustering for network-based ranking to reveal potential drug targets and its application in pancreatic ductal adenocarcinoma, BMC Medical Genomics. 2020 Apr | journal-article. doi: 10.1186/s12920-020-0681-6.
  • Na+/K+-ATPase-Targeted Cytotoxicity of (+)-Digoxin and Several Semisynthetic Derivatives, Journal of Natural Products. 2020 Mar | journal-article. doi: 10.1021/acs.jnatprod.9b01060.
  • Rational Design of Small Molecules to Enhance Genome Editing Efficiency by Selectively Targeting Distinct Functional States of CRISPR-Cas12a, Bioconjugate Chemistry. 2020 Mar | journal-article. doi: 10.1021/acs.bioconjchem.0c00062.
  • Rational design, synthesis, and evaluation of uncharged, “smart” bis-oxime antidotes of organophosphate-inhibited human acetylcholinesterase, Journal of Biological Chemistry. 2020 Mar | journal-article. doi: 10.1074/jbc.ra119.012400.
  • Semi-synthetic cinnamodial analogues: Structural insights into the insecticidal and antifeedant activities of drimane sesquiterpenes against the mosquito Aedes aegypti, PLOS Neglected Tropical Diseases. 2020 Feb | journal-article. doi: 10.1371/journal.pntd.0008073.
  • Cytotoxic and non-cytotoxic cardiac glycosides isolated from the combined flowers, leaves, and twigs of Streblus asper, Bioorganic & Medicinal Chemistry. 2020 Feb | journal-article. doi: 10.1016/j.bmc.2019.115301.
  • Carotenoids promote lateral packing and condensation of lipid membranes, Physical Chemistry Chemical Physics. 2020 Jan | journal-article. doi: 10.1039/d0cp01031f.
  • Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways, ACS Chemical Biology. 2019 Dec | journal-article. doi: 10.1021/acschembio.9b00725.
  • STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products, Journal of Chemical Information and Modeling. 2019 Nov | journal-article. doi: 10.1021/acs.jcim.9b00489.
  • Insecticidal and Antifeedant Activities of Malagasy Medicinal Plant (Cinnamosma sp.) Extracts and Drimane-Type Sesquiterpenes against Aedes aegypti Mosquitoes, Insects. 2019 Oct | journal-article. doi: 10.3390/insects10110373.
  • Structurally Modified Cyclopenta[b]benzofuran Analogues Isolated from Aglaia perviridis, Journal of Natural Products. 2019 Oct | journal-article. doi: 10.1021/acs.jnatprod.9b00631.
  • Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation, Proceedings of the National Academy of Sciences. 2019 Oct | journal-article. doi: 10.1073/pnas.1907251116.
  • A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction, Journal of the American Chemical Society. 2019 Aug | journal-article. doi: 10.1021/jacs.8b10242.
  • A new crystal form of human acetylcholinesterase for exploratory room-temperature crystallography studies, Chemico-Biological Interactions. 2019 Aug | journal-article. doi: 10.1016/j.cbi.2019.06.011.
  • 21. Molecular dynamics simulation studies of small molecules interacting with cell membranes, Characterization of Biological Membranes. 2019 Jul | book-chapter. doi: 10.1515/9783110544657-021.
  • Branched-Chain Fatty Acid Content Modulates Structure, Fluidity, and Phase in Model Microbial Cell Membranes, The Journal of Physical Chemistry B. 2019 Jul | journal-article. doi: 10.1021/acs.jpcb.9b04326.
  • Abstract 4257: Integrated network analysis reveals potentially novel molecular pathways mechanism and therapeutic targets of pancreatic ductal adenocarcinoma, Bioinformatics, Convergence Science, and Systems Biology. 2019 Jul | conference-abstract. doi: 10.1158/1538-7445.am2019-4257.
  • Productive reorientation of a bound oxime reactivator revealed in room temperature X-ray structures of native and VX-inhibited human acetylcholinesterase, Journal of Biological Chemistry. 2019 Jul | journal-article. doi: 10.1074/jbc.ra119.008725.
  • Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality, ACS Nano. 2019 Jun | journal-article. doi: 10.1021/acsnano.8b08849.
  • Biological Membrane Organization and Cellular Signaling, Chemical Reviews. 2019 May | journal-article. doi: 10.1021/acs.chemrev.8b00439.
  • Lipid Rafts: Buffers of Cell Membrane Physical Properties, The Journal of Physical Chemistry B. 2019 Mar | journal-article. doi: 10.1021/acs.jpcb.8b12126.
  • Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells, Plant Physiology. 2019 Jan | journal-article. doi: 10.1104/pp.18.01190.
  • Neutron scattering in the biological sciences: progress and prospects, Acta Crystallographica Section D Structural Biology. 2018 Dec | journal-article. doi: 10.1107/s2059798318017503.
  • Structural investigation of the enantioselectivity and thermostability mechanisms of esterase RhEst1, Journal of Molecular Graphics and Modelling. 2018 Oct | journal-article. doi: 10.1016/j.jmgm.2018.08.010.
  • RPYFMM: Parallel adaptive fast multipole method for Rotne–Prager–Yamakawa tensor in biomolecular hydrodynamics simulations, Computer Physics Communications. 2018 Jun | journal-article. doi: 10.1016/j.cpc.2018.02.005.
  • Synthesis and biological evaluation of aminothiazoles against Histoplasma capsulatum and Cryptococcus neoformans, Bioorganic & Medicinal Chemistry. 2018 May | journal-article. doi: 10.1016/j.bmc.2018.01.024.
  • Crystallographic studies of human acetylcholinesterase inhibition by organophosphates and reactivation by oximes, The FASEB Journal. 2018 Apr | journal-article. doi: 10.1096/fasebj.2018.32.1_supplement.527.10.
  • Dynamics of Organophosphate‐Induced Structural Changes in Acetylcholinesterase Revealed by Time‐Resolved Small‐Angle X‐Ray Scattering and Inelastic Neutron Scattering, The FASEB Journal. 2018 Apr | journal-article. doi: 10.1096/fasebj.2018.32.1_supplement.527.7.
  • Temperature-Dependent Lipid Extraction from Membranes by Boron Nitride Nanosheets, ACS Nano. 2018 Mar | journal-article. doi: 10.1021/acsnano.7b09095.
  • Effects of carotenoids on lipid bilayers, Physical Chemistry Chemical Physics. 2018 Jan | journal-article. doi: 10.1039/c7cp07126d.
  • Lipid extraction by boron nitride nanosheets from liquid-ordered and liquid-disordered nanodomains, Nanoscale. 2018 Jan | journal-article. doi: 10.1039/c8nr02018c.
  • Ordering of lipid membranes altered by boron nitride nanosheets, Physical Chemistry Chemical Physics. 2018 Jan | journal-article. doi: 10.1039/c7cp07136a.
  • Temperature-dependent phase behaviour of tetrahydrofuran–water alters solubilization of xylan to improve co-production of furfurals from lignocellulosic biomass, Green Chemistry. 2018 Jan | journal-article. doi: 10.1039/c7gc03608f.
  • Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis, Scientific Reports. 2017 Nov | journal-article. doi: 10.1038/s41598-017-15048-7.
  • Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane, Environmental Science & Technology. 2017 Sep | journal-article. doi: 10.1021/acs.est.7b02204.
  • Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane, The Journal of Physical Chemistry Letters. 2017 Sep | journal-article. doi: 10.1021/acs.jpclett.7b01877.
  • The in vivo structure of biological membranes and evidence for lipid domains, PLOS Biology. 2017 May | journal-article. doi: 10.1371/journal.pbio.2002214.
  • Probing the structural requirements of polybasic peptides for effective and specific amyloid reactivity, Amyloid. 2017 Mar | journal-article. doi: 10.1080/13506129.2017.1295946.
  • Serendipitous inhibition of Aβ and rVλ6Wil amyloid fibril growth by bi-functional peptides, Amyloid. 2017 Mar | journal-article. doi: 10.1080/13506129.2017.1295947.
  • Description of Hydration Water in Protein (Green Fluorescent Protein) Solution, Journal of the American Chemical Society. 2017 Jan | journal-article. doi: 10.1021/jacs.6b08845.
  • Quasielastic neutron scattering in biology: Theory and applications, Biochimica et Biophysica Acta (BBA) - General Subjects. 2017 Jan | journal-article. doi: 10.1016/j.bbagen.2016.06.015.
  • Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid, Physical Chemistry Chemical Physics. 2017 Jan | journal-article. doi: 10.1039/c7cp04013j.
  • The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time, Nature Physics. 2016 Feb | journal-article. doi: 10.1038/nphys3553.
  • Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies, The Journal of Physical Chemistry B. 2016 Jan | journal-article. .
  • Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling, Journal of computational chemistry. 2016 Jan | journal-article. .
  • Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics, Green Chemistry. 2016 Jan | journal-article. .
  • Covalent Inhibition Of Acetylcholinesterase Affects Quaternary Structure As Revealed By Small Angle X-Ray Scattering, The FASEB Journal. 2016 Jan | journal-article. .
  • Crystallographic Studies of Human Acetylcholinesterase Reactivation by Oximes: Towards a Neutron Structure, The FASEB Journal. 2016 Jan | journal-article. .
  • Enhanced sampling simulation analysis of the structure of lignin in the THF--water miscibility gap, Physical Chemistry Chemical Physics. 2016 Jan | journal-article. .
  • Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways, Methods in Enzymology. 2016 Jan | book-chapter. doi: 10.1016/bs.mie.2016.05.012.
  • Limitations in current acetylcholinesterase structure--based design of oxime antidotes for organophosphate poisoning, Annals of the New York Academy of Sciences. 2016 Jan | journal-article. .
  • Molecular Driving Forces behind the Tetrahydrofuran--Water Miscibility Gap, The Journal of Physical Chemistry B. 2016 Jan | journal-article. .
  • Preclinical validation and translation of peptide p5+ 14 as a molecular imaging agent for systemic amyloidoses, Journal of Nuclear Medicine. 2016 Jan | journal-article. .
  • Structure and Function of Photosystem I--[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study, The Journal of Physical Chemistry B. 2016 Jan | journal-article. .
  • Theoretical Study of the Initial Stages of Self-Assembly of a Carboxysome’s Facet, ACS nano. 2016 Jan | journal-article. .
  • Translocase Activity and Asymmetric Model Membranes Probed by Neutron Scattering, Biophysical Journal. 2016 Jan | journal-article. .
  • Experiment and Simulation Reveal the Bending Properties of Nanoscopic Lipid Domains, Biophysical Journal. 2015 Jan | journal-article. .
  • Interactions of the anticancer drug tamoxifen with lipid membranes, Biophysical journal. 2015 Jan | journal-article. .
  • Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes, Chemistry and physics of lipids. 2015 Jan | journal-article. .
  • Mechanical properties of nanoscopic lipid domains, Journal of the American Chemical Society. 2015 Jan | journal-article. .
  • Molecular dynamics investigation of the substrate binding mechanism in carboxylesterase, Biochemistry. 2015 Jan | journal-article. .
  • Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase, Interdisciplinary Sciences: Computational Life Sciences. 2015 Jan | journal-article. .
  • Preclinical validation of the heparin-reactive peptide p5+ 14 as a molecular imaging agent for visceral amyloidosis, Molecules. 2015 Jan | journal-article. .
  • Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding, Journal of Molecular Graphics and Modelling. 2015 Jan | journal-article. .
  • Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations, Soft matter. 2015 Jan | journal-article. .
  • All-atom molecular dynamics simulation of a photosystem i/detergent complex, The Journal of Physical Chemistry B. 2014 Jan | journal-article. .
  • Analysis of the solution structure of Thermosynechococcus elongatus, Small. 2014 Jan | journal-article. .
  • Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-$β$-d-maltoside using small-angle neutron scattering and molecular dynamics simulation, Archives of biochemistry and biophysics. 2014 Jan | journal-article. .
  • Coarse-grain model for natural cellulose fibrils in explicit water, The Journal of Physical Chemistry B. 2014 Jan | journal-article. .
  • Organocatalytic Trifluoromethylthiolation of $β$-Keto Esters, Synfacts. 2014 Jan | journal-article. .
  • Replica-Exchange Molecular Dynamics Simulations of Cellulose Solvated in Water and in the Ionic Liquid 1-Butyl-3-Methylimidazolium Chloride, The Journal of Physical Chemistry B. 2014 Jan | journal-article. .
  • Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose I$β$, Cellulose. 2014 Jan | journal-article. .
  • Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution, Cellulose. 2014 Jan | journal-article. .
  • Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase, Biophysical journal. 2014 Jan | journal-article. .
  • The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations, Soft Matter. 2014 Jan | journal-article. .
  • The role of histone tails in the nucleosome: a computational study, Biophysical journal. 2014 Jan | journal-article. .
  • AFMPB: An adaptive fast multipole Poisson--Boltzmann solver for calculating electrostatics in biomolecular systems, Computer Physics Communications. 2013 Jan | journal-article. .
  • Ab Initio Study of Molecular Interactions in Cellulose I$α$, The Journal of Physical Chemistry B. 2013 Jan | journal-article. .
  • Backbone moiety of phospholipids determines cholesterol disposition, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2013 Jan | conference-paper. .
  • Computer simulation of pretreatment of lignocellulosic biomass in cellulosic ethanol production, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2013 Jan | conference-paper. .
  • Effect of initial stagger selection on the handedness of Amyloid beta helical fibrils, FEBS Letters. 2013 Jan | journal-article. .
  • Effect of the amyloid $β$ hairpin's structure on the handedness of helices formed by its aggregates, FEBS letters. 2013 Jan | journal-article. .
  • Enantioselective Electrophilic Trifluoromethylthiolation of $β$-Ketoesters: A Case of Reactivity and Selectivity Bias for Organocatalysis, Angewandte Chemie International Edition. 2013 Jan | journal-article. .
  • Impact of resistance mutations on inhibitor binding to HIV-1 integrase, Journal of chemical information and modeling. 2013 Jan | journal-article. .
  • Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity, Biophysical journal. 2013 Jan | journal-article. .
  • Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver, Communications in Computational Physics. 2013 Jan | journal-article. .
  • Synthesis, docking, and biological studies of phenanthrene $β$-diketo acids as novel HIV-1 integrase inhibitors, Bioorganic & medicinal chemistry letters. 2013 Jan | journal-article. .
  • Homology model-guided 3D-QSAR studies of HIV-1 integrase inhibitors, Journal of chemical information and modeling. 2012 Jan | journal-article. .
  • Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations, The Journal of Physical Chemistry B. 2012 Jan | journal-article. .
  • Intramembrane proton binding site linked to activation of bacterial pentameric ion channel, Journal of Biological Chemistry. 2012 Jan | journal-article. .
  • Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver, . 2012 Jan | book. .
  • Molecular Simulation in the Energy Biosciences, Innovations in Biomolecular Modeling and Simulations. 2012 Jan | book-chapter. .
  • Molecular dynamics, Computational Toxicology: Volume I. 2012 Jan | journal-article. .
  • Multilevel Enhanced Sampling of Cellulose-Cellulase Interaction, From Computational Biophysics to Systems Biology (CBSB11)--Celebrating Harold Scheraga’s 90th Birthday. 2012 Jan | journal-article. .
  • REACH coarse-grained simulation of a cellulose fiber, Biomacromolecules. 2012 Jan | journal-article. .
  • Simulating the transport of a cellulose chain through the cellulase catalytic tunnel, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2012 Jan | conference-paper. .
  • Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core, Physical review letters. 2012 Jan | journal-article. .
  • A solvent-free coarse grain model for crystalline and amorphous cellulose fibrils, Journal of chemical theory and computation. 2011 Jan | journal-article. .
  • Docking and 3D-QSAR studies of HIV-1 integrase inhibitors, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2011 Jan | conference-paper. .
  • Editorial: Special issue on ionic fluids and its biological application, Interdisciplinary Sciences: Computational Life Sciences. 2011 Jan | journal-article. .
  • Image charge method for reaction fields in a hybrid ion-channel model, Communications in computational physics. 2011 Jan | journal-article. .
  • Ion selectivity mechanism in a bacterial pentameric ligand-gated ion channel, Biophysical journal. 2011 Jan | journal-article. .
  • The solvation structures of cellulose microfibrils in ionic liquids, Interdisciplinary Sciences: Computational Life Sciences. 2011 Jan | journal-article. .
  • Transfer matrix approach to the hydrogen-bonding in cellulose I$α$ fibrils describes the recalcitrance to thermal deconstruction, The Journal of chemical physics. 2011 Jan | journal-article. .
  • Treecode-based generalized Born method, The Journal of chemical physics. 2011 Jan | journal-article. .
  • AFMPB: an adaptive fast multipole Poisson--Boltzmann solver for calculating electrostatics in biomolecular systems, Computer physics communications. 2010 Jan | journal-article. .
  • Analysis of the Cellulose-Cellulase Interaction, Biophysical Journal. 2010 Jan | journal-article. .
  • An Adaptive Fast Multipole Boundary Element Method for Poisson- Boltzmann Electrostatics, Journal of chemical theory and computation. 2009 Jan | journal-article. .
  • Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes, . 2009 Jan | book. .
  • Characterizing loop dynamics and ligand 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 Jan | journal-article. .
  • Molecular-dynamics simulations of ELIC—a prokaryotic homologue of the nicotinic acetylcholine receptor, Biophysical journal. 2009 Jan | journal-article. .
  • Single-channel current through nicotinic receptor produced by closure of binding site C-loop, Biophysical journal. 2009 Jan | journal-article. .
  • Acetylcholinesterase: Mechanisms of covalent inhibition of H447I mutant determined by computational analyses, Chemico-biological interactions. 2008 Jan | journal-article. .
  • COMP 19-The generalized gradient-augmented Harmonic Fourier Beads: A practical method for accurate free energy calculations from multidimensional umbrella sampling, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2008 Jan | conference-paper. .
  • Control of cation permeation through the nicotinic receptor channel, PLoS Comput Biol. 2008 Jan | journal-article. .
  • PHYS 533-Cooperative permeation of ions and water through the selectivity filter of the KcsA ion channel: A novel transition path ensemble study, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2008 Jan | conference-paper. .
  • Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses, Journal of the American Chemical Society. 2007 Jan | journal-article. .
  • Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family, Journal of the American Chemical Society. 2007 Jan | journal-article. .
  • Barriers to ion translocation in the human alpha 7 nicotinic acetylcholine receptor, BIOPHYSICAL JOURNAL. 2007 Jan | conference-paper. .
  • Nanosecond-timescale conformational dynamics of the human $α$7 nicotinic acetylcholine receptor, Biophysical journal. 2007 Jan | journal-article. .
  • New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular, Issue: Journal of Computational Physics, 226. 2007 Jan | journal-article. .
  • PHYS 270-Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2007 Jan | conference-paper. .
  • PHYS 705-Multiscale modeling of gating motion in nicotinic acetylcholine receptors, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2007 Jan | conference-paper. .
  • “New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systems, Journal of computational physics. 2007 Jan | journal-article. .
  • Channel opening motion of $α$7 nicotinic acetylcholine receptor as suggested by normal mode analysis, Journal of molecular biology. 2006 Jan | journal-article. .
  • Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase, Journal of medicinal chemistry. 2006 Jan | journal-article. .
  • Order N algorithm for computation of electrostatic interactions in biomolecular systems, Proceedings of the National Academy of Sciences. 2006 Jan | journal-article. .
  • Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors, PLoS Comput Biol. 2006 Jan | journal-article. .
  • Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals, The Journal of chemical physics. 2005 Jan | journal-article. .
  • Dynamic behavior of DNA base pairs containing 8-oxoguanine, Journal of the American Chemical Society. 2005 Jan | journal-article. .
  • Modified replica exchange simulation methods for local structure refinement, The Journal of Physical Chemistry B. 2005 Jan | journal-article. .
  • Improved conformational sampling through an efficient combination of mean-field simulation approaches, The Journal of Physical Chemistry B. 2004 Jan | journal-article. .
  • AFMPB: Adaptive Fast Multipole Poisson-Boltzmann Solver, . 1 Jan | journal-article. .
  • High-performance computer simulation in the energy biosciences, . 1 Jan | journal-article. .