Background
Van is serving as a liaison for life science projects at Oak Ridge Leadership Computing Facility (OLCF). His research topics include, but not limited to, ion channels, Ras-related cancer, drug design, molecular dynamics simulations, free-energy calculations, non-equilibrium/enhanced sampling, force field developments, Markov State Modeling and machine learning/artificial intelligence applied to life sciences.
One of Van’s research goals is to find clinically efficient noncovalent drugs for targeting mutant Rat sarcoma (Ras) proteins, which are a main cause of 30% of all cancers. He aims to build an all-atom model of an entire signaling network regulated by Ras with proteins from experiments and/or predicted from AlphaFold/RosettaFold, and refined with molecular dynamics simulations. The research of complex biological processes has encountered many challenges that remain standing in the characterizations of spatial-temporal properties of complex protein networks at both atomic details and microscopic scales.
Van earned PhD in Physics and Master in Computer Science specialized in High Performance Parallel Computing & Simulations from University of Southern California. After PhD, he held two postdoctoral fellowships awarded by Alberta Innovates-Health Solutions (2015-2017) and Canadian Institutes of Health Research (2016-2018) for heart-disease research at University of Calgary in Canada. He was awarded Ed McCauley Postdoctoral Award for Excellent Research in 2016. In 2018, he joined Los Alamos National Laboratory for Director’s postdoctoral fellowship to study Ras-related cancer and develop advanced sampling algorithms using non-equilibrium theories and machine learning/artificial intelligent frameworks. He has published many peer-reviewed papers in method developments including QM/MM deMon2k/CHARMM interface, free-energy calculations, non-equilibrium sampling, and Drude polarizable force-field, and in disease-related research including drug designs, arrhythmias and Ras-related cancer. He is an expert in Markov State Modeling and molecular dynamics simulations to reveal kinetics and molecular mechanisms of many protein systems, which are fundamental to many biological processes.
Publications
2021
Kevin R. DeMarco, …, Van A. Ngo., …, Colleen E. Clancy and Igor Vorobyov. Molecular
determinants of pro-arrhythmia proclivity of d-and l-sotalol via a multi-scale modeling pipeline.
J. Molecular and Cellular Cardiology. DOI: 10.1016/j.yjmcc.2021.05.015
2021
Van A. Ngo and Ramesh K. Jha, Identifying key determinants and dynamics of SARSCoV-
2/ACE2 tight interaction, PlosOne, DOI: 10.1371/journal.pone.0257905.
2021
Van A. Ngo, Hui Li, Toby Allen, Alexander Mackerell, Benoit Roux, and Sergei Noskov,
“Polarization Effects of Water on Selective Cation Transport Across a Narrow Transmembrane
Channel”, J. Chem. Theory Comp. DOI: 10.1021/acs.jctc.0c00968.
2020
Van A. Ngo, Sumantra Sarkar, Chris Neale, and Angel E Garcia. How Anionic Lipids
Affect Spatiotemporal Properties of KRAS4B on Model Membranes. J. Phys. Chem. B 2020.
DOI: 10.1021/acs.jpcb.0c02642. (Cover Article)
2020
Yingying Zhang, Kamran Haider, Divya Kaur, Van A. Ngo, Xiuhong Cai, Junjun Mao,
Umesh Khaniya, Xuyu Zhu, Sergei Noskov, Themis Lazaridis, M.R. Gunner. Characterizing the
water wire in the gramicidin channel found by Monte Carlo sampling using continuum
electrostatics and in Molecular Dynamics trajectories with conventional or polarizable force
fields. J. of Theo. and Comp. Chem. DOI: 10.1142/S0219633620420018
2019
Trung Hai Nguyen, Van A Ngo, João Paulo Castro Zerba, Sergei Noskov, and David DL
Minh, Nonequilibrium path-ensemble averages for symmetric protocols, J. Chem. Phys. 151,
194103 (2019). DOI: 10.1063/1.5121306.
2019
Van A. Ngo, John Keenan Fanning and Sergei Yu. Noskov. Comparative Analysis of
Protein Hydration from MD simulations with Additive and Polarizable Force Fields, Advanced
Theory and Simulations (Wiley), DOI: doi.org/10.1002/adts.201800106.
2019
Yibo Wang, Rocio Finol-Urdaneta, Van A. Ngo, Sergei Noskov, and Robert French,
Bases of Bacterial Sodium Channel Selectivity Among Organic Cations, Scientific Reports.
DOI: doi.org/10.1038/s41598-019-51605-y.
2018
Williams Ernesto Miranda, Van A. Ngo, Ruiwu Wang, Lin Zhang, SR Wayne Chen,
Sergei Yu Noskov, Molecular Mechanism of Conductance Enhancement in Narrow Cation
Selective Membrane Channels, J. Phys. Chem. Lett., DOI: 10.1021/acs.jpclett.8b01005.
2017
Hristina Zhekova, Van A. Ngo, Mauricio C. da Silva, Dennis Salahub, and Sergei
Noskov, Selective Ion Binding and Transport by Membrane Proteins – A Computational
Perspective, Coord. Chem. Rev. DOI: 10.1016/j.ccr.2017.03.019.
2017
Van A. Ngo, Laura L Perissinotti, Williams Ernesto Miranda, Wayne Chen, and Sergei
Noskov, Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptor, Biophys.
J., DOI: 10.1016/j.bpj.2017.03.014
2017
Williams Ernesto Miranda, Van A. Ngo, Laura L Perissinotti, and Sergei Y. Noskov,
Computational Membrane Biophysics: Connecting Ion Channels-Ligand Interactions to Cellular
Function and Pharmacology”, BBA -Proteins and Proteomics, DOI:
10.1016/j.bbapap.2017.08.008. (Co-first authors)
2016
Van A. Ngo, Ilsoo Kim, Toby Allen, and Sergei Noskov, Estimation of Potentials of Mean
Force from Non-Equilibrium Pulling Simulations Using both Minh-Adib Estimator and Weighted
Histogram Analysis Method, J. Chem. Theory Comp. DOI: 10.1021/acs.jctc.5b01050.
2016
Van A. Ngo, Yibo Wang, Stephan Haas, Sergei Noskov, and Robert Farley, K+ Block Is
the Mechanism of Functional Asymmetry in Bacterial Nav Channels, PLoS Comput Biol 12(1):
e1004482. doi:10.1371/journal.pcbi.1004482.
2016
Williams Ernesto Miranda, Van A. Ngo, Pedro Alberto Valiente, and Sergei Yu. Noskov,
Improved QM/MM Linear Interaction Energy Model for Substrate Recognition in Zinc-
Containing Metalloenzymes, J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.6b05628.
2015
Dennis R. Salahub, Sergei Yu. Noskov, Bogdan Lev, Rui Zhang, Van A. Ngo, Annick
Goursot, Patrizia Calaminici, Andreas M. Köster, Aurelio Alvarez Ibarra, Daniel Mejía
Rodríguez, Jan Řezáč, Fabien Cailliez and Aurélien de la Lande, Review: QM/MM Calculations
with deMon2k, Molecules 2015, 20(3), 4780-4812; doi:10.3390/molecules20034780.
2015
Hui Li*, Van A. Ngo*, Mauricio Silva*, Dennis R. Salahub, Sergei Noskov and Benoit
Roux. “Representation of Ion-Protein Interactions using the Drude Polarizable Force-Field”, J.
Phys. Chem. B, 2015, 119 (29), pp 9401–9416. (Co-first Authors).
2015
Van A. Ngo, Mauricio C. da Silva, Maximilian Kubillus, Hui Li, Benoît Roux, Marcus
Elstner, Qiang Cui, Dennis R. Salahub and Sergei Noskov, Quantum Effects in Cation
Interactions with First and Second Coordination Shell Ligands in Metalloproteins, J. Chem.
Theory Comp. DOI: 10.1021/acs.jctc.5b00524.
2014
Van A. Ngo, Darko Stefanovski, Stephan Haas and Robert Farley, “Non-Equilibrium
Dynamics Contribute to Ion Selectivity in The KcsA Channel”. PLoS ONE 9(1): e86079.
DOI:10.1371/journal.pone.0086079.
2014
Van A. Ngo, Rosa Di Felice and Stephan Haas, “Is The G-quadruplex an Effective
Nanoconductor for Ions?”, J. Phys. Chem. B, 2014, 118 (4), pp 864–872 DOI:
10.1021/jp408071h.
2012
Van A. Ngo and Stephan Haas, “Demonstration of Jarzynski’s Equality in Open
Quantum Systems Using A Step-wise Pulling Protocol”, Phys. Rev. E 86, 031127
2012
Van A. Ngo, Rajiv Kalia, Aiichiro Nakano, and Priya Vashishta, “Molecular Mechanism of
Flip-flop in Triple-layer Oleic-Acid Membrane: Correlation Between Oleic Acid and Water”, J.
Phys. Chem. B, 2012, 116 (45), pp 13416–13423.
2012
Van A. Ngo, Rajiv Kalia, Aiichiro Nakano, and Priya Vashishta, “Supercrystals of DNAfunctionalized
Gold Nanoparticles: A Million-Atom Molecular Dynamics Simulation Study”, J.
Phys. Chem. C, 2012, 116 (36), pp 19579–19585.
Van A. Ngo, “Parallel-pulling Protocol for Free-Energy Evaluation”. Phys. Rev. E 85,
036702 (2012).
