Chen, Alan - University at Albany-SUNY - Department of Chemistry

个人简介

Alan A. Chen is an assistant professor of Chemistry at SUNY Albany. Prior to joining the RNA Institute, Alan was a NIH-NRSA postdoctoral fellow in the lab of Angel Garcia in the Physics department of Rensselaer Polytechnic Institute. He received his Ph.D in Molecular Biophysics in 2009 from Washington University in St. Louis where he did his thesis work with Rohit Pappu, department of Biomedical Engineering. Alan’s undergraduate degree was a dual major in physics and molecular biology from Cornell University (B.A., 2002), where he was introduced to the fascinating world of biophysics by his undergraduate mentor, Linda Nicholson.

研究领域

Our research focuses on the use of physics-based simulations of RNA as a tool for studying RNA folding and biomolecular engineering. We are located in the “Advanced Computational/Visualization Center” (LSRB 2016) in the newly constructed RNA Institute at UAlbany. This interdisciplinary hub contains state-of-the-art computational and experimental facilities dedicated to RNA research, including the labs of our many experimental collaborators. Our lab’s research is carried out on our dedicated 600 core Xeon high-performance computing cluster augmented by GPU computing and 3D visualization facilities available for RNA Institute researchers

近期论文

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Quantitative characterization of ion pairing and cluster formation in strong 1: 1 electrolytes AA Chen, RV Pappu The Journal of Physical Chemistry B 111 (23), 6469-6478, 2007 74 2007 Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements AA Chen, RV Pappu The Journal of Physical Chemistry B 111 (41), 11884-11887, 2007 71 2007 Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop AA Chen, DE Draper, RV Pappu Journal of molecular biology 390 (4), 805-819, 2009 41 2009 High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations AA Chen, AE García Proceedings of the National Academy of Sciences 110 (42), 16820-16825, 2013 33 2013 Simulations of RNA interactions with monovalent ions AA Chen, M Marucho, NA Baker, RV Pappu Methods in enzymology 469, 411-432, 2009 29 2009 Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations AA Chen, AE García Proceedings of the National Academy of Sciences 109 (24), E1530-E1539, 2012 8 2012 The Essential Role of Stacking Adenines in a Two-Base-Pair RNA Kissing Complex W Stephenson, PN Asare-Okai, AA Chen, S Keller, R Santiago, ... Journal of the American Chemical Society 135 (15), 5602-5611, 2013 5 2013 Sequence Specificity in RNA-Mediated Transcriptional Attenuation Examined by Coarse-Grained MD Simulations PM Gasper, AA Chen Biophysical Journal 108 (2), 237a-238a, 2015 2015 Reversible Folding of Hyperstable RNA Tetraloops Using Molecular Dynamics Simulations AE Garcia, J Miner, AA Chen Biophysical Journal 108 (2), 370a, 2015 2015 Force and Temperature Dependent Folding of a 2-Base-Pair RNA Kissing Complex WT Stephenson, A Colvin, A Chen, PTX Li Biophysical Journal 108 (2), 235a, 2015 2015 Molecular Modeling and Simulations of DNA at Graphene-Water Interfaces towards Developing Biosensors and Drug Delivery Vehicles S Vembanur, K Halvorsen, C Myers, A Chen, M Yigit Biophysical Journal 108 (2), 231a-232a, 2015 2015 Molecular Simulations Studies of RNA Tetraloop Hyperstability: The Effect of Stem Length on Folding Dynamics JC Miner, AA Chen, AE García Biophysical Journal 108 (2), 237a, 2015 2015 De Novo Folding of RNA Hairpins by Temperature Replica Exchange JC Miner, AA Chen, AE Garcia Biophysical Journal 106 (2), 280a, 2014 2014 High resolution reversible folding simulations of hyperstable RNA tetraloops AA Chen, AE Garcia ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 246, 2013 2013 High resolution de-novo folding of hyperstable RNA tetraloops using molecular dynamics simulations AA Chen, AE Garcia The FASEB Journal 2013 (27), 2013 2013 41 The essential adenosine stacking in a two-base-pair minimal kissing complex W Stephenson, PN Asare-Okai, AA Chen, S Tenenbaum, AE Garcia, ... Journal of Biomolecular Structure and Dynamics 31 (sup1), 25-25, 2013 2013 The Essential Adenosine Stacking in a Two-Base-Pair Minimal Kissing Complex PTX Li, W Stephenson, P Nii Asare-Okai, AA Chen, S Tenenbaum, ... Biophysical Journal 104, 411, 2013 2013 Mechanism of Enhanced Mechanical Stability of Retroviral Kissing-Loops Elucidated by Non-Equilibrium Molecular Dynamics Simulations AA Chen, AE García Biophysical Journal 102 (3), 644a-645a, 2012 2012 Rebooting science outreach A Chen ASBMB Today, 22-23, 2011 2011 Atomistic Simulations of the Force-Induced Dissociation of Retroviral RNA Kissing-Loops AA Chen, AE Garcia Biophysical Journal 100 (3), 524a, 2011