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Pratyush Tiwary - Publications

Affiliations: 
2017- Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
Area:
statistical mechanics, molecular dynamics, rare events, enhanced sampling, drug design
Website:
sites.google.com/site/pratyushtiwary/
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Zou Z, Beyerle ER, Tsai ST, Tiwary P. Driving and characterizing nucleation of urea and glycine polymorphs in water. Proceedings of the National Academy of Sciences of the United States of America. 120: e2216099120. PMID 36757888 DOI: 10.1073/pnas.2216099120  0.32
2022 Beyerle ER, Mehdi S, Tiwary P. Quantifying Energetic and Entropic Pathways in Molecular Systems. The Journal of Physical Chemistry. B. 126: 3950-3960. PMID 35605180 DOI: 10.1021/acs.jpcb.2c01782  0.344
2021 Zou Z, Tsai ST, Tiwary P. Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. The Journal of Physical Chemistry. B. PMID 34788047 DOI: 10.1021/acs.jpcb.1c07595  0.33
2020 Pant S, Smith Z, Wang Y, Tajkhorshid E, Tiwary P. Confronting pitfalls of AI-augmented molecular dynamics using statistical physics. The Journal of Chemical Physics. 153: 234118. PMID 33353347 DOI: 10.1063/5.0030931  0.345
2020 Smith Z, Ravindra P, Wang Y, Cooley R, Tiwary P. Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 32841026 DOI: 10.1021/Acs.Jpcb.0C03985  0.406
2020 Wang Y, Tiwary P. Understanding the role of predictive time delay and biased propagator in RAVE. The Journal of Chemical Physics. 152: 144102. PMID 32295373 DOI: 10.1063/5.0004838  0.313
2020 Wang Y, Lamim Ribeiro JM, Tiwary P. Machine learning approaches for analyzing and enhancing molecular dynamics simulations. Current Opinion in Structural Biology. 61: 139-145. PMID 31972477 DOI: 10.1016/J.Sbi.2019.12.016  0.415
2020 Tsai S, Tiwary P. On the distance between A and B in molecular configuration space Molecular Simulation. 1-8. DOI: 10.1080/08927022.2020.1761548  0.323
2019 Tsai ST, Smith Z, Tiwary P. Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory. The Journal of Chemical Physics. 151: 154106. PMID 31640371 DOI: 10.1063/1.5124385  0.365
2019 Wang Y, Ribeiro JML, Tiwary P. Past-future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. Nature Communications. 10: 3573. PMID 31395868 DOI: 10.1038/S41467-019-11405-4  0.401
2019 Bonomi M, Bussi G, Camilloni C, Tribello GA, Banáš P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen H, ... ... Tiwary P, et al. Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods. 16: 670-673. PMID 31363226 DOI: 10.1038/S41592-019-0506-8  0.719
2019 Pramanik D, Smith Z, Kells A, Tiwary P. Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation. The Journal of Physical Chemistry. B. PMID 30974941 DOI: 10.1021/Acs.Jpcb.9B01813  0.469
2018 Smith Z, Pramanik D, Tsai ST, Tiwary P. Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization. The Journal of Chemical Physics. 149: 234105. PMID 30579304 DOI: 10.1063/1.5064856  0.411
2018 Ribeiro JML, Tsai ST, Pramanik D, Wang Y, Tiwary P. Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet? Biochemistry. PMID 30547565 DOI: 10.1021/Acs.Biochem.8B00977  0.449
2018 Ribeiro JML, Tiwary P. Towards Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE. Journal of Chemical Theory and Computation. PMID 30525598 DOI: 10.1021/Acs.Jctc.8B00869  0.459
2018 Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K. Frequency adaptive metadynamics for the calculation of rare-event kinetics. The Journal of Chemical Physics. 149: 072309. PMID 30134721 DOI: 10.1063/1.5024679  0.59
2018 Ribeiro JML, Bravo P, Wang Y, Tiwary P. Reweighted autoencoded variational Bayes for enhanced sampling (RAVE). The Journal of Chemical Physics. 149: 072301. PMID 30134694 DOI: 10.1063/1.5025487  0.38
2017 Tiwary P. Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin. The Journal of Physical Chemistry. B. PMID 29117680 DOI: 10.1021/Acs.Jpcb.7B09510  0.41
2017 Tiwary P, Berne BJ. Predicting reaction coordinates in energy landscapes with diffusion anisotropy. The Journal of Chemical Physics. 147: 152701. PMID 29055314 DOI: 10.1063/1.4983727  0.564
2017 Tiwary P, Mondal J, Berne BJ. How and when does an anticancer drug leave its binding site? Science Advances. 3: e1700014. PMID 28580424 DOI: 10.1126/Sciadv.1700014  0.648
2017 Dickson A, Tiwary P, Vashisth H. Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review. Current Topics in Medicinal Chemistry. PMID 28413946 DOI: 10.2174/1568026617666170414142908  0.423
2017 Casasnovas R, Limongelli V, Tiwary P, Carloni P, Parrinello M. Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations. Journal of the American Chemical Society. PMID 28290199 DOI: 10.1021/Jacs.6B12950  0.644
2016 Salvalaglio M, Tiwary P, Maggioni GM, Mazzotti M, Parrinello M. Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations. The Journal of Chemical Physics. 145: 211925. PMID 28799374 DOI: 10.1063/1.4966265  0.728
2016 Tiwary P, Berne BJ. How wet should be the reaction coordinate for ligand unbinding? The Journal of Chemical Physics. 145: 054113. PMID 27497545 DOI: 10.1063/1.4959969  0.551
2016 Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. Journal of Chemical Theory and Computation. PMID 27145262 DOI: 10.1021/Acs.Jctc.6B00201  0.555
2016 Tiwary P, Berne BJ. Kramers turnover: From energy diffusion to spatial diffusion using metadynamics. The Journal of Chemical Physics. 144: 134103. PMID 27059558 DOI: 10.1063/1.4944577  0.516
2016 Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annual Review of Physical Chemistry. PMID 26980304 DOI: 10.1146/Annurev-Physchem-040215-112229  0.539
2016 Mondal J, Tiwary P, Berne BJ. How a kinase inhibitor withstands Gatekeeper residue mutations. Journal of the American Chemical Society. PMID 26954686 DOI: 10.1021/Jacs.6B01232  0.618
2016 Tiwary P, Berne BJ. Spectral gap optimization of order parameters for sampling complex molecular systems. Proceedings of the National Academy of Sciences of the United States of America. PMID 26929365 DOI: 10.1073/Pnas.1600917113  0.581
2015 Tiwary P, Dama JF, Parrinello M. A perturbative solution to metadynamics ordinary differential equation. The Journal of Chemical Physics. 143: 234112. PMID 26696051 DOI: 10.1063/1.4937945  0.464
2015 Fleming KL, Tiwary P, Pfaendtner J. A New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations. The Journal of Physical Chemistry. A. PMID 26690335 DOI: 10.1021/Acs.Jpca.5B10667  0.431
2015 Quhe R, Nava M, Tiwary P, Parrinello M. Path Integral Metadynamics. Journal of Chemical Theory and Computation. 11: 1383-8. PMID 26574350 DOI: 10.1021/Ct501002A  0.558
2015 Nava M, Quhe R, Palazzesi F, Tiwary P, Parrinello M. de Broglie Swapping Metadynamics for Quantum and Classical Sampling. Journal of Chemical Theory and Computation. 11: 5114-9. PMID 26574309 DOI: 10.1021/Acs.Jctc.5B00818  0.454
2015 Tiwary P, Mondal J, Morrone JA, Berne BJ. Role of water and steric constraints in the kinetics of cavity-ligand unbinding. Proceedings of the National Academy of Sciences of the United States of America. PMID 26371312 DOI: 10.1073/Pnas.1516652112  0.693
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation. Physical Review Letters. 115: 070601. PMID 26317704 DOI: 10.1103/Physrevlett.115.070601  0.775
2015 Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps. Proceedings of the National Academy of Sciences of the United States of America. 112: E386-91. PMID 25605901 DOI: 10.1073/Pnas.1424461112  0.69
2015 Tiwary P, Parrinello M. A time-independent free energy estimator for metadynamics. The Journal of Physical Chemistry. B. 119: 736-42. PMID 25046020 DOI: 10.1021/Jp504920S  0.575
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation Physical Review Letters. 115. DOI: 10.1103/PhysRevLett.115.070601  0.718
2015 Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps Proceedings of the National Academy of Sciences of the United States of America. 112: E386-E391. DOI: 10.1073/pnas.1424461112  0.637
2015 Tiwary P, Parrinello M. A time-independent free energy estimator for metadynamics Journal of Physical Chemistry B. 119: 736-742. DOI: 10.1021/jp504920s  0.427
2015 Quhe R, Nava M, Tiwary P, Parrinello M. Path integral metadynamics Journal of Chemical Theory and Computation. 11: 1383-1388. DOI: 10.1021/ct501002a  0.308
2014 Salvalaglio M, Tiwary P, Parrinello M. Assessing the Reliability of the Dynamics Reconstructed from Metadynamics. Journal of Chemical Theory and Computation. 10: 1420-5. PMID 26580360 DOI: 10.1021/Ct500040R  0.74
2014 Van De Walle A, Hong Q, Miljacic L, Gopal CB, Demers S, Pomrehn G, Kowalski A, Tiwary P. Ab initio calculation of anisotropic interfacial excess free energies Physical Review B - Condensed Matter and Materials Physics. 89. DOI: 10.1103/Physrevb.89.184101  0.725
2014 Salvalaglio M, Tiwary P, Parrinello M. Assessing the reliability of the dynamics reconstructed from metadynamics Journal of Chemical Theory and Computation. 10: 1420-1425. DOI: 10.1021/ct500040r  0.636
2013 Tiwary P, Parrinello M. From metadynamics to dynamics. Physical Review Letters. 111: 230602. PMID 24476246 DOI: 10.1103/Physrevlett.111.230602  0.574
2013 Tiwary P, Parrinello M. From metadynamics to dynamics Physical Review Letters. 111. DOI: 10.1103/PhysRevLett.111.230602  0.412
2013 Tiwary P, Van De Walle A. Accelerated molecular dynamics through stochastic iterations and collective variable based basin identification Physical Review B - Condensed Matter and Materials Physics. 87. DOI: 10.1103/Physrevb.87.094304  0.627
2013 Van De Walle A, Tiwary P, De Jong M, Olmsted DL, Asta M, Dick A, Shin D, Wang Y, Chen LQ, Liu ZK. Efficient stochastic generation of special quasirandom structures Calphad: Computer Coupling of Phase Diagrams and Thermochemistry. 42: 13-18. DOI: 10.1016/J.Calphad.2013.06.006  0.674
2011 Tiwary P, Van De Walle A. Hybrid deterministic and stochastic approach for efficient atomistic simulations at long time scales Physical Review B - Condensed Matter and Materials Physics. 84. DOI: 10.1103/Physrevb.84.100301  0.661
2011 Tiwary P, Van De Walle A, Jeon B, Grønbech-Jensen N. Interatomic potentials for mixed oxide and advanced nuclear fuels Physical Review B - Condensed Matter and Materials Physics. 83. DOI: 10.1103/Physrevb.83.094104  0.64
2009 Tiwary P, Van De Walle A, Grønbech-Jensen N. Ab initio construction of interatomic potentials for uranium dioxide across all interatomic distances Physical Review B - Condensed Matter and Materials Physics. 80. DOI: 10.1103/Physrevb.80.174302  0.666
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