# 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/Year | Citation | Score | |||
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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 |
0.48 | |||

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 |
0.48 | |||

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 |
0.48 | |||

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 |
0.48 | |||

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 |
0.48 | |||

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 |
1 | |||

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 |
0.48 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

2013 | Tiwary P, Parrinello M. From metadynamics to dynamics. Physical Review Letters. 111: 230602. PMID 24476246 DOI: 10.1103/PhysRevLett.111.230602 |
1 | |||

2013 | Tiwary P, Parrinello M. From metadynamics to dynamics Physical Review Letters. 111. DOI: 10.1103/PhysRevLett.111.230602 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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 |
1 | |||

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