Physics of Living Systems

Publications

Tiwary Lab

PI: Pratyush Tiwary

^, *, and ** denote postdoctoral scholars, graduate and undergraduate students respectively mentored in the Tiwary group at the University of Maryland.

  • Wang*, Ribeiro^ and Tiwary, "Machine learning approaches for analyzing and enhancing molecular dynamics simulations", arXiv (submitted)
  • Ravindra**, Smith* and Tiwary, "Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems", bioRxiv (submitted)
  • Tsai*, Smith* and Tiwary, "Reaction coordinates and rate constants for liquid droplet nucleation: quantifying the interplay between driving force and memory", J. Chem. Phys. (Emerging investigators special collection) (in press)
  • Wang*, Ribeiro^ and Tiwary, "Past-future information bottleneck framework for simultaneously sampling biomolecular reaction coordinate, thermodynamics and kinetics", Nature Communications 2019
  • Bonomi, Bussi, Camilloni et al, "Promoting transparency and reproducibility in enhanced molecular simulations", Nature Methods 2019
  • Pramanik^, Smith*, Kells* and Tiwary, "Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation", J. Phys. Chem. B 2019
  • Ribeiro^, Tsai*, Pramanik^, Wang* and Tiwary, "Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet?", Biochemistry (Future of Biochemistry: The International Issue), invited perspective article, 2019
  • Ribeiro^ and Tiwary, "Towards Achieving Reversible Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE", J. Chem. Theor. Comp. 2019

  • Smith*, Pramanik^, Tsai* and Tiwary, "Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization", J. Chem. Phys. 2018
  • Ribeiro^, Bravo**, Wang* and Tiwary, "Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)", J. Chem. Phys. 2018
  • Wang, Valsson, Tiwary, Parrinello and Lindorff-Larsen, "Frequency adaptive metadynamics for the calculation of rare event kinetics", J. Chem. Phys. 2018
  • Bussi, Laio and Tiwary, "Metadynamics: a unified framework for accelerating rare events and sampling thermodynamics and kinetics", Handbook of Materials Modeling (Springer), Ed. Sidney Yip and Wanda Andreoni, 2018

  • Tiwary, "Molecular determinants and bottlenecks in the dissociation dynamics of biotin-streptavidin", J. Phys. Chem. B 2017
Publications Prior to the University of Maryland

  • Tiwary and Berne, "Predicting reaction coordinates in energy landscapes with diffusion anisotropy" J. Chem. Phys.: Special topic issue on reaction pathways 2017. Selected as 2017 Editor's choice paper
  • Dickson, Tiwary and Vashisth, "Kinetics of ligand binding through advanced computational approaches: A review", Curr. Top. Med. Chem. 2017 (Invited review article)
  • Tiwary, Mondal and Berne, "How and when does an anti-cancer drug leave its binding site?", Science Advances 2017
  • Casasnovas, Limongelli, Tiwary, Carloni and Parrinello, "Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations", J. Amer. Chem. Soc. 2017

  • Salvalaglio, Tiwary, Maggioni, Mazzotti and Parrinello, "Overcoming timescale and finite-size limitations to compute nucleation rates from small scale well tempered metadynamics simulations" , J. Chem. Phys. 2016
  • Tiwary and Berne, "How wet should be the reaction coordinate for ligand unbinding?", J. Chem. Phys. 2016
  • Clark, Tiwary, Borrelli, Feng, Miller, Abel, Friesner and Berne, "Prediction of protein-ligand binding poses via a combination of induced fit docking and metadynamics simulations", J. Chem. Theor. Comp. 2016.
  • Mondal, Tiwary and Berne, "How a kinase inhibitor withstands gatekeeper residue mutations", J. Amer. Chem. Soc. 2016
  • Tiwary and Berne, "Kramers turnover: from energy diffusion to spatial diffusion using metadynamics", J. Chem. Phys. 2016
  • Tiwary and Berne, "Spectral gap optimization of order parameters (SGOOP) for sampling complex molecular systems", Proc. Natl. Acad. Sci. 2016
  • * Valsson, Tiwary & Parrinello, "Enhancing essential fluctuations: Rare events and metadynamics from a conceptual viewpoint", Ann. Rev. Phys. Chem. 2016 (Invited review article) (Web of Science top 1%)
  • Tiwary and van de Walle, "A review of enhanced sampling approaches for accelerated molecular dynamics", Multiscale materials modeling for nanomechanics (Springer series in materials science), 2016 (Invited book chapter)
  • Fleming, Tiwary and Pfaendtner, "A New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations", J. Phys. Chem. A 2016. Selected as ACS Editors' Choice. In top 10 most downloaded article in last year

  • Tiwary, Dama and Parrinello, "A perturbative solution to metadynamics ordinary differential equation", J. Chem. Phys. 2015
  • Nava, Quhe, Palazzesi, Tiwary and Parrinello, "De Broglie swapping metadynamics for quantum and classical sampling", J. Chem. Theor. Comp. 2015
  • Tiwary, Mondal, Morrone and Berne, "The role of water and steric effects in the kinetics of cavity-ligand unbinding", Proc. Natl. Acad. Sci. 2015 See Philip Ball's blog post from Water in Biology
  • McCarty, Valsson, Tiwary & Parrinello, "Variationally optimized free energy flooding for rate calculation", Phys. Rev. Lett. 2015
  • * Tiwary, Limongelli, Salvalaglio and Parrinello, "Kinetics of protein-ligand unbinding: predicting pathways, rates and rate-determining steps", Proc. Natl. Acad. Sci. 2015 (Web of Science top 1%)
  • Quhe, Nava, Tiwary and Parrinello, "Path-integral metadynamics", J. Chem. Theor. Comp. 2015
  • * Tiwary and Parrinello, "A time-independent free energy estimator for metadynamics", J. Phys. Chem. B 2015 (Web of Science top 1%)

  • Salvalaglio, Tiwary and Parrinello, "Assessing the reliability of dynamics reconstructed from metadynamics", J. Chem. Theor. Comp. 2014
  • van de Walle, Hong, Miljacic, Gopal, Demers, Pomrehn, Kowalski and Tiwary, "Ab initio calculation of anisotropic interfacial excess free energies", Phys. Rev. B 2014

  • * Tiwary and Parrinello, "From metadynamics to dynamics", Phys. Rev. Lett. 2013. See associated highlight in Physics
  • Tiwary and van de Walle, "SISYPHUS: Hybrid MC-MD approach in a more robust framework", Phys. Rev. B 2013
  • * van de Walle, Tiwary, de Jong, Olmstead, Asta, Dick, Shin and Wang, "Efficient stochastic generation of special quasirandom structures", Calphad 2013 (Web of Science top 1%)

  • Tiwary and van de Walle, "SISYPHUS: Hybrid MC-MD approach for extended timescales", Phys. Rev. B (Rapid Communications) 2011
  • Tiwary, van de Walle, Jeon and Gronbech-Jensen, "DFT+U and experiment fitted interatomic potentials for (U,Pu,Np)O2", Phys. Rev. B 2011

  • Tiwary, van de Walle and Gronbech-Jensen, "DFT+U and experiment fitted interatomic potentials for UO2", Phys. Rev. B 2009

  • Tiwary and Pandey, "An analytical expression for the characteristic length scale for randomly faulted close-packed structures", Acta Cryst. A 2007
  • Tiwary and Pandey, "Scaling behavior of pair correlation functions for randomly faulted close-packed structures", Acta Cryst. A 2007
  • Tiwary and Ghosh, "Cluster variation investigation of phase equilibria in Fe–Co system using simulated annealing approach", Comp. Mat. Sci. 2007