Zack Smith

Zack Smith

Graduate student in the Tiwary Lab at Unviersity of Maryland, College Park. Joining Schrödinger in August 2023.

Publications

  1. Mrinal Shekhar, Zachary Smith, Markus Seeliger, and Pratyush Tiwary. Protein flexibility and dissociation pathway differentiation can explain onset of resistance mutations in kinases Hot paper in Angewandte Chemie (134), e202200983, 2022.
  2. Zachary Smith, and Pratyush Tiwary. Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs The Journal of Physical Chemistry B 125 (40), 11150-11158, 2021.
  3. Sun-Ting Tsai, Zachary Smith, and Pratyush Tiwary. SGOOP-d: Estimating kinetic distances and reaction coordinate dimensionality for rare event systems from biased/unbiased simulations Journal of Chemical Theory and Computation 17 (11), 6757-6765, 2021.
  4. Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, and Pratyush Tiwary. Confronting pitfalls of AI-augmented molecular dynamics using statistical physics Editor’s choice, featured article, and cover of The Journal of Chemical Physics 153 (23): 234118, 2020.
  5. Zachary Smith, Pavan Ravindra, Yihang Wang, Rory Cooley, Pratyush Tiwary. Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics Machine Learning in Physical Chemistry special issue of The Journal of Physical Chemistry B 124 (38): 8221-8229, 2020.
  6. Zachary Smith, Pavan Ravindra, Pratyush Tiwary. Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems Emerging Investigators special issue of Molecular Systems Design & Engineering 5 (1): 339-348, 2020.
  7. Sun-Ting Tsai, Zachary Smith, Pratyush Tiwary. Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory The Journal of Chemical Physics 151 (15): 154106, 2019.
  8. Debabrata Pramanik, Zachary Smith, Adam Kells, Pratyush Tiwary. 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 123 (17): 3672-3678, 2019.
  9. Zachary Smith, Debabrata Pramanik, Sun-Ting Tsai, Pratyush Tiwary. Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization Markov Models of Molecular Kinetics special issue of The Journal of Chemical Physics 149 (23): 234105, 2018.