ZS
Zachary D. Smith
biophysicsMolecular Dynamics SimulationArtificial IntelligencebiochemistryLewy Body Diseasephysics.comp-phalpha-Synucleinalpha-synuclein fibrilsamplified LBD fibrilsAnti-HIV Agents
On Valency
published · living versionsW_r98kgkse·v1 · currentpublished
Learning developmental dynamics from lineage context
with Gokul Gowri, Nic Fishman, William N. Colgan, Minming Wang +8
1 version
Preprints & journals
16 papers in the corpus · 2018–2026Photonic qubit encoding interconversion for heterogeneous quantum networking2604.02081v1 · Vedansh Nehra, Richard J. Birrittella, Christopher C. Tison et al.2026 · 0 citationsarXiv
Toward Automated Physics-Based Absolute Drug Residence Time Predictions.41365673 · Smith, Zachary, Branduardi, Davide, Lupyan, Dmitry et al.2025 · 15 citationsJournal of chemical information and modeling. 2025;65(24):13360-13373
Use of Amplified Lewy Body Dementia Fibrils and Autoradiography to Characterize Binding of Radioligand Tg-1-90B to Alpha-Synuclein Fibrils in Postmortem Brain Tissue.41002442 · O'Shea, Jennifer Y, Dhavale, Dhruva D, Hwang, Helen et al.2025 · 1 citationCells. 2025;14(18)
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention.37546775 · Smith, Zachary, Strobel, Michael, Vani, Bodhi P et al.2024 · 46 citationsbioRxiv : the preprint server for biology. 2023
Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue.36711931 · Dhavale, Dhruva D, Barclay, Alexander M, Borcik, Collin G et al.2024 · 73 citationsbioRxiv : the preprint server for biology. 2023
Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases.35486370 · Shekhar, Mrinal, Smith, Zachary, Seeliger, Markus A et al.2022 · 48 citationsAngewandte Chemie (International ed. in English). 2022;61(28):e202200983
SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations.34662516 · Tsai, Sun-Ting, Smith, Zachary, Tiwary, Pratyush2021 · 35 citationsJournal of chemical theory and computation. 2021;17(11):6757-6765
Making High-Dimensional Molecular Distribution Functions Tractable through Belief Propagation on Factor Graphs.34586819 · Smith, Zachary, Tiwary, Pratyush2021 · 1 citationThe journal of physical chemistry. B. 2021;125(40):11150-11158
Confronting pitfalls of AI-augmented molecular dynamics using statistical physics.33353347 · Pant, Shashank, Smith, Zachary, Wang, Yihang et al.2021 · 25 citationsThe Journal of chemical physics. 2020;153(23):234118
Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics.32841026 · Smith, Zachary, Ravindra, Pavan, Wang, Yihang et al.2021 · 31 citationsThe journal of physical chemistry. B. 2020;124(38):8221-8229
Discovering loop conformational flexibility in T4 lysozyme mutants through Artificial Intelligence aided Molecular Dynamics10.1101/2020.04.08.032748v2 · Smith, Z., Ravindra, P., Wang, Y. et al.2020 · 1 citationbioRxiv
Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory.31640371 · Tsai, Sun-Ting, Smith, Zachary, Tiwary, Pratyush2019 · 29 citationsThe Journal of chemical physics. 2019;151(15):154106
Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems10.1101/745968v1 · Ravindra, P., Smith, Z., Tiwary, P.2019 · 67 citationsbioRxiv
Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation.30974941 · Pramanik, Debabrata, Smith, Zachary, Kells, Adam et al.2020 · 42 citationsThe journal of physical chemistry. B. 2019;123(17):3672-3678
Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization.30579304 · Smith, Zachary, Pramanik, Debabrata, Tsai, Sun-Ting et al.2019 · 41 citationsThe Journal of chemical physics. 2018;149(23):234105
Griffiths Physics in an Ultracold Bose Gas1806.07434v4 · M. E. W. Reed, Z. S. Smith, Aftaab Dewan et al.2018 · 1 citationPhys. Rev. A 99, 063611 (2019)
Career total: 27 works. 16 are in this corpus.
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