Thomas E Markland

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 48

Top Venues

The journal of physical chemistry. B

The Journal of chemical physics

The journal of physical chemistry letters

Journal of chemical information and modeling

Stanford University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Stanford University Aug 01 2018

United States

Associate Professor :: Chemistry

Stanford University Aug 01 2011 - Aug 01 2018

United States

Assistant Professor :: Chemistry

Publications

Raul P Pelaez, Guillem Simeon, Raimondas Galvelis, Antonio Mirarchi, Peter Eastman, Stefan Doerr, Philipp Thölke, Thomas E Markland, Gianni De Fabritiis
TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. Journal of chemical theory and computation 20 (10) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Raul P Pelaez, Guillem Simeon, Raimondas Galvelis, Antonio Mirarchi, Peter Eastman, Stefan Doerr, Philipp Thölke, Thomas E Markland, Gianni De Fabritiis
TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. Journal of chemical theory and computation (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Raul P Pelaez, Guillem Simeon, Raimondas Galvelis, Antonio Mirarchi, Peter Eastman, Stefan Doerr, Philipp Thölke, Thomas E Markland, Gianni De Fabritiis
TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. Journal of chemical theory and computation 20 (10) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling (2024)
Raul P Pelaez, Guillem Simeon, Raimondas Galvelis, Antonio Mirarchi, Peter Eastman, Stefan Doerr, Philipp Thölke, Thomas E Markland, Gianni De Fabritiis
TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. Journal of chemical theory and computation (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter Eastman, Thomas E Markland, John D Chodera, Gianni De Fabritiis
NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. Journal of chemical information and modeling (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Anthony J Dominic, Thomas Sayer, Siqin Cao, Thomas E Markland, Xuhui Huang, Andrés Montoya-Castillo
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (12) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B (2023)
Kenneth A Jung, Joseph Kelly, Thomas E Markland
Electron transfer at electrode interfaces via a straightforward quasiclassical fermionic mapping approach. The Journal of chemical physics 159 (1) (2023)
Michael S Chen, Yuezhi Mao, Andrew Snider, Prachi Gupta, Andrés Montoya-Castillo, Tim J Zuehlsdorff, Christine M Isborn, Thomas E Markland
Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure. The journal of physical chemistry letters (2023)
Austin O Atsango, Andrés Montoya-Castillo, Thomas E Markland
An accurate and efficient Ehrenfest dynamics approach for calculating linear and nonlinear electronic spectra. The Journal of chemical physics 158 (7) (2023)
Anthony J Dominic, Thomas Sayer, Siqin Cao, Thomas E Markland, Xuhui Huang, Andrés Montoya-Castillo
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (12) (2023)
Michael S Chen, Joonho Lee, Hong-Zhou Ye, Timothy C Berkelbach, David R Reichman, Thomas E Markland
Data-Efficient Machine Learning Potentials from Transfer Learning of Periodic Correlated Electronic Structure Methods: Liquid Water at AFQMC, CCSD, and CCSD(T) Accuracy. Journal of chemical theory and computation (2023)
Anthony J Dominic, Thomas Sayer, Siqin Cao, Thomas E Markland, Xuhui Huang, Andrés Montoya-Castillo
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (12) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Andrés Montoya-Castillo, Thomas E Markland
A derivation of the conditions under which bosonic operators exactly capture fermionic structure and dynamics. The Journal of chemical physics 158 (9) (2023)
Kenneth A Jung, Thomas E Markland
2D spectroscopies from condensed phase dynamics: Accessing third-order response properties from equilibrium multi-time correlation functions. The Journal of chemical physics 157 (9) (2022)
Steven D E Fried, Chu Zheng, Yuezhi Mao, Thomas E Markland, Steven G Boxer
Solvent Organization and Electrostatics Tuned by Solute Electronic Structure: Amide versus Non-Amide Carbonyls. The journal of physical chemistry. B 126 (31) (2022)
Chu Zheng, Yuezhi Mao, Jacek Kozuch, Austin O Atsango, Zhe Ji, Thomas E Markland, Steven G Boxer
A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site. Nature chemistry 14 (8) (2022)
Austin O Atsango, Mark E Tuckerman, Thomas E Markland
Characterizing and Contrasting Structural Proton Transport Mechanisms in Azole Hydrogen Bond Networks Using Ab Initio Molecular Dynamics. The journal of physical chemistry letters 12 (36) (2021)
Yuezhi Mao, Andrés Montoya-Castillo, Thomas E Markland
Excited state diabatization on the cheap using DFT: Photoinduced electron and hole transfer. The Journal of chemical physics 153 (24) (2021)
Michael S Chen, Tobias Morawietz, Hideki Mori, Thomas E Markland, Nongnuch Artrith
AENET-LAMMPS and AENET-TINKER: Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials. The Journal of chemical physics 155 (7) (2021)
Zhaorui Huang, Michael S Chen, Cristian P Woroch, Thomas E Markland, Matthew W Kanan
A framework for automated structure elucidation from routine NMR spectra. Chemical science 12 (46) (2021)
Siqin Cao, Andrés Montoya-Castillo, Wei Wang, Thomas E Markland, Xuhui Huang
On the advantages of exploiting memory in Markov state models for biomolecular dynamics. The Journal of chemical physics 153 (1) (2021)
Michael S Chen, Tim J Zuehlsdorff, Tobias Morawietz, Christine M Isborn, Thomas E Markland
Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. The journal of physical chemistry letters 11 (18) (2020)
Santanu Roy, Gregory K Schenter, Joseph A Napoli, Marcel D Baer, Thomas E Markland, Christopher J Mundy
Resolving Heterogeneous Dynamics of Excess Protons in Aqueous Solution with Rate Theory. The journal of physical chemistry. B 124 (27) (2020)
Zhuoran Long, Austin O Atsango, Joseph A Napoli, Thomas E Markland, Mark E Tuckerman
Elucidating the Proton Transport Pathways in Liquid Imidazole with First-Principles Molecular Dynamics. The journal of physical chemistry letters 11 (15) (2020)
Tobias Morawietz, Andres S Urbina, Patrick K Wise, Xiangen Wu, Wanjun Lu, Dor Ben-Amotz, Thomas E Markland
Hiding in the Crowd: Spectral Signatures of Overcoordinated Hydrogen-Bond Environments. The journal of physical chemistry letters 10 (20) (2019)
Mark A Boyer, Ondrej Marsalek, Joseph P Heindel, Thomas E Markland, Anne B McCoy, Sotiris S Xantheas
Beyond Badger's Rule: The Origins and Generality of the Structure-Spectra Relationship of Aqueous Hydrogen Bonds. The journal of physical chemistry letters 10 (5) (2019)
Yuezhi Mao, Andrés Montoya-Castillo, Thomas E Markland
Accurate and efficient DFT-based diabatization for hole and electron transfer using absolutely localized molecular orbitals. The Journal of chemical physics 151 (16) (2019)
Luis Ruiz Pestana, Ondrej Marsalek, Thomas E Markland, Teresa Head-Gordon
The Quest for Accurate Liquid Water Properties from First Principles. The journal of physical chemistry letters 9 (17) (2018)
Andrés Montoya-Castillo, Thomas E Markland
On the exact continuous mapping of fermions. Scientific reports 8 (1) (2018)
Tobias Morawietz, Ondrej Marsalek, Shannon R Pattenaude, Louis M Streacker, Dor Ben-Amotz, Thomas E Markland
The Interplay of Structure and Dynamics in the Raman Spectrum of Liquid Water over the Full Frequency and Temperature Range. The journal of physical chemistry letters 9 (4) (2018)
Joseph A Napoli, Ondrej Marsalek, Thomas E Markland
Decoding the spectroscopic features and time scales of aqueous proton defects. The Journal of chemical physics 148 (22) (2018)
Tim J Zuehlsdorff, Joseph A Napoli, Joel M Milanese, Thomas E Markland, Christine M Isborn
Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. The Journal of chemical physics 149 (2) (2018)
Lu Wang, Stephen D Fried, Thomas E Markland
Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. The journal of physical chemistry. B 121 (42) (2017)

Thomas E Markland.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Thomas E Markland