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Thomas E. Markland - Publications

Affiliations: 
2011- Chemistry Stanford University, Palo Alto, CA 
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69/75 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, ... ... Markland TE, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry. B. PMID 38154096 DOI: 10.1021/acs.jpcb.3c06662  0.609
2023 Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, ... ... Markland TE, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. Arxiv. PMID 37986730  0.609
2023 Atsango AO, Morawietz T, Marsalek O, Markland TE. Developing machine-learned potentials to simultaneously capture the dynamics of excess protons and hydroxide ions in classical and path integral simulations. The Journal of Chemical Physics. 159. PMID 37581418 DOI: 10.1063/5.0162066  0.805
2023 Chen MS, Mao Y, Snider A, Gupta P, Montoya-Castillo A, Zuehlsdorff TJ, Isborn CM, Markland TE. 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. 6610-6619. PMID 37459252 DOI: 10.1021/acs.jpclett.3c01444  0.789
2023 Dominic AJ, Sayer T, Cao S, Markland TE, Huang X, Montoya-Castillo A. 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: e2221048120. PMID 36920924 DOI: 10.1073/pnas.2221048120  0.782
2023 Montoya-Castillo A, Markland TE. A derivation of the conditions under which bosonic operators exactly capture fermionic structure and dynamics. The Journal of Chemical Physics. 158: 094112. PMID 36889969 DOI: 10.1063/5.0138664  0.765
2023 Atsango AO, Montoya-Castillo A, Markland TE. An accurate and efficient Ehrenfest dynamics approach for calculating linear and nonlinear electronic spectra. The Journal of Chemical Physics. 158: 074107. PMID 36813724 DOI: 10.1063/5.0138671  0.741
2023 Chen MS, Lee J, Ye HZ, Berkelbach TC, Reichman DR, Markland TE. 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. PMID 36730728 DOI: 10.1021/acs.jctc.2c01203  0.566
2023 Eastman P, Behara PK, Dotson DL, Galvelis R, Herr JE, Horton JT, Mao Y, Chodera JD, Pritchard BP, Wang Y, De Fabritiis G, Markland TE. SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Scientific Data. 10: 11. PMID 36599873 DOI: 10.1038/s41597-022-01882-6  0.571
2022 Jung KA, Markland TE. 2D spectroscopies from condensed phase dynamics: Accessing third-order response properties from equilibrium multi-time correlation functions. The Journal of Chemical Physics. 157: 094111. PMID 36075710 DOI: 10.1063/5.0107087  0.364
2022 Montoya-Castillo A, Chen MS, Raj SL, Jung KA, Kjaer KS, Morawietz T, Gaffney KJ, van Driel TB, Markland TE. Optically Induced Anisotropy in Time-Resolved Scattering: Imaging Molecular-Scale Structure and Dynamics in Disordered Media with Experiment and Theory. Physical Review Letters. 129: 056001. PMID 35960558 DOI: 10.1103/PhysRevLett.129.056001  0.77
2022 Fried SDE, Zheng C, Mao Y, Markland TE, Boxer SG. Solvent Organization and Electrostatics Tuned by Solute Electronic Structure: Amide versus Non-Amide Carbonyls. The Journal of Physical Chemistry. B. 126: 5876-5886. PMID 35901512 DOI: 10.1021/acs.jpcb.2c03095  0.543
2022 Zheng C, Mao Y, Kozuch J, Atsango AO, Ji Z, Markland TE, Boxer SG. A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site. Nature Chemistry. PMID 35513508 DOI: 10.1038/s41557-022-00937-w  0.539
2021 Atsango AO, Tuckerman ME, Markland TE. Characterizing and Contrasting Structural Proton Transport Mechanisms in Azole Hydrogen Bond Networks Using Molecular Dynamics. The Journal of Physical Chemistry Letters. 8749-8756. PMID 34478302 DOI: 10.1021/acs.jpclett.1c02266  0.547
2021 Chen MS, Morawietz T, Mori H, Markland TE, Artrith N. AENET-LAMMPS and AENET-TINKER: Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials. The Journal of Chemical Physics. 155: 074801. PMID 34418919 DOI: 10.1063/5.0063880  0.75
2021 Hu Y, Ounkham P, Marsalek O, Markland TE, Krishmoorthy B, Clark AE. Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics. Frontiers in Chemistry. 9: 624937. PMID 33748074 DOI: 10.3389/fchem.2021.624937  0.688
2020 Mao Y, Montoya-Castillo A, Markland TE. Excited state diabatization on the cheap using DFT: Photoinduced electron and hole transfer. The Journal of Chemical Physics. 153: 244111. PMID 33380087 DOI: 10.1063/5.0035593  0.784
2020 Chen MS, Zuehlsdorff TJ, Morawietz T, Isborn CM, Markland TE. Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. The Journal of Physical Chemistry Letters. PMID 32808797 DOI: 10.1021/Acs.Jpclett.0C02168  0.746
2020 Cao S, Montoya-Castillo A, Wang W, Markland TE, Huang X. On the advantages of exploiting memory in Markov state models for biomolecular dynamics. The Journal of Chemical Physics. 153: 014105. PMID 32640825 DOI: 10.1063/5.0010787  0.792
2020 Long Z, Atsango AO, Napoli JA, Markland TE, Tuckerman ME. Elucidating the Proton Transport Pathways in Liquid Imidazole with First-principles Molecular Dynamics. The Journal of Physical Chemistry Letters. PMID 32633523 DOI: 10.1021/Acs.Jpclett.0C01744  0.594
2020 Roy S, Schenter GK, Napoli JA, Baer MD, Markland TE, Mundy CJ. Resolving Heterogeneous Dynamics of Excess Protons in Aqueous Solution with Rate Theory. The Journal of Physical Chemistry. B. PMID 32482074 DOI: 10.1021/Acs.Jpcb.0C02649  0.373
2020 Wang L, Ceriotti M, Markland TE. Quantum kinetic energy and isotope fractionation in aqueous ionic solutions. Physical Chemistry Chemical Physics : Pccp. PMID 31942581 DOI: 10.1039/C9Cp06483D  0.497
2019 Mao Y, Montoya-Castillo A, Markland TE. Accurate and efficient DFT-based diabatization for hole and electron transfer using absolutely localized molecular orbitals. The Journal of Chemical Physics. 151: 164114. PMID 31675855 DOI: 10.1063/1.5125275  0.804
2019 Morawietz T, Urbina AS, Wise PK, Wu X, Lu W, Ben-Amotz D, Markland TE. Hiding in the Crowd: Spectral Signatures of Overcoordinated Hydrogen Bond Environments. The Journal of Physical Chemistry Letters. PMID 31549833 DOI: 10.1021/Acs.Jpclett.9B01781  0.74
2019 Zuehlsdorff TJ, Montoya-Castillo A, Napoli JA, Markland TE, Isborn CM. Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches. The Journal of Chemical Physics. 151: 074111. PMID 31438704 DOI: 10.1063/1.5114818  0.792
2019 Yuan R, Napoli JA, Yan C, Marsalek O, Markland TE, Fayer MD. Tracking Aqueous Proton Transfer by Two-Dimensional Infrared Spectroscopy and ab Initio Molecular Dynamics Simulations. Acs Central Science. 5: 1269-1277. PMID 31403075 DOI: 10.1021/Acscentsci.9B00447  0.71
2019 Pfalzgraff WC, Montoya-Castillo A, Kelly A, Markland TE. Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics. The Journal of Chemical Physics. 150: 244109. PMID 31255061 DOI: 10.1063/1.5095715  0.792
2019 Boyer MA, Marsalek O, Heindel J, Markland TE, McCoy AB, Xantheas SS. Beyond Badger's Rule: The Origins and Generality of the Structure-Spectra Relationship of Aqueous Hydrogen Bond. The Journal of Physical Chemistry Letters. PMID 30735052 DOI: 10.1021/Acs.Jpclett.8B03790  0.675
2019 Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, ... ... Markland TE, et al. i-PI 2.0: A universal force engine for advanced molecular simulations Computer Physics Communications. 236: 214-223. DOI: 10.1016/J.Cpc.2018.09.020  0.742
2018 Montoya-Castillo A, Markland TE. On the exact continuous mapping of fermions. Scientific Reports. 8: 12929. PMID 30154503 DOI: 10.1038/S41598-018-31162-6  0.757
2018 Ruiz Pestana L, Marsalek O, Markland TE, Head-Gordon T. The Quest for Accurate Liquid Water Properties from First Principles. The Journal of Physical Chemistry Letters. 5009-5016. PMID 30118601 DOI: 10.1021/Acs.Jpclett.8B02400  0.75
2018 Zuehlsdorff TJ, Napoli JA, Milanese JM, Markland TE, Isborn CM. Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. The Journal of Chemical Physics. 149: 024107. PMID 30007372 DOI: 10.1063/1.5025517  0.44
2018 Napoli JA, Marsalek O, Markland TE. Decoding the spectroscopic features and time scales of aqueous proton defects. The Journal of Chemical Physics. 148: 222833. PMID 29907063 DOI: 10.1063/1.5023704  0.719
2018 Morawietz T, Marsalek O, Pattenaude SR, Streacker LM, Ben-Amotz D, Markland TE. 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. PMID 29394069 DOI: 10.1021/Acs.Jpclett.8B00133  0.775
2018 Schran C, Marsalek O, Markland TE. Corrigendum to “Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond” [Chem. Phys. Lett. 678 (2017) 289–295] Chemical Physics Letters. 712: 215. DOI: 10.1016/J.Cplett.2018.09.064  0.789
2017 Wang L, Fried SD, Markland TE. Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. The Journal of Physical Chemistry. B. PMID 28915043 DOI: 10.1021/Acs.Jpcb.7B06985  0.427
2017 Marsalek O, Markland TE. Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects. The Journal of Physical Chemistry Letters. 8: 1545-1551. PMID 28296422 DOI: 10.1021/Acs.Jpclett.7B00391  0.751
2017 Lau VM, Pfalzgraff WC, Markland TE, Kanan MW. Electrostatic control of regioselectivity in Au(I)-catalyzed hydroarylation. Journal of the American Chemical Society. PMID 28225605 DOI: 10.1021/Jacs.6B11971  0.765
2017 Schran C, Marsalek O, Markland TE. Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond Chemical Physics Letters. 678: 289-295. DOI: 10.1016/J.Cplett.2017.04.034  0.789
2016 Wang L, Isborn CM, Markland TE. Simulating Nuclear and Electronic Quantum Effects in Enzymes. Methods in Enzymology. 577: 389-418. PMID 27498646 DOI: 10.1016/Bs.Mie.2016.05.047  0.498
2016 Kelly A, Montoya-Castillo A, Wang L, Markland TE. Generalized quantum master equations in and out of equilibrium: When can one win? The Journal of Chemical Physics. 144: 184105. PMID 27179469 DOI: 10.1063/1.4948612  0.819
2016 Ceriotti M, Fang W, Kusalik PG, McKenzie RH, Michaelides A, Morales MA, Markland TE. Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges. Chemical Reviews. PMID 27049513 DOI: 10.1021/Acs.Chemrev.5B00674  0.456
2016 Yan C, Yuan R, Pfalzgraff WC, Nishida J, Wang L, Markland TE, Fayer MD. Unraveling the dynamics and structure of functionalized self-assembled monolayers on gold using 2D IR spectroscopy and MD simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 27044113 DOI: 10.1073/Pnas.1603080113  0.785
2016 Marsalek O, Markland TE. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory. The Journal of Chemical Physics. 144: 054112. PMID 26851913 DOI: 10.1063/1.4941093  0.75
2015 Pfalzgraff WC, Kelly AT, Markland TE. Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations. The Journal of Physical Chemistry Letters. PMID 26563917 DOI: 10.1021/Acs.Jpclett.5B02131  0.81
2015 Kelly A, Brackbill N, Markland TE. Accurate nonadiabatic quantum dynamics on the cheap: making the most of mean field theory with master equations. The Journal of Chemical Physics. 142: 094110. PMID 25747064 DOI: 10.1063/1.4913686  0.658
2014 Wang L, Fried SD, Boxer SG, Markland TE. Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site. Proceedings of the National Academy of Sciences of the United States of America. 111: 18454-9. PMID 25503367 DOI: 10.1073/Pnas.1417923111  0.444
2014 Wang L, Ceriotti M, Markland TE. Quantum fluctuations and isotope effects in ab initio descriptions of water. The Journal of Chemical Physics. 141: 104502. PMID 25217932 DOI: 10.1063/1.4894287  0.496
2014 Luehr N, Markland TE, Martínez TJ. Multiple time step integrators in ab initio molecular dynamics. The Journal of Chemical Physics. 140: 084116. PMID 24588157 DOI: 10.1063/1.4866176  0.46
2014 Nistor RA, Markland TE, Berne BJ. Interface-limited growth of heterogeneously nucleated ice in supercooled water. The Journal of Physical Chemistry. B. 118: 752-60. PMID 24393086 DOI: 10.1021/Jp408832B  0.519
2014 Wang L, Fried SD, Wu Y, Boxer SG, Markland TE. Quantum Delocalization of Protons in the Ketosteroid Isomerase Active Site Biophysical Journal. 106: 589a. DOI: 10.1016/J.Bpj.2013.11.3263  0.456
2013 Kelly A, Markland TE. Efficient and accurate surface hopping for long time nonadiabatic quantum dynamics. The Journal of Chemical Physics. 139: 014104. PMID 23822290 DOI: 10.1063/1.4812355  0.659
2013 Habershon S, Manolopoulos DE, Markland TE, Miller TF. Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. Annual Review of Physical Chemistry. 64: 387-413. PMID 23298242 DOI: 10.1146/Annurev-Physchem-040412-110122  0.763
2013 Ceriotti M, Markland TE. Efficient methods and practical guidelines for simulating isotope effects. The Journal of Chemical Physics. 138: 014112. PMID 23298033 DOI: 10.1063/1.4772676  0.455
2012 Hocky GM, Markland TE, Reichman DR. Growing point-to-set length scale correlates with growing relaxation times in model supercooled liquids. Physical Review Letters. 108: 225506. PMID 23003622 DOI: 10.1103/Physrevlett.108.225506  0.756
2012 Zeidler A, Salmon PS, Fischer HE, Neuefeind JC, Simonson JM, Markland TE. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 24: 284126. PMID 22738936 DOI: 10.1088/0953-8984/24/28/284126  0.389
2012 Markland TE, Berne BJ. Unraveling quantum mechanical effects in water using isotopic fractionation. Proceedings of the National Academy of Sciences of the United States of America. 109: 7988-91. PMID 22566650 DOI: 10.1073/Pnas.1203365109  0.596
2012 Berkelbach TC, Markland TE, Reichman DR. Reduced density matrix hybrid approach: application to electronic energy transfer. The Journal of Chemical Physics. 136: 084104. PMID 22380029 DOI: 10.1063/1.3687342  0.604
2012 Markland TE, Morrone JA, Miyazaki K, Berne BJ, Reichman DR, Rabani E. Theory and simulations of quantum glass forming liquids. The Journal of Chemical Physics. 136: 074511. PMID 22360252 DOI: 10.1063/1.3684881  0.786
2012 Berkelbach TC, Reichman DR, Markland TE. Reduced density matrix hybrid approach: an efficient and accurate method for adiabatic and non-adiabatic quantum dynamics. The Journal of Chemical Physics. 136: 034113. PMID 22280750 DOI: 10.1063/1.3671372  0.64
2011 Zeidler A, Salmon PS, Fischer HE, Neuefeind JC, Simonson JM, Lemmel H, Rauch H, Markland TE. Oxygen as a site specific probe of the structure of water and oxide materials. Physical Review Letters. 107: 145501. PMID 22107211 DOI: 10.1103/Physrevlett.107.145501  0.373
2011 Morrone JA, Markland TE, Ceriotti M, Berne BJ. Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances. The Journal of Chemical Physics. 134: 014103. PMID 21218993 DOI: 10.1063/1.3518369  0.56
2011 Markland TE, Morrone JA, Berne BJ, Miyazaki K, Rabani E, Reichman DR. Quantum fluctuations can promote or inhibit glass formation Nature Physics. 7: 134-137. DOI: 10.1038/Nphys1865  0.684
2010 Ceriotti M, Parrinello M, Markland TE, Manolopoulos DE. Efficient stochastic thermostatting of path integral molecular dynamics. The Journal of Chemical Physics. 133: 124104. PMID 20886921 DOI: 10.1063/1.3489925  0.626
2009 Fanourgakis GS, Markland TE, Manolopoulos DE. A fast path integral method for polarizable force fields. The Journal of Chemical Physics. 131: 094102. PMID 19739844 DOI: 10.1063/1.3216520  0.608
2009 Habershon S, Markland TE, Manolopoulos DE. Competing quantum effects in the dynamics of a flexible water model. The Journal of Chemical Physics. 131: 024501. PMID 19603998 DOI: 10.1063/1.3167790  0.778
2008 Markland TE, Manolopoulos DE. An efficient ring polymer contraction scheme for imaginary time path integral simulations. The Journal of Chemical Physics. 129: 024105. PMID 18624514 DOI: 10.1063/1.2953308  0.642
2008 Markland TE, Habershon S, Manolopoulos DE. Quantum diffusion of hydrogen and muonium atoms in liquid water and hexagonal ice. The Journal of Chemical Physics. 128: 194506. PMID 18500879 DOI: 10.1063/1.2925792  0.744
2008 Markland TE, Manolopoulos DE. A refined ring polymer contraction scheme for systems with electrostatic interactions Chemical Physics Letters. 464: 256-261. DOI: 10.1016/J.Cplett.2008.09.019  0.639
Low-probability matches (unlikely to be authored by this person)
2023 Galvelis R, Varela-Rial A, Doerr S, Fino R, Eastman P, Markland TE, Chodera JD, De Fabritiis G. NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. Journal of Chemical Information and Modeling. 63: 5701-5708. PMID 37694852 DOI: 10.1021/acs.jcim.3c00773  0.267
2018 Markland TE, Ceriotti M. Nuclear quantum effects enter the mainstream Nature Reviews Chemistry. 2. DOI: 10.1038/s41570-017-0109  0.236
2023 Jung KA, Kelly J, Markland TE. Electron transfer at electrode interfaces via a straightforward quasiclassical fermionic mapping approach. The Journal of Chemical Physics. 159. PMID 37409707 DOI: 10.1063/5.0156136  0.225
2021 Huang Z, Chen MS, Woroch CP, Markland TE, Kanan MW. A framework for automated structure elucidation from routine NMR spectra. Chemical Science. 12: 15329-15338. PMID 34976353 DOI: 10.1039/d1sc04105c  0.196
2012 Zeidler A, Salmon PS, Fischer HE, Neuefeind JC, Simonson JM, Lemmel H, Rauch H, Markland TE. Zeidler etal. Reply: Physical Review Letters. 108. DOI: 10.1103/Physrevlett.108.259604  0.148
2013 Ceriotti M, Markland TE. Efficient methods and practical guidelines for simulating isotope effects Journal of Chemical Physics. 138. DOI: 10.1063/1.4772676  0.138
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