Markland, Thomas
Publication with MATCHING institution:
- Wang L, Isborn CM, Markland T (2016) Simulating Nuclear and Electronic Quantum Effects in Enzymes. None. [IF=None,
Cited=1, 27498646].
- Ceriotti M, Fang W, Kusalik PG, ..., Markland T (2016) Nuclear Quantum Effects in Water and Aqueous Systems: Experiment,
Theory, and Current Challenges. Chemical Reviews. [IF=11.712, Cited=123, 27049513].
- Galvelis R, Varela-Rial A, Doerr S, ..., De Fabritiis G (2023) NNP/MM: Accelerating Molecular Dynamics Simulations with
Machine Learning Potentials and Molecular Mechanics. Journal of Chemical Information and Modeling. [IF=1.379, Cited=6, 37694852].
- Sabanés Zariquiey F, Galvelis R, Gallicchio E, ..., De Fabritiis G (2024) Enhancing Protein-Ligand Binding Affinity
Predictions Using Neural Network Potentials. Journal of Chemical Information and Modeling. [IF=1.379, Cited=1, 38376463].
- Chen MS, Lee J, Ye HZ, ..., Markland T (2023) 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. [IF=1.512, Cited=5, 36730728].
- Pelaez RP, Simeon G, Galvelis R, ..., De Fabritiis G (2024) TorchMD-Net 2.0: Fast Neural Network Potentials for
Molecular Simulations. Journal of Chemical Theory and Computation. [IF=1.512, Cited=1, 38743033].
- Roy S, Schenter GK, Napoli JA, ..., Mundy CJ (2020) Resolving Heterogeneous Dynamics of Excess Protons in Aqueous
Solution with Rate Theory. Journal of Physical Chemistry B. [IF=0.893, Cited=5, 32482074].
- Fried SDE, Zheng C, Mao Y, ..., Boxer SG (2022) Solvent Organization and Electrostatics Tuned by Solute Electronic
Structure: Amide versus Non-Amide Carbonyls. Journal of Physical Chemistry B. [IF=0.893, Cited=1, 35901512].
- Eastman P, Galvelis R, Peláez RP, ..., Markland T (2023) OpenMM 8: Molecular Dynamics Simulation with Machine Learning
Potentials. Journal of Physical Chemistry B. [IF=0.893, Cited=4, 38154096].
- Wang L, Fried SD, Markland T (2017) Proton Network Flexibility Enables Robustness and Large Electric Fields in the
Ketosteroid Isomerase Active Site. Journal of Physical Chemistry B. [IF=0.893, Cited=11, 28915043].
- Long Z, Atsango AO, Napoli JA, ..., Tuckerman ME (2020) Elucidating the Proton Transport Pathways in Liquid Imidazole
with First-Principles Molecular Dynamics. Journal of Physical Chemistry Letters. [IF=1.158, Cited=8, 32633523].
- Chen MS, Zuehlsdorff TJ, Morawietz T, ..., Markland T (2020) Exploiting Machine Learning to Efficiently Predict
Multidimensional Optical Spectra in Complex Environments. Journal of Physical Chemistry Letters. [IF=1.158, Cited=9, 32808797].
- Atsango AO, Tuckerman ME, Markland T (2021) Characterizing and Contrasting Structural Proton Transport Mechanisms in
Azole Hydrogen Bond Networks Using Ab Initio Molecular Dynamics. Journal of Physical Chemistry Letters.
[IF=1.158, Cited=0, 34478302].
- Chen MS, Mao Y, Snider A, ..., Markland T (2023) 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. Journal of Physical Chemistry Letters. [IF=1.158, Cited=1, 37459252].
- Pfalzgraff WC, Kelly A, Markland T (2015) Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical
Theory with Generalized Quantum Master Equations. Journal of Physical Chemistry Letters. [IF=1.158, Cited=8, 26563917].
- Marsalek O, Markland T (2017) Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and
Electronic Quantum Effects. Journal of Physical Chemistry Letters. [IF=1.158, Cited=48, 28296422].
- Morawietz T, Marsalek O, Pattenaude SR, ..., Markland T (2018) The Interplay of Structure and Dynamics in the Raman
Spectrum of Liquid Water over the Full Frequency and Temperature Range. Journal of Physical Chemistry Letters.
[IF=1.158, Cited=21, 29394069].
- Ruiz Pestana L, Marsalek O, Markland T, Head-Gordon T (2018) The Quest for Accurate Liquid Water Properties from First
Principles. Journal of Physical Chemistry Letters. [IF=1.158, Cited=19, 30118601].
- Boyer MA, Marsalek O, Heindel JP, ..., Xantheas SS (2019) Beyond Badger's Rule: The Origins and Generality of the
Structure-Spectra Relationship of Aqueous Hydrogen Bonds. Journal of Physical Chemistry Letters. [IF=1.158, Cited=9, 30735052].
- Morawietz T, Urbina AS, Wise PK, ..., Markland T (2019) Hiding in the Crowd: Spectral Signatures of Overcoordinated
Hydrogen-Bond Environments. Journal of Physical Chemistry Letters. [IF=1.158, Cited=3, 31549833].
- Yuan R, Napoli JA, Yan C, ..., Fayer MD (2019) Tracking Aqueous Proton Transfer by Two-Dimensional Infrared Spectroscopy
and ab Initio Molecular Dynamics Simulations. ACS Central Science. [IF=2.363, Cited=18, 31403075].
- Lau VM, Pfalzgraff WC, Markland T, ..., Kanan MW (2017) Electrostatic Control of Regioselectivity in Au(I)-Catalyzed
Hydroarylation. Journal of the American Chemical Society. [IF=2.573, Cited=23, 28225605].
- Nistor RA, Markland T, Berne BJ (2014) Interface-limited growth of heterogeneously nucleated ice in supercooled water.
Journal of Physical Chemistry B. [IF=0.893, Cited=8, 24393086].
- Zheng C, Mao Y, Kozuch J, ..., Boxer SG (2022) A two-directional vibrational probe reveals different electric field
orientations in solution and an enzyme active site. Nature Chemistry. [IF=3.667, Cited=18, 35513508].
- Eastman P, Behara PK, Dotson DL, ..., Markland T (2023) SPICE, A Dataset of Drug-like Molecules and Peptides for
Training Machine Learning Potentials. Scientific data. [IF=2.887, Cited=14, 36599873].
- Wang L, Ceriotti M, Markland T (2020) Quantum kinetic energy and isotope fractionation in aqueous ionic solutions.
Physical Chemistry Chemical Physics. [IF=0.906, Cited=0, 31942581].
- Huang Z, Chen MS, Woroch CP, ..., Kanan MW (2021) A framework for automated structure elucidation from routine NMR
spectra. Chemical Science. [IF=1.563, Cited=2, 34976353].
- Berkelbach TC, Reichman DR, Markland T (2012) Reduced density matrix hybrid approach: an efficient and accurate method
for adiabatic and non-adiabatic quantum dynamics. Journal of Chemical Physics. [IF=1.184, Cited=30, 22280750].
- Markland T, Morrone JA, Miyazaki K, ..., Rabani E (2012) Theory and simulations of quantum glass forming liquids.
Journal of Chemical Physics. [IF=1.184, Cited=17, 22360252].
- Berkelbach TC, Markland T, Reichman DR (2012) Reduced density matrix hybrid approach: application to electronic energy
transfer. Journal of Chemical Physics. [IF=1.184, Cited=27, 22380029].
- Ceriotti M, Markland T (2013) Efficient methods and practical guidelines for simulating isotope effects. Journal of
Chemical Physics. [IF=1.184, Cited=21, 23298033].
- Kelly A, Markland T (2013) Efficient and accurate surface hopping for long time nonadiabatic quantum dynamics. Journal
of Chemical Physics. [IF=1.184, Cited=31, 23822290].
- Luehr N, Markland T, Martínez TJ (2014) Multiple time step integrators in ab initio molecular dynamics. Journal of
Chemical Physics. [IF=1.184, Cited=7, 24588157].
- Wang L, Ceriotti M, Markland T (2014) Quantum fluctuations and isotope effects in ab initio descriptions of water.
Journal of Chemical Physics. [IF=1.184, Cited=25, 25217932].
- Kelly A, Brackbill N, Markland T (2015) Accurate nonadiabatic quantum dynamics on the cheap: making the most of mean
field theory with master equations. Journal of Chemical Physics. [IF=1.184, Cited=13, 25747064].
- Marsalek O, Markland T (2016) Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer
contraction for density functional theory. Journal of Chemical Physics. [IF=1.184, Cited=21, 26851913].
- Kelly A, Montoya-Castillo A, Wang L, Markland T (2016) Generalized quantum master equations in and out of equilibrium:
When can one win? Journal of Chemical Physics. [IF=1.184, Cited=12, 27179469].
- Napoli JA, Marsalek O, Markland T (2018) Decoding the spectroscopic features and time scales of aqueous proton defects.
Journal of Chemical Physics. [IF=1.184, Cited=10, 29907063].
- Zuehlsdorff TJ, Napoli JA, Milanese JM, ..., Isborn CM (2018) Unraveling electronic absorption spectra using nuclear
quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. Journal of Chemical
Physics. [IF=1.184, Cited=9, 30007372].
- Pfalzgraff WC, Montoya-Castillo A, Kelly A, Markland T (2019) Efficient construction of generalized master equation
memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics. Journal of Chemical Physics.
[IF=1.184, Cited=2, 31255061].
- Zuehlsdorff TJ, Montoya-Castillo A, Napoli JA, ..., Isborn CM (2019) Optical spectra in the condensed phase: Capturing
anharmonic and vibronic features using dynamic and static approaches. Journal of Chemical Physics. [IF=1.184, Cited=14, 31438704].
- Mao Y, Montoya-Castillo A, Markland T (2019) Accurate and efficient DFT-based diabatization for hole and electron
transfer using absolutely localized molecular orbitals. Journal of Chemical Physics. [IF=1.184, Cited=3, 31675855].
- Cao S, Montoya-Castillo A, Wang W, ..., Huang X (2020) On the advantages of exploiting memory in Markov state models for
biomolecular dynamics. Journal of Chemical Physics. [IF=1.184, Cited=19, 32640825].
- Mao Y, Montoya-Castillo A, Markland T (2020) Excited state diabatization on the cheap using DFT: Photoinduced electron
and hole transfer. Journal of Chemical Physics. [IF=1.184, Cited=6, 33380087].
- Chen MS, Morawietz T, Mori H, ..., Artrith N (2021) AENET-LAMMPS and AENET-TINKER: Interfaces for accurate and efficient
molecular dynamics simulations with machine learning potentials. Journal of Chemical Physics. [IF=1.184, Cited=7, 34418919].
- Jung KA, Markland T (2022) 2D spectroscopies from condensed phase dynamics: Accessing third-order response properties
from equilibrium multi-time correlation functions. Journal of Chemical Physics. [IF=1.184, Cited=0, 36075710].
- Montoya-Castillo A, Markland T (2023) A derivation of the conditions under which bosonic operators exactly capture
fermionic structure and dynamics. Journal of Chemical Physics. [IF=1.184, Cited=0, 36889969].
- Atsango AO, Montoya-Castillo A, Markland T (2023) An accurate and efficient Ehrenfest dynamics approach for calculating
linear and nonlinear electronic spectra. Journal of Chemical Physics. [IF=1.184, Cited=0, 36813724].
- Jung KA, Kelly J, Markland T (2023) Electron transfer at electrode interfaces via a straightforward quasiclassical
fermionic mapping approach. Journal of Chemical Physics. [IF=1.184, Cited=0, 37409707].
- Atsango AO, Morawietz T, Marsalek O, Markland T (2023) Developing machine-learned potentials to simultaneously capture
the dynamics of excess protons and hydroxide ions in classical and path integral simulations. Journal of Chemical
Physics. [IF=1.184, Cited=1, 37581418].
- Markland T, Berne BJ (2012) Unraveling quantum mechanical effects in water using isotopic fractionation. Proceedings of
the National Academy of Sciences of the United States of America. [IF=2.765, Cited=31, 22566650].
- Wang L, Fried SD, Boxer S, ..., Markland TE (2014) 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. [IF=2.765,
Cited=43, 25503367].
- Yan C, Yuan R, Pfalzgraff WC, ..., Fayer MD (2016) 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. [IF=2.765, Cited=9, 27044113].
- Dominic AJ, Sayer T, Cao S, ..., Montoya-Castillo A (2023) 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. [IF=2.765, Cited=6, 36920924].
- Montoya-Castillo A, Chen MS, Raj SL, ..., Markland T (2022) Optically Induced Anisotropy in Time-Resolved Scattering:
Imaging Molecular-Scale Structure and Dynamics in Disordered Media with Experiment and Theory. Physical Review Letters.
[IF=2.288, Cited=3, 35960558].
- Habershon S, Manolopoulos DE, Markland T, Miller TF (2013) Ring-polymer molecular dynamics: quantum effects in chemical
dynamics from classical trajectories in an extended phase space. Annual Review of Physical Chemistry. [IF=3.733,
Cited=158, 23298242].
- Hu Y, Ounkham P, Marsalek O, ..., Clark AE (2021) Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive
Atoms in Path Integral Dynamics. Frontiers in Chemistry. [IF=1.04, Cited=1, 33748074].
- Pelaez RP, Simeon G, Galvelis R, ..., De Fabritiis G (2024) TorchMD-Net 2.0: Fast Neural Network Potentials for
Molecular Simulations. None. [IF=None, Cited=0, 38463504].
Publication with MISMATCHING institution:
- Markland T, Habershon S, Manolopoulos DE (2008) Quantum diffusion of hydrogen and muonium atoms in liquid water and
hexagonal ice. Journal of Chemical Physics. [IF=1.184, Cited=29, 18500879].
- Markland T, Manolopoulos DE (2008) An efficient ring polymer contraction scheme for imaginary time path integral
simulations. Journal of Chemical Physics. [IF=1.184, Cited=52, 18624514].
- Habershon S, Markland T, Manolopoulos DE (2009) Competing quantum effects in the dynamics of a flexible water model.
Journal of Chemical Physics. [IF=1.184, Cited=172, 19603998].
- Fanourgakis GS, Markland T, Manolopoulos DE (2009) A fast path integral method for polarizable force fields. Journal of
Chemical Physics. [IF=1.184, Cited=18, 19739844].
- Ceriotti M, Parrinello M, Markland T, Manolopoulos DE (2010) Efficient stochastic thermostatting of path integral
molecular dynamics. Journal of Chemical Physics. [IF=1.184, Cited=83, 20886921].
- Morrone JA, Markland T, Ceriotti M, Berne BJ (2011) Efficient multiple time scale molecular dynamics: Using colored
noise thermostats to stabilize resonances. Journal of Chemical Physics. [IF=1.184, Cited=22, 21218993].
Publication with MISSING institution:
- Montoya-Castillo A, Markland T (2018) On the exact continuous mapping of fermions. Scientific Reports. [IF=1.312,
Cited=0, 30154503].
- Zeidler A, Salmon PS, Fischer HE, ..., Markland T (2012) Isotope effects in water as investigated by neutron diffraction
and path integral molecular dynamics. Journal of Physics Condensed Matter. [IF=0.812, Cited=12, 22738936].
- Zeidler A, Salmon PS, Fischer HE, ..., Markland T (2011) Oxygen as a site specific probe of the structure of water and
oxide materials. Physical Review Letters. [IF=2.288, Cited=10, 22107211].
- Hocky GM, Markland T, Reichman DR (2012) Growing point-to-set length scale correlates with growing relaxation times in
model supercooled liquids. Physical Review Letters. [IF=2.288, Cited=48, 23003622].
- Eastman P, Galvelis R, Peláez RP, ..., Markland T (2023) OpenMM 8: Molecular Dynamics Simulation with Machine Learning
Potentials. None. [IF=None, Cited=0, 37986730].
- Zariquiey FS, Galvelis R, Gallicchio E, ..., de Fabritiis G (2024) Enhancing Protein-Ligand Binding Affinity Predictions
using Neural Network Potentials. None. [IF=None, Cited=0, 38351937].