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Title: Nuclear quantum effects enter the mainstream

Abstract

Atomistic simulations of chemical, biological and materials systems have become increasingly precise and predictive owing to the development of accurate and efficient techniques that describe the quantum mechanical behaviour of electrons. Nevertheless, the overwhelming majority of such simulations still assumes that the nuclei behave as classical particles. Historically, this approximation could sometimes be justified owing to the complexity and computational overhead. However, neglecting nuclear quantum effects has become one of the largest sources of error, especially when systems containing light atoms are treated using current state-of-the-art descriptions of chemical interactions. Over the past decade, this realization has spurred a series of methodological advances that have dramatically reduced the cost of including these important physical effects in the structure and dynamics of chemical systems. We discuss how these developments are now allowing nuclear quantum effects to become a mainstream feature of molecular simulations. These advances have led to new insights into phenomena that are relevant to different areas of science — from biochemistry to condensed matter — and open the door to many exciting future opportunities.

Authors:
 [1];  [2]
  1. Stanford Univ., Stanford, CA (United States). Dept. of Chemistry
  2. Swiss Federal Inst. of Technology in Lausanne (EPFL) (Switzerland). Lab. of Computational Science and Modeling. Inst. of Materials
Publication Date:
Research Org.:
Stanford Univ., CA (United States); Swiss Federal Inst. of Technology in Lausanne (EPFL) (Switzerland)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); European Research Council (ERC); Swiss National Science Foundation (SNSF)
OSTI Identifier:
1526763
Grant/Contract Number:  
SC0014437; CHE-1652960; 677013-HBMAP; 200021-159896
Resource Type:
Accepted Manuscript
Journal Name:
Nature Reviews Chemistry
Additional Journal Information:
Journal Volume: 2; Journal Issue: 3; Journal ID: ISSN 2397-3358
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; method development; statistical mechanics; structure of solids and liquids

Citation Formats

Markland, Thomas E., and Ceriotti, Michele. Nuclear quantum effects enter the mainstream. United States: N. p., 2018. Web. doi:10.1038/s41570-017-0109.
Markland, Thomas E., & Ceriotti, Michele. Nuclear quantum effects enter the mainstream. United States. https://doi.org/10.1038/s41570-017-0109
Markland, Thomas E., and Ceriotti, Michele. Wed . "Nuclear quantum effects enter the mainstream". United States. https://doi.org/10.1038/s41570-017-0109. https://www.osti.gov/servlets/purl/1526763.
@article{osti_1526763,
title = {Nuclear quantum effects enter the mainstream},
author = {Markland, Thomas E. and Ceriotti, Michele},
abstractNote = {Atomistic simulations of chemical, biological and materials systems have become increasingly precise and predictive owing to the development of accurate and efficient techniques that describe the quantum mechanical behaviour of electrons. Nevertheless, the overwhelming majority of such simulations still assumes that the nuclei behave as classical particles. Historically, this approximation could sometimes be justified owing to the complexity and computational overhead. However, neglecting nuclear quantum effects has become one of the largest sources of error, especially when systems containing light atoms are treated using current state-of-the-art descriptions of chemical interactions. Over the past decade, this realization has spurred a series of methodological advances that have dramatically reduced the cost of including these important physical effects in the structure and dynamics of chemical systems. We discuss how these developments are now allowing nuclear quantum effects to become a mainstream feature of molecular simulations. These advances have led to new insights into phenomena that are relevant to different areas of science — from biochemistry to condensed matter — and open the door to many exciting future opportunities.},
doi = {10.1038/s41570-017-0109},
journal = {Nature Reviews Chemistry},
number = 3,
volume = 2,
place = {United States},
year = {Wed Feb 28 00:00:00 EST 2018},
month = {Wed Feb 28 00:00:00 EST 2018}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 240 works
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Figures / Tables:

FIG. 1 FIG. 1: (a) Schematic representation of a ring-polymer (imaginary time path integral) simulation of a water molecule. Each replica (bead) comprises physical interaction between one oxygen (O) and two hydrogen (H) atoms, and corresponding atoms in adjacent replicas are joined by a harmonic spring. (b) Representative equilibrium configuration of amore » ring polymer on a two-dimensional potential energy surface composed of a harmonic term along $y$ and a double-well quartic term along $x$. (c) In a ring-polymer contraction scheme, the slowly varying component is evaluated on a contracted version of the ring-polymer, whereas the stiff harmonic term is evaluated on all replicas. (d) A high-order factorization achieves more rapid convergence with the number of replicas $P$ as it exploits information on the local curvature of the physical potential to achieve more accurate path integration. (e) A generalized Langevin equation can be used to accelerate the convergence of a PI calculation by selectively and automatically enhancing the fluctuations of the high-frequency vibrations.« less

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  • Eastman, Peter; Friedrichs, Mark S.; Chodera, John D.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
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On the Quantum Nature of the Shared Proton in Hydrogen Bonds
journal, February 1997


Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures
journal, February 2016

  • Pinotsi, Dorothea; Grisanti, Luca; Mahou, Pierre
  • Journal of the American Chemical Society, Vol. 138, Issue 9
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Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space
journal, April 2013


Surface Isotope Segregation as a Probe of Temperature in Water Nanoclusters
journal, June 2014

  • Videla, Pablo E.; Rossky, Peter J.; Laria, Daniel
  • The Journal of Physical Chemistry Letters, Vol. 5, Issue 13
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Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water
journal, August 2008

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  • The Journal of Chemical Physics, Vol. 129, Issue 7
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Surface Diffusion of Hydrogen on Ni(100) from Ring Polymer Molecular Dynamics
journal, May 2012

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  • The Journal of Physical Chemistry C, Vol. 116, Issue 20
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Colored-Noise Thermostats à la Carte
journal, March 2010

  • Ceriotti, Michele; Bussi, Giovanni; Parrinello, Michele
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 4
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High-Pressure Hydrogen Sulfide from First Principles: A Strongly Anharmonic Phonon-Mediated Superconductor
journal, April 2015


Nuclear Quantum Effects in Solids Using a Colored-Noise Thermostat
journal, July 2009


Monte Carlo Calculation of Quantum Systems. II. Higher Order Correction
journal, November 1984

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  • Journal of the Physical Society of Japan, Vol. 53, Issue 11
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Stability of Complex Biomolecular Structures: van der Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects
journal, October 2015

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  • The Journal of Physical Chemistry Letters, Vol. 6, Issue 21
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A fast path integral method for polarizable force fields
journal, January 2009

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  • The Journal of Chemical Physics, Vol. 131, Issue 9
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The mechanism of proton conduction in phosphoric acid
journal, April 2012

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  • Nature Chemistry, Vol. 4, Issue 6
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Displaced Path Integral Formulation for the Momentum Distribution of Quantum Particles
journal, September 2010


Nonergodicity in path integral molecular dynamics
journal, October 1984

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  • The Journal of Chemical Physics, Vol. 81, Issue 8
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Ring-polymer molecular dynamics rate-theory in the deep-tunneling regime: Connection with semiclassical instanton theory
journal, December 2009

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  • The Journal of Chemical Physics, Vol. 131, Issue 21
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Quantum nature of the hydrogen bond
journal, April 2011

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  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 16
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Quantum Thermal Bath for Molecular Dynamics Simulation
journal, November 2009


Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature
journal, March 2018

  • Litman, Yair; Donadio, Davide; Ceriotti, Michele
  • The Journal of Chemical Physics, Vol. 148, Issue 10
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Communication: On the consistency of approximate quantum dynamics simulation methods for vibrational spectra in the condensed phase
journal, November 2014

  • Rossi, Mariana; Liu, Hanchao; Paesani, Francesco
  • The Journal of Chemical Physics, Vol. 141, Issue 18
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Influence of nuclear quantum effects on frozen phonon simulations of electron vortex beam HAADF-STEM images
journal, May 2016


Efficient stochastic thermostatting of path integral molecular dynamics
journal, September 2010

  • Ceriotti, Michele; Parrinello, Michele; Markland, Thomas E.
  • The Journal of Chemical Physics, Vol. 133, Issue 12
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How to remove the spurious resonances from ring polymer molecular dynamics
journal, June 2014

  • Rossi, Mariana; Ceriotti, Michele; Manolopoulos, David E.
  • The Journal of Chemical Physics, Vol. 140, Issue 23
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Quantum-classical crossover of the transition rate in the damped double well
journal, August 1987


Direct path integral estimators for isotope fractionation ratios
journal, December 2014

  • Cheng, Bingqing; Ceriotti, Michele
  • The Journal of Chemical Physics, Vol. 141, Issue 24
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Isotopic fractionation in proteins as a measure of hydrogen bond length
journal, July 2015

  • McKenzie, Ross H.; Athokpam, Bijyalaxmi; Ramesh, Sai G.
  • The Journal of Chemical Physics, Vol. 143, Issue 4
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Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics
journal, May 2016

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  • The Journal of Physical Chemistry B, Vol. 120, Issue 33
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Accelerating equilibrium isotope effect calculations. I. Stochastic thermodynamic integration with respect to mass
journal, May 2017

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Study of an F center in molten KCl
journal, January 1984

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  • The Journal of Chemical Physics, Vol. 80, Issue 2
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Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates
journal, January 2016

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  • Physical Chemistry Chemical Physics, Vol. 18, Issue 47
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Theoretical prediction of low-energy crystal structures and hydrogen storage energetics in Li 2 N H
journal, June 2006


Tunnelling and zero-point motion in high-pressure ice
journal, March 1998

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A Feynman path centroid dynamics approach for the computation of time correlation functions involving nonlinear operators
journal, July 2000

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Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?
journal, April 2014

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  • The Journal of Chemical Physics, Vol. 140, Issue 15
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On energy estimators in path integral Monte Carlo simulations:  Dependence of accuracy on algorithm
journal, November 1989

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Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol
journal, September 2016


Importance of rain evaporation and continental convection in the tropical water cycle
journal, February 2007

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Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system
journal, March 2016

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  • Nature, Vol. 532, Issue 7597
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A comparative study of imaginary time path integral based methods for quantum dynamics
journal, April 2006

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  • The Journal of Chemical Physics, Vol. 124, Issue 15
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Proton Conductivity in Phosphoric Acid: The Role of Quantum Effects
journal, October 2016


Ring polymer molecular dynamics with surface hopping
journal, December 2012

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  • The Journal of Chemical Physics, Vol. 137, Issue 22
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Generalized path integral based quantum transition state theory
journal, October 1997


Direct Measurement of Competing Quantum Effects on the Kinetic Energy of Heavy Water upon Melting
journal, September 2013

  • Romanelli, Giovanni; Ceriotti, Michele; Manolopoulos, David E.
  • The Journal of Physical Chemistry Letters, Vol. 4, Issue 19
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Efficient methods and practical guidelines for simulating isotope effects
journal, January 2013

  • Ceriotti, Michele; Markland, Thomas E.
  • The Journal of Chemical Physics, Vol. 138, Issue 1
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Graphite-diamond phase coexistence study employing a neural-network mapping of the ab initio potential energy surface
journal, March 2010


High order path integrals made easy
journal, December 2016

  • Kapil, Venkat; Behler, Jörg; Ceriotti, Michele
  • The Journal of Chemical Physics, Vol. 145, Issue 23
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Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond
journal, June 2017


The SIESTA method for ab initio order- N materials simulation
journal, March 2002

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  • Journal of Physics: Condensed Matter, Vol. 14, Issue 11
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Path Integral Treatment of Proton Transport Processes in BaZrO 3
journal, November 2008


A new conceptual framework for enzyme catalysis: Hydrogen tunneling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes
journal, July 2002


Nuclear Quantum Effects in H + and OH Diffusion along Confined Water Wires
journal, July 2016

  • Rossi, Mariana; Ceriotti, Michele; Manolopoulos, David E.
  • The Journal of Physical Chemistry Letters, Vol. 7, Issue 15
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Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory
journal, September 2012

  • Klimeš, Jiří; Michaelides, Angelos
  • The Journal of Chemical Physics, Vol. 137, Issue 12
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Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site
journal, October 2017

  • Wang, Lu; Fried, Stephen D.; Markland, Thomas E.
  • The Journal of Physical Chemistry B, Vol. 121, Issue 42
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Competing quantum effects in the dynamics of a flexible water model
journal, July 2009

  • Habershon, Scott; Markland, Thomas E.; Manolopoulos, David E.
  • The Journal of Chemical Physics, Vol. 131, Issue 2
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Nuclear Quantum Effects and Nonlocal Exchange-Correlation Functionals Applied to Liquid Hydrogen at High Pressure
journal, February 2013


The Vapor Pressure of Isotopes
journal, December 1938


Isotopic Preferential Solvation of I in Low-Temperature Water Nanoclusters
journal, August 2015

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  • The Journal of Physical Chemistry B, Vol. 119, Issue 35
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Nuclear quantum effects and hydrogen bond fluctuations in water
journal, September 2013

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  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 39
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An alternative derivation of ring-polymer molecular dynamics transition-state theory
journal, May 2016

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Antiquity and fundamental processes of the antler cycle in Cervidae (Mammalia)
journal, December 2020

  • Rössner, Gertrud E.; Costeur, Loïc; Scheyer, Torsten M.
  • The Science of Nature, Vol. 108, Issue 1
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Ab initio phase diagram and nucleation of gallium
journal, May 2020


Gaussian Approximation Potentials: the accuracy of quantum mechanics, without the electrons
text, January 2009


Displaced path integral formulation for the momentum distribution of quantum particles
text, January 2010


Nuclear quantum effects in ab initio dynamics: theory and experiments for lithium imide
text, January 2010


Competing quantum effects in the dynamics of a flexible water model
text, January 2010


Efficient methods and practical guidelines for simulating isotope effects
text, January 2012


Effect of quantum nuclear motion on hydrogen bonding
text, January 2014


How to remove the spurious resonances from ring polymer molecular dynamics
text, January 2014


Quantum delocalization of protons in the hydrogen bond network of an enzyme active site
text, January 2015


An alternative derivation of ring-polymer molecular dynamics transition-state theory
text, January 2016


High Order Path Integrals Made Easy
text, January 2016


Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs
text, January 2016


Brownian movement and thermophoresis of nanoparticles in liquids
journal, February 2015


Works referencing / citing this record:

Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics
journal, March 2019

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Modeling absorption spectra of molecules in solution
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On the importance of anharmonicities and nuclear quantum effects in modelling the structural properties and thermal expansion of MOF-5
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Cayley modification for strongly stable path-integral and ring-polymer molecular dynamics
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Nonadiabatic quantum transition-state theory in the golden-rule limit. II. Overcoming the pitfalls of the saddle-point and semiclassical approximations
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Water is not a dynamic polydisperse branched polymer
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Path integral molecular dynamics for bosons
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Unraveling anomalous isotope effect on hydrogen diffusivities in fcc metals from first principles including nuclear quantum effects
journal, July 2019


State dependent ring polymer molecular dynamics for investigating excited nonadiabatic dynamics
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Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics
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Ab initio thermodynamics of liquid and solid water
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i-PI 2.0: A universal force engine for advanced molecular simulations
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Machine Learning Force Fields
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Vibrationally Mediated Stabilization of Electrons in Nonpolar Matter
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Thermal Engineering of Metal–Organic Frameworks for Adsorption Applications: A Molecular Simulation Perspective
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Progress and challenges in ab initio simulations of quantum nuclei in weakly bonded systems
journal, May 2021

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Quantum driven proton diffusion in brucite-like minerals under high pressure
preprint, January 2020


Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.