Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories

Domingues, Tiago S.; Coifman, Ronald R.; Haji-Akbari, Amir

doi:10.1021/acs.jpcb.3c03581

Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories

Journal Article · 27 September 2023 · Journal of Physical Chemistry. B

DOI:https://doi.org/10.1021/acs.jpcb.3c03581· OSTI ID:2420956

Domingues, Tiago S. ^[1]; Coifman, Ronald R. ^[2]; ^[3]

Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States; OSTI
Department of Mathematics, Yale University, New Haven, Connecticut 06520, United States
Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States

Not provided.

Research Organization:: Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0019112

OSTI ID:: 2420956

Journal Information:: Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 40 Vol. 127; ISSN 1520-6106

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

References (62)

Velocity autocorrelation function and diffusion coefficient in a liquid Gaskell, T. Journal of Physics C: Solid State Physics, Vol. 4, Issue 12 https://doi.org/10.1088/0022-3719/4/12/003	journal	August 1971
Polymer Conformations and Dynamics under Confinement with Two Length Scales Zhang, Tianren; Winey, Karen I.; Riggleman, Robert A. Macromolecules, Vol. 52, Issue 1 https://doi.org/10.1021/acs.macromol.8b01779	journal	December 2018
Diffusion maps Coifman, Ronald R.; Lafon, Stéphane Applied and Computational Harmonic Analysis, Vol. 21, Issue 1 https://doi.org/10.1016/j.acha.2006.04.006	journal	July 2006
Thermodynamic and kinetic anisotropies in octane thin films Haji-Akbari, Amir; Debenedetti, Pablo G. The Journal of Chemical Physics, Vol. 143, Issue 21 https://doi.org/10.1063/1.4935801	journal	December 2015
Polymer Diffusion Is Fastest at Intermediate Levels of Cylindrical Confinement Pressly, James F.; Riggleman, Robert A.; Winey, Karen I. Macromolecules, Vol. 51, Issue 23 https://doi.org/10.1021/acs.macromol.8b01728	journal	November 2018
Role of Nanoscale Interfacial Proximity in Contact Freezing in Water Hussain, Sarwar; Haji-Akbari, Amir Journal of the American Chemical Society, Vol. 143, Issue 5 https://doi.org/10.1021/jacs.0c10663	journal	January 2021
Recovering position-dependent diffusion from biased molecular dynamics simulations Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez The Journal of Chemical Physics, Vol. 140, Issue 8 https://doi.org/10.1063/1.4866448	journal	February 2014
Nadaraya–Watson estimator for I.I.D. paths of diffusion processes Marie, Nicolas; Rosier, Amélie Scandinavian Journal of Statistics, Vol. 50, Issue 2 https://doi.org/10.1111/sjos.12593	journal	May 2022
On a Nadaraya-Watson estimator with two bandwidths Comte, Fabienne; Marie, Nicolas Electronic Journal of Statistics, Vol. 15, Issue 1 https://doi.org/10.1214/21-EJS1849	journal	January 2021
Induced Charge Anisotropy: A Hidden Variable Affecting Ion Transport through Membranes Malmir, Hessam; Epsztein, Razi; Elimelech, Menachem Matter, Vol. 2, Issue 3 https://doi.org/10.1016/j.matt.2019.12.022	journal	March 2020
Confined active matter in external fields Shaik, Vaseem A.; Peng, Zhiwei; Brady, John F. Soft Matter, Vol. 19, Issue 7 https://doi.org/10.1039/D2SM01135B	journal	January 2023
On the Calculation of Diffusion Coefficients in Confined Fluids and Interfaces with an Application to the Liquid−Vapor Interface of Water ^† Liu, Pu; Harder, Edward; Berne, B. J. The Journal of Physical Chemistry B, Vol. 108, Issue 21 https://doi.org/10.1021/jp0375057	journal	May 2004
Molecular dynamics simulations of polymer transport in nanocomposites Desai, Tapan; Keblinski, Pawel; Kumar, Sanat K. The Journal of Chemical Physics, Vol. 122, Issue 13 https://doi.org/10.1063/1.1874852	journal	April 2005
Simulation of water transport through a lipid membrane Marrink, Siewert-Jan; Berendsen, Herman J. C. The Journal of Physical Chemistry, Vol. 98, Issue 15 https://doi.org/10.1021/j100066a040	journal	April 1994
Predicted Confinement-Enhanced Stability and Extraordinary Mechanical Properties for Carbon Nanotube Wrapped Chains of Linear Carbon Gao, Enlai; Li, Ruishan; Baughman, Ray H. ACS Nano, Vol. 14, Issue 12 https://doi.org/10.1021/acsnano.0c06602	journal	November 2020
Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis Chang, Joshua C.; Fok, Pak-Wing; Chou, Tom Biophysical Journal, Vol. 109, Issue 5 https://doi.org/10.1016/j.bpj.2015.07.028	journal	September 2015
Transport Coefficients from Dissipation in a Canonical Ensemble Helfand, Eugene Physical Review, Vol. 119, Issue 1 https://doi.org/10.1103/PhysRev.119.1	journal	July 1960
Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis Sicard, François; Koskin, Vladimir; Annibale, Alessia Journal of Chemical Theory and Computation, Vol. 17, Issue 4 https://doi.org/10.1021/acs.jctc.0c01151	journal	March 2021
Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes Ghysels, An; Venable, Richard M.; Pastor, Richard W. Journal of Chemical Theory and Computation, Vol. 13, Issue 6 https://doi.org/10.1021/acs.jctc.7b00039	journal	May 2017
Confinement Effect of Sub-nanometer Difference on Melting Point of Ice-Nanotubes Measured by Photoluminescence Spectroscopy Chiashi, Shohei; Saito, Yuta; Kato, Takashi ACS Nano https://doi.org/10.1021/acsnano.8b06041	journal	January 2019
Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model De Vos, Oriana; Venable, Richard M.; Van Hecke, Tanja Journal of Chemical Theory and Computation, Vol. 14, Issue 7 https://doi.org/10.1021/acs.jctc.8b00115	journal	June 2018
The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films Haji-Akbari, Amir; Debenedetti, Pablo G. The Journal of Chemical Physics, Vol. 141, Issue 2 https://doi.org/10.1063/1.4885365	journal	July 2014
Molecular dynamics of narrow, liquid‐filled pores Magda, J. J.; Tirrell, M.; Davis, H. T. The Journal of Chemical Physics, Vol. 83, Issue 4 https://doi.org/10.1063/1.449375	journal	August 1985
Two Dimensional Ice from First Principles: Structures and Phase Transitions Chen, Ji; Schusteritsch, Georg; Pickard, Chris J. Physical Review Letters, Vol. 116, Issue 2 https://doi.org/10.1103/PhysRevLett.116.025501	journal	January 2016
On the Functional Estimation of Multivariate Diffusion Processes Bandi, Federico M.; Moloche, Guillermo Econometric Theory, Vol. 34, Issue 4 https://doi.org/10.1017/S0266466617000305	journal	September 2017
Studies in Molecular Dynamics. I. General Method Alder, B. J.; Wainwright, T. E. The Journal of Chemical Physics, Vol. 31, Issue 2 https://doi.org/10.1063/1.1730376	journal	August 1959
Computational investigation of surface freezing in a molecular model of water Haji-Akbari, Amir; Debenedetti, Pablo G. Proceedings of the National Academy of Sciences, Vol. 114, Issue 13 https://doi.org/10.1073/pnas.1620999114	journal	March 2017
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture I: The van Hove correlation function Kob, Walter; Andersen, Hans C. Physical Review E, Vol. 51, Issue 5 https://doi.org/10.1103/PhysRevE.51.4626	journal	May 1995
Effect of Free Surfaces on the Glass Transition Temperature of Thin Polymer Films Forrest, J. A.; Dalnoki-Veress, K.; Stevens, J. R. Physical Review Letters, Vol. 77, Issue 10 https://doi.org/10.1103/PhysRevLett.77.2002	journal	September 1996
High-Modulus Organic Glasses Prepared by Physical Vapor Deposition Kearns, Kenneth L.; Still, Tim; Fytas, George Advanced Materials, Vol. 22, Issue 1 https://doi.org/10.1002/adma.200901673	journal	January 2010
Brownian walker in a confined geometry leading to a space-dependent diffusion coefficient Lançon, P.; Batrouni, G.; Lobry, L. Physica A: Statistical Mechanics and its Applications, Vol. 304, Issue 1-2 https://doi.org/10.1016/S0378-4371(01)00510-6	journal	February 2002
Relaxation time of confined liquids under shear Hu, Hsuan-Wei; Carson, George A.; Granick, Steve Physical Review Letters, Vol. 66, Issue 21 https://doi.org/10.1103/PhysRevLett.66.2758	journal	May 1991
Organic Glasses with Exceptional Thermodynamic and Kinetic Stability Swallen, S. F.; Kearns, K. L.; Mapes, M. K. Science, Vol. 315, Issue 5810 https://doi.org/10.1126/science.1135795	journal	January 2007
Diffusive Models of Membrane Permeation with Explicit Orientational Freedom Comer, Jeffrey; Schulten, Klaus; Chipot, Christophe Journal of Chemical Theory and Computation, Vol. 10, Issue 7 https://doi.org/10.1021/ct500209j	journal	May 2014
Liquid to quasicrystal transition in bilayer water Johnston, Jessica C.; Kastelowitz, Noah; Molinero, Valeria The Journal of Chemical Physics, Vol. 133, Issue 15 https://doi.org/10.1063/1.3499323	journal	October 2010
The interfacial density profile of a Lennard‐Jones fluid in contact with a (100) Lennard‐Jones wall and its relationship to idealized fluid/wall systems: A Monte Carlo simulation Abraham, Farid F. The Journal of Chemical Physics, Vol. 68, Issue 8 https://doi.org/10.1063/1.436229	journal	April 1978
Evaporation rate of water in hydrophobic confinement Sharma, S.; Debenedetti, P. G. Proceedings of the National Academy of Sciences, Vol. 109, Issue 12 https://doi.org/10.1073/pnas.1116167109	journal	March 2012
Anomalously low dielectric constant of confined water Fumagalli, L.; Esfandiar, A.; Fabregas, R. Science, Vol. 360, Issue 6395 https://doi.org/10.1126/science.aat4191	journal	June 2018
Confinement-induced quorum sensing of individual Staphylococcus aureus bacteria Carnes, Eric C.; Lopez, DeAnna M.; Donegan, Niles P. Nature Chemical Biology, Vol. 6, Issue 1 https://doi.org/10.1038/nchembio.264	journal	November 2009
Ridge Regression: Biased Estimation for Nonorthogonal Problems Hoerl, Arthur E.; Kennard, Robert W. Technometrics, Vol. 12, Issue 1 https://doi.org/10.1080/00401706.1970.10488634	journal	February 1970
A molecular dynamics method for simulations in the canonical ensemble Nosé, Shūichi Molecular Physics, Vol. 52, Issue 2 https://doi.org/10.1080/00268978400101201	journal	June 1984
Molecular dynamics calculation of the liquid structure up to a solid surface Toxvaerd, So/ren; Praestgaard, Eigil The Journal of Chemical Physics, Vol. 67, Issue 11 https://doi.org/10.1063/1.434707	journal	December 1977
Confinement effects on phase behavior of soft matter systems Binder, Kurt; Horbach, Jürgen; Vink, Richard Soft Matter, Vol. 4, Issue 8 https://doi.org/10.1039/b802207k	journal	January 2008
Distinct Chemistries Explain Decoupling of Slip and Wettability in Atomically Smooth Aqueous Interfaces Poggioli, Anthony R.; Limmer, David T. The Journal of Physical Chemistry Letters, Vol. 12, Issue 37 https://doi.org/10.1021/acs.jpclett.1c02828	journal	September 2021
Confined Water’s Dielectric Constant Reduction Is Due to the Surrounding Low Dielectric Media and Not to Interfacial Molecular Ordering Olivieri, Jean-François; Hynes, James T.; Laage, Damien The Journal of Physical Chemistry Letters, Vol. 12, Issue 17 https://doi.org/10.1021/acs.jpclett.1c00447	journal	April 2021
Computing committors via Mahalanobis diffusion maps with enhanced sampling data Evans, L.; Cameron, M. K.; Tiwary, P. The Journal of Chemical Physics, Vol. 157, Issue 21 https://doi.org/10.1063/5.0122990	journal	December 2022
Local and global perspectives on diffusion maps in the analysis of molecular systems Trstanova, Z.; Leimkuhler, B.; Lelièvre, T. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 476, Issue 2233 https://doi.org/10.1098/rspa.2019.0036	journal	January 2020
Two-Dimensional Water and Ice Layers: Neutron Diffraction Studies at 278, 263, and 20 K Janiak, Christoph; Scharmann, Tobias G.; Mason, Sax A. Journal of the American Chemical Society, Vol. 124, Issue 47 https://doi.org/10.1021/ja0274608	journal	November 2002
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations Hummer, Gerhard New Journal of Physics, Vol. 7 https://doi.org/10.1088/1367-2630/7/1/034	journal	January 2005
Correlation function approach for diffusion in confined geometries Palmer, Bruce J.; Chun, Jaehun; Morris, Jeffrey F. Physical Review E, Vol. 102, Issue 2 https://doi.org/10.1103/PhysRevE.102.022129	journal	August 2020
DifferentialEquations.jl – A Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia Rackauckas, Christopher; Nie, Qing Journal of Open Research Software, Vol. 5 https://doi.org/10.5334/jors.151	journal	May 2017
Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Stochastic Trajectories Domingues, Tiago S.; Coifman, Ronald R.; Haji-Akbari, Amir The Journal of Physical Chemistry B, Vol. 127, Issue 23 https://doi.org/10.1021/acs.jpcb.3c00670	journal	June 2023
Properties of a confined molecular glass-forming liquid Teboul, Victor; Simionesco, Christiane Alba Journal of Physics: Condensed Matter, Vol. 14, Issue 23 https://doi.org/10.1088/0953-8984/14/23/304	journal	May 2002
Effect of material flexibility on the thermodynamics and kinetics of hydrophobically induced evaporation of water Altabet, Y. Elia; Haji-Akbari, Amir; Debenedetti, Pablo G. Proceedings of the National Academy of Sciences, Vol. 114, Issue 13 https://doi.org/10.1073/pnas.1620335114	journal	March 2017
Molecular dynamics of a hard sphere fluid in small pores Subramanian, G.; Davis, H. T. Molecular Physics, Vol. 38, Issue 4 https://doi.org/10.1080/00268977900102241	journal	October 1979
Statistical-Mechanical Theory of Irreversible Processes. I. General Theory and Simple Applications to Magnetic and Conduction Problems Kubo, Ryogo Journal of the Physical Society of Japan, Vol. 12, Issue 6 https://doi.org/10.1143/JPSJ.12.570	journal	June 1957
Shear behavior of squalane and tetracosane under extreme confinement. III. Effect of confinement on viscosity Gupta, S. A.; Cochran, H. D.; Cummings, P. T. The Journal of Chemical Physics, Vol. 107, Issue 23 https://doi.org/10.1063/1.474173	journal	December 1997
Die mittlere Energie rotierender elektrischer Dipole im Strahlungsfeld Fokker, A. D. Annalen der Physik, Vol. 348, Issue 5 https://doi.org/10.1002/andp.19143480507	journal	January 1914
Thermodynamics Predicts How Confinement Modifies the Dynamics of the Equilibrium Hard-Sphere Fluid Mittal, Jeetain; Errington, Jeffrey R.; Truskett, Thomas M. Physical Review Letters, Vol. 96, Issue 17 https://doi.org/10.1103/PhysRevLett.96.177804	journal	May 2006
Confinement by Carbon Nanotubes Drastically Alters the Boiling and Critical Behavior of Water Droplets Chaban, Vitaly V.; Prezhdo, Victor V.; Prezhdo, Oleg V. ACS Nano, Vol. 6, Issue 3 https://doi.org/10.1021/nn3002533	journal	February 2012
Effects of confinement on material behaviour at the nanometre size scale Alcoutlabi, Mataz; McKenna, Gregory B. Journal of Physics: Condensed Matter, Vol. 17, Issue 15 https://doi.org/10.1088/0953-8984/17/15/R01	journal	April 2005

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