Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Stochastic Trajectories

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

doi:10.1021/acs.jpcb.3c00670

Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Stochastic Trajectories

Journal Article · Thu Jun 01 04:00:00 EDT 2023 · Journal of Physical Chemistry. B

DOI:https://doi.org/10.1021/acs.jpcb.3c00670· OSTI ID:2420954

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:: 2420954

Journal Information:: Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 23 Vol. 127; ISSN 1520-6106

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

References (71)

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
Phase Transition for a Hard Sphere System Alder, B. J.; Wainwright, T. E. The Journal of Chemical Physics, Vol. 27, Issue 5 https://doi.org/10.1063/1.1743957	journal	November 1957
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
Heterogeneous Surface Crystallization Observed in Undercooled Water Shaw, Raymond A.; Durant, Adam J.; Mi, Youshi The Journal of Physical Chemistry B, Vol. 109, Issue 20 https://doi.org/10.1021/jp0506336	journal	May 2005
CHEMISTRY: Water in Confinement Levinger, N. E. Science, Vol. 298, Issue 5599 https://doi.org/10.1126/science.1079322	journal	November 2002
Properties of model atomic free-standing thin films Shi, Zane; Debenedetti, Pablo G.; Stillinger, Frank H. The Journal of Chemical Physics, Vol. 134, Issue 11 https://doi.org/10.1063/1.3565480	journal	March 2011
Transport Properties of a Dense Fluid of Hard Spheres Longuet-Higgins, H. C.; Pople, J. A. The Journal of Chemical Physics, Vol. 25, Issue 5 https://doi.org/10.1063/1.1743136	journal	November 1956
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
Estimation of the coefficients of a diffusion from discrete observations Dacunha-Castelle, D.; Florens-Zmirou, D. Stochastics, Vol. 19, Issue 4 https://doi.org/10.1080/17442508608833428	journal	December 1986
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
Effects of Confinement on the Self-Organization of Microtubules and Motors Pinot, M.; Chesnel, F.; Kubiak, J. Z. Current Biology, Vol. 19, Issue 11 https://doi.org/10.1016/j.cub.2009.04.027	journal	June 2009
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
Ligand & band gap engineering: tailoring the protocol synthesis for achieving high-quality CsPbI₃ quantum dots Hassanabadi, Ehsan; Latifi, Masoud; Gualdrón-Reyes, Andrés. F. Nanoscale, Vol. 12, Issue 26 https://doi.org/10.1039/D0NR03180A	journal	January 2020
Overdamped limit and inverse-friction expansion for Brownian motion in an inhomogeneous medium Durang, Xavier; Kwon, Chulan; Park, Hyunggyu Physical Review E, Vol. 91, Issue 6 https://doi.org/10.1103/PhysRevE.91.062118	journal	June 2015
Band gap engineering of amorphous silicon quantum dots for light-emitting diodes Park, Nae-Man; Kim, Tae-Soo; Park, Seong-Ju Applied Physics Letters, Vol. 78, Issue 17 https://doi.org/10.1063/1.1367277	journal	April 2001
Confinement-induced self-organization in growing bacterial colonies You, Zhihong; Pearce, Daniel J. G.; Giomi, Luca Science Advances, Vol. 7, Issue 4 https://doi.org/10.1126/sciadv.abc8685	journal	January 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
Functionals in stochastic thermodynamics: how to interpret stochastic integrals Bo, Stefano; Lim, Soon Hoe; Eichhorn, Ralf Journal of Statistical Mechanics: Theory and Experiment, Vol. 2019, Issue 8 https://doi.org/10.1088/1742-5468/ab3111	journal	August 2019
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
Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen Einstein, A. Annalen der Physik, Vol. 322, Issue 8 https://doi.org/10.1002/andp.19053220806	journal	January 1905
Kernel-based regression of drift and diffusion coefficients of stochastic processes Lamouroux, David; Lehnertz, Klaus Physics Letters A, Vol. 373, Issue 39 https://doi.org/10.1016/j.physleta.2009.07.073	journal	September 2009
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
Effective drifts in dynamical systems with multiplicative noise: a review of recent progress Volpe, Giovanni; Wehr, Jan Reports on Progress in Physics, Vol. 79, Issue 5 https://doi.org/10.1088/0034-4885/79/5/053901	journal	April 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
Estimation of Kramers-Moyal coefficients at low sampling rates Honisch, Christoph; Friedrich, Rudolf Physical Review E, Vol. 83, Issue 6 https://doi.org/10.1103/PhysRevE.83.066701	journal	June 2011
Correlations in Space and Time and Born Approximation Scattering in Systems of Interacting Particles Van Hove, Léon Physical Review, Vol. 95, Issue 1 https://doi.org/10.1103/PhysRev.95.249	journal	July 1954
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
Confinement as a Unifying Element in Selective Catalysis Mitschke, Benjamin; Turberg, Mathias; List, Benjamin Chem, Vol. 6, Issue 10 https://doi.org/10.1016/j.chempr.2020.09.007	journal	October 2020
Single crystal texture by directed molecular self-assembly along dual axes Feng, Xunda; Kawabata, Kohsuke; Cowan, Matthew G. Nature Materials, Vol. 18, Issue 11 https://doi.org/10.1038/s41563-019-0389-1	journal	June 2019
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
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
Confinement-Driven Ferroelectricity in a Two-Dimensional Hybrid Lead Iodide Perovskite Chen, Xiao-Gang; Song, Xian-Jiang; Zhang, Zhi-Xu Journal of the American Chemical Society, Vol. 142, Issue 22 https://doi.org/10.1021/jacs.0c03710	journal	May 2020
Anisotropic diffusion in confined colloidal dispersions: The evanescent diffusivity Swan, James W.; Brady, John F. The Journal of Chemical Physics, Vol. 135, Issue 1 https://doi.org/10.1063/1.3604530	journal	July 2011
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
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
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
Nonparametric inference for fractional diffusion Saussereau, Bruno Bernoulli, Vol. 20, Issue 2 https://doi.org/10.3150/13-BEJ509	journal	May 2014
The fluctuation theorem and Green–Kubo relations Searles, Debra J.; Evans, Denis J. The Journal of Chemical Physics, Vol. 112, Issue 22 https://doi.org/10.1063/1.481610	journal	June 2000
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
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
Reciprocal Relations in Irreversible Processes. II. Onsager, Lars Physical Review, Vol. 38, Issue 12 https://doi.org/10.1103/PhysRev.38.2265	journal	December 1931
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
Computing diffusivities from particle models out of equilibrium Embacher, Peter; Dirr, Nicolas; Zimmer, Johannes Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 474, Issue 2212 https://doi.org/10.1098/rspa.2017.0694	journal	April 2018
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
Effects of Confinement on Microstructure and Charge Transport in High Performance Semicrystalline Polymer Semiconductors Himmelberger, Scott; Dacuña, Javier; Rivnay, Jonathan Advanced Functional Materials, Vol. 23, Issue 16 https://doi.org/10.1002/adfm.201202408	journal	November 2012
Markoff Random Processes and the Statistical Mechanics of Time‐Dependent Phenomena. II. Irreversible Processes in Fluids Green, Melville S. The Journal of Chemical Physics, Vol. 22, Issue 3 https://doi.org/10.1063/1.1740082	journal	March 1954
Evaporation freezing by contact nucleation inside-out Durant, Adam J. Geophysical Research Letters, Vol. 32, Issue 20 https://doi.org/10.1029/2005GL024175	journal	January 2005
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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