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Lee JH, Jung Y. Dynamical Phase Transition in Kinetically Constrained Models with Energy-Activity Double-Bias Trajectory Ensemble. J Phys Chem Lett 2024; 15:1553-1563. [PMID: 38300602 DOI: 10.1021/acs.jpclett.3c03160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
We investigate the dynamical phase transitions in two representative kinetically constrained models, the 1D Fredrickson-Andersen and East models, by utilizing a recently developed s,g double-bias ensemble approach. In this ensemble, the fields s and g are applied to bias the dynamical activity and trajectory energy, respectively, in the trajectory ensemble. We first confirm that the dynamical phase transitions are indeed first-order in both the models. The phase diagrams in (s, g, T) space obtained via extensive numerical simulations show good qualitative agreement with the mean-field results. We also demonstrate that the temperature-dependent dynamical phase transition is possible in the systems when both fields are applied simultaneously. The trajectory energy and dynamical activity exhibit strong correlations for both systems. From extensive finite-size scaling analyses using the system size and observation time, we obtain scaling functions for the susceptibility and field and find scaling exponents that are model-dependent.
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Affiliation(s)
- Jay-Hak Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - YounJoon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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2
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Poggioli AR, Limmer DT. Odd Mobility of a Passive Tracer in a Chiral Active Fluid. PHYSICAL REVIEW LETTERS 2023; 130:158201. [PMID: 37115888 DOI: 10.1103/physrevlett.130.158201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Chiral active fluids break both time-reversal and parity symmetry, leading to exotic transport phenomena unobservable in ordinary passive fluids. We develop a generalized Green-Kubo relation for the anomalous lift experienced by a passive tracer suspended in a two-dimensional chiral active fluid subjected to an applied force. This anomalous lift is characterized by a transport coefficient termed the odd mobility. We validate our generalized response theory using molecular dynamics simulations, and we show that the asymmetric tracer mobility may be understood mechanically in terms of asymmetric deformations of the tracer-fluid density distribution function. We show that the even and odd components of the mobility decay at different rates with tracer size, suggesting the possibility of size-based particle separation using a chiral active working fluid.
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Affiliation(s)
- Anthony R Poggioli
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Kavli Energy NanoScience Institute, Berkeley, California 94720, USA
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Kavli Energy NanoScience Institute, Berkeley, California 94720, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Das A, Rose DC, Garrahan JP, Limmer DT. Reinforcement learning of rare diffusive dynamics. J Chem Phys 2021; 155:134105. [PMID: 34624994 DOI: 10.1063/5.0057323] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a method to probe rare molecular dynamics trajectories directly using reinforcement learning. We consider trajectories that are conditioned to transition between regions of configuration space in finite time, such as those relevant in the study of reactive events, and trajectories exhibiting rare fluctuations of time-integrated quantities in the long time limit, such as those relevant in the calculation of large deviation functions. In both cases, reinforcement learning techniques are used to optimize an added force that minimizes the Kullback-Leibler divergence between the conditioned trajectory ensemble and a driven one. Under the optimized added force, the system evolves the rare fluctuation as a typical one, affording a variational estimate of its likelihood in the original trajectory ensemble. Low variance gradients employing value functions are proposed to increase the convergence of the optimal force. The method we develop employing these gradients leads to efficient and accurate estimates of both the optimal force and the likelihood of the rare event for a variety of model systems.
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Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, California 94609, USA
| | - Dominic C Rose
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Juan P Garrahan
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94609, USA
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Lesnicki D, Gao CY, Limmer DT, Rotenberg B. On the molecular correlations that result in field-dependent conductivities in electrolyte solutions. J Chem Phys 2021; 155:014507. [PMID: 34241409 DOI: 10.1063/5.0052860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Employing recent advances in response theory and nonequilibrium ensemble reweighting, we study the dynamic and static correlations that give rise to an electric field-dependent ionic conductivity in electrolyte solutions. We consider solutions modeled with both implicit and explicit solvents, with different dielectric properties, and at multiple concentrations. Implicit solvent models at low concentrations and small dielectric constants exhibit strongly field-dependent conductivities. We compare these results to Onsager-Wilson theory of the Wien effect, which provides a qualitatively consistent prediction at low concentrations and high static dielectric constants but is inconsistent away from these regimes. The origin of the discrepancy is found to be increased ion correlations under these conditions. Explicit solvent effects act to suppress nonlinear responses, yielding a weakly field-dependent conductivity over the range of physically realizable field strengths. By decomposing the relevant time correlation functions, we find that the insensitivity of the conductivity to the field results from the persistent frictional forces on the ions from the solvent. Our findings illustrate the utility of nonequilibrium response theory in rationalizing nonlinear transport behavior.
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Affiliation(s)
- Dominika Lesnicki
- Sorbonne Université, CNRS, Physico-Chimie des Electrolytes et Nanosystèmes Interfaciaux, Paris, France
| | - Chloe Y Gao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physico-Chimie des Electrolytes et Nanosystèmes Interfaciaux, Paris, France
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Palmer BJ, Chun J, Morris JF, Mundy CJ, Schenter GK. Correlation function approach for diffusion in confined geometries. Phys Rev E 2020; 102:022129. [PMID: 32942374 DOI: 10.1103/physreve.102.022129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/23/2020] [Indexed: 11/07/2022]
Abstract
This paper describes a formalism for extracting spatially varying transport coefficients from simulations of a molecular fluid in a nanochannel. This approach is applied to self-diffusion of a Lennard-Jones fluid confined between two parallel surfaces. A numerical grid is laid over the domain confining the fluid, and fluid properties are projected onto the grid cells. The time correlation functions between properties in different grid cells are calculated and can be used as the basis for a fitting procedure for extracting spatially varying diffusion coefficients from the simulation. Results for the Lennard-Jones system show that transport behavior varies sharply near the liquid-solid boundary and that the changes depend on the details of the liquid-solid interaction. A quantitative difference between the reduced and detailed models is discussed. It is found that the difference could be associated with assumptions about the form of the transport equations at molecular scales in lieu of problems with the method itself. The study suggests that this approach to fitting molecular simulations to continuum equations may guide the development of appropriate coarse-grained equations to model transport phenomena at nanometer scales.
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Affiliation(s)
- Bruce J Palmer
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Jaehun Chun
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA.,Levich Institute and Department of Chemical Engineering, CUNY City College of New York, New York 10031, USA
| | - Jeffrey F Morris
- Levich Institute and Department of Chemical Engineering, CUNY City College of New York, New York 10031, USA
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Bulchandani VB, Karrasch C, Moore JE. Superdiffusive transport of energy in one-dimensional metals. Proc Natl Acad Sci U S A 2020; 117:12713-12718. [PMID: 32457150 PMCID: PMC7293602 DOI: 10.1073/pnas.1916213117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metals in one spatial dimension are described at the lowest energy scales by the Luttinger liquid theory. It is well understood that this free theory, and even interacting integrable models, can support ballistic transport of conserved quantities including energy. In contrast, realistic one-dimensional metals, even without disorder, contain integrability-breaking interactions that are expected to lead to thermalization and conventional diffusive linear response. We argue that the expansion of energy when such a nonintegrable Luttinger liquid is locally heated above its ground state shows superdiffusive behavior (i.e., spreading of energy that is intermediate between diffusion and ballistic propagation), by combining an analytical anomalous diffusion model with numerical matrix-product-state calculations on a specific perturbed spinless fermion chain. Different metals will have different scaling exponents and shapes in their energy spreading, but the superdiffusive behavior is stable and should be visible in time-resolved experiments.
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Affiliation(s)
- Vir B Bulchandani
- Department of Physics, University of California, Berkeley, CA 94720;
| | - Christoph Karrasch
- Institut für Mathematische Physik, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Joel E Moore
- Department of Physics, University of California, Berkeley, CA 94720
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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Arnon E, Rabani E, Neuhauser D, Baer R. Efficient Langevin dynamics for “noisy” forces. J Chem Phys 2020; 152:161103. [DOI: 10.1063/5.0004954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eitam Arnon
- Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and The Raymond and Beverly Sackler Center for Computational Molecular and Materials Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Daniel Neuhauser
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Roi Baer
- Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Das A, Limmer DT. Variational control forces for enhanced sampling of nonequilibrium molecular dynamics simulations. J Chem Phys 2019; 151:244123. [DOI: 10.1063/1.5128956] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Kavli Energy NanoScience Institute, Berkeley, California 94720, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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9
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Gao CY, Limmer DT. Nonlinear transport coefficients from large deviation functions. J Chem Phys 2019; 151:014101. [PMID: 31272161 DOI: 10.1063/1.5110507] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nonlinear response occurs naturally when a strong perturbation takes a system far from equilibrium. Despite its omnipresence in nanoscale systems, it is difficult to predict in a general and efficient way. Here, we introduce a way to compute arbitrarily high order transport coefficients of stochastic systems, using the framework of large deviation theory. Leveraging time reversibility in the microscopic dynamics, we relate nonlinear response to equilibrium multitime correlation functions among both time reversal symmetric and asymmetric observables, which can be evaluated from derivatives of large deviation functions. This connection establishes a thermodynamiclike relation for nonequilibrium response and provides a practical route to its evaluation, as large deviation functions are amenable to importance sampling. We demonstrate the generality and efficiency of this method in predicting transport coefficients in single particle systems and an interacting system exhibiting thermal rectification.
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Affiliation(s)
- Chloe Ya Gao
- Department of Chemistry, University of California, Berkeley, California 94609, USA
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94609, USA
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Schile AJ, Limmer DT. Rate constants in spatially inhomogeneous systems. J Chem Phys 2019; 150:191102. [DOI: 10.1063/1.5092837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Addison J. Schile
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720-1460, USA
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720-1460, USA
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720-1460, USA
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Kim KS, Han MH, Kim C, Li Z, Karniadakis GE, Lee EK. Nature of intrinsic uncertainties in equilibrium molecular dynamics estimation of shear viscosity for simple and complex fluids. J Chem Phys 2018; 149:044510. [DOI: 10.1063/1.5035119] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kang-Sahn Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Myung Hoon Han
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Changho Kim
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Applied Mathematics, University of California, Merced, California 95343, USA
| | - Zhen Li
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | - George Em Karniadakis
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | - Eok Kyun Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
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Impact of Multi-Causal Transport Mechanisms in an Electrolyte Supported Planar SOFC with (ZrO 2) x-1(Y 2O 3) x Electrolyte. ENTROPY 2018; 20:e20060469. [PMID: 33265559 PMCID: PMC7512987 DOI: 10.3390/e20060469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 11/24/2022]
Abstract
The calculation of the entropy production rate within an operational high temperature solid oxide fuel cell (SOFC) is necessary to design and improve heating and cooling strategies. However, due to a lack of information, most of the studies are limited to empirical relations, which are not in line with the more general approach given by non-equilibrium thermodynamics (NET). The SOFC 1D-model presented in this study is based on non-equilibrium thermodynamics and we parameterize it with experimental data and data from molecular dynamics (MD). The validation of the model shows that it can effectively describe the behavior of a SOFC at 1300 K. Moreover, we show that the highest entropy production is present in the electrolyte and the catalyst layers, and that the Peltier heat transfer is considerable for the calculation of the heat flux in the electrolyte and cannot be neglected. To our knowledge, this is the first validated model of a SOFC based on non-equilibrium thermodynamics and this study can be extended to analyze SOFCs with other solid oxide electrolytes, with perovskites electrolytes or even other electrochemical systems like solid oxide electrolysis cells (SOECs).
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Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? ENTROPY 2018; 20:e20050348. [PMID: 33265438 PMCID: PMC7512867 DOI: 10.3390/e20050348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 01/18/2023]
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