Thermodynamic Transferability in Coarse-Grained Force Fields Using Graph Neural Networks.

Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output while removing the degrees of freedom that are less relevant. This reduction in model complexity allows coarse-grained molecular simulations to reach increased spatial and temporal scales compared with corresponding all-atom models. A core challenge in coarse-graining is to construct a force field that represents the interactions in the new representation in a way that preserves the atomistic-level properties.

The effect of temperature oscillations on energy storage rectification in harmonic systems.

Rectification, the preferential transport of a current in one direction through a system, has garnered significant attention in molecules because of its importance for controlling thermal and electronic currents at the nanoscale. Here, we report the presence of energy storage rectification effects in a molecular chain. This phenomenon is generated by subjecting a harmonic molecular chain to an oscillating temperature gradient and showing that the energy absorption rate of the system depends on the direction of the gradient.

Molecular heat transport across a time-periodic temperature gradient.

The time-periodic modulation of a temperature gradient can alter the heat transport properties of a physical system. Oscillating thermal gradients give rise to behaviors such as modified thermal conductivity and controllable time-delayed energy storage that are not present in a system with static temperatures. Here, we examine how the heat transport properties of a molecular lattice model are affected by an oscillating temperature gradient.

Energy transport between heat baths with oscillating temperatures.

Energy transport is a fundamental physical process that plays a prominent role in the function and performance of myriad systems and technologies. Recent experimental measurements have shown that subjecting a macroscale system to a time-periodic temperature gradient can increase thermal conductivity in comparison to a static temperature gradient. Here, we theoretically examine this mechanism in a nanoscale model by applying a stochastic Langevin framework to describe the energy transport properties of a particle connecting two heat baths with different temperatures, where the temperature difference between baths is oscillating in time.

Electron hopping heat transport in molecules.

The realization of single-molecule thermal conductance measurements has driven the need for theoretical tools to describe conduction processes that occur over atomistic length scales. In macroscale systems, the principle that is typically used to understand thermal conductivity is Fourier's law. At molecular length scales, however, deviations from Fourier's law are common in part because microscale thermal transport properties typically depend on the complex interplay between multiple heat conduction mechanisms.

Heat transport induced by electron transfer: A general temperature quantum calculation.

Electron transfer dominates chemical processes in biological, inorganic, and material chemistry. Energetic aspects of such phenomena, in particular, the energy transfer associated with the electron transfer process, have received little attention in the past but are important in designing energy conversion devices. This paper generalizes our earlier work in this direction, which was based on the semiclassical Marcus theory of electron transfer.

Machine learning approaches for structural and thermodynamic properties of a Lennard-Jones fluid.

Predicting the functional properties of many molecular systems relies on understanding how atomistic interactions give rise to macroscale observables. However, current attempts to develop predictive models for the structural and thermodynamic properties of condensed-phase systems often rely on extensive parameter fitting to empirically selected functional forms whose effectiveness is limited to a narrow range of physical conditions. In this article, we illustrate how these traditional fitting paradigms can be superseded using machine learning.

Determination of Structural Correlation Functions.

Determining the structural properties of condensed-phase systems is a fundamental problem in theoretical statistical mechanics. Here we present a machine learning method that is able to predict structural correlation functions with significantly improved accuracy in comparison with traditional approaches. The usefulness of this (from the machine) approach is illustrated by predicting the radial distribution functions of two paradigmatic condensed-phase systems, a Lennard-Jones fluid and a hard-sphere fluid, and then comparing those results to the results obtained using both integral equation methods and empirically motivated analytical functions.

Wiedemann-Franz Law for Molecular Hopping Transport.

The Wiedemann-Franz (WF) law is a fundamental result in solid-state physics that relates the thermal and electrical conductivity of a metal. It is derived from the predominant transport mechanism in metals: the motion of quasi-free charge-carrying particles. Here, an equivalent WF relationship is developed for molecular systems in which charge carriers are moving not as free particles but instead hop between redox sites.

Electron-Transfer-Induced Thermal and Thermoelectric Rectification.

Controlling the direction and magnitude of both heat and electronic currents using rectifiers has significant implications for the advancement of molecular circuit design. In order to facilitate the implementation of new transport phenomena in such molecular structures, we examine thermal and thermoelectric rectification effects that are induced by an electron transfer process that occurs across a temperature gradient between molecules. Historically, the only known heat conduction mechanism able to generate thermal rectification in purely molecular environments is phononic heat transport.

Upside/Downside statistical mechanics of nonequilibrium Brownian motion. II. Heat transfer and energy partitioning of a free particle.

The energy partitioning during activation and relaxation events under steady-state conditions for a Brownian particle driven by multiple thermal reservoirs of different local temperatures is investigated. Specifically, we apply the formalism derived in Paper I [G. T.

Upside/Downside statistical mechanics of nonequilibrium Brownian motion. I. Distributions, moments, and correlation functions of a free particle.

Statistical properties of Brownian motion that arise by analyzing, separately, trajectories over which the system energy increases (upside) or decreases (downside) with respect to a threshold energy level are derived. This selective analysis is applied to examine transport properties of a nonequilibrium Brownian process that is coupled to multiple thermal sources characterized by different temperatures. Distributions, moments, and correlation functions of a free particle that occur during upside and downside events are investigated for energy activation and energy relaxation processes and also for positive and negative energy fluctuations from the average energy.

Electron-transfer-induced and phononic heat transport in molecular environments.

A unified theory of heat transport in environments that sustain intersite phononic coupling and electron hopping is developed. The heat currents generated by both phononic transport and electron transfer between sites characterized by different local temperatures are calculated and compared. Using typical molecular parameters we find that the electron-transfer-induced heat current can be comparable to that of the standard phononic transport for donor-acceptor pairs with efficient bidirectional electron transfer rates (relatively small intersite distance and favorable free-energy difference).

Lagrangian descriptors of driven chemical reaction manifolds.

The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed.

Transition state theory for activated systems with driven anharmonic barriers.

Classical transition state theory has been extended to address chemical reactions across barriers that are driven and anharmonic. This resolves a challenge to the naive theory that necessarily leads to recrossings and approximate rates because it relies on a fixed dividing surface. We develop both perturbative and numerical methods for the computation of a time-dependent recrossing-free dividing surface for a model anharmonic system in a solvated environment that interacts strongly with an oscillatory external field.

Electrothermal Transistor Effect and Cyclic Electronic Currents in Multithermal Charge Transfer Networks.

A theory is developed to describe the coupled transport of energy and charge in networks of electron donor-acceptor sites which are seated in a thermally heterogeneous environment, where the transfer kinetics are dominated by Marcus-type hopping rates. It is found that the coupling of heat and charge transfer in such systems gives rise to exotic transport phenomena which are absent in thermally homogeneous systems and cannot be described by standard thermoelectric relations. Specifically, the directionality and extent of thermal transistor amplification and cyclical electronic currents in a given network can be controlled by tuning the underlying temperature gradient in the system.

Electron transfer across a thermal gradient.

Charge transfer is a fundamental process that underlies a multitude of phenomena in chemistry and biology. Recent advances in observing and manipulating charge and heat transport at the nanoscale, and recently developed techniques for monitoring temperature at high temporal and spatial resolution, imply the need for considering electron transfer across thermal gradients. Here, a theory is developed for the rate of electron transfer and the associated heat transport between donor-acceptor pairs located at sites of different temperatures.

Transition state geometry of driven chemical reactions on time-dependent double-well potentials.

Reaction rates across time-dependent barriers are difficult to define and difficult to obtain using standard transition state theory approaches because of the complexity of the geometry of the dividing surface separating reactants and products. Using perturbation theory (PT) or Lagrangian descriptors (LDs), we can obtain the transition state trajectory and the associated recrossing-free dividing surface. With the latter, we are able to determine the exact reactant population decay and the corresponding rates to benchmark the PT and LD approaches.

Deconstructing field-induced ketene isomerization through Lagrangian descriptors.

The time-dependent geometrical separatrices governing state transitions in field-induced ketene isomerization are constructed using the method of Lagrangian descriptors. We obtain the stable and unstable manifolds of time-varying transition states as dynamic phase space objects governing configurational changes when the ketene molecule is subjected to an oscillating electric field. The dynamics of the isomerization reaction are modeled through classical trajectory studies on the Gezelter-Miller potential energy surface and an approximate dipole moment model which is coupled to a time-dependent electric field.

Nonequilibrium structure in sequential assembly.

The assembly of monomeric constituents into molecular superstructures through sequential-arrival processes has been simulated and theoretically characterized. When the energetic interactions allow for complete overlap of the particles, the model is equivalent to that of the sequential absorption of soft particles on a surface. In the present work, we consider more general cases by including arbitrary aggregating geometries and varying prescriptions of the connectivity network.

Lagrangian Descriptors of Thermalized Transition States on Time-Varying Energy Surfaces.

Thermalized chemical reactions driven under dynamical load are characteristic of activated dynamics for arbitrary nonautonomous systems. Recent generalizations of transition state theory to obtain formally exact rates have required the construction of a time-dependent transition state trajectory. Here, we show that Lagrangian descriptors can be used to obtain this structure directly.

Stochastic dynamics of penetrable rods in one dimension: Entangled dynamics and transport properties.

The dynamical properties of a system of soft rods governed by stochastic hard collisions (SHCs) have been determined over a varying range of softness using molecular dynamics simulations in one dimension and analytic theory. The SHC model allows for interpenetration of the system's constituent particles in the simulations, generating overlapping clustering behavior analogous to the spatial structures observed in systems governed by deterministic bounded potentials. Through variation of an assigned softness parameter δ, the limiting ranges of intermolecular softness are bridged, connecting the limiting ensemble behavior from hard to ideal (completely soft).

Chemical reactions induced by oscillating external fields in weak thermal environments.

Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally varying external field, the transition state that the reaction must pass through during the transformation from reactant to product is no longer a fixed geometric structure, but is instead time-dependent. For a periodically forced model reaction, we develop a recrossing-free dividing surface that is attached to a transition state trajectory [T.

Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields.

When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product--for example, an energy barrier--becomes time-dependent. We show that for periodic forcing the rate of barrier crossing can be determined through stability analysis of the non-autonomous transition state. Specifically, strong agreement is observed between the difference in the Floquet exponents describing stability of the transition state trajectory, which defines a recrossing-free dividing surface [G.

Effective surface coverage of coarse-grained soft matter.

The surface coverage of coarse-grained macromolecules bound to a solid substrate is not simply proportional to the two-dimensional number density because macromolecules can overlap. As a function of the overlap probability δ, we have developed analytical formulas and computational models capable of characterizing this nonlinear relationship. For simplicity, we ignore site-site interactions that would be induced by length-scale mismatches between binding sites and the radius of gyration of the incident coarse-grained macromolecular species.