arXiv subjects

Raymond Kapral

Publications and source records attributed to Raymond Kapral.

At least 37 records · Page 2Linked to original sources

arXiv2018

Nonequilibrium thermodynamics and boundary conditions for reaction and transport in heterogeneous media

Nonequilibrium interfacial thermodynamics is formulated in the presence of surface reactions for the study of diffusiophoresis in isothermal systems. As a consequence of microreversibility and Onsager-Casimir reciprocal relations, diffusiophoresis, i.e., the coupling of the tangential components of the pressure tensor to the concentration gradients of solute species, has a reciprocal effect where the interfacial currents of solutes is coupled to the slip velocity. The presence of surface reactions is shown to modify the diffusiophoretic and reciprocal effects at the fluid-solid interface. The thin-layer approximation is used to describe the solution flowing near a reactive solid interface. Analytic formulas describing the diffusiophoretic and reciprocal effects are deduced in the thin-layer approximation and tested numerically for the Poiseuille flow of a solution between catalytic planar surfaces.

physics.chem-ph↗

arXiv2018

Dynamics of Janus motors with microscopically reversible kinetics

Janus motors with chemically active and inactive hemispheres can operate only under nonequilibrium conditions where detailed balance is broken by fluxes of chemical species that establish a nonequilibrium state. A microscopic model for reversible reactive collisions on a Janus motor surface is constructed and shown to satisfy detailed balance. The model is used to study Janus particle reactive dynamics in systems at equilibrium where generalized chemical rate laws that include time-dependent rate coefficients with power-law behavior are shown to describe reaction rates. While maintaining reversible reactions on the Janus catalytic hemisphere, the system is then driven into a nonequilibrium steady state by fluxes of chemical species that control the chemical affinity. The statistical properties of the self-propelled Janus motor in this nonequilibrium steady state are investigated and compared with predictions of a fluctuating thermodynamics theory. The model has utility beyond the examples presented here, since it allows one to explore various aspects of nonequilibrium fluctuations in systems with self-diffusiophoretic motors from a microscopic perspective.

cond-mat.soft↗

arXiv2018

Fluctuating chemohydrodynamics and the stochastic motion of self-diffusiophoretic particles

The propulsion of active particles by self-diffusiophoresis is driven by asymmetric catalytic reactions on the particle surface that generate a mechanochemical coupling between the fluid velocity and the concentration fields of fuel and product in the surrounding solution. Because of thermal and molecular fluctuations in the solution, the motion of micrometric or submicrometric active particles is stochastic. Coupled Langevin equations describing the translation, rotation, and reaction of such active particles are deduced from fluctuating chemohydrodynamics and fluctuating boundary conditions at the interface between the fluid and the particle. These equations are consistent with microreversibility and the Onsager-Casimir reciprocal relations between affinities and currents, and provide a thermodynamically consistent basis for the investigation of the dynamics of active particles propelled by diffusiophoretic mechanisms.

cond-mat.stat-mech↗

arXiv2017

Many-body dynamics of chemically propelled nanomotors

The collective behavior of chemically propelled sphere-dimer motors made from linked catalytic and noncatalytic spheres in a quasi-two-dimensional confined geometry is studied using a coarse-grained microscopic dynamical model. Chemical reactions at the catalytic spheres that convert fuel to product generate forces that couple to solvent degrees of freedom as a consequence of momentum conservation in the microscopic dynamics. The collective behavior of the many-body system is influenced by direct intermolecular interactions among the motors, chemotactic effects due to chemical gradients, hydrodynamic coupling, and thermal noise. Segregation into high and low density phases and globally homogeneous states with strong fluctuations are investigated as functions of the motor characteristics. Factors contributing to this behavior are discussed in the context of active Brownian models.

cond-mat.soft↗

arXiv2017

Chemotactic and hydrodynamic effects on collective dynamics of self-diffusiophoretic Janus motors

Collective motion in nonequilibrium steady state suspensions of self-propelled Janus motors driven by chemical reactions can arise due to interactions coming from direct intermolecular forces, hydrodynamic flow effects, or chemotactic effects mediated by chemical gradients. The relative importance of these interactions depends on the reactive characteristics of the motors, the way in which the system is maintained in a steady state, and properties of the suspension, such as the volume fraction. From simulations of a microscopic hard collision model for the interaction of fluid particles with the Janus motor we show that dynamic cluster states exist and determine the interaction mechanisms that are responsible for their formation. The relative importance of chemotactic and hydrodynamic effects is identified by considering a microscopic model in which chemotactic effects are turned off while the full hydrodynamic interactions are retained. The system is maintained in a steady state by means of a bulk reaction in which product particles are reconverted into fuel particles. The influence of the bulk reaction rate on the collective dynamics is also studied.

cond-mat.soft↗

arXiv2017

Mechanochemical fluctuation theorem and thermodynamics of self-phoretic motors

Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration fields induced by asymmetric catalytic reactions on the motor surface. The consistency between the thermodynamics of this coupling and the microscopic reversibility of the underlying molecular dynamics is investigated. For this purpose coupled Langevin equations for the translational, rotational, and chemical fluctuations of self-phoretic motors are derived. A mechanochemical fluctuation theorem for the joint probability to find the motor at position r after n reactive events have occurred during the time interval t is also derived. An important result that follows from this analysis is the identification of an effect that is reciprocal to self-propulsion by diffusiophoresis, which leads to the possibility of fuel synthesis by mechanochemical coupling to external force and torque.

cond-mat.stat-mech↗

arXiv2017

Diffusion in systems crowded by active force-dipole molecules

Experimental studies of systems containing active proteins that undergo conformational changes driven by catalytic chemical reactions have shown that the diffusion coefficients of passive tracer particles and active molecules are larger than the corresponding values when chemical activity is absent. Various mechanisms have been proposed for such behavior, including, among others, force dipole interactions of molecular motors moving on filaments and collective hydrodynamic effects arising from active proteins. Simulations of a multi-component system containing active dumbbell molecules that cycle between open and closed states, a passive tracer particle and solvent molecules are carried out. Consistent with experiments, it is shown that the diffusion coefficients of both passive particles and the dumbbells themselves are enhanced when the dumbbells are active. The dependence of the diffusion enhancement on the volume fraction of dumbbells is determined, and the effects of crowding by active dumbbell molecules are shown to differ from those due to inactive molecules.

cond-mat.soft↗

arXiv2016

Quantum Dynamics in Open Quantum-Classical Systems

Often quantum systems are not isolated and interactions with their environments must be taken into account. In such open quantum systems these environmental interactions can lead to decoherence and dissipation, which have a marked influence on the properties of the quantum system. In many instances the environment is well-approximated by classical mechanics, so that one is led to consider the dynamics of open quantum-classical systems. Since a full quantum dynamical description of large many-body systems is not currently feasible, mixed quantum-classical methods can provide accurate and computationally tractable ways to follow the dynamics of both the system and its environment. This review focuses on quantum-classical Liouville dynamics, one of several quantum-classical descriptions, and discusses the problems that arise when one attempts to combine quantum and classical mechanics, coherence and decoherence in quantum-classical systems, nonadiabatic dynamics, surface-hopping and mean-field theories and their relation to quantum-classical Liouville dynamics, as well as methods for simulating the dynamics.

quant-ph↗

arXiv2016

Microscopic and continuum descriptions of Janus motor fluid flow fields

Active media, whose constituents are able to move autonomously, display novel features that differ from those of equilibrium systems. In addition to naturally-occurring active systems such as populations of swimming bacteria, active systems of synthetic self-propelled nanomotors have been developed. These synthetic systems are interesting because of their potential applications in a variety of fields. Janus particles, synthetic motors of spherical geometry with one hemisphere that catalyzes the conversion of fuel to product and one noncatalytic hemisphere, can propel themselves in solution by self-diffusiophoresis. In this mechanism the concentration gradient generated by the asymmetric catalytic activity leads to a force on the motor that induces fluid flows in the surrounding medium. These fluid flows are studied in detail through microscopic simulations of Janus motor motion and continuum theory. It is shown that continuum theory is able to capture many but not all features of the dynamics of the Janus motor and the velocity fields of the fluid.

cond-mat.soft↗

arXiv2016

Surface hopping from the perspective of quantum-classical Liouville dynamics

Fewest-switches surface hopping is studied in the context of quantum-classical Liouville dynamics. Both approaches are mixed quantum-classical theories that provide a way to describe and simulate the nonadiabatic quantum dynamics of many-body systems. Starting from a surface-hopping solution of the quantum-classical Liouville equation, it is shown how fewest-switches dynamics can be obtained by dropping terms that are responsible for decoherence and restricting the nuclear momentum changes that accompany electronic transitions to those events that occur between population states. The analysis provides information on some of the elements that are essential for the construction of accurate and computationally tractable algorithms for nonadiabatic processes.

quant-ph↗

arXiv2016

A microscopic model for chemically-powered Janus motors

Very small synthetic motors that make use of chemical reactions to propel themselves in solution hold promise for new applications in the development of new materials, science and medicine. The prospect of such potential applications, along with the fact that systems with many motors or active elements display interesting cooperative phenomena of fundamental interest, has made the study of synthetic motors an active research area. Janus motors, comprising catalytic and noncatalytic hemispheres, figure prominently in experimental and theoretical studies of these systems. While continuum models of Janus particle systems are often used to describe motor dynamics, microscopic models that are able to account for intermolecular interactions, many-body concentration gradients, fluid flows and thermal fluctuations provide a way to explore the dynamical behavior of these complex out-of-equilibrium systems that does not rely on approximations that are often made in continuum theories. The analysis of microscopic models from first principles provides a foundation from which the range of validity and limitations of approximate theories of the dynamics may be assessed. In this paper, a microscopic model for the diffusiophoretic propulsion of Janus motors, where motor interactions with the environment occur only through hard collisions, is constructed, analyzed and compared to theoretical predictions. Microscopic simulations of both single-motor and many-motor systems are carried out to illustrate the results.

cond-mat.soft↗

arXiv2015

Nanoconfined catalytic Ångström-size motors

Self-propelled chemically powered synthetic micron and nano-scale motors are being intensively studied because of the wide range of potential applications that exploit their directed motion. This paper considers even smaller Ångström-size synthetic motors. Such very small motors in bulk solution display effects arising from their self-propulsion. Recent experiments have shown that small-molecule catalysts and single enzyme molecules exhibit properties that have been attributed to their chemical activity. Molecular dynamics is used to investigate the properties of very small Ångström-size synthetic chemically powered sphere-dimer motors in a simple atomic-like solvent confined between walls separated by distances of tens of nanometers. Evidence for strong structural ordering of the motors between the walls, which reflects the finite size of solvent molecules and depends on solvent depletion forces, is provided. Dynamical properties, such as average motor velocity, orientational relaxation, and mean square displacement, are anisotropic and depend on the distance from the walls. This research provides information needed for potential applications that use molecular-scale motors in the complex confined geometries encountered in biology and the laboratory.

cond-mat.soft↗

arXiv2015

Hydrodynamic Collective Effects of Active Protein Machines in Solution and Lipid Bilayers

The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We analyze the effects that hydrodynamic flows induced by active proteins have on other passive molecules in solution or membranes. We show that the diffusion constants of passive particles are enhanced substantially. Furthermore, when gradients of active proteins are present, a chemotaxis-like drift of passive particles takes place. In lipid bilayers, the effects are strongly nonlocal, so that active inclusions in the membrane contribute to diffusion enhancement and the drift. The results indicate that the transport properties of passive particles in systems containing active proteins machines operating under nonequilibrium conditions differ from their counterparts in systems at thermal equilibrium.

cond-mat.soft↗

arXiv2014

Chemistry in Motion: Tiny Synthetic Motors

In this Account, we describe how synthetic motors that operate by self-diffusiophoresis make use of a self-generated concentration gradient to drive motor motion. A description of propulsion by self-diffusiophoresis is presented for Janus particle motors comprising catalytic and noncatalytic faces. The properties of the dynamics of chemically powered motors are illustrated by presenting the results of particle-based simulations of sphere-dimer motors constructed from linked catalytic and noncatalytic spheres. The geometries of both Janus and sphere-dimer motors with asymmetric catalytic activity support the formation of concentration gradients around the motors. Because directed motion can occur only when the system is not in equilibrium, the nature of the environment and the role it plays in motor dynamics are described. Rotational Brownian motion also acts to limit directed motion, and it has especially strong effects for very small motors. We address the following question: how small can motors be and still exhibit effects due to propulsion, even if only to enhance diffusion? Synthetic motors have the potential to transform the manner in which chemical dynamical processes are carried out for a wide range of applications.

cond-mat.soft↗

arXiv2014

Ångström-scale chemically powered motors

Like their larger micron-scale counterparts, Ångström-scale chemically self-propelled motors use asymmetric catalytic activity to produce self-generated concentration gradients that lead to directed motion. Unlike their micron-scale counterparts, the sizes of Ångström-scale motors are comparable to the solvent molecules in which they move, they are dominated by fluctuations, and they operate on very different time scales. These new features are studied using molecular dynamics simulations of small sphere dimer motors. We show that the ballistic regime is dominated by the thermal speed but the diffusion coefficients of these motors are orders of magnitude larger than inactive dimers. Such small motors may find applications in nano-confined systems or perhaps eventually in the cell.

cond-mat.soft↗

arXiv2014

Self-propulsion through symmetry breaking

In addition to self-propulsion by phoretic mechanisms that arises from an asymmetric distribution of reactive species around a catalytic motor, spherical particles with a uniform distribution of catalytic activity may also propel themselves under suitable conditions. Reactive fluctuation-induced asymmetry can give rise to transient concentration gradients which may persist under certain conditions, giving rise to a bifurcation to self-propulsion. The nature of this phenomenon is analyzed in detail, and particle-level simulations are carried out to demonstrate its existence.

cond-mat.stat-mech↗

arXiv2013

Analysis of geometric phase effects in the quantum-classical Liouville formalism

We analyze two approaches to the quantum-classical Liouville (QCL) formalism that differ in the order of two operations: Wigner transformation and projection onto adiabatic electronic states. The analysis is carried out on a two-dimensional linear vibronic model where geometric phase (GP) effects arising from a conical intersection profoundly affect nuclear dynamics. We find that the Wigner-then-Adiabatic (WA) QCL approach captures GP effects, whereas the Adiabatic-then-Wigner (AW) QCL approach does not. Moreover, the Wigner transform in AW-QCL leads to an ill-defined Fourier transform of double-valued functions. The double-valued character of these functions stems from the nontrivial GP of adiabatic electronic states in the presence of a conical intersection. In contrast, WA-QCL avoids this issue by starting with the Wigner transform of single-valued quantities of the full problem. Since the WA-QCL approach uses solely the adiabatic potentials and non-adiabatic derivative couplings as an input, our results indicate that WA-QCL can capture GP effects in general two-state crossing problems using first-principles electronic structure calculations without prior diabatization or introduction of explicit phase factors.

quant-ph↗

arXiv2013

Analysis of the Forward-Backward Trajectory Solution for the Mixed Quantum-Classical Liouville Equation

Mixed quantum-classical methods provide powerful algorithms for the simulation of quantum processes in large and complex systems. The forward-backward trajectory solution of the mixed quantum-classical Liouville equation in the mapping basis [J. Chem. Phys. 137, 22A507 (2012)] is one such scheme. It simulates the dynamics via the propagation of forward and backward trajectories of quantum coherent state variables, and the propagation of bath trajectories on a mean-field potential determined jointly by the forward and backward trajectories. An analysis of the properties of this solution, numerical tests of its validity and an investigation of its utility for the study of nonadiabtic quantum processes are given. In addition, we present an extension of this approximate solution that allows one to systematically improve the results. This extension, termed the jump forward-backward trajectory solution, is analyzed and tested in detail and its various implementations are discussed.

physics.chem-ph↗