arXiv subjects

Raymond Kapral

Publications and source records attributed to Raymond Kapral.

At least 19 recordsLinked to original sources

arXiv2026

Colloidal logic-gate circuits can process environmental signals and autonomously perform tasks

Cooperative collective dynamics is a principal determinant of the ability of synthetic micromotors to perform specific functions. However, realizing controllable and predictable collective behavior in complex physiological environments remains a significant challenge. Here, we show that collections of enzyme-coated colloids can be designed as various chemical logic gates, which subsequently can be organized into functional logic circuits. These circuits take environmental information as input signals and process it to produce output chemical species needed to achieve specific goals. The chemical computation performed by the circuit endows the active colloidal system with the ability to sense its surroundings and autonomously coordinate its collective motion. The results of simulations of several examples are presented, where self-assembled colloidal circuits can identify invasive threats by their signals, produce and deliver chemicals to the targets to suppress their activity. The results of this work can aid in the design of experimental chemical logic circuits through micromotor self-assembly that autonomously respond to environmental cues to execute specific tasks.

physics.chem-ph↗

arXiv2024

Dynamics of Quantum-Classical Systems in Nonequilibrium Environments

The dynamics of a quantum system coupled to a classical environment and subject to constraints that drive it out of equilibrium is described. The evolution of the system is governed by the quantum-classical Liouville equation. Rather than evaluating the evolution of the mixed quantum-classical density operator, we derive exact equations of motion for the nonequilibrium average values of a set of operators or variables, along with correlation function expressions for the dissipative coefficients that enter these equations. These equations are obtained by requiring that the exact nonequilibrium averages are equal to local nonequilibrium averages that depend on auxiliary fields whose values satisfy evolution equations obtained using projection operator methods. The results are illustrated by deriving reaction-diffusion equations coupled to fluid hydrodynamic equations for a dilute solution of quantum particles that can exist in two metastable states. Nonequilibrium steady states are discussed along with the reaction rate and diffusion correlation functions that characterize such states.

cond-mat.stat-mech↗

arXiv2024

Self-organization of active colloids mediated by chemical interactions

Self-propelled colloidal particles exhibit rich non-equilibrium phenomena and have promising applications in fields such as drug delivery and self-assembled active materials. Previous experimental and theoretical studies have shown that chemically active colloids that consume or produce a chemical can self-organize into clusters with diverse characteristics depending on the effective phoretic interactions. In this paper, we investigate self-organization in systems with multiple chemical species that undergo a network of reactions and multiple colloidal species that participate in different reactions. Active colloids propelled by complex chemical reactions with potentially nonlinear kinetics can be realized using enzymatic reactions that occur on the surface of enzyme-coated particles. To demonstrate how the self-organizing behavior depends on the chemical reactions active colloids catalyze and their chemical environment, we consider first a single type of colloid undergoing a simple catalytic reaction, and compare this often-studied case with self-organization in binary mixtures of colloids with sequential reactions, and binary mixtures with nonlinear autocatalytic reactions. Our results show that in general active colloids at low particle densities can form localized clusters in the presence of bulk chemical reactions and phoretic attractions. The characteristics of the clusters, however, depend on the reaction kinetics in the bulk and on the particles and phoretic coefficients. With one or two chemical species that only undergo surface reactions, the space for possible self-organizations are limited. By considering the additional system parameters that enter the chemical reaction network involving reactions on the colloids and in the fluid, the design space of colloidal self-organization can be enlarged, leading to a variety of non-equilibrium structures.

cond-mat.soft↗

arXiv2023

Microscopic theory of a Janus motor in a non-equilibrium fluid: Surface hydrodynamics and boundary conditions

We present a derivation from first principles of the coupled equations of motion of an active self-diffusiophoretic Janus motor and the hydrodynamic densities of its fluid environment that are nonlinearly displaced from equilibrium. The derivation makes use of time-dependent projection operator techniques defined in terms of slowly varying coarse-grained microscopic densities of the fluid species number, total momentum, and energy. The exact equations of motion are simplified using time-scale arguments, resulting in Markovian equations for the Janus motor linear and angular velocities with average forces and torques that depend on the fluid densities. For a large colloid, the fluid equations are separated into bulk and interfacial contributions, and the conditions under which the dynamics of the fluid densities can be accurately represented by bulk hydrodynamic equations subject to boundary conditions on the colloid are determined. We show how the results for boundary conditions based on continuum theory can be obtained from the molecular description and provide Green-Kubo expressions for all transport coefficients, including the diffusiophoretic coupling and the slip coefficient.

cond-mat.soft↗

arXiv2023

Clustering of chemically propelled nanomotors in chemically active environments

Synthetic nanomotors powered by chemical reactions have been designed to act as vehicles for active cargo transport, drug delivery as well as a variety of other uses. Collections of such motors, acting in consort, can self-assemble to form swarms or clusters, providing opportunities for applications on various length scales. While such collective behavior has been studied when the motors move in a chemically inactive fluid environment, when the medium in which they move is a chemical network that supports complex spatial and temporal patterns, through simulation and theoretical analysis we show that collective behavior changes. Spatial patterns in the environment can guide and control motor collective states, and interactions of the motors with their environment can give rise to distinctive spatiotemporal motor patterns. The results are illustrated by studies of the motor dynamics in systems that support Turing patterns and spiral waves. This work is relevant for potential applications that involve many active nanomotors moving in complex chemical or biological environments.

cond-mat.soft↗

arXiv2023

Chemical logic gates on active colloids

Synthetic active colloidal systems are being studied extensively because of the diverse and often unusual phenomena these nonequilibrium systems manifest, and their potential applications in fields ranging from biology to material science. Recent studies have shown that active colloidal motors that use enzymatic reactions for propulsion hold special promise for applications that require motors to carry out active sensing tasks in complicated biomedical environments. In such applications it would be desirable to have active colloids with some capability of computation so that they could act autonomously to sense their surroundings and alter their own dynamics to perform specific tasks. Here we describe how small chemical networks that make use of enzymatic chemical reactions on the colloid surface can be used to construct motor-based chemical logic gates. Some basic features of coupled enzymatic reactions that are responsible for propulsion and underlie the construction and function of chemical gates are described using continuum theory and molecular simulation. Examples are given that show how colloids with specific chemical logic gates can perform simple sensing tasks. Due to the diverse functions of different enzyme gates, operating alone or in circuits, the work presented here supports the suggestion that synthetic motors using such gates could be designed to operate in an autonomous way in order to complete complicated tasks.

cond-mat.soft↗

arXiv2023

Inertial effects on rectification and diffusion of active Brownian particles in an asymmetric channel

Micro- and nano-swimmers moving in a fluid solvent confined by structures that produce entropic barriers are often described by overdamped active Brownian particle dynamics, where viscous effects are large and inertia plays no role. However, inertial effects should be considered for confined swimmers moving in media where viscous effects are no longer dominant. Here, we study how inertia affects the rectification and diffusion of self-propelled particles in a two-dimensional asymmetric channel. We show that most of the particles accumulate at the channel walls as the masses of the particles increase. Furthermore, the average particle velocity has a maximum as a function of the mass, indicating that particles with an optimal mass $M^{*}_{\rm op}$ can be sorted from a mixture with particles of other masses. In particular, we find that the effective diffusion coefficient exhibits an enhanced diffusion peak as a function of the mass, which is a signature of the accumulation of most of the particles at the channel walls. The dependence of $M^{*}_{\rm op}$ on the rotational diffusion rate, self-propulsion force, aspect ratio of the channel, and active torque is also determined. The results of this study could stimulate the development of strategies for controlling the diffusion of self-propelled particles in entropic ratchet systems.

cond-mat.soft↗

arXiv2021

Control of active polymeric filaments by chemically-powered nanomotors

Active materials with distinctive nonequilibrium properties have diverse materials science applications. Active systems are common in living matter, such as the filament network in the cell that is activated by molecular motors, and in materials science as exemplified by hydrogels activated by chemical reactions. Here we describe another class of active polymeric filament systems where the filaments are activated by embedded chemically-powered nanomotors that have catalytic and noncatalytic parts. Chemical reactions on the catalytic surfaces produce forces that act on the polymeric filaments. By changing the nonequilibrium conditions these forces can be made to change sign and thereby compress or expand the filaments. The embedded motors provide both the source of activity and the means to control the filament conformational structure. As an example of control, we show that oscillatory variations of the chemical constraints yield gel-like networks that oscillate between expanded or compressed forms, much like those of hydrogels.

cond-mat.soft↗

arXiv2020

Molecular theory of Langevin dynamics for active self-diffusiophoretic colloids

Active colloidal particles that are propelled by a self-diffusiophoretic mechanism are often described by Langevin equations that are either postulated on physical grounds or derived using the methods of fluctuating hydrodynamics. While these descriptions are appropriate for colloids of micrometric and larger size, they will break down for very small active particles. A fully microscopic derivation of Langevin equations for self-diffusiophoretic particles powered by chemical reactions catalyzed asymmetrically by the colloid is given in this paper. The derivation provides microscopic expressions for the translational and rotational friction tensors, as well as reaction rate coefficients appearing in the Langevin equations. The diffusiophoretic force and torque are expressed in terms of nonequilibrium averages of fluid fields that satisfy generalized transport equations. The results provide a description of active motion on small scales where descriptions in terms of coarse grained continuum fluid equations combined with boundary conditions that account for the presence of the colloid may not be appropriate.

cond-mat.stat-mech↗

arXiv2020

Active matter, microreversibility, and thermodynamics

Active matter, comprising many active agents interacting and moving in fluids or more complex environments, is a commonly occurring state of matter in biological and physical systems. By its very nature active matter systems exist in nonequilibrium states. In this paper the active agents are small Janus colloidal particles that use chemical energy provided by chemical reactions occurring on their surfaces for propulsion through a diffusiophoretic mechanism. As a result of interactions among these colloids, either directly or through fluid velocity and concentration fields, they may act collectively to form structures such as dynamic clusters. A general nonequilibrium thermodynamics framework for the description of such systems is presented that accounts for both self-diffusiophoresis and diffusiophoresis due to external concentration gradients, and is consistent with microreversibility. It predicts the existence of a reciprocal effect of diffusiophoresis back onto the reaction rate for the entire collection of colloids in the system, as well as the existence of a clustering instability that leads to nonequilibrium inhomogeneous system states.

cond-mat.soft↗

arXiv2019

Active rotational dynamics of a self-diffusiophoretic colloidal motor

The dynamics of a spherical chemically-powered synthetic colloidal motor that operates by a self-diffusiophoretic mechanism and has a catalytic domain of arbitrary shape is studied using both continuum theory and particle-based simulations. The motor executes active rotational motion when self-generated concentration gradients and interactions between the chemical species and colloidal motor surface break spherical symmetry. Local variations of chemical reaction rates on the motor catalytic surface with catalytic domain sizes and shapes provide such broken symmetry conditions. A continuum theoretical description of the active rotational motion is given, along with the results of particle-based simulations of the active dynamics. From these results a detailed description of the factors responsible for the active rotational dynamics can be given. Since active rotational motion often plays a significant part in the nature of the collective dynamics of many-motor systems and can be used to control motor motion in targeted cargo transport, our results should find applications beyond those considered here.

cond-mat.soft↗

arXiv2019

The 2019 Motile Active Matter Roadmap

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of active matter in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines.

cond-mat.soft↗

arXiv2019

The stochastic motion of self-thermophoretic Janus particles

Langevin equations for the self-thermophoretic dynamics of Janus motors partially coated with an absorbing layer that is heated by a radiation field are presented. The derivation of these equations is based on fluctuating hydrodynamics and radiative heat transfer theory involving stochastic equations for bulk phases and surface processes that are consistent with microscopic reversibility. Expressions for the self-thermophoretic force and torque for arbitrary slip boundary conditions are obtained. The overdamped Langevin equations for the colloid displacement and radiative heat transfer provide expressions for the self-thermophoretic velocity and its reciprocal contribution where an external force can influence the radiative heat transfer. A nonequilibrium fluctuation formula is also derived and shows how the probability density of the Janus particle displacement and radiation energy transfer during the time interval [0,t] are related to the mechanical and thermal affinities that characterize the nonequilibrium system state.

cond-mat.stat-mech↗

arXiv2018

Single particle motion and collective dynamics in Janus motor systems

The single-particle and collective dynamics of systems comprising Janus motors, solvent and reactive solute species maintained in nonequilibrium states are investigated. Reversible catalytic reactions with the solute species take place on the catalytic faces of the motors, and the nonequilibrium states are established by imposing either constant-concentration reservoirs that feed and remove reactive species, or through out-of-equilibrium fluid phase reactions. We consider general intermolecular interactions between the Janus motor hemispheres and the reactive species. For single motors, we show that the reaction rate depends nonlinearly on an applied external force when the system is displaced far from equilibrium. We also show that a finite-time fluctuation formula derived for fixed catalytic particles describes the nonequilibrium reactive fluctuations of moving Janus motors. Simulation of the collective dynamics of small ensembles of Janus motors with reversible kinetics under nonequilibrium conditions are carried out and the spatial and orientational correlations of dynamic cluster states are discussed. The conditions leading to the instability of the homogeneous motor distribution and the onset of nonequilibrium dynamical clustering are described.

cond-mat.soft↗

arXiv2018

Thermodynamics and statistical mechanics of chemically-powered synthetic nanomotors

Colloidal motors without moving parts can be propelled by self-diffusiophoresis, coupling molecular concentration gradients generated by surface chemical reactions to the velocity slip between solid Janus particles and the surrounding fluid solution. The interfacial properties involved in this propulsion mechanism can be described by nonequilibrium thermodynamics and statistical mechanics, disclosing the fundamental role of microreversibility in the coupling between motion and reaction. Among other phenomena, the approach predicts that propulsion by fuel consumption has the reciprocal effect of fuel synthesis by mechanical action.

cond-mat.stat-mech↗

arXiv2018

Finite-time fluctuation theorem for diffusion-influenced surface reactions on spherical and Janus catalytic particles

A finite-time fluctuation theorem for the diffusion-influenced surface reaction A <=> B is investigated for spherical and Janus catalytic particles. The finite-time rates and thermodynamic force are analytically calculated by solving diffusion equations with the special boundary conditions of the finite-time fluctuation theorem. Theory is compared with numerical simulations carried out with two different methods: a random walk algorithm and multiparticle collision dynamics.

cond-mat.stat-mech↗

arXiv2018

Diffusiophoretically induced interactions between chemically active and inert particles

In the presence of a chemically active particle, a nearby chemically inert particle can respond to a concentration gradient and move by diffusiophoresis. The nature of the motion is studied for two cases: first, a fixed reactive sphere and a moving inert sphere, and second, freely moving reactive and inert spheres. The continuum reaction-diffusion and Stokes equations are solved analytically for these systems and microscopic simulations of the dynamics are carried out. Although the relative velocities of the spheres are very similar in the two systems, the local and global structures of streamlines and the flow velocity fields are found to be quite different. For freely moving spheres, when the two spheres approach each other the flow generated by the inert sphere through diffu- siophoresis drags the reactive sphere towards it. This leads to a self-assembled dimer motor that is able to propel itself in solution. The fluid flow field at the moment of dimer formation changes direction. The ratio of sphere sizes in the dimer influences the characteristics of the flow fields, and this feature suggests that active self-assembly of spherical colloidal particles may be manipulated by sphere-size changes in such reactive systems.

cond-mat.soft↗

arXiv2018

Finite-time fluctuation theorem for diffusion-influenced surface reactions

A finite-time fluctuation theorem is proved for the diffusion-influenced surface reaction A<->B in a domain with any geometry where the species A and B undergo diffusive transport between the reservoir and the catalytic surface. A corresponding finite-time thermodynamic force or affinity is associated with the symmetry of the fluctuation theorem. The time dependence of the affinity and the reaction rates characterizing the stochastic process can be expressed analytically in terms of the solution of deterministic diffusion equations with specific boundary conditions.

cond-mat.stat-mech↗