arXiv subjects

Ian J. Ford

Publications and source records attributed to Ian J. Ford.

27 records · Page 2Linked to original sources

arXiv2015

Coagulation kinetics beyond mean field theory using an optimised Poisson representation

Binary particle coagulation can be modelled as the repeated random process of the combination of two particles to form a third. The kinetics can be represented by population rate equations based on a mean field assumption, according to which the rate of aggregation is taken to be proportional to the product of the mean populations of the two participants. This can be a poor approximation when the mean populations are small. However, using the Poisson representation it is possible to derive a set of rate equations that go beyond mean field theory, describing pseudo-populations that are continuous, noisy and complex, but where averaging over the noise and initial conditions gives the mean of the physical population. Such an approach is explored for the simple case of a size-independent rate of coagulation between particles. Analytical results are compared with numerical computations and with results derived by other means. In the numerical work we encounter instabilities that can be eliminated using a suitable 'gauge' transformation of the problem [P. D. Drummond, Eur. Phys. J. B38, 617 (2004)] which we show to be equivalent to the application of the Cameron-Martin-Girsanov formula describing a shift in a probability measure. The cost of such a procedure is to introduce additional statistical noise into the numerical results, but we identify an optimised gauge transformation where this difficulty is minimal for the main properties of interest. For more complicated systems, such an approach is likely to be computationally cheaper than Monte Carlo simulation.

cond-mat.stat-mech↗

arXiv2015

Free energies of molecular clusters determined by guided mechanical disassembly

The excess free energy of a molecular cluster is a key quantity in models of the nucleation of droplets from a metastable vapour phase; it is often viewed as the free energy arising from the presence of an interface between the two phases. We show how this quantity can be extracted from simulations of the mechanical disassembly of a cluster using guide particles in molecular dynamics. We disassemble clusters ranging in size from 5 to 27 argon-like Lennard-Jones atoms, thermalised at 60 K, and obtain excess free energies, by means of the Jarzynski equality, that are consistent with previous studies. We only simulate the cluster of interest, in contrast to approaches that require a series of comparisons to be made between clusters differing in size by one molecule. We discuss the advantages and disadvantages of the scheme and how it might be applied to more complex systems.

cond-mat.stat-mech↗

arXiv2012

Symmetries of cyclic work distributions for an isolated harmonic oscillator

We have calculated the distribution of work $W$ done on a 1-d harmonic oscillator that is initially in canonical equilibrium at temperature $T$, then thermally isolated and driven by an arbitrary time-dependent cyclic spring constant $κ(t)$, and demonstrated that it satisfies $P(W)=\exp(βW)P(-W)$, where $β=1/k_{B}T$, in both classical and quantum dynamics. This differs from the celebrated Crooks relation of nonequilibrium thermodynamics, since the latter relates distributions for forward and backward protocols of driving. We show that it is a special case of a symmetry that holds for non-cyclic work processes on the isolated oscillator, and that consideration of time reversal invariance shows it to be consistent with the Crooks relation. We have verified that the symmetry holds in both classical and quantum treatments of the dynamics, but that inherent uncertainty in the latter case leads to greater fluctuations in work performed for a given process.

cond-mat.stat-mech↗

arXiv2012

Entropy production from stochastic dynamics in discrete full phase space

The stochastic entropy generated during the evolution of a system interacting with an environment may be separated into three components, but only two of these have a non-negative mean. The third component of entropy production is associated with the relaxation of the system probability distribution towards a stationary state and with nonequilibrium constraints within the dynamics that break detailed balance. It exists when at least some of the coordinates of the system phase space change sign under time reversal, and when the stationary state is asymmetric in these coordinates. We illustrate the various components of entropy production, both in detail for particular trajectories and in the mean, using simple systems defined on a discrete phase space of spatial and velocity coordinates. These models capture features of the drift and diffusion of a particle in a physical system, including the processes of injection and removal and the effect of a temperature gradient. The examples demonstrate how entropy production in stochastic thermodynamics depends on the detail that is included in a model of the dynamics of a process. Entropy production from such a perspective is a measure of the failure of such models to meet Loschmidt's expectation of dynamic reversibility.

cond-mat.stat-mech↗

arXiv2012

Bistable collective behavior of polymers tethered in a nanopore

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence of the two phases suggests a transport mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations.

cond-mat.soft↗

arXiv2012

Entropy production in full phase space for continuous stochastic dynamics

The total entropy production and its three constituent components are described both as fluctuating trajectory-dependent quantities and as averaged contributions in the context of the continuous Markovian dynamics, described by stochastic differential equations with multiplicative noise, of systems with both odd and even coordinates with respect to time reversal, such as dynamics in full phase space. Two of these constituent quantities obey integral fluctuation theorems and are thus rigorously positive in the mean by Jensen's inequality. The third, however, is not and furthermore cannot be uniquely associated with irreversibility arising from relaxation, nor with the breakage of detailed balance brought about by non-equilibrium constraints. The properties of the various contributions to total entropy production are explored through the consideration of two examples: steady state heat conduction due to a temperature gradient, and transitions between stationary states of drift-diffusion on a ring, both in the context of the full phase space dynamics of a single Brownian particle.

cond-mat.stat-mech↗

arXiv2012

Non-equilibrium thermodynamics of stochastic systems with odd and even variables

The total entropy production of stochastic systems can be divided into three quantities. The first corresponds to the excess heat, whilst the second two comprise the house-keeping heat. We denote these two components the transient and generalised house-keeping heat and we obtain an integral fluctuation theorem for the latter, valid for all Markovian stochastic dynamics. A previously reported formalism is obtained when the stationary probability distribution is symmetric for all variables that are odd under time reversal which restricts consideration of directional variables such as velocity.

cond-mat.stat-mech↗

arXiv2012

Fluctuation relations: a pedagogical overview

The fluctuation relations have received considerable attention since their emergence and development in the 1990s. We present a summary of the main results and suggest ways to interpret this material. Starting with a consideration of the under-determined time evolution of a simple open system, formulated using continuous Markovian stochastic dy- namics, an expression for the entropy generated over a time interval is developed in terms of the probability of observing a trajectory associated with a prescribed driving protocol, and the probability of its time-reverse. This forms the basis for a general theoretical description of non-equilibrium thermodynamic pro- cesses. Having established a connection between entropy production and an inequivalence in probability for forward and time-reversed events, we proceed in the manner of Sekimoto and Seifert, in particular, to derive results in stochastic thermodynamics: a description of the evolution of a system between equilibrium states that ties in with well-established thermodynamic expectations. We derive fluctuation relations, state conditions for their validity, and illustrate their op- eration in some simple cases, thereby providing some introductory insight into the various celebrated symmetry relations that have emerged in this field.

cond-mat.stat-mech↗

arXiv2007

Fluctuation-driven heterogeneous chemical processes

We explore a new framework for describing the kinetics of a heterogeneous chemical reaction where two particles of the same chemical species form a reaction product of another chemical species on the surface of a seed particle. Traditional treatments neglect the effect of statistical fluctuations in populations. We employ techniques in a manner analogous to the treatment of quantum systems to develop a stochastic description of processes beyond the mean field approximation.

cond-mat.other↗