Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userEfficient Reactive Brownian Dynamics
161
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and disassociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion, and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as Reaction-Diffusion Master Equation (RDME) algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction- and diffusion-limited irreversible association in three dimensions. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. We find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.
rate research
Read More
A framework for performant Brownian Dynamics (BD) many-body simulations with adaptive timestepping is presented. Contrary to the Euler-Maruyama scheme in common non-adaptive BD, we employ an embedded Heun-Euler integrator for the propagation of the overdamped coupled Langevin equations of motion. This enables the derivation of a local error estimate and the formulation of criteria for the acceptance or rejection of trial steps and for the control of optimal stepsize. Introducing erroneous bias in the random forces is avoided by Rejection Sampling with Memory (RSwM) due to Rackauckas and Nie, which makes use of the Brownian bridge theorem and guarantees the correct generation of a specified random process even when rejecting trial steps. For test cases of Lennard-Jones fluids in bulk and in confinement, it is shown that adaptive BD solves performance and stability issues of conventional BD, already outperforming the latter even in standard situations. We expect this novel computational approach to BD to be especially helpful in long-time simulations of complex systems, e.g. in non-equilibrium, where concurrent slow and fast processes occur.
The disordering of an initially phase segregated system of finite size, induced by the presence of highly mobile vacancies, is shown to exhibit dynamic scaling in its late stages. A set of characteristic exponents is introduced and computed analytically, in excellent agreement with Monte Carlo data. In particular, the characteristic time scale, controlling the crossover between increasing disorder and saturation, is found to depend on the exponent scaling the number of vacancies in the sample.
Exact quantum master equation for a driven Brownian oscillator system is constructed via a Wigner phase-space Gaussian wave packet approach. The interplay between external field and dissipation leads to this system an effective field correction that enhances the polarization. This cooperative property is resulted from an effective bath response to the external field applied on the system. It is important in the low-frequency driving and intermediate bath memory region. We demonstrate this non-Markovian effect on the linear response and nonlinear dynamics and analyze the results together with analytical asymptotic expressions.
We endow a system of interacting particles with two distinct, local, Markovian and reversible microscopic dynamics. Using common field-theoretic techniques used to investigate the presence of a glass transition, we find that while the first, standard, dynamical rules lead to glassy behavior, the other one leads to a simple exponential relaxation towards equilibrium. This finding questions the intrinsic link that exists between the underlying, thermodynamical, energy landscape, and the dynamical rules with which this landscape is explored by the system. Our peculiar choice of dynam- ical rules offers the possibility of a direct connection with replica theory, and our findings therefore call for a clarification of the interplay between replica theory and the underlying dynamics of the system.
A number of random processes in various fields of science is described by phenomenological equations containing a stochastic force, the best known example being the Langevin equation (LE) for the Brownian motion (BM) of particles. Long ago Vladimirsky (1942) proposed a simple method for solving such equations. The method, based on the classical Gibbs statistics, consists in converting the stochastic LE into a deterministic one, and is applicable to linear equations with any kind of memory. When the memory effects are taken into account in the description of the BM, the mean square displacement of the particle at long times can exhibit an anomalous (different from that in the Einstein theory) time dependence. In the present paper we show how some general properties of such anomalous BM can be easily derived using the Vladimirsky approach. The method can be effectively used in solving many of the problems currently considered in the literature. We apply it to the description of the BM when the memory kernel in the Volterra-type integro-differential LE exponentially decreases with the time. The problem of the hydrodynamic BM of a charged particle in an external magnetic field is also solved.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
