8,567 research outputs found
Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations
In this paper we propose a new class of coupling methods for the sensitivity
analysis of high dimensional stochastic systems and in particular for lattice
Kinetic Monte Carlo. Sensitivity analysis for stochastic systems is typically
based on approximating continuous derivatives with respect to model parameters
by the mean value of samples from a finite difference scheme. Instead of using
independent samples the proposed algorithm reduces the variance of the
estimator by developing a strongly correlated-"coupled"- stochastic process for
both the perturbed and unperturbed stochastic processes, defined in a common
state space. The novelty of our construction is that the new coupled process
depends on the targeted observables, e.g. coverage, Hamiltonian, spatial
correlations, surface roughness, etc., hence we refer to the proposed method as
em goal-oriented sensitivity analysis. In particular, the rates of the coupled
Continuous Time Markov Chain are obtained as solutions to a goal-oriented
optimization problem, depending on the observable of interest, by considering
the minimization functional of the corresponding variance. We show that this
functional can be used as a diagnostic tool for the design and evaluation of
different classes of couplings. Furthermore the resulting KMC sensitivity
algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz
algorithm's philosophy, where here events are divided in classes depending on
level sets of the observable of interest. Finally, we demonstrate in several
examples including adsorption, desorption and diffusion Kinetic Monte Carlo
that for the same confidence interval and observable, the proposed
goal-oriented algorithm can be two orders of magnitude faster than existing
coupling algorithms for spatial KMC such as the Common Random Number approach
The instanton method and its numerical implementation in fluid mechanics
A precise characterization of structures occurring in turbulent fluid flows
at high Reynolds numbers is one of the last open problems of classical physics.
In this review we discuss recent developments related to the application of
instanton methods to turbulence. Instantons are saddle point configurations of
the underlying path integrals. They are equivalent to minimizers of the related
Freidlin-Wentzell action and known to be able to characterize rare events in
such systems. While there is an impressive body of work concerning their
analytical description, this review focuses on the question on how to compute
these minimizers numerically. In a short introduction we present the relevant
mathematical and physical background before we discuss the stochastic Burgers
equation in detail. We present algorithms to compute instantons numerically by
an efficient solution of the corresponding Euler-Lagrange equations. A second
focus is the discussion of a recently developed numerical filtering technique
that allows to extract instantons from direct numerical simulations. In the
following we present modifications of the algorithms to make them efficient
when applied to two- or three-dimensional fluid dynamical problems. We
illustrate these ideas using the two-dimensional Burgers equation and the
three-dimensional Navier-Stokes equations
Control of stochastic and induced switching in biophysical networks
Noise caused by fluctuations at the molecular level is a fundamental part of
intracellular processes. While the response of biological systems to noise has
been studied extensively, there has been limited understanding of how to
exploit it to induce a desired cell state. Here we present a scalable,
quantitative method based on the Freidlin-Wentzell action to predict and
control noise-induced switching between different states in genetic networks
that, conveniently, can also control transitions between stable states in the
absence of noise. We apply this methodology to models of cell differentiation
and show how predicted manipulations of tunable factors can induce lineage
changes, and further utilize it to identify new candidate strategies for cancer
therapy in a cell death pathway model. This framework offers a systems approach
to identifying the key factors for rationally manipulating biophysical
dynamics, and should also find use in controlling other classes of noisy
complex networks.Comment: A ready-to-use code package implementing the method described here is
available from the authors upon reques
Negative differential response in chemical reactions
Reaction currents in chemical networks usually increase when increasing their
driving affinities. But far from equilibrium the opposite can also happen. We
find that such negative differential response (NDR) occurs in reaction schemes
of major biological relevance, namely, substrate inhibition and autocatalysis.
We do so by deriving the full counting statistics of two minimal representative
models using large deviation methods. We argue that NDR implies the existence
of optimal affinities that maximize the robustness against environmental and
intrinsic noise at intermediate values of dissipation. An analogous behavior is
found in dissipative self-assembly, for which we identify the optimal working
conditions set by NDR.Comment: Main text and S
Forward Flux Sampling for rare event simulations
Rare events are ubiquitous in many different fields, yet they are notoriously
difficult to simulate because few, if any, events are observed in a conventiona
l simulation run. Over the past several decades, specialised simulation methods
have been developed to overcome this problem. We review one recently-developed
class of such methods, known as Forward Flux Sampling. Forward Flux Sampling
uses a series of interfaces between the initial and final states to calculate
rate constants and generate transition paths, for rare events in equilibrium or
nonequilibrium systems with stochastic dynamics. This review draws together a
number of recent advances, summarizes several applications of the method and
highlights challenges that remain to be overcome.Comment: minor typos in the manuscript. J.Phys.:Condensed Matter (accepted for
publication
Controlled diffusion processes with markovian switchings for modeling dynamical engineering systems
A modeling approach to treat noisy engineering systems is presented. We
deal with controlled systems that evolve in a continuous-time over finite time intervals,
but also in continuous interaction with environments of intrinsic variability. We face the complexity of these systems by introducing a methodology based on Stochastic
Differential Equations (SDE) models. We focus on specific type of complexity derived
from unpredictable abrupt and/or structural changes. In this paper an approach based on
controlled Stochastic Differential Equations with Markovian Switchings (SDEMS) is
proposed. Technical conditions for the existence and uniqueness of the solution of these models are provided. We treat with nonlinear SDEMS that does not have closed
solutions. Then, a numerical approximation to the exact solution based on the Euler-
Maruyama Method (EM) is proposed. Convergence in strong sense and stability are
provided. Promising applications for selected industrial biochemical systems are
showed
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