arXiv subjects

Pegah Torkaman

Publications and source records attributed to Pegah Torkaman.

5 recordsLinked to original sources

arXiv2019

Stochastic modeling of gene expression: application of ensembles of trajectories

It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with ensembles of trajectories for long but fixed times, instead of states or configurations, to study dynamics of these Markovian stochastic processes and glean more information. In this paper we aim to show that the concept of ensemble of trajectories can be applied to a variety of stochastic models of gene expression ranging from a simple birth-death process to a more sophisticate model containing burst and switch. By considering the protein numbers as a relevant dynamical observable, apart from asymptotic behavior of remote tails of probability distribution, generating function for the cumulants of this observable can also be obtained. We discuss the unconditional stochastic Markov processes which generate the statistics of rare events in these models.

physics.bio-ph↗

arXiv2019

Effective dynamics in an asymmetric death-branching process

In this paper we study activity fluctuations in an asymmetric death-branching process in one-dimension. The model, which is a variant of the asymmetric Glauber model, has already been studied in [12]. It is known that in the low-activity region i.e. below the typical activity in the steady-state, the dynamical free energy of the system can be calculated exactly. However, the behavior of the system in the high-activity region is different and more interesting. The system undergoes a series of dynamical phase transitions. In present work we justify the hierarchy of dynamical phase transitions in terms of effective interactions in the system. It turns out that the effective interactions are long-range and that they can be described in terms of interactions between repelling shock fronts.

cond-mat.stat-mech↗

arXiv2015

On Effective Stochastic Generators for Conditioned Dynamics at an Atypical Reaction-Diffusion Current

We consider the fluctuations of a time-integrated particle current around an atypical value in a generic stochastic Markov process involving classical particles with two-site interaction and hardcore repulsion on a finite one-dimensional lattice with open boundaries. We address the question of which interactions one has to impose on such process to make the atypical value of the current typical. It is known that a corresponding effective stochastic Markov process might exist whose typical value of the current is equal to the atypical value of the current in the original process within a time-translational invariant regime. This effective process has, in principle, non-local transition rates. Nevertheless, it turns out that under some conditions the stochastic generator of the effective process has the same dynamical rules as the stochastic generator of the original process. We find these conditions and show that our approach can be generalized to any time-integrated observable.

cond-mat.stat-mech↗

arXiv2014

Rare-event trajectory ensemble approach to study dynamical phase transitions in the zero temperature Glauber model

The dynamics of a one-dimensional stochastic system of classical particles consisting of asymmetric death and branching processes is studied. The dynamical activity, defined as the number of configuration changes in a dynamical trajectory, is considered as a proper dynamical order parameter. By considering an ensemble of dynamical trajectories and applying the large deviation method, we have found that the system might undergo both continuous and discontinuous dynamical phase transitions at critical values of the counting field. Exact analytical results are obtained for an infinite system. Numerical investigations confirm our analytical calculations.

cond-mat.stat-mech↗

arXiv2013

Particle current fluctuations in a particle-nonconserving process

We have considered a one-dimensional coagulation-decoagulation system of classical particles on a finite lattice with reflecting boundaries. It is known that the system undergoes a phase transition from a high-density to a low-density phase. Using a matrix product approach we have obtained an exact expression for the average entropy production rate of the system in the thermodynamic limit. We have also performed a large deviation analysis for fluctuations of entropy production rate and particle current. It turns out that the characteristics of the kink in the large deviation function can be used to spot the phase transition point. We have found that for very weak driving field (when the system approaches to its equilibrium) and also for very strong driving field (when the system is in the low-density phase) the large deviation function for fluctuations of entropy production rate is almost parabolic while in the high-density phase it prominently deviates from Gaussian behavior. The validity of the Gallavotti-Cohen fluctuation relation for the large deviation function for particle current is also verified.

cond-mat.stat-mech↗