arXiv subjects

Kavita Jain

Publications and source records attributed to Kavita Jain.

51 records · Page 3Linked to original sources

arXiv2008

Particle current in symmetric exclusion process with time-dependent hopping rates

In a recent study, (Jain et al 2007 Phys. Rev. Lett. 99 190601), a symmetric exclusion process with time-dependent hopping rates was introduced. Using simulations and a perturbation theory, it was shown that if the hopping rates at two neighboring sites of a closed ring vary periodically in time and have a relative phase difference, there is a net DC current which decreases inversely with the system size. In this work, we simplify and generalize our earlier treatment. We study a model where hopping rates at all sites vary periodically in time, and show that for certain choices of relative phases, a DC current of order unity can be obtained. Our results are obtained using a perturbation theory in the amplitude of the time-dependent part of the hopping rate. We also present results obtained in a sudden approximation that assumes large modulation frequency.

cond-mat.stat-mech↗

arXiv2008

Loss of least-loaded class in asexual populations due to drift and epistasis

We consider the dynamics of a non-recombining haploid population of finite size which accumulates deleterious mutations irreversibly. This ratchet like process occurs at a finite speed in the absence of epistasis, but it has been suggested that synergistic epistasis can halt the ratchet. Using a diffusion theory, we find explicit analytical expressions for the typical time between successive clicks of the ratchet for both non-epistatic and epistatic fitness functions. Our calculations show that the inter-click time is of a scaling form which in the absence of epistasis gives a speed that is determined by size of the least-loaded class and the selection coefficient. With synergistic interactions, the ratchet speed is found to approach zero rapidly for arbitrary epistasis. Our analytical results are in good agreement with the numerical simulations.

q-bio.PE↗

arXiv2008

Adaptation dynamics of the quasispecies model

We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic space and have many local peaks separated by low fitness valleys. We mainly focus on the Eigen's model that describes the deterministic dynamics of an infinite number of self-replicating molecules. In the stationary state, for small mutation rates such a population forms a {\it quasispecies} which consists of the fittest genotype and its closely related mutants. The quasispecies dynamics on rugged fitness landscape follow a punctuated (or step-like) pattern in which a population jumps from a low fitness peak to a higher one, stays there for a considerable time before shifting the peak again and eventually reaches the global maximum of the fitness landscape. We calculate exactly several properties of this dynamical process within a simplified version of the quasispecies model.

q-bio.PE↗

arXiv2007

Relaxation times of unstable states in systems with long range interactions

We consider several models with long-range interactions evolving via Hamiltonian dynamics. The microcanonical dynamics of the basic Hamiltonian Mean Field (HMF) model and perturbed HMF models with either global anisotropy or an on-site potential are studied both analytically and numerically. We find that in the magnetic phase, the initial zero magnetization state remains stable above a critical energy and is unstable below it. In the dynamically stable state, these models exhibit relaxation time scales that increase algebraically with the number $N$ of particles, indicating the robustness of the quasistationary state seen in previous studies. In the unstable state, the corresponding time scale increases logarithmically in $N$.

cond-mat.stat-mech↗

arXiv2007

Driving particle current through narrow channels using classical pump

We study a symmetric exclusion process in which the hopping rates at two chosen adjacent sites vary periodically in time and have a relative phase difference. This mimics a colloidal suspension subjected to external space and time dependent modulation of the diffusion constant. The two special sites act as a classical pump by generating an oscillatory current with a nonzero ${\cal DC}$ value whose direction depends on the applied phase difference. We analyze various features in this model through simulations and obtain an expression for the $\cal{DC}$ current via a novel perturbative treatment.

cond-mat.stat-mech↗

arXiv2007

Evolutionary dynamics of the most populated genotype on rugged fitness landscapes

We consider an asexual population evolving on rugged fitness landscapes which are defined on the multi-dimensional genotypic space and have many local optima. We track the most populated genotype as it changes when the population jumps from a fitness peak to a better one during the process of adaptation. This is done using the dynamics of the shell model which is a simplified version of the quasispecies model for infinite populations and standard Wright-Fisher dynamics for large finite populations. We show that the population fraction of a genotype obtained within the quasispecies model and the shell model match for fit genotypes and at short times, but the dynamics of the two models are identical for questions related to the most populated genotype. We calculate exactly several properties of the jumps in infinite populations some of which were obtained numerically in previous works. We also present our preliminary simulation results for finite populations. In particular, we measure the jump distribution in time and find that it decays as $t^{-2}$ as in the quasispecies problem.

q-bio.PE↗

arXiv2006

Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes

We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length $L$. The population evolves in a maximally rugged fitness landscape with a large number of local optima. We find that whether the evolutionary trajectory is deterministic or stochastic depends on the effective mutational distance $d_{\mathrm{eff}}$ upto which the population can spread in genotype space. For $d_{\mathrm{eff}}=L$, the deterministic quasispecies theory operates while for $d_{\mathrm{eff}} < 1$, the evolution is completely stochastic. Between these two limiting cases, the dynamics are described by a local quasispecies theory below a crossover time $T_{\times}$ while above $T_{\times}$, the population gets trapped at a local fitness peak and manages to find a better peak either via stochastic tunneling or double mutations. In the stochastic regime $d_\mathrm{eff} < 1$, we identify two subregimes associated with clonal interference and uphill adaptive walks, respectively. We argue that our findings are relevant to the interepretation of evolution experiments with microbial populations.

q-bio.PE↗

arXiv2005

Adaptation in simple and complex fitness landscapes

This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different types of mutation-selection dynamics are defined and their relation to problems of statistical physics are outlined. Then the stationary population distribution in simple, single peak fitness landscapes is discussed at length, with particular emphasis on the error threshold phenomenon. Extensions of the theory covering e.g. epistatic interactions, diploid organisms, semiconservative replication and time-dependent fitness peaks are briefly described. A further section is devoted to randomly rugged fitness landscapes, which may display fitness correlations of various degree as well as extended neutral networks. The final two sections address evolutionary dynamics in both rugged and smooth fitness landscapes, and provide a brief overview of pertinent experiments.

q-bio.PE↗

arXiv2005

Evolutionary trajectories in rugged fitness landscapes

We consider the evolutionary trajectories traced out by an infinite population undergoing mutation-selection dynamics in static, uncorrelated random fitness landscapes. Starting from the population that consists of a single genotype, the most populated genotype \textit{jumps} from a local fitness maximum to another and eventually reaches the global maximum. We use a strong selection limit, which reduces the dynamics beyond the first time step to the competition between independent mutant subpopulations, to study the dynamics of this model and of a simpler one-dimensional model which ignores the geometry of the sequence space. We find that the fit genotypes that appear along a trajectory are a subset of suitably defined fitness \textit{records}, and exploit several results from the record theory for non-identically distributed random variables. The genotypes that contribute to the trajectory are those records that are not \textit{bypassed} by superior records arising further away from the initial population. Several conjectures concerning the statistics of bypassing are extracted from numerical simulations. In particular, for the one-dimensional model, we propose a simple relation between the bypassing probability and the dynamic exponent which describes the scaling of the typical evolution time with genome size. The latter can be determined exactly in terms of the extremal properties of the fitness distribution.

q-bio.PE↗

arXiv2005

A simple sandpile model of active-absorbing state transitions

We study a simple sandpile model of active-absorbing state transitions in which a particle can hop out of a site only if the number of particles at that site is above a certain threshold. We show that the active phase has product measure whereas nontrivial correlations are found numerically in the absorbing phase. It is argued that the system relaxes to the latter phase slower than exponentially. The critical behavior of this model is found to be different from that of the other known universality classes.

cond-mat.stat-mech↗

arXiv2005

Nonuniversal exponents in sandpiles with stochastic particle number transfer

We study fixed density sandpiles in which the number of particles transferred to a neighbor on relaxing an active site is determined stochastically by a parameter $p$. Using an argument, the critical density at which an active-absorbing transition occurs is found exactly. We study the critical behavior numerically and find that the exponents associated with both static and time-dependent quantities vary continuously with $p$.

cond-mat.stat-mech↗

arXiv2004

Breaking records in the evolutionary race

We explore some aspects of the relationship between biological evolution processes and the mathematical theory of records. For Eigen's quasispecies model with an uncorrelated fitness landscape, we show that the evolutionary trajectories traced out by a population initially localized at a randomly chosen point in sequence space can be described in close analogy to record dynamics, with two complications. First, the increasing number of genotypes that become available with increasing distance from the starting point implies that fitness records are more frequent than for the standard case of independent, identically distributed random variables. Second, fitness records can be bypassed, which strongly reduces the number of genotypes that take part in an evolutionary trajectory. For exponential and Gaussian fitness distributions, this number scales with sequence length $N$ as $\sqrt{N}$, and it is of order unity for distributions with a power law tail. This is in strong contrast to the number of records, which is of order $N$ for any fitness distribution.

q-bio.PE↗

arXiv2003

Dynamics of a disordered, driven zero range process in one dimension

We study a driven zero range process which models a closed system of attractive particles that hop with site-dependent rates and whose steady state shows a condensation transition with increasing density. We characterise the dynamical properties of the mass fluctuations in the steady state in one dimension both analytically and numerically and show that the transport properties are anomalous in certain regions of the density-disorder plane. We also determine the form of the scaling function which describes the growth of the condensate as a function of time, starting from a uniform density distribution.

cond-mat.stat-mech↗

arXiv2001

Locating the minimum : Approach to equilibrium in a disordered, symmetric zero range process

We consider the dynamics of the disordered, one-dimensional, symmetric zero range process in which a particle from an occupied site $k$ hops to its nearest neighbour with a quenched rate $w(k)$. These rates are chosen randomly from the probability distribution $f(w) \sim (w-c)^{n}$, where $c$ is the lower cutoff. For $n > 0$, this model is known to exhibit a phase transition in the steady state from a low density phase with a finite number of particles at each site to a high density aggregate phase in which the site with the lowest hopping rate supports an infinite number of particles. In the latter case, it is interesting to ask how the system locates the site with globally minimum rate. We use an argument based on local equilibrium, supported by Monte Carlo simulations, to describe the approach to the steady state. We find that at large enough time, the mass transport in the regions with a smooth density profile is described by a diffusion equation with site-dependent rates, while the isolated points where the mass distribution is singular act as the boundaries of these regions. Our argument implies that the relaxation time scales with the system size $L$ as $L^{z}$ with $z=2+1/(n+1)$ for $n > 1$ and suggests a different behaviour for $n < 1$.

cond-mat.stat-mech↗

arXiv2001

Phases of a conserved mass model of aggregation with fragmentation at fixed sites

To study the effect of quenched disorder in a class of reaction-diffusion systems, we introduce a conserved mass model of diffusion and aggregation in which the mass moves as a whole to a nearest neighbour on most sites while it fragments off as a single monomer (i.e. chips off) from certain fixed sites. Once the mass leaves any site, it coalesces with the mass present on its neighbour. We study in detail the effect of a \emph{single} chipping site on the steady state in arbitrary dimensions, with and without bias. In the thermodynamic limit, the system can exist in one of the following phases -- (a) Pinned Aggregate (PA) phase in which an infinite aggregate (with mass proportional to the volume of the system) appears with probability one at the chipping site but not in the bulk. (b) Unpinned Aggregate (UA) phase in which $\emph{both}$ the chipping site and the bulk can support an infinite aggregate simultaneously. (c) Non Aggregate (NA) phase in which there is no infinite cluster. Our analytical and numerical studies show that the system exists in the UA phase in all cases except in 1d with bias. In the latter case, there is a phase transition from the NA phase to the PA phase as density is increased. A variant of the above aggregation model is also considered in which total particle number is conserved and chipping occurs at a fixed site, but the particles do not interact with each other at other sites. This model is solved exactly by mapping it to a Zero Range Process. With increasing density, it exhibits a phase transition from the NA phase to the PA phase in all dimensions, irrespective of bias. Finally, we discuss the likely behaviour of the system in the presence of extensive disorder.

cond-mat.stat-mech↗