arXiv subjects

Niraj Kumar

Publications and source records attributed to Niraj Kumar.

69 records · Page 4Linked to original sources

arXiv2014

Exact distributions for stochastic gene expression models with bursting and feedback

Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to phenotypic variation across a population of genetically identical cells. Recent experiments indicate that bursting and feedback mechanisms play important roles in controlling noise in gene expression and phenotypic variation. A quantitative understanding of the impact of these factors requires analysis of the corresponding stochastic models. However, for stochastic models of gene expression with feedback and bursting, exact analytical results for protein distributions have not been obtained so far. Here, we analyze a model of gene expression with bursting and feedback regulation and obtain exact results for the corresponding protein steady-state distribution. The results obtained provide new insights into the role of bursting and feedback in noise regulation and optimization. Furthermore, for a specific choice of parameters, the system studied maps on to a two-state biochemical switch driven by a bursty input noise source. The analytical results derived thus provide quantitative insights into diverse cellular processes involving noise in gene expression and biochemical switching.

q-bio.MN↗

arXiv2014

Moment Closure Approximations in a Genetic Negative Feedback Circuit

Auto-regulation, a process wherein a protein negatively regulates its own production, is a common motif in gene expression networks. Negative feedback in gene expression plays a critical role in buffering intracellular fluctuations in protein concentrations around optimal value. Due to the nonlinearities present in these feedbacks, moment dynamics are typically not closed, in the sense that the time derivative of the lower-order statistical moments of the protein copy number depends on high-order moments. Moment equations are closed by expressing higher-order moments as nonlinear functions of lower-order moments, a technique commonly referred to as moment closure. Here, we compare the performance of different moment closure techniques. Our results show that the commonly used closure method, which assumes a priori that the protein population counts are normally distributed, performs poorly. In contrast, conditional derivative matching, a novel closure scheme proposed here provides a good approximation to the exact moments across different parameter regimes. In summary our study provides a new moment closure method for studying stochastic dynamics of genetic negative feedback circuits, and can be extended to probe noise in more complex gene networks.

q-bio.SC↗

arXiv2013

Quantum Algorithm to Solve a Maze: Converting the Maze Problem into a Search Problem

We propose a different methodology towards approaching a Maze problem. We convert the problem into a Quantum Search Problem (QSP), and its solutions are sought for using the iterative Grover's Search Algorithm. Though the category of mazes we are looking at are of the NP complete class, we have redirected such a NP complete problem into a QSP. Our solution deals with two dimensional perfect mazes with no closed loops. We encode all possible individual paths from the starting point of the maze into a quantum register. A quantum fitness operator applied on the register encodes each individual with its fitness value. We propose an oracle design which marks all the individuals above a certain fitness value and use the Grover search algorithm to find one of the marked states. Iterating over this method, we approach towards the optimum solution.

quant-ph↗

arXiv2013

Exploring the Role of Logically Related Non-Question Phrases for Answering Why-Questions

In this paper, we show that certain phrases although not present in a given question/query, play a very important role in answering the question. Exploring the role of such phrases in answering questions not only reduces the dependency on matching question phrases for extracting answers, but also improves the quality of the extracted answers. Here matching question phrases means phrases which co-occur in given question and candidate answers. To achieve the above discussed goal, we introduce a bigram-based word graph model populated with semantic and topical relatedness of terms in the given document. Next, we apply an improved version of ranking with a prior-based approach, which ranks all words in the candidate document with respect to a set of root words (i.e. non-stopwords present in the question and in the candidate document). As a result, terms logically related to the root words are scored higher than terms that are not related to the root words. Experimental results show that our devised system performs better than state-of-the-art for the task of answering Why-questions.

cs.CL↗

arXiv2012

Stochastically driven single level quantum dot: a nano-scale finite-time thermodynamic machine and its various operational modes

We describe a single-level quantum dot in contact with two leads as a nanoscale finite-time thermodynamic machine. The dot is driven by an external stochastic force that switches its energy between two values. In the isothermal regime, it can operate as a rechargeable battery by generating an electric current against the applied bias in response to the stochastic driving, and re-delivering work in the reverse cycle. This behavior is reminiscent of the Parrondo paradox. If there is a thermal gradient the device can function as a work-generating thermal engine, or as a refrigerator that extracts heat from the cold reservoir via the work input of the stochastic driving. The efficiency of the machine at maximum power output is investigated for each mode of operation, and universal features are identified.

cond-mat.stat-mech↗

arXiv2012

Efficiency of isothermal molecular machines at maximum power

We derive upper and lower bounds for the efficiency of an isothermal molecular machine operating at maximum power. The upper bound is reached when the activated state is close to the fueling or reactant state (Eyring-like), while the lower bound is reached when the activated state is close to the product state (Kramers-like).

cond-mat.stat-mech↗

arXiv2011

Thermodynamics of a stochastic twin elevator

We study the non-equilibrium thermodynamics of a single particle with two available energy levels, in contact with a classical (Maxwell-Boltzmann) or quantum (Bose-Einstein) heat bath. The particle can undergo transitions between the levels via thermal activation or deactivation. The energy levels are alternately raised at a given rate regardless of occupation by the particle, maintaining a fixed energy gap equal to epsilon between them. We explicitly calculate the work, heat and entropy production rates. The efficiency in both the classical and the quantum case goes to a limit between 100% and 50% that depends on the relative rates of particle transitions and level elevation. In the classical problem we explicitly find the large deviation functions for heat, work, and internal energy.

cond-mat.stat-mech↗

arXiv2010

Memory-induced anomalous dynamics: emergence of diffusion, subdiffusion, and superdiffusion from a single random walk model

We present a random walk model that exhibits asymptotic subdiffusive, diffusive, and superdiffusive behavior in different parameter regimes. This appears to be the first instance of a single random walk model leading to all three forms of behavior by simply changing parameter values. Furthermore, the model offers the great advantage of analytic tractability. Our model is non-Markovian in that the next jump of the walker is (probabilistically) determined by the history of past jumps. It also has elements of intermittency in that one possibility at each step is that the walker does not move at all. This rich encompassing scenario arising from a single model provides useful insights into the source of different types of asymptotic behavior.

math-ph↗

arXiv2008

Extinction of Populations and the Schrödinger Equation: Analytic Calculations for Abrupt Transitions

We study bifurcations in a spatially extended nonlinear system representing population dynamics with the help of analytic calculations based on the time-independent Schrödinger equation for a quantum particle subjected to a uniform gravitational field. Despite the linear character of the Schrödinger equation, the result we obtain helps in the understanding of the onset of abrupt transitions leading to extinction of biological populations. The result is expressed in terms of Airy functions and sheds light on the behavior of bacteria in a Petri dish as well as of large animals such as rodents moving over a landscape.

nlin.AO↗

arXiv2008

Theory of possible effects of the Allee phenomenon on refugia of the Hantavirus epidemic

We investigate possible effects of high order nonlinearities on the shapes of infection refugia of the Hantavirus epidemic. We replace Fisher-like equations that have been recently used to describe Hantavirus spread in mouse populations by generalizations capable of describing Allee effects that are a consequence of the high order nonlinearities. We analyze the equations to calculate steady state solutions. We study the stability of those solutions under physical conditions and compare to the earlier Fisher-like case. We consider spatial modulation of the environment and find that unexpected results appear, including a bifurcation that has not been studied before.

nlin.AO↗

arXiv2008

Nonlinearity in Bacterial Population Dynamics: Proposal for Experiments for the Observation of Abrupt Transitions in Patches

An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic theory. The theory provides accurately the transition expressions in spite of the fact that the actual solutions, which involve strong nonlinearity, are inaccessible to it. The analytic expressions are verified through numerical solutions of the relevant nonlinear equation. The experimental set-up suggested uses opaque masks in a Petri dish bathed in ultraviolet radiation as in Lin et al., Biophys. J. {\bf 87}, 75 (2004) and Perry, J. R. Soc. Interface {\bf 2}, 379 (2005) but is based on the interplay of two distances the bacteria must traverse, one of them favorable and the other adverse. As a result of this interplay feature, the experiments proposed introduce highly enhanced reliability in interpretation of observations and in the potential for extraction of system parameters.

nlin.AO↗

arXiv2006

Front propagation in A$\to$2A, A$\to$3A process in 1d: velocity, diffusion and velocity correlations

We study front propagation in the reaction diffusion process $\{A\stackrelε\to2A, A\stackrel {ε_t}\to3A\}$ on a one dimensional (1d) lattice with hard core interaction between the particles. Using the leading particle picture, velocity of the front in the system is computed using different approximate methods, which is in good agreement with the simulation results. It is observed that in certain ranges of parameters, the front velocity varies as a power law of $ε_t$, which is well captured by our approximate schemes. We also observe that the front dynamics exhibits temporal velocity correlations and these must be taken care of in order to find the exact estimates for the front diffusion coefficient. This correlation changes sign depending upon the sign of $ε_t-D$, where $D$ is the bare diffusion coefficient of $A$ particles. For $ε_t=D$, the leading particle and thus the front moves like an uncorrelated random walker, which is explained through an exact analysis.

cond-mat.stat-mech↗

arXiv2006

Two site self consistent method for front propagation in reaction-diffusion system

We study front propagation in the reaction diffusion process $A\leftrightarrow2A$ on one dimensional lattice with hard core interaction between the particles. We propose a two site self consistent method (TSSCM) to make analytic estimates for the front velocity and are in excellent agreement with the simulation results for all parameter regimes. We expect that the simplicity of the method will allow one to use this technique for estimating the front velocity in other reaction diffusion processes as well.

cond-mat.stat-mech↗

arXiv2006

Velocity of front propagation in the epidemic model $A+B\to2A$

We study front propagation in the irreversible epidemic model $A+B\to 2A$ in one dimension. Here, we allow the particles $A$ and $B$ to diffuse with rates $D_A$ and $D_B$, which, in general, may be different. We find analytic estimates for the front velocity by writing truncated master equation in a frame moving with the rightmost $A$ particle. The results obtained are in reasonable agreement with the simulation results and are amenable to systematic improvement. We also observe a crossover from the linear dependence of front velocity $V$ on $D_A$ for smaller values of $D_A$ to $V\propto \sqrt{D_A}$ for larger $D_A$, but numerically still significantly different from the mean field value. The deviations reflect the role of internal fluctuations which is neglected in the mean field description.

cond-mat.stat-mech↗

arXiv2005

Velocity and diffusion coefficient of $A+A\leftrightarrow A$ reaction fronts in one dimension

We study front propagation in the reversible reaction-diffusion system A + A <-> A on a 1-d lattice. Extending the idea of leading particle in studying the motion of the front we write a master equation in the stochastically moving frame attached to this particle. This approach provides a systematic way to improve on estimates of front speed obtained earlier. We also find that the leading particle performs a correlated random walk and this correlation needs to be taken into account to get correct value of the front diffusion coefficient.

cond-mat.stat-mech↗