arXiv subjects

P. K. Mohanty

Publications and source records attributed to P. K. Mohanty.

89 records · Page 5Linked to original sources

arXiv2009

Dynamics of path aggregation in the presence of turnover

We investigate the slow time scales that arise from aging of the paths during the process of path aggregation. This is studied using Monte-Carlo simulations of a model aiming to describe the formation of fascicles of axons mediated by contact axon-axon interactions. The growing axons are represented as interacting directed random walks in two spatial dimensions. To mimic axonal turnover, random walkers are injected and whole paths of individual walkers are removed at specified rates. We identify several distinct time scales that emerge from the system dynamics and can exceed the average axonal lifetime by orders of magnitude. In the dynamical steady state, the position-dependent distribution of fascicle sizes obeys a scaling law. We discuss our findings in terms of an analytically tractable, effective model of fascicle dynamics.

physics.bio-ph↗

arXiv2009

MicroRNA Interaction network in human: implications of clustered microRNA in biological pathways and genetic diseases

A novel group of small non-coding RNA, known as microRNA (miRNA) is predicted to regulate as high as 90% of the coding genes in human. The diversity and abundance of miRNA targets offer an enormous level of combinatorial possibilities and suggest that miRNAs and their targets form a complex regulatory network. In the present study, we analyzed 711 miRNAs and their 34, 525 predicted targets in the miRBase database which generate a complex bipartite network having numerous numbers of genes forming the hub. Genes at the hub (total 9877) are significantly over represented in genes with specific molecular functions, biological processes and biological pathways as revealed from the analysis using PANTHER. We further construct a miRNA co-target network by linking every pair of miRNAs which co-target at least one gene. The weight of the link, which is taken to be the number of co-targets of the pair of miRNAs vary widely, and we could erase several links while keeping the relevant features of the network intact. The largest connected sub-graph, thus obtained, contains 479 miRNAs. More than 75% of the miRNAs deregulated in 15 different diseases collected from published data are found to be in this largest sub graph. We further analyze this sub-graph to obtain 70 small clusters containing total 330 miRNAs of 479. We identified the biological pathways where the co-targeted genes in the clusters are significantly over- represented in comparison to that obtained with that are not co-targeted by the miRNAs in the cluster. Using published data, we identified that specific clusters of miRNAs are associated with specific diseases by altering particular pathways. We propose that instead of single miRNA, clusters of miRNA that co-targets the genes are important for the regulation of miRNA in diseases.

q-bio.GN↗

arXiv2009

Stochastic Modeling of Single Molecule Michaelis Menten Kinetics

We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic processes, (a) the substrate arrives at the enzyme site in intervals which fluctuates in time and (b) the enzymatic reaction takes place at that site stochastically. We argue that distribution of arrival time is a two parameter function specified by the substrate and the disorder densities, and that it correctly reproduce the distribution of turnover time obtained from Monte-Carlo simulations of single enzyme kinetics in two dimension, both in absence and presence of disorder. The decoupled dynamics model is simple to implement and generic enough to describe both normal and anomalous diffusion of substrates. It also suggests that the diffusion of substrates in the single enzyme systems could explain the different distributions of turnover time observed in recent experiments.

physics.chem-ph↗

arXiv2008

Forbush decreases and turbulence levels at CME fronts

We seek to estimate the average level of MHD turbulence near coronal mass ejection (CME) fronts as they propagate from the Sun to the Earth. We examine the cosmic ray data from the GRAPES-3 tracking muon telescope at Ooty, together with the data from other sources for three well observed Forbush decrease events. Each of these events are associated with frontside halo Coronal Mass Ejections (CMEs) and near-Earth magnetic clouds. In each case, we estimate the magnitude of the Forbush decrease using a simple model for the diffusion of high energy protons through the largely closed field lines enclosing the CME as it expands and propagates from the Sun to the Earth. We use estimates of the cross-field diffusion coefficient $D_{\perp}$ derived from published results of extensive Monte Carlo simulations of cosmic rays propagating through turbulent magnetic fields. Our method helps constrain the ratio of energy density in the turbulent magnetic fields to that in the mean magnetic fields near the CME fronts. This ratio is found to be $\sim$ 2% for the 11 April 2001 Forbush decrease event, $\sim$ 6% for the 20 November 2003 Forbush decrease event and $\sim$ 249% for the much more energetic event of 29 October 2003.

astro-ph↗

arXiv2007

Analytical results for stochastically growing networks: connection to the zero range process

We introduce a stochastic model of growing networks where both, the number of new nodes which joins the network and the number of connections, vary stochastically. We provide an exact mapping between this model and zero range process, and use this mapping to derive an analytical solution of degree distribution for any given evolution rule. One can also use this mapping to infer about a possible evolution rule for a given network. We demonstrate this for protein-protein interaction (PPI) network for Saccharomyces Cerevisiae.

cond-mat.stat-mech↗

arXiv2007

Critical Behavior of Sandpile Models with Sticky Grains

We revisit the question whether the critical behavior of sandpile models with sticky grains is in the directed percolation universality class. Our earlier theoretical arguments in favor, supported by evidence from numerical simulations [ Phys. Rev. Lett., {\bf 89} (2002) 104303], have been disputed by Bonachela et al. [Phys. Rev. E {\bf 74} (2004) 050102] for sandpiles with no preferred direction. We discuss possible reasons for the discrepancy. Our new results of longer simulations of the one-dimensional undirected model fully support our earlier conclusions.

cond-mat.stat-mech↗

arXiv2007

Why only few are so successful ?

In many professons employees are rewarded according to their relative performance. Corresponding economy can be modeled by taking $N$ independent agents who gain from the market with a rate which depends on their current gain. We argue that this simple realistic rate generates a scale free distribution even though intrinsic ability of agents are marginally different from each other. As an evidence we provide distribution of scores for two different systems (a) the global stock game where players invest in real stock market and (b) the international cricket.

physics.pop-ph↗

arXiv2007

Energy diffusion in hard-point systems

We investigate the diffusive properties of energy fluctuations in a one-dimensional diatomic chain of hard-point particles interacting through a square--well potential. The evolution of initially localized infinitesimal and finite perturbations is numerically investigated for different density values. All cases belong to the same universality class which can be also interpreted as a Levy walk of the energy with scaling exponent 3/5. The zero-pressure limit is nevertheless exceptional in that normal diffusion is found in tangent space and yet anomalous diffusion with a different rate for perturbations of finite amplitude. The different behaviour of the two classes of perturbations is traced back to the "stable chaos" type of dynamics exhibited by this model. Finally, the effect of an additional internal degree of freedom is investigated, finding that it does not modify the overall scenario

cond-mat.stat-mech↗

arXiv2006

Driven diffusive systems of active filament bundles

The cytoskeleton is an important subsystem of cells that is involved for example in cell division and locomotion. It consists of filaments that are cross-linked by molecular motors that can induce relative sliding between filaments and generate stresses in the network. In order to study the effects of fluctuations on the dynamics of such a system we introduce here a new class of driven diffusive systems mimicking the dynamics of active filament bundles where the filaments are aligned with respect to a common axis. After introducing the model class we first analyze an exactly solvable case and find condensation. For the general case we perform a mean-field analysis and study the behavior on large length scales by coarse-graining. We determine conditions for condensation and establish a relation between the hopping rates and the tension generated in the bundle.

cond-mat.stat-mech↗

arXiv2006

A new approach to partial synchronization in globally coupled rotators

We develop a formalism to analyze the behaviour of pulse--coupled identical phase oscillators with a specific attention devoted to the onset of partial synchronization. The method, which allows describing the dynamics both at the microscopic and macroscopic level, is introduced in a general context, but then the application to the dynamics of leaky integrate-and-fire (LIF) neurons is analysed. As a result, we derive a set of delayed equations describing exactly the LIF behaviour in the thermodynamic limit. We also investigate the weak coupling regime by means of a perturbative analysis, which reveals that the evolution rule reduces to a set of ordinary differential equations. Robustness and generality of the partial synchronization regime is finally tested both by adding noise and considering different force fields.

cond-mat.dis-nn↗

arXiv2006

Generic features of the wealth distribution in ideal-gas-like markets

We provide an exact solution to the ideal-gas-like models studied in econophysics to understand the microscopic origin of Pareto-law. In these class of models the key ingredient necessary for having a self-organized scale-free steady-state distribution is the trading or collision rule where agents or particles save a definite fraction of their wealth or energy and invests the rest for trading. Using a Gibbs ensemble approach we could obtain the exact distribution of wealth in this model. Moreover we show that in this model (a) good savers are always rich and (b) every agent poor or rich invests the same amount for trading. Nonlinear trading rules could alter the generic scenario observed here.

physics.soc-ph↗

arXiv2004

Modelling one-dimensional driven diffusive systems by the Zero-Range Process

The recently introduced correspondence between one-dimensional two-species driven models and the Zero-Range Process is extended to study the case where the densities of the two species need not be equal. The correspondence is formulated through the length dependence of the current emitted from a particle domain. A direct numerical method for evaluating this current is introduced, and used to test the assumptions underlying this approach. In addition, a model for isolated domain dynamics is introduced, which provides a simple way to calculate the current also for the non-equal density case. This approach is demonstrated and applied to a particular two-species model, where a phase separation transition line is calculated.

cond-mat.stat-mech↗

arXiv2004

First-order Synchronization Transition in Locally Coupled Maps

We study a family of diffusively coupled chaotic maps on periodic d-dimensional square lattices. Even and odd sub-lattices are updated alternately, introducing an effective delay. As the coupling strength is increased, the system undergoes a first order phase transition from a multi-stable to a synchronized phase. Further increase in coupling strength shows de-synchronization where the phase space splits into two ergodic regions. We argue that the de-synchronization transition is discontinuous for piece-wise linear maps, and is continuous for non-linear maps which are differentiable.

cond-mat.stat-mech↗

arXiv2002

Generic Sandpile Models Have Directed Percolation Exponents

We study sandpile models with stochastic toppling rules and having sticky grains so that with a non-zero probability no toppling occurs, even if the local height of pile exceeds the threshold value. Dissipation is introduced by adding a small probability of particle loss at each toppling. Generically, for models with a preferred direction, the avalanche exponents are those of critical directed percolation clusters. For undirected models, avalanche exponents are those of directed percolation clusters in one higher dimension.

cond-mat.stat-mech↗

arXiv1999

Transport in a class of exactly solvable models of interacting fermions

We study transport in a class of exactly solvable models of interacting fermions in one dimension. We contrast these models with models of non-interacting fermions in an Aharanov-Bohm ring to which they are superficially similar. We introduce magnetic and non-magnetic impurities at a site, through either a weak $δ$-function potential or through a weak link. Using a renormalisation group analysis, we show that the strength of the nonmagnetic impurity is not affected by the interaction, whereas the magnetic impurity cuts the wire at the impurity site.

cond-mat.str-el↗

arXiv1998

Exactly Solvable Fermionic N-chain Models

Motivated by the problem of N coupled Hubbard chains, we investigate a generalisation of the Schulz-Shastry model containing two species of one-dimensional fermions interacting via a gauge field that depends on the positions of all the particles of the other species. The exact many body ground state of the model can be easily obtained through a unitary transformation of the model. The correlation functions are Luttinger-like - i.e., they decay through power laws with non-integer exponents. Through the interaction dependent correlation functions of the two-particle operators, we identify the relevant perturbations and hence, possible instabilities.

cond-mat.stat-mech↗

arXiv1997

Order Parameter Symmetry in Doped YBCO Systems

Intense experimental and theoretical efforts have recently been brought to bear on the determination of the symmetry of superconducting order parameter in high T$_c$ Cuprates as this would shed light on the nature of microscopic interactions that are responsible for superconductivity in these unusual systems. We use a two band model that reproduces the Fermi surface seen in ARPES experiments of Shen et al., and study the symmetry of order parameter in the YBCO system. The model incorporates the effects of tunnelling in the c-direction between the planes and chains of these Cuprates. It is observed that a suitable choice of the phase of the pair wave-function in the planes and chains lead to both s- and d-wave like features. We calculate the detailed phase diagram of this system, observe the shift in the position of the node(s) of the order parameter(s) on the Fermi surface with doping and explain the seemingly contradictory experimental observations about the presence of both s- and/or d-wave symmetry in these systems.

cond-mat.supr-con↗