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V. M. Kenkre

Publications and source records attributed to V. M. Kenkre.

At least 19 recordsLinked to original sources

Misconceptions about quantifying animal encounter and interaction processes

Quantifying animal interactions is crucial for understanding various ecological processes, including social community structures, predator-prey dynamics, spreading of pathogens and information. Despite the ubiquity of interaction processes among animals and the advancements in tracking technologies enabling simultaneous monitoring of multiple individuals, a common theoretical framework to analyse movement data is still lacking. The diverse mechanisms governing how organisms perceive the proximity of others have led to species-specific theoretical approaches, hindering a common currency with which to evaluate and compare findings across taxa. We propose a general framework, borrowing tools from statistical physics, specifically from the theory of reaction diffusion processes. While some of these tools have been employed to predict pathogen transmission events, they have not yet pervaded the movement ecology literature. Using both continuous and discrete variables, we demonstrate the suitability of our framework to study interaction processes. Defining interactions as the transfer of information between individuals, we show that the probability of information transfer for the first time is equivalent to the first-passage probability of reacting in a multi-target environment. As interaction events reduce to encounter events for perfectly efficient information transfer, we compare our formalism to a recent approach that takes the joint occupation probability of two animals over a region of interaction as a measure of the encounter probability, rather than the first-encounter probability. We show the discrepancy between the two approaches by comparing analytically their predictions with continuous variables, while with discrete variables we quantify their difference over time. We conclude by pointing to some of the open problems that reaction diffusion formalism might be able to tackle.

cond-mat.stat-mech↗

Numerical studies for an ab initio investigation into the Boltzmann prescription in statistical mechanics of large systems

We present numerical investigations into the question of the validity of the Boltzmann prescription in Statistical Mechanics for large systems, addressing the issue of whether extensivity of energy implies the extensivity of the Boltzmann entropy. The importance of the question stems from the fact that it is currently considered open by some investigators but quite settled by others. We report ab initio results for gas-like Hamiltonian systems with long-range as well as short-range interactions, based on simulations that explicitly consider more than $2^{30} \approx 10^9$ states of the full Hilbert space. The basis of the technique is Monte Carlo algorithms. Despite the largeness of the numbers used, careful inspection shows that the systems studied are still too small to settle uniquely the issues raised. Therefore, the new approach outlined represents a first step in addressing on first principles the question of non-extensive statistical mechanics. General theoretical comments are also supplied to supplement the numerical investigations.

cond-mat.stat-mech↗

Quantum Oscillations between weakly coupled Bose-Einstein Condensates: Evolution in a Non-degenerate Double Well

We discuss coherent atomic oscillations between two weakly coupled Bose-Einstein condensates that are energetically different. The weak link is notionally provided by a laser barrier in a (possibly asymmetric) multi-well trap or by Raman coupling between condensates in different hyperfine levels. The resultant boson Josephson junction dynamics is described by a double-well nonlinear Gross-Pitaevskii equation. On the basis of a new set of Jacobian elliptic function solutions, we describe the period of the oscillations as well as associated quantities and predict novel observable consequences of the interplay of the energy difference and initial phase difference between the two condensate populations.

cond-mat.quant-gas↗

Energy Exchange Calculations in a Simple Mechanical System to Investigate the Origin of Friction

The microscopic origin of friction is an important topic in science and technology. To date, noteworthy aspects of it remain unsolved. In an effort to shed some light on the possible mechanisms that could give rise to the macroscopic emergence of friction, a simple 1Dd system of two particles is considered, one of them free but moving with an initial velocity, and the other confined by a harmonic potential. The two particles interact via a repulsive Gaussian potential. While it represents in a straightforward manner a tip substrate system in the real world, no analytical solutions can be found for its motion. Because of the interaction, the free particle (tip) may overcome the bound particle (substrate) losing part of its kinetic energy. We solve the Newton's equations of the two particles numerically and calculate the net exchange of energy in the asymptotic state in terms of the relevant parameters of the problem. The effective dissipation that emerges from this simple, classical model with no ad hoc terms shows, surprisingly, a range of rich, non-trivial, behavior. We give theoretical reasoning which provides a satisfactory qualitative description. The essential ingredient of that reasoning is that the transfer of energy from the incoming particle to the confined one can be regarded as the source of the emergent dissipation force, the friction experienced by the incoming particle.

cond-mat.mes-hall↗

Confined Random Walkers in Dimensions Higher Than One and Analysis of Transmission of Infection in Epidemics

A pair of random walkers, the motion of each of which in two dimensions is confined spatially by the action of a quadratic potential centered at different locations for the two walks, are analyzed in the context of reaction-diffusion. The application sought is to the process of transmission of infection in epidemics. The walkers are animals such as rodents in considerations of the Hantavirus epidemic, infected or susceptible, the reaction is the transmission of infection, and the confining potential represents the tendency of the animals to stay in the neighborhood of their home range centers. Calculations are based on a recently developed formalism (Kenkre and Sugaya, Bull. Math. Bio. 76, 3016 (2014)) structured around analytic solutions of a Smoluchowski equation and one of its aims is the resolution of peculiar but well-known problems of reaction-diffusion theory in 2-dimensions. In the present analysis, reaction occurs not at points but in spatial regions of dimensions larger than 0. The analysis uncovers interesting nonintuitive phenomena one of which is similar to that encountered in the 1-dimensional analysis given in the quoted article, and another specific to the fact that the reaction region is spatially extended. The analysis additionally provides a realistic description of observations on animals transmitting infection while moving on what is effectively a 2-dimensional landscape. Along with the general formalism and explicit 1-dimensional analysis given in Bull. Math. Bio. 76, 3016 (2014), the present work forms a model calculational tool for the analysis for the transmission of infection in dilute systems.

physics.bio-ph↗

Theory of the Transmission of Infection in the Spread of Epidemics: Interacting Random Walkers with and without Confinement

A theory of the spread of epidemics is formulated on the basis of pairwise interactions in a dilute system of random walkers (infected and susceptible animals) moving in n dimensions. The motion of an animal pair is taken to obey a Smoluchowski equation in 2n-dimensional space that combines diffusion with confinement of each animal to its particular home range. An additional (reaction) term that comes into play when the animals are in close proximity describes the process of infection. Analytic solutions are obtained, confirmed by numerical procedures, and shown to predict a surprising effect of confinement. The effect is that infection spread has a non-monotonic dependence on the diffusion constant and/or the extent of the attachment of the animals to the home ranges. Optimum values of these parameters exist for any given distance between the attractive centers. Any change from those values, involving faster/slower diffusion or shallower/steeper confinement, hinders the transmission of infection. A physical explanation is provided by the theory. Reduction to the simpler case of no home ranges is demonstrated. Effective infection rates are calculated and it is shown how to use them in complex systems consisting of dense populations.

physics.bio-ph↗

Reaction-Diffusion Theory in the Presence of an Attractive Harmonic Potential

Problems involving the capture of a moving entity by a trap occur in a variety of physical situations, the moving entity being an electron, an excitation, an atom, a molecule, a biological object such as a receptor cluster, a cell, or even an animal such as a mouse carrying an epidemic. Theoretical considerations have almost always assumed that the particle motion is translationally invariant. We study here the case when that assumption is relaxed, in that the particle is additionally subjected to a harmonic potential. This tethering to a center modifies the reaction-diffusion phenomenon. Using a Smoluchowski equation to describe the system, we carry out a study which is explicit in 1 dimension but can be easily extended for arbitrary dimensions. Interesting features emerge depending on the relative location of the trap, the attractive center and the initial placement of the diffusing particle.

cond-mat.stat-mech↗

Approach to Equilibrium of a Nondegenerate Quantum System: Decay of Oscillations and Detailed Balance as Separate Effects of a Reservoir

The approach to equilibrium of a nondegenerate quantum system involves the damping of microscopic population oscillations, and, additionally, the bringing about of detailed balance, i.e. the achievement of the correct Boltzmann factors relating the populations. These two are separate effects of interaction with a reservoir. One stems from the randomization of phases and the other from phase space considerations. Even the meaning of the word `phase' differs drastically in the two instances in which it appears in the previous statement. In the first case it normally refers to quantum phases whereas in the second it describes the multiplicity of reservoir states that corresponds to each system state. The generalized master equation theory for the time evolution of such systems is here developed in a transparent manner and both effects of reservoir interactions are addressed in a unified fashion. The formalism is illustrated in simple cases including in the standard spin-boson situation wherein a quantum dimer is in interaction with a bath consisting of harmonic oscillators. The theory has been constructed for application in energy transfer in molecular aggregates and in photosynthetic reaction centers.

cond-mat.stat-mech↗

Explaining the observed long coherence effects by 2D photon echo experiments in photosynthetic EET : Two-Component Phonon Spectrum model

We propose a simple stochastic model which successfully explains the long coherence effects observed in photosynthetic Excitation Energy Transport (EET) by 2D photon echo experiments of G. S. Engel et. al. (Nature, {\bf 446} 782, (2007)). Our Two-Component Phonon Spectrum (TCPS) model is based upon the division of phonon degrees of freedom into a systematic component which is treated through polaron transformation and a stochastic component which is treated through dynamical disorder. This model successfully explains the observed long coherence upto $ \sim 600 fsec$ in EET experiments.

physics.chem-ph↗

Resonance Effects in the Nonadiabatic Nonlinear Quantum Dimer

The quantum nonlinear dimer consisting of an electron shuttling between the two sites and in weak interaction with vibrations, is studied numerically under the application of a DC electric field. A field-induced resonance phenomenon between the vibrations and the electronic oscillations is found to influence the electronic transport greatly. For initially delocalization of the electron, the resonance has the effect of a dramatic increase in the transport. Nonlinear frequency mixing is identified as the main mechanism that influences transport. A characterization of the frequency spectrum is also presented.

cond-mat.other↗

Phase transitions induced by complex nonlinear noise in a system of self-propelled agents

We propose a comprehensive dynamical model for cooperative motion of self-propelled particles, e.g., flocking, by combining well-known elements such as velocity-alignment interactions, spatial interactions, and angular noise into a unified Lagrangian treatment. Noise enters into our model in an especially realistic way: it incorporates correlations, is highly nonlinear, and it leads to a unique collective behavior. Our results show distinct stability regions and an apparent change in the nature of one class of noise-induced phase transitions, with respect to the mean velocity of the group, as the range of the velocity-alignment interaction increases. This phase-transition change comes accompanied with drastic modifications of the microscopic dynamics, from nonintermittent to intermittent. Our results facilitate the understanding of the origin of the phase transitions present in other treatments.

cond-mat.stat-mech↗

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↗

Extensions of Effective Medium Theory of Transport in Disordered Systems

Effective medium theory of transport in disordered systems, whose basis is the replacement of spatial disorder by temporal memory, is extended in several practical directions. Restricting attention to a 1-dimensional system with bond disorder for specificity, a transformation procedure is developed to deduce, from given distribution functions characterizing the system disorder, explicit expressions for the memory functions. It is shown how to use the memory functions in the Lapace domain forms in which they first appear, and in the time domain forms which are obtained via numerical inversion algorithms, to address time evolution of the system beyond the asymptotic domain of large times normally treated. An analytic but approximate procedure is provided to obtain the memories, in addition to the inversion algorithm. Good agreement of effective medium theory predictions with numerically computed exact results is found for all time ranges for the distributions used except near the percolation limit as expected. The use of ensemble averages is studied for normal as well as correlation observables. The effect of size on effective mediumtheory is explored and it is shown that, even in the asymptotic limit, finite size corrections develop to the well known harmonic mean prescription for finding the effective rate. A percolation threshold is shown to arise even in 1-d for finite (but not infinite) systems at a concentration of broken bonds related to the system size. Spatially long range transfer rates are shown to emerge naturally as a consequence of the replacement of spatial disorder by temporal memories, in spite of the fact that the original rates possess nearest neighbor character. Pausing time distributions in continuous time random walks corresponding to the effective medium memories are calculated.

cond-mat.stat-mech↗

Spatial features of population dynamics arising from mutual interaction of different age groups in rodents

We study the dynamics of the transmission of the hanta virus infection among mouse populations, taking into account, simultaneously, seasonal variations of the environment and interactions within two classes in the mouse population: adults and subadults. The interactions considered are not symmetric between the two age-organized classes and are responsible for driving the younger members away from home ranges. We consider the case of a bounded habitat affected by seasonal variations.

nlin.PS↗

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↗

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↗

Random Walk Access Times on Partially-Disordered Complex Networks: an Effective Medium Theory

An analytic effective medium theory is constructed to study the mean access times for random walks on hybrid disordered structures formed by embedding complex networks into regular lattices, considering transition rates $F$ that are different for steps across lattice bonds from the rates $f$ across network shortcuts. The theory is developed for structures with arbitrary shortcut distributions and applied to a class of partially-disordered traversal enhanced networks in which shortcuts of fixed length are distributed randomly with finite probability. Numerical simulations are found to be in excellent agreement with predictions of the effective medium theory on all aspects addressed by the latter. Access times for random walks on these partially disordered structures are compared to those on small-world networks, which on average appear to provide the most effective means of decreasing access times uniformly across the network.

cond-mat.dis-nn↗

Effects of disorder in location and size of fence barriers on molecular motion in cell membranes

The effect of disorder in the energetic heights and in the physical locations of fence barriers encountered by transmembrane molecules such as proteins and lipids in their motion in cell membranes is studied theoretically. The investigation takes as its starting point a recent analysis of a periodic system with constant distances between barriers and constant values of barrier heights, and employs effective medium theory to treat the disorder. The calculations make possible, in principle, the extraction of confinement parameters such as mean compartment sizes and mean intercompartmental transition rates from experimentally reported published observations. The analysis should be helpful both as an unusual application of effective medium theory and as an investigation of observed molecular movements in cell membranes.

physics.bio-ph↗