arXiv subjects

Indrani Bose

Publications and source records attributed to Indrani Bose.

At least 55 records · Page 3Linked to original sources

arXiv2005

Thermal entanglement properties of small spin clusters

Exchange interactions in spin systems can give rise to quantum entanglement in the ground and thermal states of the systems. In this paper, we consider a spin tetramer, with spins of magnitude 1/2, in which the spins interact via nearest-neighbour, diagonal and four-spin interactions of strength J1, J2 and K respectively. The ground and thermal state entanglement properties of the tetramer are calculated analytically in the various limiting cases. Signatures of quantum phase transition (QPT) in terms of appropriate entanglement measures are obtained. The magnetic properties of a S = 1/2 AFM polyoxovanadate compound, V12, are well explained by spin tetramers with only nearest-neighbour exchange interactions. Treating the magnetic susceptibility chi as an entanglement witness (EW), an estimate of the lower bound of the critical entanglement temperature, T_c, above which the multipartite entanglement disappears in the experimental compound, is determined. A second EW based on energy provides an estimate of the entanglement temperature T_E, below which bipartite entanglement is certainly present in the system, is determined. The cases of the symmetric trimer and the tetrahedron are also considered.

cond-mat.str-el↗

arXiv2005

A stochastic model of wealth distribution

We propose a stochastic model of evolution of wealth in a society of economic agents. In the model, an agent can be in two states: inactive and active. Transitions between the states occur at random time intervals. In the active state, the rate at which wealth increases is greater than that in the inactive state. In both the states, wealth diminishes at a rate proportional to the current wealth. The probability density function describing the wealth distribution in the steady state is found to have the form of a beta distribution. Wealth distributions for the poor, middle and the rich classes are obtained separately. In economic literature, beta distribution and its generalisations, namely, the generalised beta distribution functions have been proposed to describe the income distributions of different economic societies. Our stochastic model provides a simple basis for the appearance of beta-type distributions.

physics.soc-ph↗

arXiv2005

Spin gap antiferromagnets: materials and phenomena

There are several interacting spin systems which have a gap in their spin excitation spectrum. The gap does not occur due to anisotropies present in the system but is quantum mechanical in origin. We give a brief overview on the different types of spin gap (SG) antiferromagnets, the models proposed to describe their physical properties and experimental realizations of such systems. Our special focus is on exactly-solvable models and rigorous theories which provide the correct physical picture for the novel phenomena exhibited by SG systems

cond-mat.mtrl-sci↗

arXiv2004

Graded and Binary Responses in Stochastic Gene Expression

Recently, several theoretical and experimental studies have been undertaken to probe the effect of stochasticity on gene expression (GE). In experiments, the GE response to an inducing signal in a cell, measured by the amount of mRNAs/proteins synthesized, is found to be either graded or binary. The latter type of response gives rise to a bimodal distribution in protein levels in an ensemble of cells. One possible origin of binary response is cellular bistability achieved through positive feedback or autoregulation. In this paper, we study a simple, stochastic model of GE and show that the origin of binary response lies exclusively in stochasticity. The transitions between the active and inactive states of the gene are random in nature. Graded and binary responses occur in the model depending on the relative stability of the activated and deactivated gene states with respect to that of mRNAs/proteins.The theoretical results on binary response provide a good description of the ``all-or-none'' phenomenon observed in an eukaryotic system.

q-bio.OT↗

arXiv2004

Noise Characteristics of Feed Forward Loops

A prominent feature of gene transcription regulatory networks is the presence in large numbers of motifs, i.e, patterns of interconnection, in the networks. One such motif is the feed forward loop (FFL) consisting of three genes X, Y and Z. The protein product of x of X controls the synthesis of protein product y of Y. Proteins x and y jointly regulate the synthesis of z proteins from the gene Z. The FFLs, depending on the nature of the regulating interactions, can be of eight different types which can again be classified into two categories: coherent and incoherent. In this paper, we study the noise characteristics of FFLs using the Langevin formalism and the Monte Carlo simulation technique based on the Gillespie algorithm. We calculate the variances around the mean protein levels in the steady states of the FFLs and find that, in the case of coherent FFLs, the most abundant FFL, namely, the Type-1 coherent FFL, is the least noisy. This is however not so in the case of incoherent FFLs. The results suggest possible relationships between noise, functionality and abundance.

q-bio.MN↗

arXiv2004

Reaction diffusion processes on random and scale-free networks

We study the discrete Gierer-Meinhardt model of reaction-diffusion on three different types of networks: regular, random and scale-free. The model dynamics lead to the formation of stationary Turing patterns in the steady state in certain parameter regions. Some general features of the patterns are studied through numerical simulation. The results for the random and scale-free networks show a marked difference from those in the case of the regular network. The difference may be ascribed to the small world character of the first two types of networks.

cond-mat.stat-mech↗

arXiv2003

Mathematical models of haploinsufficiency

We study simple mathematical models of gene expression to explore the possible origins of haploinsufficiency (HI). In a diploid organism, each gene exists in two copies and when one of these is mutated, the amount of proteins synthesized is reduced and may fall below a threshold level for the onset of some desired activity. This can give rise to HI, a manifestation of which is in the form of a disease. We consider both deterministic and stochastic models of gene expression and suggest possible scenarios for the occurrence of HI in the two cases. In the stochastic case, random fluctuations around the mean protein level give rise to a finite probability that the protein level falls below a threshold. Increased gene copy number and faster gene expression kinetics reduce the variance around the mean protein level. The difference between slow and fast gene expression kinetics, as regards response to a signaling gradient, is further pointed out. The majority of results reported in the paper are derived analytically.

q-bio.OT↗

arXiv2003

Simple Models of Plant Learning and Memory

Plants are capable of intelligent responses to complex environmental signals. Learning and memory play fundamental roles in such responses. Two simple models of plant memory are proposed based on the calcium-signalling system. The memory states correspond to steady state distributions of calcium ions.

cond-mat↗

arXiv2003

Stochastic Simulation of Gene Expression in a Single Cell

In this paper, we consider two stochastic models of gene expression in prokaryotic cells. In the first model, sixteen biochemical reactions involved in transcription, translation and transcriptional regulation in the presence of inducer molecules are considered. The time evolution of the number of biomolecules of a particular type is determined using the stochastic simulation method based on the Gillespie Algorithm. The results obtained show that if the number of inducer molecules, N(I), is greater than or equal to the number of regulatory molecules, N(R), the average protein level is high in the steady state (state 2). The magnitude of the level is the same as long as N{I) greater than or equal to N(R). When N(I) is very very less than N(R), the average protein level is low, practically zero (state 1). As N(I) increases, the protein level continues to remain low. When N(I)becomes close to N(R), protein levels in the steady state are intermediate between high and low.In the presence of autocatalysis, a cell mostly exists in either state 1 or state 2 giving rise to a bimodal distribution in the protein levels in an ensemble of cells. This corresponds to the "all or none'' phenomenon observed in experiments. In the second model, the inducer molecules are not considered explicitly. An exhaustive simulation over the parameter space of the model shows that there are three major patterns of gene expression, Type A, Type B and Type C. The effect of varying the cellular parameters on the patterns, in particular, the transition from one type of pattern to another, is studied. Type A and Type B patterns have been observed in experiments. Simple mathematical models of transcriptional regulation predict Type C pattern of gene expression in certain parameter regimes.

cond-mat↗

arXiv2002

Macroscopic entanglement jumps in model spin systems

In this paper, we consider some frustrated spin models for which the ground states are known exactly. The concurrence, a measure of the amount of entanglement can be calculated exactly for entangled spin pairs. Quantum phase transitions involving macroscopic magnetization changes at critical values of the magnetic field are accompanied by macroscopic jumps in the (T=0) entanglement. A specific example is given in which magnetization plateaus give rise to a plateau structure in the amount of entanglement associated with nearest-neighbour bonds. We further show that macroscopic entanglement changes can occur in quantum phase transitions brought about by the tuning of exchange interaction strengths.

cond-mat↗

arXiv2002

The Physical Basis of Integrable Spin Models

Integrable models are often constructed with real systems in mind. The exact solvability of the models leads to results which are unambiguous and provide the correct physical picture. In this review, we discuss the physical basis of some integrable spin models and their relevance in the study of real systems. The emphasis in the review is on physical understanding rather than on the mathematical aspects of integrability.

cond-mat↗

arXiv2002

Bacterial Evolution and Bak-Sneppen Model

Recently, Lenski et al [Elena,Lenski,Travisano] have carried out several experiments on bacterial evolution. Their findings support the theory of punctuated equilibrium in biological evolution. They have further quantified the relative contributions of adaptation, chance and history to bacterial evolution. In this paper, we show that a modified $M$-trait Bak-Sneppen model can explain many of the experimental results in a qualitative manner.

cond-mat.stat-mech↗

arXiv2002

Magnetization plateaux in a generalised ladder model

A spin-1/2 antiferromagnetic(AFM) generalised ladder model is constructed which consists of four-spin plaquettes, coupled through weaker exchange interactions, to two-spin rungs. In an extended parameter regime, the exact ground state of the ladder is determined. In this state, the four-spin plaquettes and the rungs are in their ground state spin configurations. In the presence of an external magnetic field, the magnetization/site has a plateau structure as a function of the magnetic field.

cond-mat↗

arXiv2002

Biological Networks

In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction networks, nonlinear dynamics in gene regulatory networks and in particular the design of synthetic genetic networks using the concepts and techniques of nonlinear physics and lastly the effect of stochasticity on the dynamics. The examples chosen illustrate the usefulness of interdisciplinary approaches in the study of biological networks.

cond-mat↗

arXiv2002

Magnetization of coupled spin clusters in Ladder Geometry

In this paper, we construct a class of spin-1/2 antiferromagnetic (AFM) two-chain ladder models consisting of blocks of n-spin tetrahedral clusters alternating with two-spin rungs. For n=4 and 6 and in extended parameter regimes, the exact ground state of the ladder is shown to be a product of the ground states of the rungs and the n-spin blocks, in both zero and finite magnetic fields. In the latter case, magnetization/site (m) versus magenetic field (h) plot exhibits well-defined magnetization plateaus.

cond-mat.str-el↗

arXiv2001

Quantum magnets: a brief overview

Quantum magnetism is one of the most active areas of research in condensed matter physics. There is significant research interest specially in low-dimensional quantum spin systems. Such systems have a large number of experimental realizations and exhibit a variety of phenomena the origin of which can be attributed to quantum effects and low dimensions. In this review, an overview of some aspects of quantum magnetism in low dimensions is given. The emphasis is on key concepts, theorems and rigorous results as well as models of spin chains, ladders and frustated magnetic systems.

cond-mat.str-el↗

arXiv2001

A Cooperative Stochastic Model of Gene Expression

Recent experiments at the level of a single cell have shown that gene expression occurs in abrupt stochastic bursts. Further, in an ensemble of cells, the levels of proteins produced have a bimodal distribution. In a large fraction of cells, the gene expression is either off or has a high value. We propose a stochastic model of gene expression the essential features of which are stochasticity and cooperative binding of RNA polymerase. The model can reproduce the bimodal behaviour seen in experiments.

cond-mat.soft↗

arXiv2001

Bacterial evolution and the Bak-Sneppen model

Recently, Lenski et al \cite{Elena,Lenski,Travisano} have carried out several experiments on bacterial evolution. Their findings support the theory of punctuated equilibrium in biological evolution. They have further quantified the relative contributions of adaptation, chance and history to bacterial evolution. In this Brief Report, we show that a modified M-trait Bak-Sneppen model can explain many of the experimental results in a qualitative manner.

cond-mat.stat-mech↗