arXiv subjects

Indrani Bose

Publications and source records attributed to Indrani Bose.

At least 19 recordsLinked to original sources

arXiv2025

Brightening of dark trions in monolayer WS$_2$ via localization of surface plasmons

Among all excitonic complexes in transition-metal dichalcogenides (TMDs), dark and semi-dark trions are poised to play a stellar role in future quantum technologies due to their long lifetimes, about two orders of magnitude greater than those of their bright counterparts. In monolayer (ML) tungsten disulphide (WS$_2$), accessing these states via a suitable brightening mechanism remains challenging, specially, at elevated temperatures. Here, we demonstrate the brightening of dark trions from ML WS$_2$ over the temperature range, 83 K-115 K, enabled by localized surface plasmon modes in a disordered gold substrate. The resulting photoluminescence (PL) spectrum reveals a distinct spectral doublet with the twin peaks of semi-dark and bright trion states, separated by $\sim$ 45 meV. The origin of the semi-dark trion state lies in intervalley electron-electron scatterings, while its visibility in the PL spectrum is made possible by the enhanced out-of-plane electromagnetic field associated with plasmon localization. We also report on the negative degree of circular polarization in ML WS$_2$ at the energy of the semi-dark trion state. Our results establish a scalable plasmonic route to access valley-polarized semi-dark trions, opening new opportunities for quantum and valleytronic applications.

cond-mat.mes-hall↗

arXiv2025

Universal features of epidemic and vaccine models

In this paper, we study a stochastic susceptible-infected-susceptible (SIS) epidemic model that includes an additional immigration process. In the presence of multiplicative noise, generated by environmental perturbations, the model exhibits noise-induced transitions. The bifurcation diagram has two distinct regions of unimodality and bimodality in which the steady-state probability distribution has one and two peaks, respectively. Apart from first-order transitions between the two regimes, a critical-point transition occurs at a cusp point with the transition belonging to the mean-field Ising universality class. The epidemic model shares these features with the well-known Horsthemke-Lefever model of population genetics. The effect of vaccination on the spread/containment of the epidemic in a stochastic setting is also studied. We further propose a general vaccine-hesitancy model, along the lines of Kirman's ant model, with the steady-state distribution of the fraction of the vaccine-willing population given by the Beta distribution. The distribution is shown to give a good fit to the COVID-19 data on vaccine hesitancy and vaccination. We derive the steady-state probability distribution of the basic reproduction number, a key parameter in epidemiology, based on a beta-distributed fraction of the vaccinated population. Our study highlights the universal features that epidemic and vaccine models share with other dynamical models.

q-bio.PE↗

arXiv2025

Alloying as a new route to generating interlayer excitons

Heterobilayers formed by stacking two-dimensional atomic crystals are particularly promising for low-dimensional semiconductor optics, as they host interlayer excitons, bound states of electrons and holes residing in different layers. They inherit the valley-contrasting physics of the individual monolayers, leading to a range of unique properties that distinguish them from other solid-state nanostructures. Here, we propose a novel route for the generation of interlayer excitons based on the synthesis of a transition metal dichalcogenide bilayer alloy material, WS$_{2x}$Se$_{2(1-x)}$. Using piezoelectric force microscopy, we demonstrate the existence of an internal electric field oriented in the out-of-plane direction. Interlayer excitons have so far been mostly observed in heterostructures with a type-II band alignment. In the presence of an internal electric field, a similar alignment occurs in the alloy bilayer resulting in an efficient generation of interlayer excitons. Photoluminescence spectroscopy measurements involving circularly polarised light come up with key observations like a negative degree of circular polarization of the interlayer excitons which increases as a function of temperature. A simple theoretical model provides a physical understanding of the major experimentally observed features. With experimentally fitted parameter values, the dominant contribution to the degree of circular polarization is shown to arise from spin polarization and not from valley polarization, a consequence of the spin-valley-layer coupling characteristic of a TMDC bilayer. The room-temperature interlayer excitonic transition in bilayer TMDCs has key implications for fundamental physics, including Bose-Einstein condensation and high-temperature superfluidity, while enabling advanced valleytronic and quantum information functionalities.

cond-mat.mes-hall↗

arXiv2023

Valley polarization and photocurrent generation in transition metal dichalcogenide alloy MoS$_{2x}$Se$_{2(1-x)}$

Monolayer transition metal dichalcogenides (TMDCs) constitute the core group of materials in the emerging semiconductor technology of valleytronics. While the coupled spin-valley physics of pristine TMDC materials and their heterstructures has been extensively investigated, less attention was given to TMDC alloys, which could be useful in optoelectronic applications due to the tunability of their band gaps. We report here our experimental investigations of the spin-valley physics of the monolayer and bilayer TMDC alloy, MoS$_{2x}$Se$_{2(1-x)}$, in terms of valley polarization and the generation as well as electrical control of a photocurrent utilising the circular photogalvanic effect. Piezoelectric force microscopy provides evidence for an internal electric field perpendicular to the alloy layer, thus breaking the out-of-plane mirror symmetry. The experimental observation is supported by first principles calculations based on the density functional theory. A comparison of the photocurrent device, based on the alloy material, is made with similar devices involving other TMDC materials.

cond-mat.mes-hall↗

arXiv2023

Growth, Poverty Trap and Escape

The well-known Solow growth model is the workhorse model of the theory of economic growth, which studies capital accumulation in a model economy as a function of time with capital stock, labour and technology-based production as the basic ingredients. The capital is assumed to be in the form of manufacturing equipment and materials. Two important parameters of the model are: the saving fraction $s$ of the output of a production function and the technology efficiency parameter $A$, appearing in the production function. The saved fraction of the output is fully invested in the generation of new capital and the rest is consumed. The capital stock also depreciates as a function of time due to the wearing out of old capital and the increase in the size of the labour population. We propose a stochastic Solow growth model assuming the saving fraction to be a sigmoidal function of the per capita capital $k_p$. We derive analytically the steady state probability distribution $P(k_p)$ and demonstrate the existence of a poverty trap, of central concern in development economics. In a parameter regime, $P(k_p)$ is bimodal with the twin peaks corresponding to states of poverty and well-being respectively. The associated potential landscape has two valleys with fluctuation-driven transitions between them. The mean exit times from the valleys are computed and one finds that the escape from a poverty trap is more favourable at higher values of $A$. We identify a critical value of $A_c$ below (above) which the state of poverty (well-being) dominates and propose two early signatures of the regime shift occurring at $A_c$. The economic model, with conceptual foundation in nonlinear dynamics and statistical mechanics, shares universal features with dynamical models from diverse disciplines like ecology and cell biology.

physics.soc-ph↗

arXiv2023

Tipping the Balance: a criticality perspective

Cell populations are often characterised by phenotypic heterogeneity in the form of two distinct subpopulations. We consider a model of tumour cells consisting of two subpopulations: non-cancer promoting (NCP) and cancer-promoting (CP). Under steady state conditions, the model has similarities with a well-known model of population genetics which exhibits a purely noise-induced transition from unimodality to bimodality at a critical value of the noise intensity $\sigma^2$. The noise is associated with a parameter $\lambda$ representing the system-environment coupling. In the case of the tumour model, $\lambda$ has a natural interpretation in terms of the tissue microenvironment which has considerable influence on the phenotypic composition of the tumour. Oncogenic transformations give rise to considerable fluctuations in the parameter. We compute the $\lambda-\sigma^2$ phase diagram in a stochastic setting, drawing analogies between bifurcations and phase transitions. In the region of bimodality, a transition from a state of balance to a state of dominance, in terms of the competing subpopulations, occurs at $\lambda=0$. Away from this point, the NCP (CP) subpopulation becomes dominant as $\lambda$ changes towards positive (negative) values. The variance of the steady state probability density function as well as two entropic measures provide characteristic signatures at the transtion point.

cond-mat.stat-mech↗

arXiv2023

Emergent phenomena in living systems: a statistical mechanical perspective

A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key processes like gene expression and cell differentiation give rise to fluctuations (noise) in the levels of the biomolecules and this combined with nonlinear interactions give rise to a number of emergent phenomena. In this review, we describe and discuss some of these phenomena which have the character of phase transitions in physical systems. We specifically focus on noise-induced transitions in a stochastic model of gene expression and in a population genetics model which have no analogs when the dynamics are solely deterministic in nature. Some of these transitions exhibit critical-point phenomena belonging to the mean-field Ising universality class of equilibrium phase transitions. A number of other examples, ranging from biofilms to homeostasis in adult tissues, are also discussed which exhibit behavior similar to critical phenomena in equilibrium and nonequilbrium phase transitions. The examples illustrate how the subject of statistical mechanics provides a bridge between theoretical models and experimental observations.

cond-mat.stat-mech↗

arXiv2020

Criticality in Tissue Homeostasis: Models and Experiments

There is considerable theoretical and experimental support to the proposal that tissue homeostasis in the adult skin can be represented as a critical branching process. The homeostatic condition requires that the proliferation rate of the progenitor (P) cells (capable of cell division) is counterbalanced by the loss rate due to the differentiation of a P cell into differentiated (D) cells so that the total number of P cells remains constant. We consider the two-branch and three-branch models of tissue homeostasis to establish homeostasis as a critical phenomenon. It is first shown that some critical branching process theorems correctly predict experimental observations. A number of temporal signatures of the approach to criticality are investigated based on simulation and analytical results. The analogy between a critical branching process and mean-field percolation and sandpile models is invoked to show that the size and lifetime distributions of the populations of P cells have power-law forms. The associated critical exponents have the same magnitudes as in the cases of the mean-field lattice statistical models. The results indicate that tissue homeostasis provides experimental opportunities for testing critical phenomena.

cond-mat.stat-mech↗

arXiv2019

Bifurcation and Criticality

Equilibrium and nonequilibrium systems exhibit power-law singularities close to their critical and bifurcation points respectively. A recent study has shown that biochemical nonequilibrium models with positive feedback belong to the universality class of the mean-field Ising model. Through a mapping between the two systems, effective thermodynamic quantities like temperature, magnetic field and order parameter can be expressed in terms of biochemical parameters. In this paper, we demonstrate the equivalence using a simple deterministic approach. As an illustration we consider a model of population dynamics exhibiting the Allee effect for which we determine the exact phase diagram. We further consider a two-variable model of positive feedback, the genetic toggle, and discuss the conditions under which the model belongs to the mean-field Ising universality class. In the biochemical models, the supercritical pitchfork bifurcation point serves as the critical point. The dynamical behaviour predicted by the two models is in qualitative agreement with experimental observations and opens up the possibility of exploring critical point phenomena in laboratory populations and synthetic biological circuits.

q-bio.QM↗

arXiv2017

Allee dynamics: Growth, extinction and range expansion

In population biology, the Allee dynamics refer to negative growth rates below a critical population density. In this Letter, we study a reaction-diffusion (RD) model of population growth and dispersion in one dimension, which incorporates the Allee effect in both the growth and mortality rates. In the absence of diffusion, the bifurcation diagram displays regions of both finite population density and zero population density, i.e., extinction. The early signatures of the transition to extinction at a bifurcation point are computed in the presence of additive noise. For the full RD model, the existence of travelling wave solutions of the population density is demonstrated. The parameter regimes in which the travelling wave advances (range expansion) and retreats are identified. In the weak Allee regime, the transition from the pushed to the pulled wave is shown as a function of the mortality rate constant. The results obtained are in agreement with the recent experimental observations on budding yeast populations.

q-bio.CB↗

arXiv2016

Criticality in Cell Differentiation

Cell differentiation is an important process in living organisms. Differentiation is mostly based on binary decisions with the progenitor cells choosing between two specific lineages. The differentiation dynamics have both deterministic and stochastic components. Several theoretical studies suggest that cell differentiation is a bifurcation phenomenon, well-known in dynamical systems theory. The bifurcation point has the character of a critical point with the system dynamics exhibiting specific features in its vicinity. These include the critical slowing down, rising variance and lag-1 autocorrelation function, strong correlations between the fluctuations of key variables and non-Gaussianity in the distribution of fluctuations. Recent experimental studies provide considerable support to the idea of criticality in cell differentiation and in other biological processes like the development of the fruit fly embryo. In this Review, an elementary introduction is given to the concept of criticality in cell differentiation. The correspondence between the signatures of criticality and experimental observations on blood cell differentiation in mice is further highlighted.

q-bio.CB↗

arXiv2016

Functional Characteristics of Gene Expression Motifs with Single and Dual Strategies of Regulation

Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation are well investigated, the dynamics of motifs with dual strategies of regulation, i.e., both transcriptional and post-transcriptional regulation, have not been studied as extensively. In this paper, we probe the dynamics of a four-gene motif with dual strategies of regulation of gene expression. Some of the functional characteristics are compared with those of a two-gene motif, the genetic toggle, employing only transcriptional regulation. Both the motifs define positive feedback loops with the potential for bistability and hysteresis. The four-gene motif, contrary to the genetic toggle, is found to exhibit bistability even in the absence of cooperativity in the regulation of gene expression. The four-gene motif further exhibits a novel dynamical feature in which two regions of monostability with linear threshold response are separated by a region of bistability with digital response. Using the linear noise approximation (LNA), we further show that the coefficient of variation (a measure of noise), associated with the protein levels in the steady state, has a lower magnitude in the case of the four-gene motif as compared to the case of the genetic toggle. We next compare transcriptional with post-transcriptional regulation from an information theoretic perspective. We focus on two gene expression motifs, Motif 1 with transcriptional regulation and Motif 2 with post-transcriptional regulation. We show that amongst the two motifs, Motif 2 has a greater capacity for information transmission for an extended range of parameter values.

q-bio.CB↗

arXiv2014

Non-genetic heterogeneity criticality and cell differentiation

The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of large-scale microarray data establish the key role played by a two-gene motif in cell differentiation in a number of cell systems. The two genes express transcription factors which repress each other's expression and autoactivate their own production. A number of theoretical models have recently been proposed based on the two-gene motif to provide a physical understanding of how cell differentiation occurs. In this paper, we study a simple model of cell differentiation which assumes no cooperativity in the regulation of gene expression by the transcription factors. The latter repress each other's activity directly through DNA binding and indirectly through the formation of heterodimers. We specifically investigate how deterministic processes combined with stochasticity contribute in bringing about cell differentiation. The deterministic dynamics of our model give rise to a supercritical pitchfork bifurcation from an undifferentiated stable steady state to two differentiated stable steady states. The stochastic dynamics of our model are studied using the approaches based on the Langevin equations and the linear noise approximation. The simulation results provide a new physical understanding of recent experimental observations. We further propose experimental measurements of quantities like the variance and the lag-1 autocorrelation function in protein fluctuations as the early signatures of an approaching bifurcation point in the cell differentiation process.

q-bio.CB↗

arXiv2013

Noise-induced Regime Shifts: A Quantitative Characterization

Diverse complex dynamical systems are known to exhibit abrupt regime shifts at bifurcation points of the saddle-node type. The dynamics of most of these systems, however, have a stochastic component resulting in noise driven regime shifts even if the system is away from the bifurcation points. In this paper, we propose a new quantitative measure, namely, the propensity transition point as an indicator of stochastic regime shifts. The concepts and the methodology are illustrated for the one-variable May model, a well-known model in ecology and the genetic toggle, a two-variable model of a simple genetic circuit. The general applicability and usefulness of the method for the analysis of regime shifts is further demonstrated in the case of the mycobacterial switch to persistence for which experimental data are available.

cond-mat.stat-mech↗

arXiv2013

Early signatures of regime shifts in gene expression dynamics

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a fold-bifurcation model involving bistability and hysteresis. We consider two alternative models, Models 1 and 2, of competence development in the bacterial population B. subtilis and determine some early signatures of the regime shifts between competence and noncompetence. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence.

q-bio.MN↗

arXiv2013

Markovian evolution of classical and quantum correlations in transverse-field XY model

The transverse-field XY model in one dimension is a well-known spin model for which the ground state properties and excitation spectrum are known exactly. The model has an interesting phase diagram describing quantum phase transitions (QPTs) belonging to two different universality classes. These are the transverse-field Ising model and the XX model universality classes with both the models being special cases of the transverse-field XY model. In recent years, quantities related to quantum information theoretic measures like entanglement, quantum discord (QD) and fidelity have been shown to provide signatures of QPTs. Another interesting issue is that of decoherence to which a quantum system is subjected due to its interaction, represented by a quantum channel, with an environment. In this paper, we determine the dynamics of different types of correlations present in a quantum system, namely, the mutual information, the classical correlations and the quantum correlations, as measured by the quantum discord, in a two-qubit state. The density matrix of this state is given by the nearest-neighbour reduced density matrix obtained from the ground state of the transverse-field XY model in 1d. We assume Markovian dynamics for the time-evolution due to system-environment interactions. The quantum channels considered include the bit-flip, bit-phase-flip and phase-flip channels. Two different types of dynamics are identified for the channels in one of which the quantum correlations are greater in magnitude than the classical correlations in a finite time interval. The origins of the different types of dynamics are further explained. For the different channels, appropriate quantities associated with the dynamics of the correlations are identified which provide signatures of QPTs. We also report results for further-neighbour two-qubit states and finite temperatures.

quant-ph↗

arXiv2013

Quantum Discord, Decoherence and Quantum Phase Transitions

Quantum discord is a more general measure of quantum correlations than entanglement and has been proposed as a resource in certain quantum information processing tasks. The computation of discord is mostly confined to two-qubit systems for which an analytical calculational scheme is available. The utilization of quantum correlations in quantum information-based applications is limited by the problem of decoherence, i.e., the loss of coherence due to the inevitable interaction of a quantum system with its environment. The dynamics of quantum correlations due to decoherence may be studied in the Kraus operator formalism for different types of quantum channels representing system-environment interactions. In this review, we describe the salient features of the dynamics of classical and quantum correlations in a two-qubit system under Markovian (memoryless) time evolution. The two-qubit state considered is described by the reduced density matrix obtained from the ground state of a spin model. The models considered include the transverse-field XY model in one dimension, a special case of which is the transverse-field Ising model, and the $XXZ$ spin chain. The quantum channels studied include the amplitude damping, bit-flip, bit-phase-flip and phase-flip channels. The Kraus operator formalism is briefly introduced and the origins of different types of dynamics discussed. One can identify appropriate quantities associated with the dynamics of quantum correlations which provide signatures of quantum phase transitions in the spin models. Experimental observations of the different types of dynamics are also mentioned.

quant-ph↗

arXiv2012

Origins of Binary Gene Expression in Post-transcriptional Regulation by MicroRNAs

MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to describe the dynamics of post-transcriptional regulation by microRNAs. The model explains the observations made in single cell experiments quite well. In this paper, we introduce some additional features into the model and consider two specific cases. In the first case, a non-cooperative positive feedback loop is included in the transcriptional regulation of the target gene expression. In the second case, a stochastic version of the original model is considered in which there are random transitions between the inactive and active expression states of the gene. In the first case we show that bistability is possible in a parameter regime, due to the presence of a non-linear protein decay term in the gene expression dynamics. In the second case, we derive the conditions for obtaining stochastic binary gene expression. We find that this type of gene expression is more favourable in the case of regulation by microRNAs as compared to the case of unregulated gene expression. The theoretical predictions relating to binary gene expression are experimentally testable.

q-bio.QM↗