arXiv subjects

Supratim Sengupta

Publications and source records attributed to Supratim Sengupta.

16 recordsLinked to original sources

arXiv2025

Bayesian tit-for-tat fosters cooperation in evolutionary stochastic games

Learning from experience is a key feature of decision-making in cognitively complex organisms. Strategic interactions involving Bayesian inferential strategies can enable us to better understand how evolving individual choices to be altruistic or selfish can affect collective outcomes in social dilemmas. Bayesian strategies are distinguished, from their reactive opponents, in their ability to modulate their actions in the light of new evidence. We investigate whether such strategies can be resilient against reactive strategies when actions not only determine the immediate payoff but can affect future payoffs by changing the state of the environment. We use stochastic games to mimic the change in environment in a manner that is conditioned on the players' actions. By considering three distinct rules governing transitions between a resource-rich and a resource-poor states, we ascertain the conditions under which Bayesian tit-for-tat strategy can resist being invaded by reactive strategies. We find that the Bayesian strategy is resilient against a large class of reactive strategies and is more effective in fostering cooperation leading to sustenance of the resource-rich state. However, the extent of success of the Bayesian strategies depends on the other strategies in the pool and the rule governing transition between the two different resource states.

physics.bio-ph↗

arXiv2023

Inferring to C or not to C: Evolutionary games with Bayesian inferential strategies

Strategies for sustaining cooperation and preventing exploitation by selfish agents in repeated games have mostly been restricted to Markovian strategies where the response of an agent depends on the actions in the previous round. Such strategies are characterized by lack of learning. However, learning from accumulated evidence over time and using the evidence to dynamically update our response is a key feature of living organisms. Bayesian inference provides a framework for such evidence-based learning mechanisms. It is therefore imperative to understand how strategies based on Bayesian learning fare in repeated games with Markovian strategies. Here, we consider a scenario where the Bayesian player uses the accumulated evidence of the opponent's actions over several rounds to continuously update her belief about the reactive opponent's strategy. The Bayesian player can then act on her inferred belief in different ways. By studying repeated Prisoner's dilemma games with such Bayesian inferential strategies, both in infinite and finite populations, we identify the conditions under which such strategies can be evolutionarily stable. We find that a Bayesian strategy that is less altruistic than the inferred belief about the opponent's strategy can outperform a larger set of reactive strategies, whereas one that is more generous than the inferred belief is more successful when the benefit-to-cost ratio of mutual cooperation is high. Our analysis reveals how learning the opponent's strategy through Bayesian inference, as opposed to utility maximization, can be beneficial in the long run, in preventing exploitation and eventual invasion by reactive strategies.

q-bio.PE↗

arXiv2018

Bribery Games on Interdependent Complex Networks

Bribe demands present a social conflict scenario where decisions have wide-ranging economic and ethical consequences. Nevertheless, such incidents occur daily in many countries across the globe. Harassment bribery constitute a significant sub-set of such bribery incidents where a government official demands a bribe for providing a service to a citizen legally entitled to it. We employ an evolutionary game-theoretic framework to analyse the evolution of corrupt and honest strategies in structured populations characterized by an interdependent complex network. The effects of changing network topology, average number of links and asymmetry in size of the citizen and officer population on the proliferation of incidents of bribery are explored. A complex network topology is found to be beneficial for the dominance of corrupt strategies over a larger region of phase space when compared with the outcome for a regular network, for equal citizen and officer population sizes. However, the extent of the advantage depends critically on the network degree and topology. A different trend is observed when there is a difference between the citizen and officer population sizes. Under those circumstances, increasing randomness of the underlying citizen network can be beneficial to the fixation of honest officers up to a certain value of the network degree. Our analysis reveals how the interplay between network topology, connectivity and strategy update rules can affect population level outcomes in such asymmetric games.

physics.soc-ph↗

arXiv2012

Stuttering Min oscillations within E. coli bacteria: A stochastic polymerization model

We have developed a 3D off-lattice stochastic polymerization model to study subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding, and fragmentation of MinD filaments due to MinE. Each of processivity, protection, and fragmentation reduces stuttering, speeds oscillations, and reduces MinD filament lengths. Neither processivity or tip-protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations are consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization in experimental conditions.

q-bio.SC↗

arXiv2007

Modeling partitioning of Min proteins between daughter cells after septation in Escherichia coli

Ongoing sub-cellular oscillation of Min proteins is required to block minicelling in E. coli. Experimentally, Min oscillations are seen in newly divided cells and no minicells are produced. In model Min systems many daughter cells do not oscillate following septation because of unequal partitioning of Min proteins between the daughter cells. Using the 3D model of Huang et al., we investigate the septation process in detail to determine the cause of the asymmetric partitioning of Min proteins between daughter cells. We find that this partitioning problem arises at certain phases of the MinD and MinE oscillations with respect to septal closure and it persists independently of parameter variation. At most 85% of the daughter cells exhibit Min oscillation following septation. Enhanced MinD binding at the static polar and dynamic septal regions, consistent with cardiolipin domains, does not substantially increase this fraction of oscillating daughters. We believe that this problem will be shared among all existing Min models and discuss possible biological mechanisms that may minimize partitioning errors of Min proteins following septation.

q-bio.SC↗

arXiv2007

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.

q-bio.PE↗

arXiv2005

Stochastic Resonance in Underdamped, Bistable Systems

We carry out a detailed numerical investigation of stochastic resonance in underdamped systems in the non-perturbative regime. We point out that an important distinction between stochastic resonance in overdamped and underdamped systems lies in the lack of dependence of the amplitude of the noise-averaged trajectory on the noise strength, in the latter case. We provide qualitative explanations for the observed behavior and show that signatures such as the initial decay and long-time oscillatory behaviour of the temporal correlation function and peaks in the noise and phase averaged power spectral density, clearly indicate the manifestation of resonant behaviour in noisy, underdamped bistable systems in the weak to moderate noise regime.

nlin.PS↗

arXiv2005

A Unified Model of Codon Reassignment in Alternative Genetic Codes

Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment, based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA for the reassigned codon, or the gain of function of an existing tRNA due to a mutation or a base modification. In the codon disappearance mechanism, the codon disappears from the genome during the period of reassignment. In the other mechanisms, the codon does not disappear. In the ambiguous intermediate mechanism, the gain precedes the loss; in the unassigned codon mechanism, the loss precedes the gain; and in the compensatory change mechanism, the loss and gain spread through the population simultaneously. We present simulations of the gain-loss model and demonstrate that all four mechanisms are possible. The frequencies of the different mechanisms are influenced by selection strengths, number of codons undergoing reassignment, directional mutation pressure and the possibility of selection for reduced genome size.

q-bio.PE↗

arXiv2003

Nonequilibrium Evolution of Correlation Functions: A Canonical Approach

We study nonequilibrium evolution in a self-interacting quantum field theory invariant under space translation only by using a canonical approach based on the recently developed Liouville-von Neumann formalism. The method is first used to obtain the correlation functions both in and beyond the Hartree approximation, for the quantum mechanical analog of the $ϕ^{4}$ model. The technique involves representing the Hamiltonian in a Fock basis of annihilation and creation operators. By separating it into a solvable Gaussian part involving quadratic terms and a perturbation of quartic terms, it is possible to find the improved vacuum state to any desired order. The correlation functions for the field theory are then investigated in the Hartree approximation and those beyond the Hartree approximation are obtained by finding the improved vacuum state corrected up to ${\cal O}(λ^2)$. These correlation functions take into account next-to-leading and next-to-next-to-leading order effects in the coupling constant. We also use the Heisenberg formalism to obtain the time evolution equations for the equal-time, connected correlation functions beyond the leading order. These equations are derived by including the connected 4-point functions in the hierarchy. The resulting coupled set of equations form a part of infinite hierarchy of coupled equations relating the various connected n-point functions. The connection with other approaches based on the path integral formalism is established and the physical implications of the set of equations are discussed with particular emphasis on thermalization.

hep-ph↗

arXiv2001

Stochastic Production Of Kink-Antikink Pairs In The Presence Of An Oscillating Background

We numerically investigate the production of kink-antikink pairs in a $(1+1)$ dimensional $ϕ^4$ field theory subject to white noise and periodic driving. The twin effects of noise and periodic driving acting in conjunction lead to considerable enhancement in the kink density compared to the thermal equilibrium value, for low dissipation coefficients and for a specific range of frequencies of the oscillating background. The dependence of the kink-density on the temperature of the heat bath, the amplitude of the oscillating background and value of the dissipation coefficient is also investigated. An interesting feature of our result is that kink-antikink production occurs even though the system always remains in the broken symmetry phase.

hep-ph↗

arXiv2001

Multiple-Scale Analysis and Renormalization of Quenched Second Order Phase Transitions

A quenched second order phase transition is modeled by an effective $Φ^4$-theory with a time-dependent Hamiltonian $\hat{H} (t)$, whose symmetry is broken spontaneously in time. The quantum field evolves out of equilibrium (nonequilibrium) during the phase transition as the density operator significantly deviates from $\hatρ (t) = e^{- β\hat{H} (t)}/Z_H$. The recently developed Liouville-von Neumann (LvN) method provides various quantum states for the phase transition in terms of a complex solution to the mean-field equation, which is equivalent to the Gaussian effective potential in the static case and to the time-dependent Hartree-Fock equation in the nonequilibrium case. Using the multiple scale perturbation theory (MSPT) we solve analytically the mean-field equation to the first order of coupling constant and find the quantum states during the quenched second order phase transition. We propose a renormalization scheme during the process of phase transition to regularize the divergences, which originate from the mode coupling between hard and hard modes or between the soft and hard modes. The effect of mode coupling is discussed.

hep-ph↗

arXiv2000

Electroweak Baryogenesis in a Cold Universe

We discuss the possibility of generating the baryon asymmetry of the Universe when the temperature of the Universe is much below the electroweak scale. In our model the evaporation of primordial black holes or the decay of massive particles re-heats the surrounding plasma to temperatures above the electroweak transition temperature leading to the restoration of electroweak symmetry locally. The symmetry is broken again spontaneously as the plasma cools and a baryon asymmetry is generated during the phase transition. This mechanism generates sufficient asymmetry for a second order electroweak phase transition. For a first order phase transition, sufficient asymmetry is generated if viscous effects slow down the heated plasma as it moves away from the black hole. In our scenario there is no wash-out of the asymmetry after the phase transition as the plasma rapidly cools to lower temperatures thereby shutting off the sphaleron processes.

hep-ph↗

arXiv1999

Resonant Production of Topological Defects

We describe a novel phenomenon in which vortices are produced due to resonant oscillations of a scalar field which is driven by a periodically varying temperature T, with T remaining much below the critical temperature $T_c$. Also, in a rapid heating of a localized region to a temperature {\it below} $T_c$, far separated vortex and antivortex can form. We compare our results with recent models of defect production during reheating after inflation. We also discuss possible experimental tests of our predictions of topological defect production {\it without} ever going through a phase transition.

hep-ph↗

arXiv1998

Simulation of Vortex-Antivortex Pair Production in a Phase Transition with Explicit Symettry Breaking

We carry out numerical simulation of the formation of U(1) global vortices in a first order phase transition in 2+1 dimensions in the presence of small explicit symmetry breaking. Bubbles of broken symmetry phase are randomly nucleated, which grow and coalesce. Vortices form at junctions of bubbles via standard Kibble mechanism as well as due to a new mechanism, recently proposed by us, where defect-antidefect pairs are produced due to field oscillations. In a simulation involving nucleation of 63 bubbles, with bias in phase distribution inside bubbles arising from explicit symmetry breaking, we find that not a single vortex/antivortex is produced via the Kibble mechanism, while the new mechanism leads to production of 104 vortices and antivortices. Even without biasing the phase distribution inside bubbles, the vortex production is completely dominated by this new mechanism, which accounts for the production of about 80% of the vortices and antivortices, remaining 20% being produced via the Kibble mechanism. We study the dependence of the effectiveness of the new mechanism on the magnitude of explicit symmetry breaking, as well as on the nucleation rate of bubbles. We also study the effect of damping on this mechanism and show that damping suppresses this mode of vortex production.

hep-ph↗

arXiv1997

Vortex-Antivortex Pair Production in a First Order Phase Transition

We carry out numerical simulation of a first order phase transition in 2+1 dimensions by randomly nucleating bubbles, and study the formation of global U(1) vortices. Bubbles grow and coalesce and vortices are formed at junctions of bubbles via standard Kibble mechanism as well as due to a new mechanism, recently proposed by us, where defect-antidefect pairs are produced due to field oscillations. We make a comparative study of the contribution of both of these mechanisms for vortex production. We find that, for high nucleation rate of bubbles, vortex-antivortex pairs produced via the new mechanism have overlapping configurations, and annihilate quickly; so only those vortices survive till late which are produced via the Kibble mechanism. However, for low nucleation rates, bubble collisions are energetic enough to lead to many well separated vortex-antivortex pairs being produced via the new mechanism. For example, in a simulation involving nucleation of 20 bubbles, a total of 14 non-overlapping vortices and antivortices formed via this new mechanism of pair creation (6 of them being very well separated), as compared to 6 vortices and antivortices produced via the Kibble mechanism. Our results show the possibility that in extremely energetic bubble collisions, such as those in the inflationary models of the early Universe, this new mechanism may drastically affect the defect production scenario.

hep-ph↗

arXiv1996

Defect-Antidefect pair production via field oscillations

We show that the mechanism of vortex-antivortex pair production via field oscillations, earlier proposed by two of us for systems with first order transitions in presence of explicit symmetry breaking, is in fact very generally applicable. We further argue that this mechanism applies to all sorts of topological defects (e.g. strings, monopoles, textures) and for second order transitions as well. We also show this explicitly by numerically simulating production of vortex-antivortex pairs by decay of bubble walls for a U(1) global theory in the absence of any explicit symmetry breaking.

hep-ph↗