arXiv subjects

Sayantan Mondal

Publications and source records attributed to Sayantan Mondal.

At least 19 recordsLinked to original sources

arXiv2026

Chirality-Driven Hierarchical Phase Morphologies in Self-Assembled Biaxial Amphiphiles

Chirality plays a crucial role in determining the structure of many systems in nature. Twisted or helical aggregates as a consequence of self-assembly can be seen in many biological and synthetic materials. Despite extensive theoretical and experimental efforts, how molecular-scale chirality gives rise to complex twisted morphologies in amphiphiles still remains unexplored. Here we study the interplay between molecular hydrophobicity, shape anisotropy and chirality using molecular dynamics simulation. Variation of relative molecular concentration and intrinsic chirality of molecules drive a sequence of twisted liquid crystalline variants of lamellar, cylindrical and vesicular phases. These structures emerge spontaneously under equilibrium conditions and are characterized by orientational correlation functions. We demonstrate that variation in molecular chirality gives rise to the development of hierarchical chiral order within the system. Further increment of chirality competes with hydrophobic interactions, leading to morphological instabilities. Our findings establish a direct link between microscopic chirality and mesoscale structure formation and their instabilities. Qualitative comparison of liquidity and pitch of the observed phase morphologies with the amount of chirality has been reported.

cond-mat.soft↗

arXiv2026

Velocity Resetting of Inertial Run-and-Tumble Particles in Non-Newtonian Media: Velocity Distribution, Diffusion and First-Passage Time

We study the dynamics of an athermal inertial run-and-tumble particle moving through a non-Newtonian medium in $d=1$, where the particle's velocity $v$ is reset to zero at a constant rate $r$. The drag force from the non-Newtonian medium is represented by a nonlinear velocity-dependent function $g(v)$. The run-and-tumble dynamics is modeled by a symmetric dichotomous noise with strength $Σ$ and flipping rate $λ$. We begin with the Fokker-Planck (FP) equation for the velocity distribution $P(v,t)$ of the particle. In the presence of resetting, however, the FP equation does not yield a closed-form solution even in the steady state. We therefore compute the steady-state velocity distribution $P_s(v)$ directly from particle trajectories and compare it with the numerical solution of the FP equation, finding good agreement between the two approaches. For sufficiently large $r$, $P_s(v)$ shows a cusp-like singularity at $v=0$ and the particles display diffusive motion at long times. The effective diffusion coefficient $D_{\mathrm{eff}}$ decays as $r^{-2}$ in the large-$r$ regime. These results hold irrespective of the specific form of $g(v)$ and the values of $λ$ and $Σ$. However, the mean first-passage time exhibits a strong dependence on the nature of the medium as the resetting rate $r$ is varied. In shear-thickening media, there exists an optimal resetting rate that minimizes the time required to reach the target velocity $v_t$. In contrast, no such optimal resetting rate is observed in shear-thinning media.

cond-mat.soft↗

arXiv2026

Derivation and Analysis of Amplitude Equation for Generalized AMB+ in Presence of Chemical Reaction

We derive and analyze the amplitude equation for the roll patterns in case of generalized Active Model B+ (AMB+) in the presence of chemical reactions. The generalized AMB+ differs from the original AMB+ introduced by Tjhung \textit{et al.} [E. Tjhung \textit{et al.}, Phys. Rev. X \textbf{8}, 031080 (2018)] by the addition of a quadratic term, $gϕ^2$, in the expression for the equilibrium part of the current. Also, the model includes a rotation-free active current of strength $λ$ and a rotational current of strength $ξ$. The inclusion of a chemical reaction with rate $Γ$ removes the conservation constraint and introduces a preferred wavenumber that governs the pattern formation below a critical reaction rate $Γ_c$. We argue for the analytical form of the amplitude equation based on symmetry considerations and explicitly derived it using multiscale analysis. By taking different limits of $g$, $λ$, and $ξ$, we recover amplitude equations for several well-known physical models as special cases and determine the nature transitions close to the onset of instability. We find that for $g = 0$, the transition is always supercritical, whereas for $g \ne 0$, the transition between the supercritical and subcritical regimes depends sensitively on the model parameters. Further, we derive the condition for the \textit{Eckhaus instability} from the stability analysis of the amplitude equation as well as from the phase diffusion equation, and find that it is independent of $g$.

cond-mat.stat-mech↗

arXiv2025

Velocity Distribution and Diffusion of an Athermal Inertial Run-and-Tumble Particle in a Shear-Thickening Medium

We study the dynamics of an athermal inertial run-and-tumble particle moving in a shear-thickening medium in $d=1$. The viscosity of the medium is represented by a nonlinear function $f(v)\sim\tan(v)$, while a symmetric dichotomous noise of strength $Σ$ and flipping rate $λ$ models the activity of the particle. Starting from the Fokker-Planck~(FP) equation for the time-dependent probability distribution $W_{\pmΣ}(v, t)$ of the particle's velocity $v$ at time $t$ and the active force is $\pmΣ$, we analytically derive the steady-state velocity distribution function $W_s(v)$ and a quadrature expression for the effective diffusion coefficient $D_{\rm eff}$. For a fixed $Σ$, $W_s(v)$ undergoes multiple transitions with varying $λ$, and we have identified the corresponding transition points. We then numerically compute $W_s(v)$, the mean-squared velocity $\langle v^2\rangle(t)$, and the diffusion coefficient $D_{\rm eff}$, all of which show excellent agreement with the analytical results in the steady-state. Finally, we test the robustness of the transitions in $W_s(v)$ by considering an alternative $f(v)$ function that also capture the shear-thickening behavior of the medium.

cond-mat.stat-mech↗

arXiv2025

Surface Induced Frustration of Inherent Dipolar Order in Nanoconfined Water

Surface effects could play a dominant role in modifying the natural liquid order. In some cases, the effects of the surface interactions can propagate inwards, and even can interfere with a similar propagation from opposite surfaces. This can be particularly evident in liquid water under nano-confinement. The large dipolar cross-correlations among distinct molecules that give rise to the unusually large dielectric constant of water (and in turn owe their origin to the extended hydrogen bond (HB) network) can get perturbed by surfaces. The perturbation can propagate inwards and then interfere with the one from the opposite surface if confinement is only a few layers wide. This can give rise to short-to-intermediate range solvent-mediated interaction between two surfaces. Here we study the effects of such interactions on the dielectric constant of nano-confined liquids, not just water but also ordering at protein surfaces. The surfaces work at two levels: (i) induce orientational realignment, and (ii) alter the cross-correlations between water molecules. Molecular dynamics simulations and statistical analyses are used to address these aspects in confinement of slit pores, nano tube/cylinder, and nano sphere. In addition, we consider the hydration layers of multiple proteins with vastly different structural features. These studies give us a measure of the extent or the length scale of cross-correlations between dipole moments of water molecules. We find an interesting orientational arrangement in the protein hydration layers, giving rise to long-range molecular cross-correlations. To decouple the effect of HB from the effect of geometry, we additionally study acetonitrile under nanoconfinement. Importantly, while a protein's interior is characterized by a small dielectric constant, the dipole moment of a peptide bond is large, and thus susceptible to fluctuations in water.

cond-mat.soft↗

arXiv2025

Multipurpose in situ cell design for 3D X-ray imaging of electrochemical processes

We present the design of a modular multipurpose cell for monitoring the degradation of materials in extreme environments. This cell decouples the reference electrode from the working and counter electrodes, permitting precise electrochemical control and measurement reliability. The design is compatible with 4th generation synchrotron light sources, and its emphasis on modularity facilitates adaptation to different beamlines, where there may be variations in sample stage requirements and X-ray imaging techniques. Experimental tests with the novel design demonstrate its support of real-time corrosion and hydrogen embrittlement measurements under both Bragg Coherent Diffraction Imaging (BCDI) and Dark Field X-ray Microscopy (DFXM) configurations.

physics.ins-det↗

arXiv2025

Role of structural biaxiality on the phase behaviour of chiral liquid crystals

We report a computer simulation study on the effect of molecular structural biaxiality in the phase formation of chiral molecules. In this study, we have done coarse-grained modeling to observe self-assembled phase behavior. In our molecular dynamics simulation study we varied both the chiral interaction strength and molecular biaxiality. Uniaxial molecules give rise to cholesteric phase, blue phase whereas molecular biaxiality favours cholesteric phase. At higher chirality, small chiral domains are formed creating twisted cylindrical networks with each cylinder having elliptical cross-sections instead of circular nature as found in uniaxial systems. The value of cholesteric pitch decreases when chirality and molecular biaxiality becomes higher. Coaction of biaxiality and chirality is crucial for fabricating liquid crystal materials with optical properties suitable for displays, sensors and chiral photonic devices.

cond-mat.soft↗

arXiv2025

Phase Separation in Active Binary Mixtures With Chemical Reaction

We study motility-induced phase separation~(MIPS) in active AB binary mixtures undergoing the chemical reaction $A \rightleftharpoons B$. Starting from the evolution equations for the density fields $ρ_i(\vec r, t)$ describing MIPS, we phenomenologically incorporate the effects of the reaction through the reaction rate $Γ$ into the equations. The steady-state domain morphologies depend on $Γ$ and the relative activity of the species, $Δ$. For a sufficiently large $Γ$ and $Δ\ne 1$, the more active component of the mixture forms a droplet morphology. We characterize the morphology of domains by calculating the equal-time correlation function $C(r, t)$ and the structure factor $S(k, t)$, exhibiting scaling violation. The average domain size, $L(t)$, follows a diffusive growth as $L(t)\sim t^{1/3}$ before reaching the steady state domain size, $L_{\rm ss}$. Additionally, $L_{\rm ss}$ shows the scaling relation $L_{\rm ss}\simΓ^{-1/4}$, independent of $Δ$.

cond-mat.soft↗

arXiv2025

Velocity Distribution and Diffusion of an Athermal Inertial Run-and-Tumble Particle in a Shear-Thinning Medium

We study the dynamics of an athermal inertial active particle moving in a shear-thinning medium in $d=1$. The viscosity of the medium is modeled using a Coulomb-tanh function, while the activity is represented by an asymmetric dichotomous noise with strengths $-Δ$ and $μΔ$, transitioning between these states at a rate $λ$. Starting from the Fokker-Planck~(FP) equation for the time-dependent probability distributions $P(v,-Δ,t)$ and $P(v,μΔ,t)$ of the particle's velocity $v$ at time $t$, moving under the influence of active forces $-Δ$ and $μΔ$ respectively, we analytically derive the steady-state velocity distribution function $P_s(v)$, explicitly dependent on $μ$. Also, we obtain a quadrature expression for the effective diffusion coefficient $D_e$ for the symmetric active force case~($μ=1$). For a given $Δ$ and $μ$, we show that $P_s(v)$ exhibits multiple transitions as $λ$ is varied. Subsequently, we numerically compute $P_s(v)$, the mean-squared velocity $\langle v^2\rangle(t)$, and the diffusion coefficient $D_e$ by solving the particle's equation of motion, all of which show excellent agreement with the analytical results in the steady-state. Finally, we examine the universal nature of the transitions in $P_s(v)$ by considering an alternative functional form of medium's viscosity that also capture the shear-thinning behavior.

cond-mat.stat-mech↗

arXiv2024

Unique Dielectric Behaviour and Anomalies in Nanoconfined Liquids

The dielectric properties of a bulk dipolar liquid have been subjects of intense interest during the past decades. A surprising result was the discovery of a strong wavenumber dependence in the bulk homogeneous state. Such behaviour seems to suggest the possibility of a strong system size dependence of the dielectric constant (DC) of a nanoconfined liquid, although details have been revealed only recently. Dielectric properties of nanoconfined water indeed show marked sensitivity not only to the size and shape (dielectric boundaries) of confinement but also to the nature of surface-water interactions. For geometries widely studied, namely, water confined in a narrow slit, nanocylinder, and nanospherical cavity, the asymptotic approach to the bulk value of the DC with the increase in confinement size, is found to be surprisingly slow. This seems to imply the appearance of a dipolar cross-correlation length, much larger than the molecular length-scale of water. In narrow slit and narrow cylinder, the dielectric function becomes both inhomogeneous and anisotropic, and the longitudinal and transverse components display markedly different system size dependencies. This sensitivity can be traced back to the dependence of the DC on the ratio of the mean square dipole moment fluctuation to the volume of the system. The observed sensitivity of collective dipole moment fluctuations to the length scale of confinement points to the possibility of using DC to estimate orientational correlation length scale which has been an elusive quantity. Furthermore, the determination of volume also requires special consideration when the system size is in nanoscale. We discuss these and several other interesting issues along with several applications that have emerged in recent years.

cond-mat.soft↗

arXiv2024

Domain Growth Kinetics in Active Binary Mixtures

We study motility-induced phase separation (MIPS) in symmetric and asymmetric active binary mixtures. We start with the coarse-grained run-and-tumble bacterial model that provides evolution equations for the density fields $ρ_i(\vec r, t)$. Next, we study the phase separation dynamics by solving the evolution equations using the Euler discretization technique. We characterize the morphology of domains by calculating the equal-time correlation function $C(r, t)$ and the structure factor $S(k, t)$, both of which show dynamical scaling. The form of the scaling functions depends on the mixture composition and the relative activity of the species, $Δ$. For $k\rightarrow\infty$, $S(k, t)$ follows Porod's law: $S(k, t)\sim k^{-(d+1)}$ and the average domain size $L(t)$ shows a diffusive growth as $L(t)\sim t^{1/3}$ for all mixtures.

cond-mat.soft↗

arXiv2021

Emergence of Dynamical Coherence in a Driven One-dimensional Interacting Rotor Model

In order to understand the dynamics of active matter, we examine a minimalistic model where interacting spins on a one-dimensional lattice are driven by a self-propelled spin at the centre with a fixed rotational velocity $(ω_{0})$. The other spins execute rotational Brownian motion by following the Shore-Zwanzig model of rotational dynamics. The simplicity of the model allows us to inquire about several relevant microscopic quantities. The continuous 'active' torque on the central spin is propagated through nearest neighbour interactions with a uniform coupling parameter, J. We have found a bounded region in the J-$ω_{0}$ plane where the system exhibits 'active matter like behaviour'. Interestingly, in the limits of large J and $ω_{0}$, we observe a 'slipping behaviour'. The site specific average rotational velocity of the spin, as one moves away from the central spin exhibits a nearly exponential decay with distance, allowing the definition of a correlation length $(ξ)$ which grows rapidly with an increase of the coupling (J) between the spins. Site specific average velocity exhibits a change from a single exponential to biexponential decay pattern as the system enters the active region of the phase diagram, accompanied by a non-monotonic behavior of the correlation length. We conclude that a macroscopic coherent state can emerge in the presence of a small concentration of active molecules. We discuss experimental relevance of our results.

cond-mat.stat-mech↗

arXiv2021

Effect of vibronic relaxation in fluorescence resonance energy transfer: An exact analytical solution

Fluorescence resonance energy transfer (FRET) is widely used as a 'spectroscopic ruler' to measure fluctuations in macromolecules because of the strong dependence of the rate on the separation (R) between the donor (D) and acceptor (A). However, the well-known Forster rate expression that predicts an $R^{-6}$ dependence, is limited by several approximations. Notable among them is the neglect of the vibronic relaxation in the reactant (donor) and product (acceptor) manifolds. Vibronic relaxation can play an important role when the energy transfer rate is faster than the vibronic relaxation rate. Under such conditions, donor to acceptor energy transfer can occur from the excited vibronic states. This phenomenon is not captured by the usual formulation based on the overlap of donor emission and acceptor absorption spectra. Here, we attempt to eliminate this lacuna, by allowing relaxation in the vibronic energy levels and adopting a relaxation model to account for vibronic cascading down in the donor manifold. We develop a Green's function based generalized formalism and provide an exact solution for the excited state population relaxation and the rate of energy transfer in the presence of vibronic relaxation. We find and verify that the neglect of vibronic relaxations can significantly alter the energy transfer rate and overestimates the distance between D and A.

physics.chem-ph↗

arXiv2020

Origin of Multiple Infection Waves in a Pandemic: Effects of Inherent Susceptibility and External Infectivity Distributions

Two factors that are often ignored but could play a crucial role in the progression of an infectious disease are the distributions of inherent susceptibility ($σ_{inh}$) and external infectivity ($ι_{ext}$), in a given population. While the former is determined by the immunity of an individual towards a disease, the latter depends on the duration of exposure to the infection. We model the spatio-temporal propagation of a pandemic using a generalized SIR (Susceptible-Infected-Removed) model by introducing the susceptibility and infectivity distributions to understand their combined effects, which appear to remain inadequately addressed till date. We consider the coupling between $σ_{inh}$ and $ι_{ext}$ through a new Critical Infection Parameter (CIP) ($γ_c$). We find that the neglect of these distributions, as in the naive SIR model, results in an overestimation of the amount of infection in a population, which leads to incorrect (higher) estimates of the infections required to achieve the herd immunity threshold. Additionally, we include the effects of seeding of infection in a population by long-range migration. We solve the resulting master equations by performing Kinetic Monte Carlo Cellular Automata (KMC-CA) simulations. Importantly, our simulations can reproduce the multiple infection peak scenario of a pandemic. The latent interactions between disease migration and the distributions of susceptibility and infectivity can render the progression a character vastly different from the naive SIR model. In particular, inclusion of these additional features renders the problem a character of a living percolating system where the disease cluster survives by migrating from region to region.

q-bio.PE↗

arXiv2020

Attainment of Herd Immunity: Mathematical Modelling of Survival Rate

We study the influence of the rate of the attainment of herd immunity (HI), in the absence of an approved vaccine, on the vulnerable population. We essentially ask the question: how hard the evolution towards the desired herd immunity could be on the life of the vulnerables? We employ mathematical modelling (chemical network theory) and cellular automata based computer simulations to study the human cost of an epidemic spread and an effective strategy to introduce HI. Implementation of different strategies to counter the spread of the disease requires a certain degree of quantitative understanding of the time dependence of the outcome. In this paper, our main objective is to gather understanding of the dependence of outcome on the rate of progress of HI. We generalize the celebrated SIR model (Susceptible-Infected-Removed) by compartmentalizing the susceptible population into two categories- (i) vulnerables and (ii) resilients, and study dynamical evolution of the disease progression. We achieve such a classification by employing different rates of recovery of vulnerables vis-a-vis resilients. We obtain the relative fatality of these two sub-categories as a function of the percentages of the vulnerable and resilient population, and the complex dependence on the rate of attainment of herd immunity. Our results quantify the adverse effects on the recovery rates of vulnerables in the course of attaining the herd immunity. We find the important result that a slower attainment of the HI is relatively less fatal. However, a slower progress towards HI could be complicated by many intervening factors.

q-bio.PE↗

arXiv2020

Dynamical Theory and Cellular Automata Simulations of Pandemic Spread: Understanding Different Temporal Patterns of Infections

Here we propose and implement a generalized mathematical model to find the time evolution of population in infectious diseases and apply the model to study the recent COVID-19 pandemic. Our model at the core is a non-local generalization of the widely used Kermack-McKendrick(KM) model where the susceptible(S) population evolves into two other categories, namely infectives(I) and removed(R). This is the well-known SIR model in which we further divide both S and I into high and low risk categories. We first formulate a set of non-local dynamical equations for the time evolution of distinct population distributions under this categorization in an attempt to describe the general scenario of infectious disease progression. We then solve the non-linear coupled differential equations-(i) numerically by the method of propagation, and (ii) a more flexible and versatile cellular automata (CA) simulation which provides a coarse-grained description of the generalized non-local model. In order to account for multiple factors such as role of spreaders before containment, we introduce a time dependent rate which appears to be essential to explain the sudden spikes before the plateau observed in many cases (for example like China). We demonstrate how this generalized approach allows us to handle the effects of (i) time-dependence of the rate-constants of spread, (ii) different population density, (iii) the age ratio, (iv) quarantine, (v) lockdown, and (vi) social distancing. Our study allows us to make certain predictions regarding the nature of spread with respect to several external parameters, treated as control variables. Analysis of the model clearly shows that due to the strong heterogeneity in the epidemic process originating from the distribution of initial infectives, the theory must be local in character but at the same time connect to a global perspective.

q-bio.PE↗

arXiv2019

Ice-water Interface: Correlation between Structure and Dynamics

To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, the interface. The deviation from bulk values of structural and dynamical quantities at the interface are obtained by computer simulations. Water molecules are found to get exchanged between the ice-like and water-like domains of the interface with a time scale of the order of ~10 ps. To investigate the effect of interfaces in general, we study three other systems, namely (i) water between two hydrophobic nano-slabs, (ii) water at protein and (iii) DNA surfaces. In all these systems, we find that the difference from bulk properties become negligible beyond ~1 nm, with structural features converging to bulk values faster than the dynamical properties. Even in the case of the latter, we find that single-particle and collective properties behave differently. The approach to bulk values is rapid except for collective shell-dipole moments. We present a new insightful characterization of the surfaces by establishing a quantitative correlation between tetrahedrality order parameter (q_td) and dynamics by diffusion (D) and angular jumps. In the ice-water system, we find that the variation of qtd, as we move from solid to the liquid phase, correlated well with D. The correlation is found to be present in all the interfaces studied. Our results can be used to explain the experimental outcomes of the likes of dielectric relaxation and solvation dynamics.

cond-mat.soft↗

arXiv2019

Altered Dielectric Behaviour, Structure and Dynamics of Nanoconfined Dipolar Liquids: Signatures of Enhanced Cooperativity

Spherical confinement can alter the properties of a dipolar fluid in several different ways. In an atomistic molecular dynamics simulation study of two different dipolar liquids (SPC/E water and a model Stockmayer fluid) confined to nanocavities of different radii ranging from Rc=1nm to 4nm, we find that the Kirkwood correlation factor remains surprisingly small in water, but not so in model Stockmayer liquid. This gives rise to an anomalous ultrafast relaxation of the total dipole moment time correlation function (DMTCF). The static dielectric constant of water under nanoconfinement (computed by employing Clausius-Mossotti equation, the only exact relation) exhibits a strong dependence on the size of the nanocavity with a remarkably slow convergence to the bulk value. Interestingly, the value of the volume becomes ambiguous in this nanoworld. It is determined by the liquid-surface interaction potential and is to be treated with care because of the sensitivity of the Clausius-Mossotti equation to the volume of the nanosphere. We discover that the DMTCF for confined water exhibit a bimodal 1/f noise power spectrum. We also comment on the applicability of certain theoretical formalisms that become dubious in the nanoworld.

cond-mat.soft↗