arXiv subjects

Souvik Mondal

Publications and source records attributed to Souvik Mondal.

13 recordsLinked to original sources

arXiv2026

Electromagnetic filament coalescence as magnetic island merging with diamagnetic effects

We investigate the nonlinear coalescence of two current-carrying ELM filaments using a three-dimensional electromagnetic fluid model. In the flat-density limit, the coalescence exhibits magnetic island-like reconnection, characterized by X-point formation, current-sheet development, and Sweet-Parker-like resistive scaling. Introducing a blob-like density perturbation modifies the reconnection dynamics: while the peak reconnection rate remains nearly unchanged for weak perturbations, it decreases and is increasingly delayed for larger density amplitudes. Analysis of the induction equation reveals a transition from resistive to increasingly density-dependent advective dynamics. Finite density perturbations also enhance the post-compression rebound, or sloshing, of the filaments. The sloshing amplitude increases with the density-gradient pressure force, establishing density perturbation as an additional control parameter for both reconnection and filament sloshing. These results highlight the coupled electromagnetic and pressure-driven dynamics governing the nonlinear evolution of ELM filaments in the tokamak edge.

physics.plasm-ph↗

arXiv2026

Nonlinear Dynamics of Current-Carrying ELM Filaments: Spiral Vorticity, Rotation, and Velocity Suppression

In this work, we investigate the nonlinear dynamics of isolated current-carrying edge-localized mode (ELM) filaments using a reduced electromagnetic fluid model in slab geometry. Numerical simulations show that unidirectional parallel current significantly suppresses radial filament velocity and reduces the outward propagation velocity by weakening the curvature-driven interchange force. The reduction in radial velocity is found to follow a modified scaling relation, demonstrating that increasing current progressively weakens outward filament propagation. Analysis of the vorticity equation shows that the electromagnetic current source changes from a dipolar structure to a remarkable spiral pattern, and overcomes the conventional curvature drive in the nonlinear phase. This current-driven source directly imprints its topology on the vorticity field, resulting in spiral vorticity, enhanced angular momentum, increased rotational energy, and localized shear layers. The filament therefore undergoes a transition from a conventional propagating state to a rotationally self-organized electromagnetic structure. These findings demonstrate that parallel current acts as an effective electromagnetic vorticity source and provides new insight into the nonlinear dynamics of ELM filaments in tokamak edge plasmas.

physics.plasm-ph↗

arXiv2026

From Enhanced Sampling to Human-Readable Representations of Protein Dynamics

Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of timescales and the complexity of collective motions. Enhanced sampling methods overcome timescale limitations of conventional molecular dynamics, yet their effectiveness depends on the choice of collective variables (CVs), which are often difficult to define and may lack physical interpretability. In particular, collective variables derived from machine learning or collective vibrational modes can efficiently capture slow dynamics but are not easily mapped onto intuitive structural descriptors. Here, we present a fully automated framework that transforms enhanced sampling trajectories into human-readable representations of protein dynamics. Our approach combines enhanced sampling along CVs derived from frequency-selective anharmonic mode analysis with a post hoc analysis of biased trajectories using weighted dynamic cross-correlation matrices. From these, we identify residue pairs and domains exhibiting correlated and anti-correlated motions, yielding simple domain-domain distances that serve as physically interpretable CVs. We apply this method to five proteins, including KRAS and HIV-1 protease, and show that it consistently identifies biologically relevant domains and motions without prior system-specific knowledge. Projection onto these distances produces free energy surfaces that reproduce known conformational states with low statistical uncertainty while maximizing independent dynamical information. This workflow enables systematic recasting of complex CVs into simple geometric descriptors without loss of essential dynamics. Its generality and automation make it broadly applicable for interpreting enhanced sampling simulations and generating interpretable conformational ensembles for integration with emerging machine learning approaches.

cond-mat.stat-mech↗

arXiv2026

Finite Ion Temperature Effects on the Merging of Current-Carrying ELM Filaments in the edge region of a tokamak

Edge-localized-mode (ELM) filaments are crucial for cross-field transport at the tokamak edge; yet, their dynamics are often analyzed using the cold-ion approximation, despite experimental data indicating that Ti~Te . This study employs a normalized three-dimensional fluid model to investigate the influence of finite ion temperature on the dynamics of unidirectional current-carrying ELM-like filaments. We demonstrate that increasing ion temperature substantially alters filament propagation and interaction, resulting in a delay of filament merging despite an increase in total kinetic energy due to a stronger pressure-gradient drive. The examination of single-filament dynamics indicates that finite ion temperature generates asymmetric potential structures, strong poloidal flows, and persistent rotational motion, which channel kinetic energy from radial propagation into vortical dynamics. A comprehensive examination of the ion-to-electron temperature ratio reveals a distinct transition from radially dominated to rotation-dominated behavior as ion temperature increases. These results provide a unified physical explanation for reduced radial transport and delayed merging in the warm-ion domain, emphasizing the necessity of incorporating ion temperature effects in the modeling of ELM filament dynamics and edge plasma transport.

physics.plasm-ph↗

arXiv2025

All optical chaos synchronization between nonidentical optomechanical cavities

Optomechanical cavities, with nonlinear photon-phonon interactions, offer a more compact approach to chaos generation than conventional feedback-based optical systems. However, proper study on chaos synchronization of two optomechanical cavities connected by optical means is still unexplored. In this work, we theoretically investigate all-optical complete synchronization between unidirectionally coupled optomechanical cavities in the master-slave configuration. Traditionally, achieving complete synchronization in nonlinear coupled oscillators and in optical systems necessitates identical systems. Our findings, which arise naturally from the fundamental mathematical properties of optomechanical cavities, demonstrate that parameter heterogeneity can, in fact, not only enable complete synchronization but make it stable.

physics.optics↗

arXiv2025

Fast Sampling of Protein Conformational Dynamics

Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed compared to state-of-the-art protein structure prediction. Molecular simulations provide unique opportunities to study protein dynamics, but the timescales associated with conformational changes generate substantial challenges. Enhanced sampling algorithms with collective variables can greatly reduce the computational cost of sampling slow processes. However, defining collective variables suitable to enhance sampling of protein conformational transitions is non-trivial. Low-frequency vibrations have long been considered as promising candidates for collective variable but their identification so far relied on assumptions inherently invalid at low frequencies. We recently introduced an analysis of molecular vibrations that does not rely on such approximations and remains accurate at low frequencies. Here, we modified this approach to efficiently isolate low-frequency vibrations in proteins and applied it to a set of five proteins of varying complexity. We demonstrate that our approach is not only highly reproducible but results in collective variables that consistently enhance sampling of protein conformational transitions and associated free energy surfaces on timescales compatible with high throughput applications. This enables the efficient generation of protein conformational ensembles, which will be key for future prediction algorithms aiming beyond static protein structures.

cond-mat.stat-mech↗

arXiv2025

High-Throughput Computation of Anharmonic Low-Frequency Protein Vibrations

At room temperature, low frequency vibrations at far-infrared frequencies are thermally excited ($k_B T > h ν$) and not restricted to harmonic fluctuations around a single potential energy minimum. For folded proteins, these intrinsically anharmonic vibrations can contain information on slow conformational transitions. Recently, we have developed FREquency-SElective ANharmonic (FRESEAN) mode analysis, a method based on time correlation functions that isolates low-frequency vibrational motions from molecular dynamics simulation trajectories without relying on harmonic approximations. We recently showed that low-frequency vibrations obtained from FRESEAN mode analysis are effective collective variables in enhanced sampling simulations of conformational ensembles. However, FRESEAN mode analysis is based on velocity time correlations between all degrees of freedom, which creates computational challenges for large biomolecules. To facilitate future applications, we demonstrate here how coarse-graining of all-atom simulation trajectories can be combined with FRESEAN mode analysis to extract information on low-frequency vibrations at minimal computational cost.

cond-mat.stat-mech↗

arXiv2024

Merging dynamics of plasma blobs in the Scrape-off Layer of a tokamak

The emergence and merging of high-density coherent structures - plasma blobs - is a recurrent phenomenon in the Scrape-off layer (SOL) of a tokamak plasma that has a significant impact on the rate of convective transport in that region. We report on a model study of the merging of two electromagnetically interacting blobs in a high beta plasma. Our detailed numerical simulations show that the merging process is akin to the coalescence instability between two magnetic islands but with important differences due to the density perturbation. The blobs are found to rotate about each other during merging and the merging occurs with an acceleration in the poloidal direction that is directly proportional to the square of the current density of the blobs and inversely proportional to its density. The separation distance between two high current density blobs is also seen to oscillate indicating a sloshing behavior.

physics.plasm-ph↗

arXiv2024

Chaotic dynamics under the influence of synthetic magnetic field in optomechanical system

The optomechanical systems produce chaotic behaviour due to nonlinear interaction between photons and phonons, and the same systems are used to understand the synthetic fields as well. Here, we report on the study of chaotic behaviour in the presence of a phononic synthetic magnetic field in a closed loop configuration consisting of a single optical mode and two mechanical modes. The modulation phase of the mechanical coupling between the two mechanical modes plays a critical role in determining the mechanical and optical intensity dynamics in the nonlinear regime. Our study shows the dark mode breaking effect in the presence of a synthetic magnetic field, which brings about a complex way of mechanical energy exchange that causes the cavity field to alternate between chaotic and regular behaviour periodically in temporal domain. However in the stronger nonlinear regime the temporal dynamics demonstrate predominantly chaotic behaviour. Besides, with the advent of advanced fabrication technologies, this study holds promises in developing phase tunable integrated low-power chaotic light sources to support efficient optical secure communication systems.

physics.optics↗

arXiv2024

Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations

We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on timescales faster than conformational transitions but describe a path of least resistance towards structural change. A key challenge is that harmonic approximations are ill-suited to characterize these vibrations, which are observed at far-infrared frequencies and are easily excited by thermal collisions at room temperature. Here, we approached this problem with a frequency-selective anharmonic (FRESEAN) mode analysis that does not rely on harmonic approximations and successfully isolates anharmonic low-frequency vibrations from short molecular dynamics simulation trajectories. We applied FRESEAN mode analysis to simulations of alanine dipeptide, a common test system for enhanced sampling simulation protocols, and compare the performance of isolated low-frequency vibrations to conventional user-defined collective variables (here backbone dihedral angles) in enhanced sampling simulations. The comparison shows that enhanced sampling along anharmonic low-frequency vibrations not only reproduces known conformational dynamics but can even further improve sampling of slow transitions compared to user-defined collective variables. Notably, free energy surfaces spanned by low-frequency anharmonic vibrational modes exhibit lower barriers associated with conformational transitions relative to representations in backbone dihedral space. We thus conclude that anharmonic low-frequency vibrations provide a promising path for highly effective and fully automated enhanced sampling simulations of conformational dynamics in biomolecules.

cond-mat.stat-mech↗

arXiv2023

Exceptional point induced quantum phase synchronization and entanglement dynamics in mechanically coupled gain-loss oscillators

The optomechanical cavity (OMC) system has been a paradigm in the manifestation of continuous variable quantum information over the past decade. This paper investigates how quantum phase synchronization relates to bipartite Gaussian entanglement in coupled gain-loss mechanical oscillators, where the gain and loss rates are engineered by driving the cavity with blue and red detuned lasers, respectively. We examine the role of exceptional point in a deterministic way of producing self-sustained oscillations that induce robust quantum correlations among quadrature fluctuations of the oscillators. Particularly, steady phase synchronization dynamics along with the entanglement phenomena are observed in the effective weak coupling regime above a critical driving power. These phenomena are further verified by observing the mechanical squeezing and phase space rotations of the Wigner distributions. Additionally, we discuss how the oscillators frequency mismatches and decoherence due to thermal phonons impact the system dynamics. These findings hold promise for applications in phonon-based quantum communication and information processing.

quant-ph↗

arXiv2023

Controllable optical sideband generation by breaking mechanical Parity-Time symmetry

The interaction between light and mechanical vibrations in a cavity is often exploited to produce higher order sidebands (HOS) /combs, which are used in optical communication networks, spectroscopy, and others. Although a considerable study of optomechanically induced HOS has been done, its proper control and manipulation using only continuous wave (CW) laser drive are still to be explored. Here, we employed mechanical Parity-Time (PT) Symmetric structure with optically induced gain and loss. It has allowed us to manipulate the flow of mechanical energies (phonons) between the cavities, which has consequences on the optical response of the cavities. Based on our numerical investigations, we found that the higher order optical sidebands start to emerge by breaking PT symmetry. We precisely controlled the number of higher order sideband lines by adjusting the coupling rate between the cavities with fixed drive power. In addition, we observe that the Exceptional Point (EP) induces the formation of two synchronized higher order optical sideband spectra, which opens a promising EP based platform towards realization of optical readout of various mechanical synchronization phenomena, memory applications, sensing, synchronization of remote clock time and others.

physics.optics↗

arXiv2016

Nonequilibrium steady states in a closed inhomogeneous asymmetric exclusion process with particle nonconservation

We study asymmetric exclusion processes (TASEP) on a nonuniform one-dimensional ring consisting of two segments having unequal hopping rates, or {\em defects}. We allow weak particle nonconservation via Langmuir kinetics (LK), that are parameterised by generic unequal attachment and detachment rates. For an extended defect, in the thermodynamic limit the system generically displays inhomogeneous density profiles in the steady state - the faster segment is either in a phase with spatially varying density having no density discontinuity, or a phase with a discontinuous density changes. Nonequilibrium phase transitions between them are controlled by the inhomogeneity and LK. The slower segment displays only macroscopically uniform bulk density profiles in the steady states, reminiscent of the maximal current phase of TASEP but with a bulk density generally different from half. With a point defect, there are low and high density spatially uniform phases as well, in addition to the inhomogeneous density profiles observed for an extended defect. In all the cases, it is argued that the the mean particle density in the steady state is controlled only by the ratio of the LK attachment and detachment rates.

cond-mat.stat-mech↗