arXiv subjects

Rakesh Das

Publications and source records attributed to Rakesh Das.

18 recordsLinked to original sources

arXiv2026

DNA end tethering through break-induced DNA--protein condensation

Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA double-strand break, a DNA--protein condensate can tether the broken DNA ends before they disperse away, a critical step for subsequent repair biochemistry. However, it remains puzzling how such condensation reliably achieves spatiotemporal localization at the break site and captures both broken ends despite intrinsic stochasticity. Here, we propose that broken DNA ends can trigger a conversion of proteins from a soluble state to a condensate-competent state. Combining this idea with Brownian dynamics simulations and theory, we propose a physical mechanism for reliable DNA-end tethering. Simulations show that such break-induced conversion can drive local DNA--protein condensation with two possible outcomes: successful or failed tethering. To rationalize this, we construct an effective free energy landscape, identify the corresponding stationary states, and demonstrate that tethering is governed by a kinetic competition between polymer relaxation and condensation dynamics. Together, our study shows that DNA end-dependent conversion, coupled with DNA--protein condensation, can reliably tether broken DNA ends.

physics.bio-ph↗

arXiv2026

Conclusive Identification Via Noisy Classical Channel: Superactivation and Quantum Advantage

We introduce conclusive identification task for classical channels: a receiver identifies transmitted inputs without error when possible, and responds inconclusively when outputs are ambiguous. For a symmetric not-fully-corrupted channel $N : X \to X$, the single-shot conclusive identification index $\mathrm{ci}_\circ(N)$ counts the maximum number of conclusively identifiable inputs. We show $\mathrm{ci}_\circ(N)$ exhibits a striking superactivation phenomenon: a channel with $\mathrm{ci}_\circ(N) = 0$ achieves $\mathrm{ci}_\circ(N \otimes \mathrm{id}^c_\beta) = |X|$ when assisted by a perfect classical channel of dimension $\beta < |X|$. The minimum classical assistance required equals the chromatic number $\chi(\mathtt{S}_N)$ of the channel's support graph $\mathtt{S}_N$. We provide channel families where the superactivation gap $\mathrm{ci}_\circ(N \otimes \mathrm{id}^c_\beta) - \mathrm{ci}_\circ(\mathrm{id}^c_\beta)$ can be made arbitrarily large. A noiseless quantum channel of dimension equal to the orthogonal rank $\xi(\mathtt{S}_N)$ suffices, yielding a strict quantum advantage whenever $\xi(\mathtt{S}_N) < \chi(\mathtt{S}_N)$. This advantage is demonstrated through three explicit constructions motivated by combinatorial and algebraic state-independent, and state-dependent proofs of Kochen-Specker contextuality. Via the co-normal product of graphs, we analyze the scaling of the quantum advantage ratio $\chi_f(\mathtt{S}_N)/\xi(\mathtt{S}_N)$, and present a channel for which quantum assistance is exponentially more efficient than classical. Our results establish $\mathtt{S}_N$, rather than the confusability graph $\mathtt{G}_N$, as the natural combinatorial object for conclusive identification, revealing that channels deemed useless under Shannon's zero-error framework can exhibit rich superactivation and quantum advantage, with deep connections to quantum contextuality.

quant-ph↗

arXiv2026

Superadditivity of Zero-Error Capacity in Noisy Classical and Perfect Quantum Channel Pairs

We demonstrate superadditivity of one-shot zero-error classical capacity in an asymmetric communication setting where a noisy classical channel is used in parallel with a perfect quantum channel. Each channel individually supports only a fixed number of perfectly distinguishable messages. Their joint use enables transmission of strictly more messages than permitted by the product of the individual capacities. We present explicit constructions achieving this enhancement and establish that replacing the perfect quantum channel with a perfect classical channel eliminates the effect. Finally, we identify a structural criterion on the noisy channel governing this effect and show that the quantum advantage is rooted in Kochen-Specker contextuality.

quant-ph↗

arXiv2025

Motifs in self-organising cells

In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another. Simultaneously, the motifs can also interact, causing new coarse-grained properties to emerge in the system. In this paper, we found motifs in a simulated system of Dynamically Self-Organising cells. We also found that quantifying these motifs with a set of physically interpretable structural and dynamic features efficiently captures the interaction dynamics of the motifs' underlying cells. Using these motif features, we revealed packing strain and defects in large compact aggregates, semi-periodicity in motif ensembles, and phase space classes with unsupervised machine learning. Additionally, we trained neural networks to infer the critical hidden microscopic interaction parameters within each motif from coarse-grained motif features extracted from snapshots of the system. Furthermore, we uncovered emergent features that can predict the movement of cell collectives by hierarchically coarse-graining smaller motifs into larger ones (e.g. motif clusters). We speculate that this concept of motif hierarchies may be applied broadly to many-body interacting systems that are otherwise too complex to understand.

physics.bio-ph↗

arXiv2025

CLAReSNet: When Convolution Meets Latent Attention for Hyperspectral Image Classification

Hyperspectral image (HSI) classification faces critical challenges, including high spectral dimensionality, complex spectral-spatial correlations, and limited training samples with severe class imbalance. While CNNs excel at local feature extraction and transformers capture long-range dependencies, their isolated application yields suboptimal results due to quadratic complexity and insufficient inductive biases. We propose CLAReSNet (Convolutional Latent Attention Residual Spectral Network), a hybrid architecture that integrates multi-scale convolutional extraction with transformer-style attention via an adaptive latent bottleneck. The model employs a multi-scale convolutional stem with deep residual blocks and an enhanced Convolutional Block Attention Module for hierarchical spatial features, followed by spectral encoder layers combining bidirectional RNNs (LSTM/GRU) with Multi-Scale Spectral Latent Attention (MSLA). MSLA reduces complexity from $\mathcal{O}(T^2D)$ to $\mathcal{O}(T\log(T)D)$ by adaptive latent token allocation (8-64 tokens) that scales logarithmically with the sequence length. Hierarchical cross-attention fusion dynamically aggregates multi-level representations for robust classification. Experiments conducted on the Indian Pines and Salinas datasets show state-of-the-art performance, achieving overall accuracies of 99.71% and 99.96%, significantly surpassing HybridSN, SSRN, and SpectralFormer. The learned embeddings exhibit superior inter-class separability and compact intra-class clustering, validating CLAReSNet's effectiveness under severe class imbalance.

cs.CV↗

arXiv2025

Nano-size fragmentation of Tantalum in Copper composite using additive manufacturing

The biggest challenge in manufacturing an immiscible system is phase segregation and non-uniformity inside the composite matrix. Additive manufacturing has the potential to overcome these difficulties due to the high cooling rate achieved during the process. Here we have developed immiscible Copper-based composites reinforced with Tantalum, which were fabricated using the powder bed fusion melting (PBF-M) technique. The distinct advantage of utilizing Tantalum in this process resides in its high melting point, allowing it to remain in particle form within the composite and contribute to its mechanical and surface/wear properties. The PBF-M results in the in situ fragmentation of micron-size Tantalum particles into nanoparticle form through a surface roughening process during laser interaction, enhancing its mechanical and wear properties. The microstructural evolution of Cu-Ta composites is explained through multiscale numerical modeling. The enhanced yield strength and the dynamics of the Ta particles were corroborated by molecular dynamics simulations. The maximum yield strength is exhibited by Cu-5wt%Ta of 80 MPa. Addition of Ta also have significant improvement in wear properties of composites. The current results can be exploited to develop complex shape, high energy efficient copper-based composites.

cond-mat.mtrl-sci↗

arXiv2024

Probing the massive scalar mode in the levitated sensor detector of gravitational wave

Owing to the mass scale associated with it the scalar longitudinal polarization mode of gravitational wave predicted in various modified theories of gravity should propagate at a subluminal speed and thus arrive with a time delay (for burst signals) or a phase difference (for persistent signals) at the detector site compared to the massless tensor polarization modes which move at the speed of light and are present in both standard general relativity and modified theories. The longitudinal massive scalar mode interacts non-trivially with detectors along the signal propagation direction in contrast to massless the tensor modes which interact only in the transverse plane. Identifying the signature of these distinctive features in a gravitational wave signal can provide observational evidence in favour of modified theories of gravity over general relativity. In this work we argue that owing to its compact design and tunability of operational frequency the recently proposed levitated sensor detectors \cite{Aggarwal} that works on the principle of gravitational wave induced resonant oscillation of a optically trapped \cite{Ashkin_1970} dielectric nanosphere sensor \cite{Geraci} can be useful in this regard. We demonstrate that the dynamics of the levitated sensor mass obeys a geodesic deviation equation in the proper detector frame and construct a quantum mechanical description of this system in modified gravity framework to compute the probabilities of resonant transitions in response to incoming gravitational wave signals of both periodic and aperiodic kind.

gr-qc↗

arXiv2024

Chromatin remodeling due to transient-link-and-pass activity enhances subnuclear dynamics

Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.

physics.bio-ph↗

arXiv2022

Quantum mechanical interaction of matter with the scalar mode of gravitational wave in modified gravity theories

We study the interaction of a quantum mechanical particle with gravitational wave (GW) in the framework of modified theory of gravity (MTG) where apart from the two standard tensorial modes of polarization of GW there exists another massless scalar mode. The purpose of using the MTG framework in our study is to uncover key features in matter's response to GWs that, if observed in actual GW data, can serve as observational evidence in favor of MTG over standard General Relativity.

gr-qc↗

arXiv2021

How enzymatic activity is involved in chromatin organization

Spatial organization of chromatin plays a critical role in genome regulation. Various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at the mechanistic level, enzymes act in their unique ways. Here, we construct a polymer physics model following the mechanistic scheme of Topoisomerase-II, an enzyme resolving topological constraints of chromatin, and investigate its role on interphase chromatin organization. Our computer simulations demonstrate Topoisomerase-II's ability to phase separate chromatin into eu- and heterochromatic regions with a characteristic wall-like organization of the euchromatic regions. Exploiting a mean-field framework, we argue that the ability of the euchromatic regions crossing each other due to enzymatic activity of Topoisomerase-II induces this phase separation. Motivated from a recent experimental observation on different structural states of the eu- and the heterochromatic units, we further extend our model to a bidisperse setting and show that the characteristic features of the enzymatic activity driven phase separation survives there. The existence of these characteristic features, even under the non-localized action of the enzyme, highlights the critical role of enzymatic activity in chromatin organization, and points out the importance of further experiments along this line.

physics.bio-ph↗

arXiv2020

Liquid-phase reinforced Metal matrix (LMM) composite with non-intuitive properties

Over the ages, efforts have been made to use composite design to reinforce metals and alloys in order to increase their strength and modulus. On the other hand, nature herself improves the strength, ductility, stiffness and toughness of materials by strengthening them with liquids having zero strength/modulus. Here, emulating nature, efforts have been made to develop a new class of tin based alloy/composite with liquid metal reinforcement (LMM). Based on thermodynamic calculations, a composition has been designed such that on melting and casting it forms a solid metal (tin solid solution) and the eutectic mixture remains in liquid form at room temperature. The composite structure named as LMM shows multifold improvement in hardness, strength, ductility, toughness and wear resistance as compared to conventional solder alloys. A Finite Element Method (FEM) based simulation shows strain distribution in the composite which results in the unique behavior. The LMM also shows a negative coefficient of thermal expansion which is further verified using in-situ microscopy and thermodynamic calculations.

physics.app-ph↗

arXiv2020

Nonquenched rotators ease flocking and memorise it

We introduce a minimal model for a two-dimensional polar flock with nonquenched rotators, and show that the rotators make the usual macroscopic long-range order of the flock more robust than the clean system. The rotators memorise the flock-information which helps in establishing the robustness. Moreover, the memory of the rotators assists in probing the moving flock. We also formulate a hydrodynamic framework for the microscopic model that makes our study comprehensive. Using linearised hydrodynamics, it is shown that the presence of such nonquenched heterogeneities increases the sound speeds of the flock. The enhanced sound speeds lead to faster convection of information and consequently the robust ordering in the system. We argue that similar nonquenched heterogeneities may be useful in monitoring and controlling large crowds.

cond-mat.stat-mech↗

arXiv2019

Enhanced dynamics of active Brownian particles in periodic obstacle arrays and corrugated channels

We study the motion of an active Brownian particle (ABP) using overdamped Langevin dynamics on a two-dimensional substrate with periodic array of obstacles and in a quasi-one-dimensional corrugated channel comprised of periodically arrayed obstacles. The periodic arrangement of the obstacles enhances the persistent motion of the ABP in comparison to its motion in the free space. Persistent motion increases with the activity of the ABP. We note that the periodic arrangement induces directionality in ABP motion at late time, and it increases with the size of the obstacles. We also note that the ABP exhibits a super-diffusive dynamics in the corrugated channel. The transport property is independent of the shape of the channel; rather it depends on the packing fraction of the obstacles in the system. However, the ABP shows the usual diffusive dynamics in the quasi-one-dimensional channel with flat boundary.

cond-mat.soft↗

arXiv2018

Polar flock in the presence of random quenched rotators

We study a collection of polar self-propelled particles (SPPs) on a two-dimensional substrate in the presence of random quenched rotators. These rotators act like obstacles which rotate the orientation of the SPPs by an angle determined by their intrinsic orientations. In the zero self-propulsion limit, our model reduces to the equilibrium $XY$ model with quenched disorder, while for the clean system, it is similar to the Vicsek model for polar flock. We note that a small amount of the quenched rotators destroys the long-range order usually noted in the clean SPPs. The system shows a quasi-long range order state upto some moderate density of the rotators. On further increment in the density of rotators, the system shows a continuous transition from the quasi-long-range order to disorder state at some critical density of rotators. Our linearized hydrodynamic calculation predicts anisotropic higher order fluctuation in two-point structure factors for density and velocity fields of the SPPs. We argue that nonlinear terms probably suppress this fluctuation such that no long-range order but only a quasi-long-range order prevails in the system.

cond-mat.stat-mech↗

arXiv2018

Ordering dynamics of self-propelled particles in an inhomogeneous medium

Ordering dynamics of self-propelled particles in an inhomogeneous medium in two-dimensions is studied. We write coarse-grained hydrodynamic equations of motion for coarse-grained density and velocity fields in the presence of an external random disorder field, which is quenched in time. The strength of inhomogeneity is tuned from zero disorder (clean system) to large disorder. In the clean system, the velocity field grows algebraically as $L_{\rm V} \sim t^{0.5}$. The density field does not show clean power-law growth; however, it follows $L_{\rm ρ} \sim t^{0.8}$ approximately. In the inhomogeneous system, we find a disorder dependent growth. For both the density and the velocity, growth slow down with increasing strength of disorder. The velocity shows a disorder dependent power-law growth $L_{\rm V}(t,Δ) \sim t^{1/\bar z_{\rm V}(Δ)}$ for intermediate times. At late times, there is a crossover to logarithmic growth $L_{\rm V}(t,Δ) \sim (\ln t)^{1/φ}$, where $φ$ is a disorder independent exponent. Two-point correlation functions for the velocity shows dynamical scaling, but the density does not.

cond-mat.stat-mech↗

arXiv2017

Order-disorder transition in active nematic: A lattice model study

We introduce a lattice model for active nematic composed of self-propelled apolar particles,study its different ordering states in the density-temperature parameter space, and compare with the corresponding equilibrium model. The active particles interact with their neighbours within the framework of the Lebwohl-Lasher model, and move anisotropically along their orientation to an unoccupied nearest neighbour lattice site. An interplay of the activity, thermal fluctuations and density gives rise distinct states in the system. For a fixed temperature, the active nematic shows a disordered isotropic state, a locally ordered inhomogeneous mixed state, and bistability between the inhomogeneous mixed and a homogeneous globally ordered state in different density regime. In the low temperature regime, the isotropic to the inhomogeneous mixed state transition occurs with a jump in the order parameter at a density less than the corresponding equilibrium disorder-order transition density. Our analytical calculations justify the shift in the transition density and the jump in the order parameter. We construct the phase diagram of the active nematic in the density-temperature plane.

cond-mat.soft↗

arXiv2016

Magnetic instability and $f-d$ hybridization in CeFe$_2$ on substituting Cr, Ag and Au for Fe

Hybridization between Ce $f$ and conduction $d$ states has been speculatively known to be one of the mechanisms responsible for magnetic instability of the ferromagnetic ground state of CeFe$_2$. Substituting Fe by small amounts of certain elements stabilizes it to an antiferromagnetic state below the Curie temperature via a first-order second phase transition. In the present work, we seek any direct relation between the $f-d$ hybridization and the second transition by measuring primarily dc magnetization and Ce M$_{4,5}$ edge x-ray absorption spectra of Ce(Fe$_{1-x}$M$_x$)$_2$ pseudobinaries, with M = Cr, Ag and Au. X-ray diffraction and x-ray photoelectron spectroscopy measurements are also performed essentially to monitor the quality of the samples. Whereas Cr impurity is found to cause the second transition, Ag and Au apparently do not induce any. In the former, the Curie and second transition temperatures vary systematically, but differently, with $x$. Our results imply that there is a definite proportionality between the $x$ dependences of the second transition temperature and the $f-d$ hybridization strength estimated qualitatively from the absorption spectra.

cond-mat.str-el↗

arXiv2015

Density Induced Phases in Active Nematic

We introduce a minimal model for a collection of self-propelled apolar active particles, also called as `active nematic', on a two-dimensional substrate and study the order-disorder transition with the variation of density. The particles interact with their neighbours within the framework of the Lebwohl-Lasher model and move asymmetrically, along their orientation, to unoccupied nearest neighbour lattice sites. At a density lower than the equilibrium isotropic-nematic transition density, the active nematic shows a first order transition from the isotropic state to a banded state. The banded state extends over a range of density, and the scalar order parameter of the system shows a plateau like behaviour, similar to that of the magnetic systems. In the large density limit the active nematic shows a bistable behaviour between a homogeneous ordered state with global ordering and an inhomogeneous mixed state with local ordering. The study of the above phases with density variation is scant and gives significant insight of complex behaviours of many biological systems.

cond-mat.stat-mech↗