arXiv subjects

Priyanka

Publications and source records attributed to Priyanka.

At least 19 recordsLinked to original sources

arXiv2026

Catalytic Crosstalk: Cooperative Enzyme Dynamics in Artificial Crowded Environments

In cellular environments, enzymes operate under densely crowded conditions that often hinder catalytic efficiency by limiting substrate diffusion and essential conformational dynamics. While reports suggest that crowding can often lead to inhibition of enzyme's catalytic activity, persistent efficiency of cellular biochemistry hints at underlying cooperative mechanisms among these molecules. Here, we experimentally demonstrate catalytic crosstalk between two enzymes - catalase and urease - in artificially crowded environments. Our results reveal that when co-localized in dense media, these enzymes mutually enhance each other's catalytic activity and dynamic behavior. This cooperative interaction leads to a net increase in reaction rates and mobility, suggesting an emergent many-body effect in enzyme assemblies. Modeling enzymes as dimeric active particles, we propose a minimal simulation framework that qualitatively captures the observed synergy. Our findings show that inter-enzyme cooperation can counteract the detrimental effects of crowding, offering insights into how enzymatic efficiency is sustained in complex biological milieu.

cond-mat.soft↗

arXiv2026

Asymmetry-Induced Chiral Dynamics in Coupled Self-Propelled Robots: Spinning and Circular Motion

Motivated by the chiral motility of microswimmers, we investigate how geometric asymmetry in a system of two self-propelled active Brownian robots coupled by a spring gives rise to rich collective dynamics. We demonstrate that asymmetry in the propulsion directions of the robots generates net torques that induce persistent rotational motion. Depending on the choice of propulsion angles $\alpha_1$ and $\alpha_2$, the system exhibits three distinct dynamical regimes -- run-and-tumble motion, circular trajectories, and spinning -- with the geometric configuration primarily determining the realized regime. We further show that spring stiffness and rotational noise act as additional tuning parameters governing the stability of these regimes. These results demonstrate how the interplay of mechanical coupling and activity produces diverse self-organized dynamics in simple robotic dimers, providing a bridge between artificial active systems and biological microswimmers such as bacteria, Chlamydomonas reinhardtii, and spermatozoa.

cond-mat.soft↗

arXiv2025

EnzyCLIP: A Cross-Attention Dual Encoder Framework with Contrastive Learning for Predicting Enzyme Kinetic Constants

Accurate prediction of enzyme kinetic parameters is crucial for drug discovery, metabolic engineering, and synthetic biology applications. Current computational approaches face limitations in capturing complex enzyme-substrate interactions and often focus on single parameters while neglecting the joint prediction of catalytic turnover numbers (Kcat) and Michaelis-Menten constants (Km). We present EnzyCLIP, a novel dual-encoder framework that leverages contrastive learning and cross-attention mechanisms to predict enzyme kinetic parameters from protein sequences and substrate molecular structures. Our approach integrates ESM-2 protein language model embeddings with ChemBERTa chemical representations through a CLIP-inspired architecture enhanced with bidirectional cross-attention for dynamic enzyme-substrate interaction modeling. EnzyCLIP combines InfoNCE contrastive loss with Huber regression loss to learn aligned multimodal representations while predicting log10-transformed kinetic parameters. The model is trained on the CatPred-DB database containing 23,151 Kcat and 41,174 Km experimentally validated measurements, and achieved competitive performance with R2 scores of 0.593 for Kcat and 0.607 for Km prediction. XGBoost ensemble methods applied to the learned embeddings further improved Km prediction (R2 = 0.61) while maintaining robust Kcat performance.

q-bio.BM↗

arXiv2024

Investigating the fission-like fragments in the $^{12}$C + $^{208}$Pb system at E$^{\star}$ $\approx$ 31.8--45.4 MeV

In this work, the cross-sections of 25 fission-like fragments within the mass range 76$\leq$A$\leq$141, expected to be populated via fission of moderately excited compound nucleus produced as a result of complete and/or incomplete fusion in $^{12}$C+$^{208}$Pb reaction at E$_{\rm lab}$ = 81.9 and 75.8 MeV, have been measured using activation technique followed by offline $\gamma$-ray spectroscopy. The yields of different fission-like fragments have been analyzed to generate isotopic and isobaric yield distributions. The value of the mass dispersion parameter, $\sigma^2_A$, is found to be 2.93 and 2.65 for Antimony (Sb) isotope at excitation energy E$^{\star}$ = 45.4 and 39.6 MeV, and 1.24 for Indium (In) isotope at E$^{\star}$ = 45.4 MeV. The charge dispersion parameter $\sigma_Z$ for Sb is estimated to be 0.769 and 0.714 at E$^{\star}$ = 45.4 and 39.6 MeV, respectively. For In isotopes, the value of $\sigma_Z$ is estimated to be 0.430 at E$^{\star}$ = 45.4 MeV. The value of mass and charge dispersion parameters for Sb and In isotopes have been found to be in good agreement with the values reported in the literature for similar systems. The mass distribution of fission-like fragments is found to be fitted with a Gaussian function, except for a few data points, indicating their population via compound nucleus fission. Further, the mass variance ($\sigma^2_M$) displays linear increment with an increase in excitation energy. Two medically important isotopes, $^{99m}$Tc and $^{111}$In, are populated in this system, suggesting a potential formation route.

nucl-ex↗

arXiv2024

Exploring $\beta^+$ decay/EC residues in $^{118}$Sn($^{12}$C,x)$^{130}$Ba reaction

The fusion cross-sections of $^{126}$Ba, $^{127,126,125}$Cs, $^{125,123,122}$Xe and $^{124,123}$I residues, populated via $x$n, p$x$n, $\alpha$$x$n, and $\alpha$p$x$n channels, have been measured in $^{12}$C+$^{118}$Sn system at E$_{\textrm{lab}}$ $\approx$ 65-85 MeV using offline $\gamma$-spectroscopy. To gain insights into the formation and decay modes of these residues, experimentally measured cross-sections have been analyzed using the statistical model codes PACE4 and EMPIRE. In the analysis, the cross-sections of p$x$n ($^{127,126,125}$Cs), $\alpha$xn ($^{125}$Xe), and $\alpha$p$x$n ($^{123}$I) channels are substantially fed from their higher charge isobars via $\beta^+$ decay and electron capture. The contribution of $\beta^+$ decay and electron capture has been calculated using the prescription of Cavinato $et$ $al.$\cite{cavinato1995study} and the independent cross-sections of these residues have been compared with PACE4 and EMPIRE calculations, which fairly reproduce the independent cross-sections of evaporation-residue within the experimental uncertainties. Interestingly, it has been observed that the $\alpha$-emitting channels, contrary to established findings in reactions involving $\alpha$ cluster projectiles (e.g., $^{12}$C, $^{16}$O, etc.) at the studied energy range, display negligible or no contribution of incomplete fusion (ICF) in $^{12}$C+$^{118}$Sn system. The absence of ICF has been verified through a complementary experiment in which the forward recoil ranges of $^{126}$Ba(4n) and $^{125}$Xe($\alpha$n) channels have been measured. Present measurements reveal anomalous suppression of ICF in the $^{12}$C+$^{118}$Sn system, providing new constraints on entrance-channel mass-asymmetry systematics absent in prior data.

nucl-ex↗

arXiv2024

Incomplete fusion in $^{193}$Ir($^{12}$C, x)$^{205}$Bi reaction at $E_{lab}$ $\approx$ 5-7 AMeV

Low-energy heavy-ion induced reactions often involve incomplete fusion, but the dependence of ICF on various entrance-channel parameters remains unclear. In this work, we measure channel-by-channel production cross-sections of different evaporation residues populated via complete and/or incomplete fusion in $^{12}$C+$^{193}$Ir system at $E_{lab}$ $\approx$ 64--84 MeV ($\approx$ 5--7 AMeV) using the stacked-foil activation technique followed by offline $\gamma$-spectroscopy. Experimentally measured excitation functions have been analyzed in the framework of the statistical model code PACE4 using different values of the level-density parameter ($a$ = A/9-A/15 MeV${^{-1}}$). In the analysis of excitation functions, the $xn$ and $pxn$ channels (after correcting with their precursor contributions) have been explained fairly well with $a$ = A/13 MeV${^{-1}}$; however, almost all $\alpha$-emitting channels showed substantial enhancement over PACE4 predictions, which has been attributed to incomplete fusion. The incomplete fusion fraction ($F_{ICF}$) increases linearly with energy from 12\% to 18\% at 64 and 84 MeV, respectively. For better insights into the onset and strength of ICF, the variations of $F_{ICF}$ have been studied as a function of different entrance-channel parameters, which are found to increase with mass asymmetry, Coulomb factor, and neutron skin thickness. Further analysis of the data suggests the onset of ICF below the critical angular momentum ($\ell<\ell_{crit}$). Projectile breakup-driven incomplete fusion is found to suppress complete fusion by $\approx12\%$ and $\approx6\%$ w.r.t. the universal fusion function and the improved fusion function, respectively. These findings highlight the critical role of projectile structure at 5--7 AMeV energies, with implications for high-spin spectroscopy and reaction modeling.

nucl-ex↗

arXiv2024

Intrinsic phenomena of delta shock waves in a more realistic Chaplygin Aw-Rascle model

The motivation of this study is to find the Riemann solutions of the Aw-Rascle model with a more realistic version of extended Chaplygin gas. Firstly, we establish the Riemann solutions with two different structures, viz., a shock wave followed by the contact discontinuity and a rarefaction wave followed by the contact discontinuity. Further, by analyzing the limiting behavior, it is found that one of the Riemann solutions converges to a $ \delta $-shock solution as the pressure approaches the generalized Chaplygin gas pressure. Moreover, numerical simulations have been performed to validate the theoretical analysis.

math.AP↗

arXiv2024

Ground state properties and bubble structure of the isotopic chains of Z = 125 and 126 using the relativistic mean-field formalism

The ground state properties of Z = 125 and 126 nuclei are investigated, taking the isotopic series from the proton to neutron drip-lines. This analysis is conducted using the relativistic mean-field approach with NL3 and the Relativistic-Hartree-Bogoliubov model with DD-ME2 parameterization. The bulk properties under examination include the binding energy, the neutron separation energies, the differential variation of the separation energy, the quadrupole deformation parameter $\beta_2$, and the single-particle energy. We observed the stability at N = 172 and 184 over the isotopic chain for both parameter sets. The quadrupole deformation parameter reveals a shape transition from prolate to spherical and back to prolate with mass number. No signature of a super- and/or hyper-deformed structure is found over the isotopic chain. Furthermore, the analysis is extended to examine the bubble structure, revealing a bubble/semi-bubble structure for a few neutron-rich isotopes.

nucl-th↗

arXiv2024

Investigating radioactivity in soil samples from neutral and vegetation land of Punjab/India

In this work, radioactivity investigations of soil samples from neutral and agricultural sites in Punjab/India have been carried out to study the impact of land use patterns. The analysis of radiological, mineralogical, physicochemical, and morphological attributes of soil samples has been performed employing state-of-the-art techniques. The mean activity concentration of 238U, 232Th, 40K, 235U, and 137Cs, measured using a carbon-loaded p-type HPGe detector, in neutral land was observed as 58.03, 83.95, 445.18, 2.83, and 1.16Bq kg-1, respectively. However, in vegetation land, it was found to be 40.07, 64.68, 596.74, 2.26 and 2.11Bq kg-1, respectively. In the detailed activity analysis, radium equivalent (Raeq) radioactivity is found to be in the safe prescribed limit of 370Bq kg-1 for all investigated soil samples. However, the dosimetric investigations revealed that the outdoor absorbed gamma dose rate (96.08nGy h-1) and consequent annual effective dose rate (0.12mSv y-1) for neutral land, and the gamma dose rate (82.46nGy h-1) and subsequent annual effective dose rate (0.10mSv y-1) for vegetation land marginally exceeded the global average. The surface morphology of neutral land favored more compactness, while agricultural land favored high porosity. Various heavy metals of health concern, namely As, Cd, Co, Cr, Cu, Hg, Pb, Se, and Zn, were also evaluated in all soil samples using Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS). Pollution Load Index (PLI) and Ecological Risk Index (RI) revealed that vegetation land was more anthropogenically contaminated than neutral land, with maximum contamination from Hg and As.

physics.geo-ph↗

arXiv2021

Dynein-inspired multilane exclusion process with open boundary conditions

Motivated by the sidewise motions of dynein motors shown in experiments, we use a variant of the exclusion process to model the multistep dynamics of dyneins on a cylinder with open ends. Due to the varied step sizes of the particles in a quasi-two-dimensional topology, we observe the emergence of a novel phase diagram depending on the various load conditions. Under high-load conditions, our numerical findings yield results similar to the TASEP model with the presence of all three standard TASEP phases, namely the low-density (LD), high-density (HD), and maximal-current (MC) phases. However, for medium- to low-load conditions, for all chosen influx and outflux rates, we only observe the LD and HD phases, and the maximal-current phase disappears. Further, we also measure the dynamics for a single dynein particle which is logarithmically slower than a TASEP particle with a shorter waiting time. Our results also confirm experimental observations of the dwell time distribution. The dwell time distribution for dyneins is exponential in less crowded conditions, whereas a double exponential emerges under overcrowded conditions.

cond-mat.stat-mech↗

arXiv2021

The role of the non-linearity in controlling the surface roughness in the one-dimensional Kardar--Parisi--Zhang growth process

We explore linear control of the one-dimensional non-linear Kardar--Parisi--Zhang (KPZ) equation with the goal to understand the effects the control process has on the dynamics and on the stationary state of the resulting stochastic growth kinetics. In linear control, the intrinsic non-linearity of the system is maintained at all times. In our protocol, the control is applied to only a small number $n_c$ of Fourier modes. The stationary-state roughness is obtained analytically in the small-$n_c$ regime with weak non-linear coupling wherein the controlled growth process is found to result in Edwards--Wilkinson dynamics. Furthermore, when the non-linear KPZ coupling is strong, we discern a regime where the controlled dynamics shows scaling in accordance to the KPZ universality class. We perform a detailed numerical analysis to investigate the controlled dynamics subject to weak as well as strong non-linearity. A first-order perturbation theory calculation supports the simulation results in the weak non-linear regime. For strong non-linearity, we find a temporal crossover between KPZ and dispersive growth regimes, with the crossover time scaling with the number $n_c$ of controlled Fourier modes. We observe that the height distribution is positively skewed, indicating that as a consequence of the linear control, the surface morphology displays fewer and smaller hills than in the uncontrolled growth process, and that the inherent size-dependent stationary-state roughness provides an upper limit for the roughness of the controlled system.

cond-mat.stat-mech↗

arXiv2020

Slow quench dynamics in classical systems: kinetic Ising model and zero-range process

While a large number of studies have focused on the nonequilibrium dynamics of a system when it is quenched instantaneously from a disordered phase to an ordered phase, such dynamics have been relatively less explored when the quench occurs at a finite rate. Here we study the slow quench dynamics in two paradigmatic models of classical statistical mechanics, {viz.}, one-dimensional kinetic Ising model and mean-field zero-range process, when the system is annealed slowly to the critical point. Starting from the time evolution equations for the spin-spin correlation function in the Ising model and the mass distribution in the zero-range process, we derive the Kibble-Zurek scaling laws. We then test a recent proposal that critical coarsening which is ignored in the Kibble-Zurek argument plays a role in the nonequilibrium dynamics close to the critical point. We find that the defect density in the Ising model and a scaled mass distribution in the zero-range process decay linearly to the respective value at the critical point with the time remaining until the end of the quench provided the final quench point is approached sufficiently fast, and sublinearly otherwise. As the linear scaling for the approach to the critical point also holds when a system following an instantaneous quench is allowed to coarsen for a finite time interval, we conclude that critical coarsening captures the scaling behavior in the vicinity of the critical point if the annealing is not too slow.

cond-mat.stat-mech↗

arXiv2020

Parallel Temperature Interfaces in the Katz-Lebowitz-Spohn Driven Lattice Gas

We explore a variant of the Katz-Lebowitz-Spohn (KLS) driven lattice gas in two dimensions, where the lattice is split into two regions that are coupled to heat baths with distinct temperatures. The temperature boundaries are oriented parallel to the external particle drive. If the hopping rates at the interfaces satisfy particle-hole symmetry, the current difference across them generates a vector flow diagram akin to a vortex sheet. We have studied the finite-size scaling of the particle density fluctuations in both temperature regions, and observed that it is controlled by the respective temperature values. If the colder subsystem is maintained at the KLS critical temperature, while the hotter subsystem's temperature is set much higher, the interface current greatly suppresses particle exchange between the two regions. As a result of the ensuing effective subsystem decoupling, strong fluctuations persist in the critical region, whence the particle density fluctuations scale with the KLS critical exponents. However, if both temperatures are set well above the critical temperature, the particle density fluctuations scale according to the totally asymmetric exclusion process (TASEP). We have also measured the entropy production rate in both subsystems; it displays intriguing algebraic decay in the critical region, while it saturates quickly at a small but non-zero level in the hotter region. We have also considered another possible choice of the hopping rates across the temperature interfaces that explicitly breaks particle-hole symmetry. In that case the boundary rates induce a net particle flux across the interfaces that displays power-law behavior, until ultimately the particle exclusion constraints generate a clogging transition to an inert state.

cond-mat.stat-mech↗

arXiv2020

Study of lockdown/testing mitigation strategies on stochastic SIR model and its comparison with South Korea, Germany and New York data

We are currently facing a highly critical case of a world-wide pandemic. The novel coronavirus (SARS-CoV-2, a.k.a. COVID-19) has proved to be extremely contagious and the original outbreak from Asia has now spread to all continents. This situation will fruitfully profit from the study in regards of the spread of the virus, assessing effective countermeasures to weight the impact of the adopted strategies. The standard Susceptible-Infectious-Recovered (SIR) model is a very successful and widely used mathematical model for predicting the spread of an epidemic. We adopt the SIR model on a random network and extend the model to include control strategies {\em lockdown} and {\em testing} -- two often employed mitigation strategies. The ability of these strategies in controlling the pandemic spread is investigated by varying the effectiveness with which they are implemented. The possibility of a second outbreak is evaluated in detail after the mitigation strategies are withdrawn. We notice that, in any case, a sudden interruption of such mitigation strategies will likely induce a resurgence of a second outbreak, whose peak will be correlated to the number of susceptible individuals. In fact, we find that a population will remain vulnerable to the infection until the herd immunity is achieved. We also test our model with real statistics and information on the epidemic spread in South Korea, Germany, and New York and find a remarkable agreement with the simulation data.

physics.soc-ph↗

arXiv2020

Social distancing and epidemic resurgence in agent-based Susceptible-Infectious-Recovered models

Once an epidemic outbreak has been effectively contained through non-pharmaceutical interventions, a safe protocol is required for the subsequent release of social distancing restrictions to prevent a disastrous resurgence of the infection. We report individual-based numerical simulations of stochastic susceptible-infectious-recovered model variants on four distinct spatially organized lattice and network architectures wherein contact and mobility constraints are implemented. We robustly find that the intensity and spatial spread of the epidemic recurrence wave can be limited to a manageable extent provided release of these restrictions is delayed sufficiently (for a duration of at least thrice the time until the peak of the unmitigated outbreak) and long-distance connections are maintained on a low level (limited to less than five percent of the overall connectivity).

physics.soc-ph↗

arXiv2020

One Dimensional Exclusion Process with Dynein Inspired Hops: Simulation and Mean Field Analysis

We introduce a one-dimensional non-equilibrium lattice gas model representing the processive motion of dynein molecular motors over the microtubule. We study both dynamical and stationary state properties for the model consisting of hardcore particles hopping on the lattice with variable step sizes. We find that the stationary state gap-distribution exhibits striking peaks around gap sizes that are multiples of the maximum step size, for both open and periodic boundary conditions. We verified this feature using a mean-field calculation. For open boundary conditions, we observe intriguing damped oscillator-like distribution of particles over the lattice with a periodicity equal to the maximum step size. To characterize transient dynamics, we measure the mean square displacement that shows weak superdiffusive growth with exponent $\gamma \approx 1.34$ for periodic boundary and ballistic growth ($\gamma \approx 2$) for open boundary conditions at early times. We also study the effect of Langmuir dynamics on the density profile.

cond-mat.stat-mech↗

arXiv2019

Feedback control of surface roughness in a one-dimensional KPZ growth process

Control of generically scale-invariant systems, i.e., targeting specific cooperative features in non-linear stochastic interacting systems with many degrees of freedom subject to strong fluctuations and correlations that are characterized by power laws, remains an important open problem. We study the control of surface roughness during a growth process described by the Kardar--Parisi--Zhang (KPZ) equation in $(1+1)$ dimensions. We achieve the saturation of the mean surface roughness to a prescribed value using non-linear feedback control. Numerical integration is performed by means of the pseudospectral method, and the results are used to investigate the coupling effects of controlled (linear) and uncontrolled (non-linear) KPZ dynamics during the control process. While the intermediate time kinetics is governed by KPZ scaling, at later times a linear regime prevails, namely the relaxation towards the desired surface roughness. The temporal crossover region between these two distinct regimes displays intriguing scaling behavior that is characterized by non-trivial exponents and involves the number of controlled Fourier modes. Due to the control, the height probability distribution becomes negatively skewed, which affects the value of the saturation width.

cond-mat.stat-mech↗

arXiv2019

Transverse Temperature Interfaces in the Katz-Lebowitz-Spohn Driven Lattice Gas

We explore the intriguing spatial patterns that emerge in a two-dimensional spatially inhomogeneous Katz-Lebowitz-Spohn (KLS) driven lattice gas with attractive nearest-neighbor interactions. The domain is split into two regions with hopping rates governed by different temperatures T > T_c and T_c, respectively, where T_c indicates the critical temperature for phase ordering, and with the temperature boundaries oriented perpendicular to the drive. In the hotter region, the system behaves like the (totally) asymmetric exclusion processes (TASEP), and experiences particle blockage in front of the interface to the critical region. To explain this particle density accumulation near the interface, we have measured the steady-state current in the KLS model at T > T_c and found it to decay as 1/T. In analogy with TASEP systems containing "slow" bonds, we argue that transport in the high-temperature subsystem is impeded by the lower current in the cooler region, which tends to set the global stationary particle current value. This blockage is induced by the extended particle clusters, growing logarithmically with system size, in the critical region. We observe the density profiles in both high-and low-temperature subsystems to be similar to the well-characterized coexistence and maximal-current phases in (T)ASEP models with open boundary conditions, which are respectively governed by hyperbolic and trigonometric tangent functions. Yet if the lower temperature is set to T_c, we detect marked fluctuation corrections to the mean-field density profiles, e.g., the corresponding critical KLS power law density decay near the interfaces into the cooler region.

cond-mat.stat-mech↗