arXiv subjects

Rajib Biswas

Publications and source records attributed to Rajib Biswas.

14 recordsLinked to original sources

arXiv2025

Infrared Spectral Signature of Water as a Probe to Demystify Urea Aggregation and Force Field Accuracy

Urea is widely used as a protein denaturant. However, the potential of urea to form self-assembled structures at higher concentrations and the influence of its self-interactions on water structure and dynamics remains elusive. This open question demands tracking of molecular-level rearrangements. In this work, we explore the influence of urea on local structure of water and dynamics and relate it to urea self-association. We correlate vibrational spectral response and orientational dynamics of water with concentration-dependent self-association of urea by looking at the interface surface area, hydrogen bond strength, and population of relevant donor-acceptor pairs. We compare the response of four urea force fields (KBFF, OPLS-S, OPLS-AA-D, GAFF-D3) with simple point charge extented water. The KBFF model reproduces experimental IR spectra. Both variants of the Duffy model (OPLS-S, OPLS-AA-D) show blue shifts with reasonable broadening and intense concentration-dependent responses, while GAFF-D3 shows random peak shifts with prominent broadening. Regarding urea self-aggregation, KBFF is mildly repulsive, Duffy models are attractive, and GAFF-D3 is neutral with high variability. Only KBFF and GAFF-D3 capture the expected deceleration in water-orientational dynamics. We conclude urea does not self-aggregate significantly in water, even at higher concentrations. KBFF emerges as the most reliable classical non-polarizable model of urea for capturing both structural and dynamic properties of water.

cond-mat.soft↗

arXiv2024

Azurin-Based Peptide p28 Arrests the p53-HDM2 Interactions: A Novel Anti-Cancer Pathway

Azurin and its derived peptides, notably p28, exhibit significant anticancer properties, primarily by stabilizing the tumor suppressor protein p53 and preventing its degradation. Previous studies have shown that p28 binds to p53's DNA-binding domain, protecting it from degradation mechanisms. Expanding on these findings, our research explored whether p28 acts on additional cancer pathways beyond p53 stabilization. Specifically, we examined the interactions between p28 and Human Double Minute 2 (HDM2), a protein that downregulates p53's tumor-suppressive activity by binding to its transactivation domain (TAD). HDM2 is crucial in diminishing p53's function, and our study aimed to determine if p28 disrupts this HDM2-p53 interaction. Using HADDOCK docking and molecular dynamics simulations, we identified three stable conformations of the HDM2-p28 complex. These conformations effectively block HDM2's hydrophobic pocket, allowing for sustained inter-chain interactions and showing favorable binding energies. Further analysis pinpointed essential residues in these interactions, and we calculated interaction energies using the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method. Our findings reveal that by blocking HDM2's binding sites, p28 helps maintain p53's transcriptional activity, thus enhancing its tumor-suppressive functions, including apoptosis and cell cycle arrest in cancer cells. This study enhances understanding of azurin-derived peptides' anticancer mechanisms and highlights p28's potential as a peptide-based anticancer agent. These findings also suggest the possibility of designing additional peptide therapies targeting HDM2 and other cancer-related pathways, opening new directions in anticancer therapeutics.

cond-mat.soft↗

arXiv2023

A brief overview of Turkiye Earthquake: insight into the building damage

The month of February 2023 had been a nightmare for the people of Turkiye. On 6th Feb, there was a devastating earthquake which jolted Turkiye like never before. The aftershock which followed later added more fuel to the overall damages. Till now, there has been reports several aftershocks which is believed to continue for another considerable span of time. In terms of damage, the loss was totally irreparable. Millions of people were rendered homeless, and a large chunk of population had lost their lives due to building collapse. This mini communication overviews the past seismicity of Turkiye. As per preliminary report, there has been substantial liquefaction and ground subsidence in and around the epicenters. Accordingly, the liquefaction is also briefly detailed along with types of prevalent sediments Further, the damages as well as building collapsed are detailed here along with probable causes as well as lacunae observed in building construction. Future strategies may possibly involve such as base isolation or isolators can be introduced in order to make the buildings more resilient earthquakes. However, strict monitoring and compliance of structures to building code should be implemented with strict measures. Any violation of such codes should be penalized. All these measures can lead to earthquake resilient society.

physics.geo-ph↗

arXiv2021

Effects of hydrophobic solute on water normal modes

The vibrational modes of water get significantly modified by external solutes; this becomes particularly important when the solute is hydrophobic. In this work, we examine the effects of a tiny hydrophobe, methane, on the normal modes of water, using small cluster-based harmonic normal mode analysis of aqueous methane system. We estimate the vibrational density of states and also the infrared spectral density. We compare the methane-water data with the bulk water response. We decompose these modes based on different vibrational characters. The stretch-bend decomposition reflects a pronounced coupling between the methane asymmetric stretch mode and the water symmetric stretch mode. We examine the methane-water data in terms of the symmetry of the central water molecule's vibrations and find that asymmetric modes do not contribute. We also find that the vibrational modes having non-zero contributions from methane molecule are extremely localized in nature.

cond-mat.soft↗

arXiv2021

Spatial variation of Coda Q in Kopili fault zone of northeast India as a probe for heterogeneous media

Kopili fault has been experiencing higher seismic and tectonic activity ([1], [2]) during the recent years. These kinds of active tectonics can be inspected by examining coda-wave attenuation and its dependence with frequency. Here, we report spatial variation of coda attenuation of this region. The obtained results reveal that there is velocity anomaly at depth 210-220 km as there arises sharp changes in attenuation coefficient (γ) and frequency parameter (n) which are supported by available data reported by other researchers for this region.

physics.geo-ph↗

arXiv2020

Theoretical Spectroscopic Investigation of Hydrogen Bonding and Hydrophobicity

Hydrophobic solutes significantly alters water hydrogen bond network. The local alteration of solvation struc-tures get reflected in the vibrational spectroscopic signal. Although it is possible to detect this microscopicfeatures by modern infrared spectroscopy, however, bulk phase spectra often comes with formidable challengeof establishing the connection among the experimental spectra to molecular structures. Theoretical spec-troscopy can serve as more powerful tool even where spectroscopic data cannot provide microscopic picture.In the present work, we build a theoretical spectroscopic map based on mixed quantum-classical molecularsimulation approach using methane in water system. The single oscillator level O-H stretch frequency is wellcorrelated with a collective variable solvation energy. We construct the spectroscopic maps for fundamentaltransition frequencies and also the transition dipoles. A bimodal frequency distribution with a blue shiftedpopulation of transition frequency illustrates presence of gas like water molecules in the hydration shell ofmethane. This observation is further complemented by a shell-wise decomposition of the O-H stretch fre-quencies. We observe a significant increase in ordering of the first solvation water except the water molecules,which are directly facing the methane molecule. This is manifested in redshift of the observed transition fre-quencies. Temperature dependent simulations depict that the water molecules facing to the methane moleculebehave similar to the high temperature water and the rest of the first shell water molecules behave more likecold water.

physics.chem-ph↗

arXiv2020

CodaQback: A simplified Python Code facilitating auto-windowing for estimating Seismic Coda attenuation parameter

Attenuation study of a province is considered as a basic quantity for seismic hazard assessment, ground motion simulation process and source parameter studies. It is already established that the study of two physical processes, first, the seismic sources and second, propagation of the waves, is essential for seismic-hazard mapping, attenuation being one of the properties paying importance to the latter. Here, a computational tool entitled CodaQback is presented. Based on back scattering model, this versatile software is equipped with user friendly graphical user interface. It also allows quick picking of phases for computing coda attenuation parameter. All outputs after each execution step in CodaQback are efficiently exported stepwise into a separate folder in excel and text formats. This CodaQback is checked in real data analysis and there is found to be good matching of computed values with already established ones. It is envisioned that this package will enable user to derive quick and reliable estimation of coda attenuation parameter irrespective of geological and geo-morphological units.

physics.geo-ph↗

arXiv2017

Assessing site response through H/V ratio in a seismic prone area of northeast India

We endeavor to assess site response exploiting ambient noise measurements which we carried out at 70 sites in different parts of Shillong City, one of the seismically active regions. We estimate the spectral ratio from these recordings. The spectral ratios reveal the resonant frequency for Shillong City in the range of 3 to 8 Hz. Short scale spatial variation in the resonant frequencies suggests that there is prominent lateral heterogeneity in the underlying layers. Besides, a non-linear earthquake site response analysis is also attempted using available geotechnical data. A good correlation is observed between site response analysis and HVSR results constrained by wide variation of resonant frequency at short distances. The results are found to be tallying well with the geological data.

physics.geo-ph↗

arXiv2017

Quantifying Regional Body-wave attenuation in a seismic prone zone of northeast India

We evaluated the body wave attenuation parameter in Kopili region of northeast India. Using the modified algorithm of coda normalization method, we delineated frequency-dependent attenuation for both P and S waves. Taking more than 300 seismograms as input, we comprehensively studied microearthquake spectra in the frequency range of 1.5 to 12 Hz. The estimated values of $Q_P^{-1}$ and $Q_S^{-1}$ show strong frequency dependence. The relationships emerge to be $Q_P^{-1}=(23.8\pm 6)\times10^{-3}f^{-1.2\pm 0.008}$ and $Q_S^{-1}=(10.2\pm 2)\times10^{-3}f^{-1.3\pm 0.02}$, respectively. The ratio $Q_P^{-1}/Q_S^{-1}$ is found to be larger than unity for the entire frequency band which implies profound seismic activity and macroscale heterogeneity prevailing in the region. The study may act as the building block towards determination of source parameter and hazard related studies in the region.

physics.geo-ph↗

arXiv2014

Diffusion in a rough potential revisited

Rugged energy landscapes find wide applications in diverse fields ranging from astrophysics to protein folding. We study the dependence of diffusion coefficient $(D)$ of a Brownian particle on the distribution width $(\varepsilon)$ of randomness in a Gaussian random landscape by simulations and theoretical analysis. We first show that the elegant expression of Zwanzig [PNAS, 85, 2029 (1988)] for $D(\varepsilon)$ can be reproduced exactly by using the Rosenfeld diffusion-entropy scaling relation. Our simulations show that Zwanzig's expression overestimates $D$ in an uncorrelated Gaussian random lattice - differing by almost an order of magnitude at moderately high ruggedness. The disparity originates from the presence of "three-site traps" (TST) on the landscape -- which are formed by the presence of deep minima flanked by high barriers on either side. Using mean first passage time formalism, we derive a general expression for the effective diffusion coefficient in the presence of TST, that quantitatively reproduces the simulation results and which reduces to Zwanzig's form only in the limit of infinite spatial correlation. We construct a continuous Gaussian field with inherent correlation to establish the effect of spatial correlation on random walk. The presence of TSTs at large ruggedness $(\varepsilon \gg k_{B}T)$ give rise to an apparent breakdown of ergodicity of the type often encountered in glassy liquids.

physics.chem-ph↗

arXiv2014

Melting/freezing transition in polydisperse Lennard-Jones system: Remarkable agreement between predictions of inherent structure, bifurcation phase diagram, Hansen-Verlet rule and Lindemann criteria

We use polydispersity in size as a control parameter to explore certain aspects of melting and freezing transitions in a system of Lennard-Jones spheres. Both analytical theory and computer simulations are employed to establish a potentially interesting relationship between observed terminal polydispersity in Lennard-Jones polydisperse spheres and prediction of the same in the integral equation based theoretical analysis of liquid-solid transition. As we increase polydispersity, solid becomes inherently unstable because of the strain built up due to the size disparity. This aspect is studied here by calculating the inherent structure (IS) calculation. With polydispersity at constant volume fraction we find initially a sharp rise of the average IS energy of the crystalline solid until transition polydispersity, followed by a cross over to a weaker dependence of IS energy on polydispersity in the amorphous state. This cross over from FCC to amorphous state predicted by IS analysis agrees remarkably well with the solid-liquid phase diagram (with extension into the metastable phase) generated by non-linear integral equation theories of freezing. Two other well-known criteria of freezing/melting transitions, the Hansen-Verlet rule of freezing and the Lindemann criterion of melting are both shown to be remarkably in good agreement with the above two estimates. Together they seem to indicate a small range of metastability in the liquid-solid transition in polydisperse solids.

cond-mat.soft↗

arXiv2012

Phase transition in magnetically coupled spins on a ring (SOR) model

We have considered a new type of 'XY' model where spins are placed on concentric ring with constant spin density in every ring. The spin executes continuous rotation under a modified Shore-Zwanzig Hamiltonian (J. Chem. Phys. 63, 5445 (1975)). We have performed Monte Carlo simulation using Glauber acceptance criteria. Computations of Binder's cumulant, specific heat and magnetic susceptibility all show presence of a finite temperature order-disorder phase transition in this spin system. The system size dependence of Binder's cumulant suggests the existence of a phase transition with a transition temperature of T* = 1.2. However, we have found no signature of the occurrence of vortex in our SOR model. The absence of hysteresis rules out the possibility of first order phase transition. We have found two "stable" states for T* = 0 phase. The perfectly ordered true ground state is obtained by gradual cooling of the system, while the other is obtained by starting the simulation with a random configuration at T* = 0. This second state has higher energy than the perfectly aligned ground state.

cond-mat.stat-mech↗

arXiv2010

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of ATP and AMP to ADP by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of LID and NMP domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motions of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis and multi-dimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed RMSD variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder type theoretical model to explain the observed dynamic coupling between the motions of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations.

cond-mat.stat-mech↗

arXiv2010

A kinetic Ising model study of dynamical correlations in confined fluids: Emergence of both fast and slow time scales

Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation of molecules in confined systems such as water in reverse micelles, cyclodextrin cavities and nano-tubes. Here we introduce a novel finite length one dimensional Ising model to investigate the propagation and the annihilation of dynamical correlations in finite systems and to understand the intriguing shortening of the orientational relaxation time that has been reported for small sized reverse micelles. In our finite sized model, the two spins at the two end cells are oriented in the opposite directions, to mimic the effects of surface that in real system fixes water orientation in the opposite directions. This produces opposite polarizations to propagate inside from the surface and to produce bulk-like condition at the centre. This model can be solved analytically for short chains. For long chains we solve the model numerically with Glauber spin flip dynamics (and also with Metropolis single-spin flip Monte Carlo algorithm). We show that model nicely reproduces many of the features observed in experiments. Due to the destructive interference among correlations that propagate from the surface to the core, one of the rotational relaxation time components decays faster than the bulk. In general, the relaxation of spins is non-exponential due to the interplay between various interactions. In the limit of strong coupling between the spins or in the limit of low temperature, the nature of relaxation of the spins undergoes a qualitative change with the emergence of a homogeneous dynamics where decay is predominantly exponential, again in agreement with experiments.

cond-mat.stat-mech↗