arXiv subjects

Prabal K. Maiti

Publications and source records attributed to Prabal K. Maiti.

At least 37 records · Page 2Linked to original sources

arXiv2023

Effect of Confinement and Topology: 2-TIPS vs MIPS

2-TIPS (Two Temperature induced phase separation) refers to the phase separation phenomenon observed in mixtures of active and passive particles which are modelled using scalar activity. The active particles are connected to a thermostat at high temperature while the passive particles are connected to the thermostat at low temperature and the relative temperature difference between "hot" and "cold" particles is taken as the measure of the activity of the non-equilibrium system. The study of such binary mixtures of hot and cold particles under various kinds of confinement is an important problem in many physical and biological processes. The nature and extent of phase separation are heavily influenced by the geometry of confinement, activity, and density of the non-equilibrium binary mixture. Investigating such 3D binary mixtures confined by parallel walls, we observe that, the active and passive particles phase separate, but the extent of phase separation is reduced compared to bulk phase separation at high densities and enhanced at low densities. However, when the binary mixture of active and passive particles is confined inside a spherical cavity, the phase separation is radial for small radii of the confining sphere and the extent of phase separation is higher compared to their bulk counterparts. Confinement leads to interesting properties in the passive(cold) region like enhanced layering and high compression in the direction parallel to the confining wall. In 2D, both the bulk and confined systems of the binary mixture show a significant decrement in the extent of phase separation at higher densities. This observation is attributed to the trapping of active particles inside the passive cluster, which increases with density. similar phase co-existence.

cond-mat.soft↗

arXiv2023

Entropy of different phases formed by soft rods

Computation of entropy in liquids and liquid crystal phases is a big challenge in statistical physics. In this work, we extend the two-phase thermodynamic model (2PT) to shape anisotropic soft repulsive spherocylinders (SRSs) and report the absolute values of entropy for different liquid crystal (LC) phases for a range of aspect ratios L/D = 2-5. We calculate the density of states (DoS) for different LC phases and decompose it into contributions arising from translational and rotational degrees of freedom. The translational and rotational modes are further partitioned into diffusive, gas-like, and non-diffusive, solid-like components using a fluidicity factor. In the dilute limit, the entropy values obtained from the 2PT method match exactly those of an ideal rigid rotor. We find that, for a given packing fraction, the magnitude of the total entropy is roughly equal regardless of the different LC phases associated with different aspect ratios. We also compute the excess entropy (for L/D = 5) and compare those with the values obtained using the standard integration approach of molecular dynamics (MD) or Monte Carlo (MC) equation of state (EOS) of SRS. The values obtained using both approaches match very well. The rotational and translational fluidicity factors are further used to determine the phase boundaries of different liquid crystal phases for the respective aspect ratios.

cond-mat.soft↗

arXiv2022

Does twist angle affect the properties of water confined inside twisted bilayer graphene?

Graphene nanoslit pore is used for nanofluidic devices like water desalination, ion-selective channels, ionic transistors, sensing, molecular sieving, blue energy harvesting, and protein sequencing. It is a strenuous task to prepare nanofluidic devices because a small misalignment leads to a significant alteration in various properties of the devices. Here we focus on the rotational misalignment between two parallel graphene sheets. Using molecular dynamics simulation, we probe the structure and dynamics of monolayer water confined inside graphene nanochannels for a range of commensurate twist angles. With SPC/E and TIP4P/2005 water model, our simulations reveal the independence of equilibrium number density $(n \sim 13 nm^{-2})$ for SPC/E and $(n \sim 11.5 nm^{-2})$ for TIP4P/2005) across twists. Based on the respective densities of water models, the structure and dielectric constant are invariant of twist angles. The confined water structure at this shows square ice ordering for SPC/E water only. TIP4P/2005 shows ordering at the vicinity of a critical density $(n \sim 12.5 nm^{-2})$. The average perpendicular dielectric constant of the confined water remains anomalously low ($\sim 2$ for SPC/E and $\sim 6$ for TIP4P/2005) for studied twist angles. We find that the friction coefficient of confined water molecules varies for small twist angles while becoming independent for twists greater than $5.1^{o}$. Our results indicate that small angular misalignment will not impair the dielectric properties of monolayer water within graphene slit-pore but can significantly influence its dynamics.

cond-mat.soft↗

arXiv2022

Molecular insights into the physics of poly(amidoamine)-dendrimer-based supercapacitors

Increasing the energy density in electric double layer capacitors (EDLCs), also known as supercapacitors, remains an active area of research. Specifically, there is a need to design and discover electrode and electrolyte materials with enhanced electrochemical storage capacity. Here, using fully atomistic molecular dynamics (MD) simulations, we investigate the performance of hyper-branched 'poly(amidoamine) (PAMAM)' dendrimer as an electrolyte and an electrode coating material in a graphene based supercapacitor. We investigate the performance of the capacitor using two different modeling approaches, namely the constant charge method (CCM) and the constant potential method (CPM). These simulations facilitated the direct calculation of the charge density, electrostatic potential and field, and hence the differential capacitance. We found that the presence of the dendrimer in the electrodes and the electrolyte increased the capacitance by about 65.25 % and 99.15 % respectively, compared to the bare graphene electrode based aqueous EDLCs. Further analysis revealed that these increases were due to the enhanced electrostatic screening and reorganization of the double layer structure of the dendrimer based electrolyte.

cond-mat.soft↗

arXiv2022

Probing the microscopic structure and flexibility of oxidized DNA by molecular simulations

The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the microscopic structural changes in physical properties of DNA and the resulting influence on its function due to oxidative damage of its nucleotide bases, we have conducted all-atom molecular dynamic simulations of double-stranded DNA (dsDNA) with its guanine bases being oxidized. The guanine bases are more prone to oxidative damage due to the lowest value of redox potential among all nucleobases. We have analyzed the local as well as global mechanical properties of native and oxidized dsDNA and explained those results by microscopic structural parameters and thermodynamic calculations. Our results show that the oxidative damage of dsDNA does not deform the Watson-Crick geometry; instead, the oxidized DNA structures are found to be better stabilized through electrostatic interactions. Moreover, oxidative damage changes the mechanical, helical, and groove parameters of dsDNA. The persistence length, stretch modulus, and torsional stiffness are found to be 48.87 nm, 1239.26 pN, and 477.30 pN.nm^2, respectively, for native dsDNA, and these values are 61.31 nm, 659.91 pN, and 407.79 pN.nm^2, respectively, when all the guanine bases of the dsDNA are oxidized. Compared to the global mechanical properties, the changes in helical and groove properties are found to be more prominent, concentrated locally at the oxidation sites, and causing the transition of the backbone conformations from BI to BII at the regions of oxidative damage.

physics.bio-ph↗

arXiv2022

Packing and emergence of ordering of rods in a spherical monolayer

Spatially ordered systems confined to surfaces such as spheres exhibit interesting topological structures because of curvature induced frustration in orientational as well as translational order. The study of these structures is important for investigating the interplay between geometry, topology, and elasticity, and for their potential applications in materials science. In this work we numerically simulate a spherical monolayer of soft repulsive spherocylinders (SRS) and study the packing of rods and their ordering transition as a function of the packing fraction. In the model that we study, centers of mass of the spherocylinders (situated at their geometric centers) are constrained to move on a spherical surface. The spherocylinders are free to rotate about any axis that passes through their respective centers of mass. We show that at relatively lower packing fractions, there is a continuous transition from a disordered fluid to a novel, orientationally ordered, spherical fluid monolayer as the packing fractions is increased. This monolayer of orientationally ordered SRS particles resembles a hedgehog -- long axes of the SRS particles are aligned along the local normal to the sphere. At higher packing fractions, system undergoes transition to the solid phase, which is riddled with topological point defects (disclinations) and grain boundaries that divide the whole surface into several domains.

cond-mat.soft↗

arXiv2022

Heating leads to liquid-crystal and crystalline order in a two-temperature active fluid of rods

We report phase separation and liquid-crystal ordering induced by scalar activity in a system of Soft Repulsive Spherocylinders (SRS) of aspect ratio $L/D = 5 $. Activity was introduced by increasing the temperature of half of the SRS (labeled \textit{`hot'}) while maintaining the temperature of the other half constant at a lower value (labeled \textit{`cold'}). The difference between the two temperatures scaled by the lower temperature provides a measure of the activity. Starting from different equilibrium initial phases, we find that activity leads to segregation of the hot and cold particles. Activity also drives the cold particles through a phase transition to a more ordered state and the hot particles to a state of less order compared to the initial equilibrium state. The cold components of a homogeneous isotropic (I) structure acquire nematic (N) and, at higher activity, crystalline (K) order. Similarly, the cold zone of a nematic initial state undergoes smectic (Sm) and crystal ordering above a critical value of activity while the hot component turns isotropic. We find that the hot particles occupy a larger volume and exert an extra kinetic pressure, confining, compressing and provoking an ordering transition of the cold-particle domains.

cond-mat.soft↗

arXiv2022

Two-temperature activity induces liquid-crystal phases inaccessible in equilibrium

In equilibrium hard-rod fluids, and in effective hard-rod descriptions of anisotropic soft-particle systems, the transition from the isotropic (I) phase to the nematic phase (N) is observed above the rod aspect ratio L/D = 3.70 as predicted by Onsager. We examine the fate of this criterion in a molecular dynamics study of a system of soft repulsive spherocylinders rendered active by coupling half the particles to a heat bath at a higher temperature than that imposed on the other half. We show that the system phase separates and self-organizes into various liquid-crystalline phases that are not observed in equilibrium for the respective aspect ratios. In particular, we find a nematic phase for L/D = 3 and a smectic phase for L/D = 2 above a critical activity.

cond-mat.soft↗

arXiv2022

Ultra-high permeable phenine nanotube membranes for water desalination

Nanopore desalination technology hinges on high water-permeable membranes which, at the same time, block ions efficiently. In this study, we consider a recently synthesized [Science 363, 151-155 (2019)] phenine nanotube (PNT) for water desalination applications. Using both equilibrium and non-equilibrium molecular dynamics simulations, we show that the PNT membrane completely rejects salts, but permeates water at a rate which is an order-of-magnitude higher than that of all the membranes used for water filtration. We provide the microscopic mechanisms of salt rejection and fast water-transport by calculating the free-energy landscapes and electrostatic potential profiles. A collective diffusion model accurately predicts the water permeability obtained from the simulations over a wide range of pressure gradients. We propose a method to calculate the osmotic water permeability from the equilibrium simulation data and find that it is very high for the PNT membrane. These remarkable properties of PNT can be applied in various nanofluidic applications, such as ion-selective channels, ionic transistors, sensing, molecular sieving, and blue energy harvesting.

physics.app-ph↗

arXiv2022

Molecular rectifiers with very high rectification ratio enabled by oxidative damage in double-stranded DNA

In this work, we report a novel strategy to construct molecular diodes with a record tunable rectification ratio of as high as 10^6 using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers constant oxidative damages leading to oxidation of guanine to 8-Oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising of molecular dynamics, density functional theory and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its CT properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operates as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.

cond-mat.soft↗

arXiv2021

Role of Entropy in Determining the Phase Behavior of Protein Solutions Induced by Multivalent Ions

Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex hydration effects that result in a net entropy gain upon phase separation. To decipher the underlying molecular mechanism, we use all-atom molecular dynamics simulations along with the two-phase thermodynamic method for entropy calculation. Based on simulations of a single BSA protein in various salt solutions (NaCl, CaCl_2, MgCl_2, and YCl_3) at temperatures (T) ranging 283-323 K, we find that the cation-protein binding affinity increases with T, reflecting its thermodynamic driving force to be entropic in origin. We show that in the cation binding process, many tightly bound water molecules from the solvation shells of a cation and the protein are released to the bulk, resulting in entropy gain. To rationalize the LCST behavior, we calculate the ζ-potential that shows charge inversion of the protein for solutions containing multivalent ions. The ζ-potential increases with T. Performing simulations of two BSA proteins, we demonstrate that the protein-protein binding is mediated by multiple cation bridges and involves similar dehydration effects that cause a large entropy gain which more than compensates for rotational and translational entropy losses of the proteins. Thus, the LCST behavior is entropy-driven, but the associated solvation effects are markedly different from hydrophobic hydration. Our findings have direct implications for tuning the phase behavior of biological and soft-matter systems, e.g., protein condensation and crystallization.

cond-mat.soft↗

arXiv2021

A minimal coarse-grained model to study the gelation of multi-armed DNA nanostars

DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and five arms and study their self-assembly using molecular dynamics simulations. Our simulations show that the DNA nanostars form thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from the arrested gel phase to an unstructured liquid phase has been modelled using two-state theoretical model. We find that this transition is enthalpic driven and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends which is giving rise to gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using two-phase thermodynamic model, also substantiate the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature, demonstrating the phase transition to the gel phase. The detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, easily extensible to other polymeric systems, and has remarkable implications in the DNA nanotechnology field.

cond-mat.soft↗

arXiv2021

Dipole alignment of water molecules flowing through a carbon nanotube

The fast flow rate of water through nanochannels has promising applications in desalination, energy conversion, and nanomedicine. We have used molecular dynamics simulations to show that the water molecules passing through a wide single-walled carbon nanotube (CNT) cavity get aligned by flow to have a net dipole moment along the flow direction. With increasing flow velocity, the net dipole moment first increases and eventually saturates to a constant value. This behavior is similar to the Langevin theory of paraelectricity with the flow velocity acting as an effective aligning field. We show conclusively that the microscopic origin of this behavior is the preferential entry of water molecules with their dipole vectors pointing inward along the CNT axis.

cond-mat.soft↗

arXiv2021

Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA

The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length ranging from 12 base-pairs (bps) to 56 bps, paranemic crossover (PX) DNA, and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grain models $-$ Martini and oxDNA. To calculate the persistence length ($L_p$) and the stretch modulus ($γ$) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for DNT, we implement our previously developed theoretical framework. We compare and contrast all the results with previously reported all-atom molecular dynamics (MD) simulation and experimental results. The mechanical properties of dsDNA ($L_p$ $\sim$ 50nm, $γ\sim$ 800-1500 pN), PX DNA ($γ\sim$ 1600-2000 pN) and DNTs ($L_p \sim 1-10\ μ$m, $γ\sim$ 6000-8000 pN) estimated using Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces order of magnitude higher values of $L_p$ and $γ$. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. OxDNA captures the salt concentration effect on small dsDNA mechanics. But it is found to be ineffective to reproduce the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.

cond-mat.soft↗

arXiv2021

Reconstruction of moiré lattices in twisted transition metal dichalcogenide bilayers

An important step in understanding the exotic electronic, vibrational, and optical properties of the moiré lattices is the inclusion of the effects of structural relaxation of the un-relaxed moiré lattices. Here, we propose novel structures for twisted bilayer of transition metal dichalcogenides (TMDs). For $θ\gtrsim 58.4^{\circ}$, we show a dramatic reconstruction of the moiré lattices, leading to a trimerization of the unfavorable stackings. We show that the development of curved domain walls due to the three-fold symmetry of the stacking energy landscape is responsible for such lattice reconstruction. Furthermore, we show that the lattice reconstruction notably changes the electronic band-structure. This includes the occurrence of flat bands near the edges of the conduction as well as valence bands, with the valence band maximum, in particular, corresponding to localized states enclosed by the trimer. We also find possibilities for other complicated, entropy stabilized, lattice reconstructed structures.

cond-mat.mtrl-sci↗

arXiv2020

Fine-tuning the DNA conductance by intercalation of drug molecules

In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites which leads to modifications of the density-of-states in the near-Fermi energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance/tune the DNA conductance which opens new possibilities for their potential applications in nanoelectronics.

cond-mat.soft↗

arXiv2020

Using Multiscale Molecular Dynamics Simulations to Obtain Insights into Pore Forming Toxin Mechanisms

Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse grained MARTINI models and structure based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.

cond-mat.soft↗

arXiv2020

DNA versus RNA -- which shows higher electronic conduction?

In this study, we compare the charge transport properties of multiple (double stranded) dsRNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA:RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has smaller end-to-end length relative to that of dsDNA.

cond-mat.soft↗