Prabal K. Maiti
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View article: Phase behaviour and defect structure of soft rods on a sphere
Phase behaviour and defect structure of soft rods on a sphere Open
Using particle-resolved molecular-dynamics simulations, we compute the phase diagram for soft repulsive spherocylinders confined on the surface of a sphere. While crystal (K), smectic (Sm), and isotropic (I) phases exhibit a stability regi…
View article: Computational Insight into the Complexation of DNA-Functionalized Gold Nanoparticles
Computational Insight into the Complexation of DNA-Functionalized Gold Nanoparticles Open
Ensuring the stability of the AuNP-gene complex until it reaches the target sites is a crucial factor for the success of gene therapy. Though different AuNP sizes and AuNP-to-DNA ratios are investigated for specific therapeutic needs, thei…
View article: Clade-specific influences of glycans on the interactions between HIV-1 envelope and broadly neutralizing antibodies
Clade-specific influences of glycans on the interactions between HIV-1 envelope and broadly neutralizing antibodies Open
N-linked glycans are important in the elicitation and the activity of many broadly neutralizing antibodies (bNAbs) against HIV-1. The high conformational flexibility of glycans hindered detailed atomistic investigations of glycan-bNAb inte…
View article: AT vs. GC binding of protamine-template: A microscopic understanding through molecular dynamics and binding free energies
AT vs. GC binding of protamine-template: A microscopic understanding through molecular dynamics and binding free energies Open
Protamine, an arginine-rich protein, compacts DNA more tightly than histones in somatic cells, yet its sequence-specific binding remains unclear. Using all-atom MD simulations with an arginine-rich short cationic peptide that mimics the pr…
View article: Mechanistic Insights into Crossover-Dependent Stability and Exceptional Resistance of PX/JX Nanostructures to DNase I using Enhanced Sampling
Mechanistic Insights into Crossover-Dependent Stability and Exceptional Resistance of PX/JX Nanostructures to DNase I using Enhanced Sampling Open
Designing biostable DNA nanocarriers for precise therapeutic delivery remains a key challenge in DNA nanotechnology due to susceptibility to nuclease degradation. Multi-stranded DNA nanostructures, such as Paranemic crossover (PX) DNA, sho…
View article: Freezing in flat monolayers of soft spherocylinders
Freezing in flat monolayers of soft spherocylinders Open
Lamellar or smectic phases often have an intricate intralamellar structure that remains scarcely understood from a microscopic viewpoint. In this work, we use molecular dynamics simulations to study the effect of volume exclusion on the ph…
View article: Orientation Dependence of Current Blockade in Single Amino Acid Translocation through a Graphene Nanopore<sup>†</sup>
Orientation Dependence of Current Blockade in Single Amino Acid Translocation through a Graphene Nanopore<sup>†</sup> Open
After successful commercialization of DNA sequencing with biological nanopores, the next frontier of the nanopore technology is protein sequencing which is far more daunting a task. Molecules passing through solid-state nanopores produce c…
View article: Melting of rods on a sphere via an intermediate hexatic phase
Melting of rods on a sphere via an intermediate hexatic phase Open
We have studied, using molecular dynamics simulations, the pressure-induced melting in a monolayer of soft repulsive spherocylinders whose centers of mass are constrained to move on the surface of a sphere. We show that the orientational d…
View article: Prediction of thermal conductivity in CALF-20 with first-principles accuracy via machine learning interatomic potentials
Prediction of thermal conductivity in CALF-20 with first-principles accuracy via machine learning interatomic potentials Open
Understanding the thermal transport properties of CALF-20, a recent addition to the metal-organic framework family, is crucial for its effective utilization in greenhouse gas capture. Here, we report the thermal transport study of CALF-20 …
View article: Enhanced and Efficient Extraction of Uranyl Ions from Aqueous Waste through Graphene/CNT-PAMAM Nanocomposites
Enhanced and Efficient Extraction of Uranyl Ions from Aqueous Waste through Graphene/CNT-PAMAM Nanocomposites Open
The increasing threat of uranium contamination to environmental and human health due to its radiotoxicity demands the development of novel and efficient adsorbents for remediation. In this study, we investigated the potential of poly(amido…
View article: Freezing in flat monolayers of soft spherocylinders
Freezing in flat monolayers of soft spherocylinders Open
Lamellar or smectic phases often have an intricate intralamellar structure that remains scarcely understood from a microscopic viewpoint. In this work, we use molecular dynamics simulations to study the effect of volume exclusion and elect…
View article: Understanding the Role of Cnt in Piezoelectric Properties of Pvdf and Pvdf-Trfe: Combined Experimental and Simulation Study
Understanding the Role of Cnt in Piezoelectric Properties of Pvdf and Pvdf-Trfe: Combined Experimental and Simulation Study Open
View article: Deciphering Interstellar Ice Morphology: Atomistic Simulations Reveal the Complex Behavior of Ethanethiol
Deciphering Interstellar Ice Morphology: Atomistic Simulations Reveal the Complex Behavior of Ethanethiol Open
Ethanethiol (C$_2$H$_5$SH), a molecule detected in the interstellar medium (ISM), indicates the rich chemistry involving sulfur atoms. However, its behavior at low temperatures remains elusive, particularly the reported transition from an …
View article: Self-assembly of mycolic acid in water: monolayer or bilayer
Self-assembly of mycolic acid in water: monolayer or bilayer Open
The enduring pathogenicity of Mycobacterium tuberculosis can be attributed to its lipid-rich cell wall, with mycolic acids (MAs) being a significant constituent. Different MAs’ fluidity and structural adaptability within the bacterial cell…
View article: Unifying mixed gas adsorption in molecular sieve membranes and MOFs using machine learning
Unifying mixed gas adsorption in molecular sieve membranes and MOFs using machine learning Open
View article: Data-Driven Approaches to Predict Dendrimer Cytotoxicity
Data-Driven Approaches to Predict Dendrimer Cytotoxicity Open
Dendrimers are employed as functional elements in contrast agents and are proposed as nontoxic vehicles for drug delivery. Toxicity is a property that is to be evaluated for this novel class of bionanomaterials for in vivo applications. Th…
View article: Amorphous 1-propanol interstellar ice beyond its melting point
Amorphous 1-propanol interstellar ice beyond its melting point Open
The recent discovery of 1-propanol (CH3CH2CH2OH) in the interstellar medium (ISM) is of tremendous interest since fatty alcohols have been proposed as constituents of proto-cell membranes. Motivated by this discovery, we present the labora…
View article: Ab initio Investigation of Thermal Transport in Insulators: Unveiling the Roles of Phonon Renormalization and Higher-Order Anharmonicity
Ab initio Investigation of Thermal Transport in Insulators: Unveiling the Roles of Phonon Renormalization and Higher-Order Anharmonicity Open
The occurrence of thermal transport phenomena is widespread, exerting a pivotal influence on the functionality of diverse electronic and thermo-electric energy-conversion devices. The traditional first-principles theory governing the therm…
View article: Highly Selective Molecular-Sieving Membranes by Interfacial Polymerization for H2 Purification
Highly Selective Molecular-Sieving Membranes by Interfacial Polymerization for H2 Purification Open
View article: Unifying Mixed Gas Adsorption in Molecular Sieve Membranes and Mofs Using Machine Learning
Unifying Mixed Gas Adsorption in Molecular Sieve Membranes and Mofs Using Machine Learning Open
View article: Stability of the chiral crystal phase and breakdown of the cholesteric phase in mixtures of active–passive chiral rods
Stability of the chiral crystal phase and breakdown of the cholesteric phase in mixtures of active–passive chiral rods Open
We explored the effect of chirality on the phase behaviour of soft helices and the stability of cholesteric phase under scalar activity.
View article: Trajectory-Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane
Trajectory-Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane Open
With renewed interest in CO2 separations, carbon molecular sieving (CMS) membrane performance evaluation requires diffusion coefficients as inputs to have a reliable estimate of the permeability. An optimal material is desired t…
View article: Stability of chiral crystal phase and breakdown of cholesteric phase in mixtures of active-passive chiral rods
Stability of chiral crystal phase and breakdown of cholesteric phase in mixtures of active-passive chiral rods Open
In this study, we aim to explore the effect of chirality on the phase behavior of active helical particles driven by two-temperature scalar activity. We first calculate the equation of state of soft helical particles of various intrinsic c…
View article: Trajectory Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane
Trajectory Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane Open
With renewed interest in CO2 separations, carbon molecular sieving (CMS) membrane performance evaluation requires diffusion coefficients as inputs to have reliable estimate of the permeability. An optimal material is desired to have both h…
View article: Effect of Confinement and Topology: 2-TIPS vs MIPS
Effect of Confinement and Topology: 2-TIPS vs MIPS Open
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 a…
View article: Drug-bacterial membrane interactions: A Tale of two force fields
Drug-bacterial membrane interactions: A Tale of two force fields Open
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), a gram-positive bacteria, is known to infect and kill millions of people worldwide, specifically in poor and developing countries. M.tb has unique characteristics in terms of …
View article: DNA Tetrahedral Nanocages as a Promising Nanocarrier for Dopamine Delivery in Neurological Disorders
DNA Tetrahedral Nanocages as a Promising Nanocarrier for Dopamine Delivery in Neurological Disorders Open
Dopamine is a neurotransmitter in the central nervous system that is essential for many bodily and mental processes, and a lack of it can cause Parkinson’s disease. DNA tetrahedral (TD) nanocages are promising in bio-nanotechnology, especi…
View article: Gold Nanoparticles Aggregation on Graphene Using Reactive Force Field: A Molecular Dynamic Study
Gold Nanoparticles Aggregation on Graphene Using Reactive Force Field: A Molecular Dynamic Study Open
We examine the aggregation behavior of AuNPs of different sizes on graphene as function of temperature using molecular dynamic simulations with Reax Force Field (ReaxFF). In addition, the consequences of such aggregation on the morphology …
View article: <i>C</i>-4-Modified Isotetrones Prevent Biofilm Growth and Persister Cell Resuscitation in <i>Mycobacterium smegmatis</i>
<i>C</i>-4-Modified Isotetrones Prevent Biofilm Growth and Persister Cell Resuscitation in <i>Mycobacterium smegmatis</i> Open
Hyperphosphorylated nucleotide (p)ppGpp, synthesized by Rel protein, regulates the stringent response pathway responsible for biofilm and persister cell growth in mycobacteria. The discovery of vitamin C as an inhibitor of Rel protein acti…
View article: Dipole alignment of water molecules flowing through a carbon nanotube
Dipole alignment of water molecules flowing through a carbon nanotube Open
The flow 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 carbo…