Searcharxiv⌕ Search

arXiv subjects

Prabal K. Maiti

Publications and source records attributed to Prabal K. Maiti.

68 records · Page 4Linked to original sources

Strong Correlations and Fickian Water Diffusion in Narrow Carbon Nanotubes

We have used atomistic molecular dynamics (MD) simulations to study the structure and dynamics of water molecules inside an open ended carbon nanotube placed in a bath of water molecules. The size of the nanotube allows only a single file of water molecules inside the nanotube. The water molecules inside the nanotube show solid-like ordering at room temperature, which we quantify by calculating the pair correlation function. It is shown that even for the longest observation times, the mode of diffusion of the water molecules inside the nanotube is Fickian and not sub-diffusive. We also propose a one-dimensional random walk model for the diffusion of the water molecules inside the nanotube. We find good agreement between the mean-square displacements calculated from the random walk model and from MD simulations, thereby confirming that the water molecules undergo normal-mode diffusion inside the nanotube. We attribute this behavior to strong positional correlations that cause all the water molecules inside the nanotube to move collectively as a single object. The average residence time of the water molecules inside the nanotube is shown to scale quadratically with the nanotube length.

cond-mat.stat-mech↗

Binding of Nucleobases with Single-Walled Carbon Nanotubes

We have calculated the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotubes (SWNTs) using ab-initio Hartre-Fock method (HF) together with force field calculations. The gas phase binding energies follow the sequence G $>$ A $>$ T $>$ C. We show that main contribution to binding energy comes from van-der Wall (vdW) interaction between nanotube and nucleobases. We compare these results with the interaction of nucleobases with graphene. We show that the binding energy of bases with SWNTs is much lower than the graphene but the sequence remains same. When we include the effect of solvation energy (Poisson-Boltzman (PB) solver at HF level), the binding energy follow the sequence G $>$ T $>$ A $>$ C $>$, which explains the experiment\cite{zheng} that oligonucleotides made of thymine bases are more effective in dispersing the SWNT in aqueous solution as compared to poly (A) and poly (C). We also demonstrate experimentally that there is differential binding affinity of nucleobases with the single-walled carbon nanotubes (SWNTs) by directly measuring the binding strength using isothermal titration (micro) calorimetry. The binding sequence of the nucleobases varies as thymine (T) $>$ adenine (A) $>$ cytosine (C), in agreement with our calculation.

cond-mat.mtrl-sci↗

Structure and Dynamics of DNA-dendrimer complexation: Role of counterions, water and base pair sequence

We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free energy surface in the initial stage is found to be funnel-like with a significant barrier arising in the late stage due to the occurrence of misfolded states of DNA. Complexation shows surprisingly strong sensitivity to the ssDNA sequence which is found to arise from a competition between enthalpic versus entropic rigidity of ssDNA.

cond-mat.soft↗

Structure of poly(propyl ether imine) (PETIM) dendrimer from fully atomistic molecular Dynamics Simulation and by Small Angle X-ray scattering

We study the structure of carboxylic acid terminated neutral poly (propyl ether imine) (PETIM) dendrimer from generation 1 through 6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation such structural properties as: radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by Small Angle X-Ray Scattering (SAXS) experiment on dendrimer of generation 2 to 4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as ~ N^x with the number of monomers. We find two distinct exponents depending on the generations: x = 0.47 for G1-G3 and x = 0.28 for G3-G6 which reveals their non-space filling nature. In comparison with the amine terminated PAMAM dendrimer, we find Rg of G-th generation PETIM dendrimer is nearly equal to that of (G+1)-th generation of PAMAM dendrimer as observed by Maiti et. al. [Macromolecules,38, 979 2005]. We find substantial back folding of the outer sub generations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules suggesting using PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.

cond-mat.soft↗

Collapse of Double-Walled Carbon Nanotube Bundles under Hydrostatic Pressure

We use classical molecular dynamics simulations to study the collapse of single (SWNT) and double-walled (DWNT) carbon nanotube bundles under hydrostatic pressure. The collapse pressure (pc) varies as 1/R^3, where R is the SWNT radius or the DWNT effective radius. The bundles show ~ 30% hysteresis and the hexagonally close packed lattice is completely restored on decompression. The pc of DWNT is found to be close to the sum of its values for the inner and the outer tubes considered separately as SWNT, demonstrating that the inner tube supports the outer tube and that the effective bending stiffness of DWNT, D(DWNT) ~ 2D(SWNT) . We use an elastica formulation to derive the scaling and the collapse behavior of DWNT and multi-walled carbon nanotubes.

cond-mat.other↗

Entropy driven formation of Smectic C in system of Zig-zag shaped molecules

We have carried out Monte Carlo simulations of zig-zag shaped molecules where the the molecules is composed of three rigidly linked hard spherocylinder arranged in a zigzag fashion. By varying zigzag angle we have mapped out the whole phase diagram as a function of pressure, molecular density and zigzag angle $Ψ$. For $Ψ$ between $35^0$ and $80^0$ our model simulation exhibits SmC phase. This is the first conclusive evidence where steric interaction arising out of molecular shape alone induce the occurrence of SmC phase for a wide range of zigzag angle. For smaller $Ψ$, a transition from tilted crystal (XT) to nontlted crystal is observed.

cond-mat.stat-mech↗

Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.

cond-mat.stat-mech↗

Phase Behavior of Bent-Core Molecules

Recently, a new class of smectic liquid crystal phases (SmCP phases) characterized by the spontaneous formation of macroscopic chiral domains from achiral bent-core molecules has been discovered. We have carried out Monte Carlo simulations of a minimal hard spherocylinder dimer model to investigate the role of excluded volume interations in determining the phase behavior of bent-core materials and to probe the molecular origins of polar and chiral symmetry breaking. We present the phase diagram as a function of pressure or density and dimer opening angle $ψ$. With decreasing $ψ$, a transition from a nonpolar to a polar smectic phase is observed near $ψ= 167^{\circ}$, and the nematic phase becomes thermodynamically unstable for $ψ< 135^{\circ}$. No chiral smectic or biaxial nematic phases were found.

cond-mat.stat-mech↗

Self-assembly in Lyotropic Chromonic Liquid Crystals

We have developed a class of idealized models of chromonic molecules which are miscible in water, but which can form aggregates which in turn organize into lyotropic liquid crystal (LC) phases. By carrying out Monte Carlo simulation in a binary mixture of model chromonic and water molecules, we have studied the effect of concentration and molecular shape on the nature of resulting mesophases. We have also computed the free energy associated with the formation of chromonic columnar aggregates by umbrella sampling. Our free energy computation helps us to verify the isodesmic behavior which is characteristic of chromonic systems. For isodesmic behavior the addition of each chromonic molecule to the columnar aggregates is accompanied by a constant free energy increment and the net free energy decreases with increasing column length.

cond-mat.stat-mech↗

Induced Anticlinic Ordering and Nanophase Segregation of Bow-Shaped Molecules in a Smectic Solvent

Recent experiments indicate that doping low concentrations of bent-core molecules into calamitic smectic solvents can induce anticlinic and biaxial smectic phases. We have carried out Monte Carlo (MC) simulations of mixtures of rodlike molecules (hard spherocylinders with length/breadth ratio $L_{\rm rod}/D = 5$) and bow- or banana-shaped molecules (hard spherocylinder dimers with length/breadth ratio $L_{ban}/D = 5$ or 2.5 and opening angle $ψ$) to probe the molecular-scale organization and phase behavior of rod/banana mixtures. We find that a low concentration (3%) of $L_{ban}/D = 5$ dimers induces anticlinic (SmC$_A$) ordering in an untilted smectic (SmA) phase for $100^\circ \le ψ< 150^\circ$. For smaller $ψ$, half of each bow-shaped molecule is nanophase segregated between smectic layers, and the smectic layers are untilted. For $L_{ban}/D = 2.5$, no tilted phases are induced. However, with decreasing $ψ$ we observe a sharp transition from {\sl intralamellar} nanophase segregation (bow-shaped molecules segregated within smectic layers) to {\sl interlamellar} nanophase segregation (bow-shaped molecules concentrated between smectic layers) near $ψ= 130^\circ$. These results demonstrate that purely entropic effects can lead to surprisingly complex behavior in rod/banana mixtures.

cond-mat.stat-mech↗

Cross-linking of micelles by gemini surfactants

We investigate the effects of gemini surfactants, telechelic chain and lipids on the nature of micelles formed by conventional single-tail surfactants in water by carrying out Monte Carlo simulations. In a mixture of gemini and single-tail surfactants in water we find direct evidence of micelles of predominantly single-tail surfactants some of which are dynamically cross-linked by gemini surfactants when the concentrations of the geminis is only a few mole percent and their spacers are {\it hydrophilic}. In contrast, mixtures of lipids and single-tail surfactants in water form only isolated micelles, each consisting of a mixture of both species, without cross-links.

cond-mat.stat-mech↗

A Microscopic Model of Gemini Surfactants: Self-assemblies in Water and at Air-Water Interface

We report the results of large scale Monte Carlo (MC) simulations of novel microscopic models of gemini surfactants to elucidate (i) their spontaneous aggregation in bulk water and (ii) their spatial organization in a system where water is separated from the air above it by a sharp well defined interface. We study the variation of the critical micellar concentration (CMC) with the variation of the (a) length of the spacer, (b) length of the hydrophobic tail and (c) the bending rigidity of the hydrocarbon chains forming the spacer and the tail; some of the trends of variation are counter-intuitive but are in excellent agreement with the available experimental results. Our simulations elucidate the effects of the geometrical shape, size and density of the surfactant molecules, the ionic nature of the heads and hydrophobicity/hydrophilicity of the spacer not only on the shapes of the micellar aggregates and the magnitude of the CMC, but also on their conformations close to the air-water interface.

cond-mat.soft↗

Micellar Aggregates of Gemini Surfactants: Monte Carlo Simulation of a Microscopic Model

We propose a "microscopic" model of gemini surfactants in aqueous solution. Carrying out extensive Monte Carlo simulations, we study the variation of the critical micellar concentration (CMC) of these model gemini surfactants with the variation of the (a) length of the spacer connecting the two hydrophilic heads, (b) length of the hydrophobic tail and (c) the bending rigidity of the hydrocarbon chains forming the spacer and the tail; some of the trends of variation are counter-intuitive but are in excellent agreement with the available experimental results. Our simulations also elucidate the dependence of the shapes of the micellar aggregates and the magnitude of the CMC on the geometrical shape and size of the surfactant molecules and the electrical charge on the hydrophilic heads.

cond-mat.soft↗