arXiv subjects

Biman Bagchi

Publications and source records attributed to Biman Bagchi.

At least 55 records · Page 3Linked to original sources

arXiv2019

Altered Dielectric Behaviour, Structure and Dynamics of Nanoconfined Dipolar Liquids: Signatures of Enhanced Cooperativity

Spherical confinement can alter the properties of a dipolar fluid in several different ways. In an atomistic molecular dynamics simulation study of two different dipolar liquids (SPC/E water and a model Stockmayer fluid) confined to nanocavities of different radii ranging from Rc=1nm to 4nm, we find that the Kirkwood correlation factor remains surprisingly small in water, but not so in model Stockmayer liquid. This gives rise to an anomalous ultrafast relaxation of the total dipole moment time correlation function (DMTCF). The static dielectric constant of water under nanoconfinement (computed by employing Clausius-Mossotti equation, the only exact relation) exhibits a strong dependence on the size of the nanocavity with a remarkably slow convergence to the bulk value. Interestingly, the value of the volume becomes ambiguous in this nanoworld. It is determined by the liquid-surface interaction potential and is to be treated with care because of the sensitivity of the Clausius-Mossotti equation to the volume of the nanosphere. We discover that the DMTCF for confined water exhibit a bimodal 1/f noise power spectrum. We also comment on the applicability of certain theoretical formalisms that become dubious in the nanoworld.

cond-mat.soft↗

arXiv2019

Fractional size dependence of surface tension of a growing nucleus with an inhomogeneous interface

The surface energy of the nucleus of a stable phase growing in the presence of several amorphous metastable phases of character intermediate between the initial and the final phases may depend non-trivially on the size of the nucleus. This size dependence is being increasingly used to explain diverse non-equilibrium phase selection, and relaxation, as in the random first-order transition (RFOT) theory of glasses. Here we develop an order parameter based Ginzburg-Landau approach that explicitly includes the rugged free energy landscape due to the metastable phases. The fractional dependence of total surface energy between melt and stable solid phase on the number of metastable phases($N_{MS}$) has been interrogated in this study. We have also analyzed how this fractional dependence gets modified with temperature. We find that the fractional size dependence of surface energy is omnipresent, arises from the minimization of free energy and demands certain ordering of metastable phases in the interface. Our results could recover the celebrated result of Villain that forms the basis of RFOT theory of glasses. We find the additional result that the surface tension saturates to a finite size independent value.

cond-mat.soft↗

arXiv2019

Translation-Rotation Coupling in the Dynamics of Linear Molecules in Water

We study by computer simulations the coupled rotational and translational dynamics of three important linear diatomic molecules, namely, carbon monoxide (CO), nitric oxide (NO) and cyanide ion (CN-) in water. Translational diffusion of these molecules is found to be strongly coupled to their own rotational dynamics which in turn are coupled to similar motions of surrounding water. We examined the validity of hydrodynamic predictions and found them to be largely insufficient, particularly for rotational diffusion. A mode coupling theory approach is developed and applied to understand the complexity of translation-rotation coupling.

cond-mat.soft↗

arXiv2019

Tetrahedral entropy captures non-monotonicity of electrical conductivity in aqueous monatomic ions

The intriguing relationship between entropy and diffusion is a subject of much current interest. However, the experimentally observed unusual non-monotonic dependence of limiting ionic conductivity on inverse ion size is neither described by the Adam-Gibbs entropy crisis theory nor by the Rosenfeld entropy scaling. This failure is obvious because throughout the size variation the bulk entropy of the solvent remains the same, or undergoes infinitesimal change. We show that it is the entropy experienced by the tagged ion that needs to be calculated. This entropy can be quantified, at least partly, by the change in the tetrahedral ordering of water molecules in the hydration layer of the ions which exhibits a nonmonotonic size dependence.

cond-mat.soft↗

arXiv2019

Interference effects between ion induced solvent polarisations in Liquid water

We calculate the effective force between two oppositely charged and similarly charged ions fixed in water as a function of separation distance R. At short separations, R less than 1 nm, the effective force is vastly different from the $1/ε_{s}R^2$ dependence advocated by the screened Coulomb force law (SCFL); $ε_{s}$ being the static dielectric constant of the medium. We also find an interesting asymmetry in the force between +ve and -ve ions. This breakdown of SCFL is shown to be due to the persistent interference between the polarizations created by the two charges, in a manner similar to the vortex-antivortex pair formation in XY model Hamiltonian. The distance dependence of dielectric constants, $ε_{s}$(R) extracted from our simulation exhibit interesting features and can be used in future modelling.

cond-mat.soft↗

arXiv2018

Exploration of vitrification of water and Kauzmann entropy through complex specific heat: A journey through 'No Man's Land'

Frequency dependent specific heat, introduced by Grest and Nagel, offers valuable insight into the vitrification of supercooled liquid. We calculate this quantity and other thermodynamic properties of supercooled liquid water by varying temperature and density across the "no man's land" all the way to the formation of amorphous ice. The calculations are aided by very long computer simulations, often more than 50 $μs$ long. Density fluctuations that arise from the proximity to a putative liquid-liquid (LL) transition at 228 K, cast a long shadow on the properties of water, both above and below the LL transition. We carry out the calculation of the quantum mechanical static and frequency-dependent specific heats by combining seminal works by Lebowitz, Percus, and Verlet and Grest and Nagel with the harmonic approximation for the density of states. The obtained values are in quantitative agreement with all available experimental and numerical results of specific heats for both supercooled water and ice. We calculate the entropy at all the state points by integrating the specific heat. We find that the quantum corrected-contributions of intermolecular vibrational entropy dominate the excess entropy of amorphous phases over the crystal over a wide range of temperature. Interestingly, the vibrational entropy lowers the Kauzmann temperature, $T_{\rm K}$, to 130 K, just below the experimental glass-to-liquid water transition temperature, $T_{\rm g}$, of 136 K and the calculated $T_{\rm g}$ of 135 K in our previous study. A straightforward extrapolation of high temperature entropy from 250 K to below however would give a much higher value of $T_{\rm K}$ $\sim$ 190 K. The calculation of Lindemann ratios places the melting of amorphous ice $\sim$ 135 K. The amorphous state exhibits an extremely short correlation length for the distance dependence of orientational correlation.

cond-mat.soft↗

arXiv2018

Crucial role of fragmented and isolated defects in persistent relaxation of deeply supercooled water

Properties of water have been well elucidated for temperatures above $\sim$230 K and yet mysteries remain in the deeply supercooled region. By performing extensive molecular dynamics simulations on this supercooled region, we find that structural and dynamical instabilities are hidden in the experimentally inaccessible region between 235 K and 150 K. We find a hitherto undiscovered fragmentation from 220 K to 190 K, which is the break-up of large clusters consisting of molecules with locally distorted tetrahedral structure into small pieces with one or two isolated defects. The fragmentation leads to considerable changes in the relaxation dynamics of water. We reveal a crucial role of specific three-coordinated defects in slow but persistent structural relaxation. The presence of relaxation due to these specific defects makes water glass transition temperature $T_{\rm g}$ (= 136 K) extremely low and explains why the $T_{\rm g}$ of water is $\sim$ 1/2 of the melting temperature Tm, much lower than the commonly obeyed 2/3 rule of $T_{\rm g}/T_{\rm m}$.

cond-mat.soft↗

arXiv2018

Diffusion in the presence of correlated dynamical disorder and coherent exciton transfer in the non-Markovian limit

The presence of static off-diagonal disorder promotes coherent exciton transport while diffusive motion can be recovered in the presence of fluctuations in the diagonal and off-diagonal elements of the Hamiltonian. Here we study the crossover induced by correlated dynamical disorder.We uncover a novel role of the excited bath states (ExBS) in dictating quantum coherence and quantum transport in dissipative quantum systems interacting with correlated bath.We solve both analytically and numerically the temperature dependent Quantum Stochastic Liouville equation (TD-QSLE) to study temperature dependence of quantum coherence in both linear chains and cyclic trimer (first three subunits of Fenna-Matthews-Olson(FMO) and also heptamer) complexes, using Haken-Strobl-Reineker Hamiltonian. In the non-Markovian limit where the lowering of temperature induces long-lasting quantum coherences, ExBSnot only determines the lifetime of coherences but also dictates the long time population distribution. We find a parallelism between classical and quantum systems through transitions among excited bath states that provides a deeper insight about role of temperature in equilibrium distribution.The effects of dynamic disorder and excited bath stat eon quantum entanglement (through the calculation of concurrence) in single exciton manifold are demonstrated.

cond-mat.stat-mech↗

arXiv2018

Transport in a binary mixture of non-spherical molecules: Is hydrodynamics at fault?

We consider a new class of model systems to study systematically the role of molecular shape in the transport properties of dense liquids. Our model is a liquid binary mixture where both the molecules are non-spherical and characterized by a collection of parameters. Although in the real world most of the molecules are non-spherical, only a limited number of theoretical studies exist on the effects of molecular shapes and hardly any have addressed the validity of the hydrodynamic predictions of rotational and translational diffusion of these shapes in liquids. In this work, we study a model liquid consisting of a mixture of prolate and oblate (80:20 mixture) ellipsoidals with interactions governed by a modified Gay-Berne potential for a particular aspect ratio (ratio of the length and diameter of the ellipsoids), at various temperature and pressure conditions. We report calculations of transport properties of this binary mixture by varying temperature over a wide range, at a fixed pressure. We find that for the pressure-density conditions studied, there is no signature of any phase separation, except transitions to the crystalline phase at low temperatures and relatively low pressure (the reason we largely confined our studies to high pressure). We find that for our model binary mixture, both the stick and slip hydrodynamic predictions break down in a major fashion, for both prolates and oblates and particularly so for rotation. Moreover, prolates and oblates themselves display different dynamical features in the mean square displacement and in orientational time correlation functions.

physics.comp-ph↗

arXiv2018

Hidden role of metastable phases on surface tension and in the selection of solid polymorphs from melt

The preferential formation of one solid over the other, as it precipitates out from the melt at specific temperatures, is often explained by invoking a competition between thermodynamic and kinetic control. A quantitative theory, however, could not be developed because of the lack of accurate values of relevant surface tension terms. Motivated by the observations that wetting of the interface between two stable phases by multiple metastable phases of intermediate order can reduce the surface tension significantly (Kirkpatrick-Thirumalai-Wolynes (KTW), Phys. Rev. A 1989, 40 (2), 1045; Santra et al., J. Phys. Chem. B, 2013, 117, 13154 ), we develop a statistical mechanical approach based on a Landau-Ginzburg type free energy functional to calculate the surface tension between two stable phases in the presence of N number of metastable phases. Simple model calculations are performed that show the surface tension between two coexisting stable phases (melt and the stable crystalline forms) depends significantly on the number, relative depths and arrangements of the free energy minima of the metastable phases, in addition to the size of the nucleus. We provide an explanation of the quickly disappearing polymorphs (QDPMs) that often melt back to the liquid (or, the sol) phase. It is shown that our model systems could describe some aspects of solid formation in real polymorphic systems, like phosphates and zeolites.

cond-mat.stat-mech↗

arXiv2018

Adverse effect of ethanol on insulin dimer stability

Alcohol is widely believed to have an effect on diabetes, often considered beneficial in small amounts but detrimental in excess. The reasons are not fully known but questions have been asked about the stability of insulin oligomers in the presence of ethanol. We compute the free energy surface (FES) and the pathway of insulin dimer dissociation in water and in 5% and 10% water-ethanol mixture. We find that in the presence of ethanol the barrier energy of dissociation reaction decreases by about 40% even in 5% water-ethanol solution. In addition, ethanol induces a significant change in the reaction pathway. We obtain estimates of the rate of reaction and binding energy for all the three systems and those agree well with the previous experimental results for the insulin dimer dissociation in water. The computed FES in water exhibits ruggedness due to the existence of a number of intermediate states surrounded by high and broad transition state region. However, the presence of ethanol smoothens out the ruggedness. We extracted the conformations of the intermediate states along the minimum energy pathway in all the three systems and analyzed the change in microscopic structures in the presence of ethanol. Interestingly, we discover a stable intermediate state in water-ethanol mixtures where the monomers are separated (center-to-center) by about 3 nm and the contact order parameter is close to zero. This intermediate is stabilized by the distribution of ethanol and water molecules at the interface and which, significantly, serves to reduce the dissociation rate constant .The solvation of the two monomers during the dissociation and proteins' departure from native state configuration are analyzed to obtain insight into the dimer dissociation processes.

q-bio.BM↗

arXiv2018

In search of the origin of long-time power-law decay in DNA solvation dynamics

Experiments reveal that DNA solvation dynamics (SD) is characterized by multiple time scales ranging from a few ps to hundreds of ns and in some cases even up to microseconds. The last part of decay is slow and is characterized by a power law (PL). The microscopic origin of this PL is not yet clearly understood. Here we present a theoretical study based on time dependent statistical mechanics and computer simulations. Our investigations show that the primary candidates responsible for this exotic nature of SD are the counterions and ions from the buffer solution. We employ the model developed by Oosawa for polyelectrolyte solution that includes effects of counterion fluctuations to construct a frequency dependent dielectric function. We use it in the continuum model of Bagchi, Fleming and Oxtoby only to find that it fails to explain the slow PL decay of DNA solvation dynamics. We then extend the model by employing the continuous time random walk technique developed by Scher-Montroll-Lax. This approach can explain the long time PL decay, in terms of the collective response of the counter ions. From MD simulations we find frequent occurrence of random walk of tagged counter ions along the phosphate backbone. We propose a generalized random walk model for counterion hopping and carry out kinetic Monte Carlo simulations to show that the nonexponential contribution to solvation dynamics can indeed arise from dynamics of such ions. We also employ a Mode Coupling Theory analysis to understand the slow relaxation that originates from ions in solution. Explicit evaluation suggests that buffer ion contribution could explain logarithmic time dependence in the ns time scale, but not a power law. From MD simulations we find log-normal distributions of relaxation times of water dynamics inside the grooves. This is responsible for the initial faster multiexponential decay of SD.

cond-mat.stat-mech↗

arXiv2018

Polymorph selection during crystallization of a model colloidal fluid with a free energy landscape containing a metastable solid

The free energy landscape responsible for crystallization can be complex even for relatively simple systems like hard sphere and charged stabilized colloids. In this work, using hard-core repulsive Yukawa model, which is known to show complex phase behavior consisting of fluid, FCC and BCC phases, we studied the interplay between the free energy landscape and polymorph selection during crystallization. When the stability of the BCC phase with respect to the fluid phase is gradually increased by changing the temperature and pressure at a fixed fluid-FCC stability, the final phase formed by crystallization is found to undergo a switch from the FCC to the BCC phase, even though FCC remains thermodynamically the most stable phase. We further show that the nature of local bond-orientational order parameter fluctuations in the metastable fluid phase as well as the composition of the critical cluster depend delicately on the free energy landscape, and play a decisive role in the polymorph selection during crystallization.

cond-mat.soft↗

arXiv2018

A unified picture of roto-translational dynamics in aqueous polyatomic ions

Mode-coupling theory provides a unified description of the rotational and translational dynamics of polyatomic ions. These molecular ions are distinct from usual models of ion diffusion, such as K+ , Cl- etc., and also different from rotational dynamics of dipolar molecules often modeled in dielectric continuum models as point dipoles. Both these approaches are untenable for polyatomic ions. Here rotational and translational dynamics are so strongly coupled that one obtains a more coherent description by treating them together. We carry out theoretical and computational studies of a series of well-known polyatomic ions, namely sulfate, nitrate and acetate ions. All the three ions exhibit different rotational diffusivity, with that of nitrate ion being considerably larger than the other two. They all defy the hydrodynamic laws of size dependence. Study of the local structure around the ions provides valuable insight into the origin of these differences. We carry out a detailed study of the rotational diffusion of these ions by extensive computer simulation and using the theoretical approaches of the dielectric friction developed by Fatuzzo-Mason (FM) and Nee-Zwanzig (NZ), and subsequently generalized by Alavi and Waldeck. We develop a self-consistent mode-coupling theory (SC-MCT) formalism that helps elucidating the role of coupling between translational and rotational motion of these ions. In fact, these two motions self-consistently determine the value of each other. The RISM-based MCT suggests an interesting relation between the torque-torque and the force-force time correlation function with the proportionality constant being determined by the geometry and the charge distribution of the polyatomic molecule.We point out several parallelism between the theories of translational and rotation friction calculations of ions in dipolar liquids.

cond-mat.soft↗

arXiv2018

Towards Understanding the Structure, Dynamics and Bio-activity of Diabetic Drug Metformin

Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows anti-tumour activities and increases the survival rate of patients suffering from certain types of cancer namely colorectal, breast, pancreas and prostate cancer. However, theoretical studies of structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three mono-protonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to that of the experimental findings. Nevertheless, we discover that the non-planar tautomeric form is the most stable. Metformin forms strong hydrogen bonds with surrounding water molecules and its solvation dynamics show unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry and metadynamics simulation. We find a non-intercalating mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT rich domains. A significant decrease in the free-energy of binding is observed when it binds to a minor groove of DNA.

q-bio.BM↗

arXiv2017

Cavity Waters Govern Insulin Association and Release: Inferences from Experimental Data and Molecular Dynamics Simulations

While a monomer of the ubiquitous hormone insulin is the biologically active form in the human body, its hexameric assembly acts as an efficient storage unit. However, the role of water molecules in the structure, stability and dynamics of the insulin hexamer is poorly understood. Here we combine experimental data with molecular dynamics simulations to investigate the shape, structure and stability of an insulin hexamer focusing on the role of water molecules. Both X-Ray analysis and computer simulations show that the core of the hexamer cavity is barrel-shaped, holding, on an average, sixteen water molecules. These encapsulated and constrained molecules impart structural stability to the hexamer. Apart from the electrostatic interactions with Zn2+ ions, an intricate hydrogen bond network amongst cavity water and neighboring protein residues stabilizes the hexameric association. These water molecules solvate six glutamate residues inside the cavity decreasing electrostatic repulsions amongst the negatively charged carboxylate groups. They also prevent association between glutamate residues and Zn2+ ions and maintain the integrity of the cavity. Simulations reveal that removal of these waters results in a collapse of the cavity. Subsequent analyses also show that the hydrogen bond network among these water molecules and protein residues that face the inner side of the cavity is more rigid with a slower relaxation as compared to that of the bulk solvent. Dynamics of cavity water reveal certain slow water molecules which form the back bone of the stable hydrogen bond network. The analysis presented here suggests a dominant role of structurally conserved water molecules in maintaining the integrity of the hexameric assembly and potentially modulating the dissociation of this assembly into the functional monomeric form.

q-bio.BM↗

arXiv2017

On the origin of diverse time scales in the protein hydration layer solvation dynamics: A molecular dynamics simulation study

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely, Lysozyme, Myoglobin and sweet protein Monellin. In these experiments we mutate the charges of the neighbouring amino acid side chains of certain natural probes (Tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component in the ~20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component may arise from various sources namely, adjacent charges in amino acid side chains, the water molecules that are hydrogen bonded to them and a dynamically coupled motion between side chain and water. The charges, in addition, enforce a structural ordering of nearby water molecules and helps to form local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component whereas the initial ultrafast decay arise predominantly (~80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi quantitative manner.

cond-mat.soft↗

arXiv2017

A mode-coupling theory analysis of the rotation driven translational motion of aqueous polyatomic ions

In contrast to simple monatomic alkali and halide ions, complex polyatomic ions like nitrate, acetate, nitrite, chlorate etc. have not been studied in any great detail. Experiments have shown that diffusion of polyatomic ions exhibits many remarkable anomalies, notable among them is the fact that polyatomic ions with similar size show large difference in their diffusivity values. This fact has drawn relatively little interest in scientific discussions. We show here that a mode-coupling theory (MCT) can provide a physically meaningful interpretation of the anomalous diffusivity of polyatomic ions in water, by including the contribution of rotational jumps on translational friction. The two systems discussed here, namely aqueous nitrate ion and aqueous acetate ion, although have similar ionic radii exhibit largely different diffusivity values due to the differences in the rate of their rotational jump motions. We have further verified the mode-coupling theory formalism by comparing it with experimental and simulation results that agrees well with the theoretical prediction.

physics.chem-ph↗