arXiv subjects

Biman Bagchi

Publications and source records attributed to Biman Bagchi.

At least 127 records · Page 7Linked to original sources

arXiv2006

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↗

arXiv2006

Anisotropic translational diffusion in the nematic phase: Dynamical signature of the coupling between orientational and translational order in the energy landscape

We find in a model system of thermotropic liquid crystals that the translational diffusion coefficient parallel to the director $D_{\parallel}$ first increases and then decreases as temperature drops through the nematic phase, and this reversal occurs where the smectic order parameter of the underlying inherent structures becomes significant for the first time. We argue, based on an energy landscape analysis, that the coupling between orientational and translational order can play a role in inducing the non-monotonic temperature behavior of $D_{\parallel}$. Such a view is likely to form the foundation of a theoretical framework to explain the anisotropic translation diffusion.

cond-mat.soft↗

arXiv2006

Power law relaxation and glassy dynamics in Lebwohl-Lasher model near isotropic-nematic phase transition

Orientational dynamics in a liquid crystalline system near the isotropic-nematic (I-N) phase transition is studied using Molecular Dynamics simulations of the well-known Lebwohl-Lasher (LL) model. As the I-N transition temperature is approached from the isotropic side, we find that the decay of the orientational time correlation functions (OTCF) slows down noticeably, giving rise to a power law decay at intermediate timescales. The angular velocity time correlation function also exhibits a rather pronounced power law decay near the I-N boundary. In the mean squared angular displacement at comparable timescales, we observe the emergence of a \emph{subdiffusive regime} which is followed by a \emph{superdiffusive regime} before the onset of the long-time diffusive behavior. We observe signature of dynamical heterogeneity through \emph{pronounced non-Gaussian behavior in orientational motion} particularly at lower temperatures. This behavior closely resembles what is usually observed in supercooled liquids. We obtain the free energy as a function of orientational order parameter by the use of transition matrix Monte Carlo method. The free energy surface is flat for the system considered here and the barrier between isotropic and nematic phases is vanishingly small for this weakly first-order phase transition, hence allowing large scale, collective and correlated orientational density fluctuations. This might be responsible for the observed power law decay of the OTCFs.

cond-mat.soft↗

arXiv2005

Complete breakdown of the Debye model of rotational relaxation near the isotropic-nematic phase boundary: Effects of intermolecular correlations in orientational dynamics

The Debye-Stokes-Einstein (DSE) model of rotational diffusion predicts that the rotational correlation times $τ_{l}$ vary as $[l(l+1)]^{-1}$, where $l$ is the rank of the orientational correlation function (given in terms of the Legendre polynomial of rank $l$). One often finds significant deviation from this prediction, in either direction. In supercooled molecular liquids where the ratio $τ_{1}/τ_{2}$ falls considerably below three (the Debye limit), one usually invokes a jump diffusion model to explain the approach of the ratio $τ_{1}/τ_{2}$ to unity. Here we show in a computer simulation study of a standard model system for thermotropic liquid crystals that this ratio becomes much less than unity as the isotropic-nematic phase boundary is approached from the isotropic side. Simultaneously, the ratio $τ_2/η$ (where $η$ is the shear viscosity of the liquid) becomes {\it much larger} than hydrodynamic value near the I-N transition. We have also analyzed the break down of the Debye model of rotational diffusion in ratios of higher order rotational correlation times. We show that the break down of the DSE model is due to the growth of orientational pair correlation and provide a mode coupling theory analysis to explain the results.

cond-mat.soft↗

arXiv2005

Decoupling phenomena in supercooled liquids: Signatures in the energy landscape

A significant deviation from the Debye model of rotational diffusion in the dynamics of orientational degrees of freedom in an equimolar mixture of ellipsoids of revolution and spheres is found to begin precisely at a temperature at which the average inherent structure energy of the system starts falling with drop in temperature. We argue that this onset temperature corresponds to the emergence of the alpha-process as a distinct mode of orientational relaxation. Equally important, we find that the coupling between the rotational and translational diffusion breaks down at a still lower temperature where a sharp change occurs in the temperature dependence of the average inherent structure energy.

cond-mat.soft↗

arXiv2005

Universal power law in the orientational relaxation in thermotropic liquid crystals

We observe a surprisingly general power law decay at short to intermediate times in orientational relaxation in a variety of model systems (both calamitic and discotic, and also discrete) for thermotropic liquid crystals. As all these systems transit across the isotropic-nematic phase boundary, two power law relaxation regimes, separated by a plateau, emerge giving rise to a step-like feature (well-known in glassy liquids) in the single-particle second-rank orientational time correlation function. In contrast to its probable dynamical origin in supercooled liquids, we show that the power law here can originate from the thermodynamic fluctuations of the orientational order parameter, driven by the rapid growth in the second-rank orientational correlation length.

cond-mat.soft↗

arXiv2005

Anomalous glassy relaxation near the isotropic-nematic phase transition

Dynamical heterogeneity in a system of Gay-Berne ellipsoids near its isotropic-nematic (I-N) transition and also in an equimolar mixture of Lennard-Jones spheres and Gay-Berne ellipsoids in deeply supercooled regime is probed by the time evolution of non-Gaussian parameter (NGP). The appearance of a dominant second peak in the rotational NGP near the I-N transition signals the growth of pseudonematic domains. Surprisingly such a second peak is instead observed in the translational NGP for glassy binary mixture. Localization of orientational motion near the I-N transition is found to be responsible for the observed anomalous orientational relaxation.

cond-mat.soft↗

arXiv2005

Bridging the Gap Between the Mode Coupling and the Random First Order Transition Theories of Structural Relaxation in Liquids

A unified treatment of structural relaxation in a deeply supercooled glassy liquid is developed which extends the existing mode coupling theory (MCT) by incorporating the effects of activated events by using the concepts from the random first order transition (RFOT) theory. We show how the decay of the dynamic structure factor is modified by localized activated events (called instantons) which lead to the spatial reorganization of molecules in the region where the instanton pops up. The instanton vertex added to the usual MCT depicts the probability and consequences of such an event which can be derived from the random first order transition theory. The vertex is proportional to $exp(-A/s_{c})$ where $s_{c}$ is the configurational entropy. Close to the glass transition temperature, $T_{g}$, since $s_{c}$ is diminishing, the activated process slows beyond the time window and this eventually leads to an arrest of the structural relaxation as expected for glasses. The combined treatment describes the dynamic structure factor in deeply supercooled liquid fairly well, with a hopping dominated decay following the MCT plateau.

cond-mat.dis-nn↗

arXiv2005

Anisotropic Local Stress and Particle Hopping in a Deeply Supercooled Liquid

The origin of the microscopic motions that lead to stress relaxation in deeply supercooled liquid remains unclear. We show that in such a liquid the stress relaxation is locally anisotropic which can serve as the driving force for the hopping of the system on its free energy surface. However, not all hopping are equally effective in relaxing the local stress, suggesting that diffusion can decouple from viscosity even at local level. On the other hand, orientational relaxation is found to be always coupled to stress relaxation.

physics.chem-ph↗

arXiv2004

Frequency dependent heat capacity within a kinetic model of glassy dynamics

There has been renewed interest in the frequency dependent specific heat of supercooled liquids in recent years with computer simulation studies exploring the whole frequency range of relaxation. The simulation studies can thus supplement the existing experimental results to provide an insight into the energy landscape dynamics. We here investigate a kinetic model of cooperative dynamics within the landscape paradigm for the dynamic heat capacity behavior. In this picture, the beta-process is modeled as a thermally activated event in a two-level system and the alpha-process is described as a beta-relaxation mediated cooperative transition in a double well. The model provides a description of the activated hopping in the energy landscape in close relation with the cooperative nature of the hopping event. For suitable choice of parameters, the model predicts a frequency dependent heat capacity that reflects the two-step relaxation behavior. Although experimentally obtained specific heat spectra of supercooled liquids till date could not capture the two-step relaxation behavior, this has been observed in a computer simulation study by Scheidler et. al. [Phys. Rev. B 63, 104204 (2001)]. The temperature dependence of the position of the low-frequency peak, due to the alpha-relaxation, shows a non-Arrhenius behavior as observed experimentally by Birge and Nagel [Phys. Rev. Lett. 54, 2674 (1985)]. The shape of the alpha-peak is, however, found to be temperature independent, in agreement with the simulation result. The high-frequency peak appears with considerably larger amplitude than the alpha-peak. We attempt a plausible reason for this observation that is in contrast with the general feature revealed by the dielectric spectroscopy.

cond-mat.soft↗

arXiv2004

Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect

Rotational friction on proteins and macromolecules is known to derive contributions from at least two distinct sources -- hydrodynamic (due to viscosity) and dielectric friction (due to polar interactions). In the existing theoretical approaches, the effect of the latter is taken into account in an {\it ad hoc} manner, by increasing the size of the protein with the addition of a hydration layer. Here we calculate the rotational dielectric friction on a protein ($ζ_{DF}$) by using a generalized arbitrary charge distribution model (where the charges are obtained from quantum chemical calculation) and the hydrodynamic friction with stick boundary condition, ($ζ_{hyd}^{stick}$) by using the sophisticated theoretical technique known as tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp. Biol. Med. {\bf 12}, 75 (1982)]. The calculation of hydrodynamic friction is done with only the dry volume of the protein (no hydration layer). We find that the total friction obtained by summing up $ζ_{DF}$ and $ζ_{hyd}^{stick}$ gives reasonable agreement with the experimental results, i.e., $ζ_{exp} \approx ζ_{DF} + ζ_{hyd}^{stick}$.

physics.bio-ph↗

arXiv2004

Self-consistent mode-coupling theory for the viscosity of rod-like polyelectrolyte solutions

A self-consistent mode-coupling theory is presented for the viscosity of solutions of charged rod-like polymers. The static structure factor used in the theory is obtained from polymer integral equation theory; the Debye-Hückel approximation is inadequate even at low concentrations. The theory predicts a non-monotonic dependence of the reduced excess viscosity, $η_R$, on concentration from the behaviour of the static structure factor in polyelectrolyte solutions. The theory predicts that the peak in $η_R$ occurs at concentrations slightly lower than the overlap threshold concentration, $c^\ast$. The peak height increases dramatically with increasing molecular weight and decreases with increased concentrations of added salt. The position of the peak, as a function of concentration divided by $c^\ast$ is independent of salt concentration or molecular weight. The predictions can be tested experimentally.

cond-mat.soft↗

arXiv2004

Relaxation in open one-dimensional systems

A new master equation to mimic the dynamics of a collection of interacting random walkers in an open system is proposed and solved numerically.In this model, the random walkers interact through excluded volume interaction (single-file system); and the total number of walkers in the lattice can fluctuate because of exchange with a bath.In addition, the movement of the random walkers is biased by an external perturbation. Two models for the latter are considered: (1) an inverse potential (V $\propto$ 1/r), where r is the distance between the center of the perturbation and the random walker and (2) an inverse of sixth power potential ($V \propto 1/r^6 $). The calculated density of the walkers and the total energy show interesting dynamics. When the size of the system is comparable to the range of the perturbing field, the energy relaxation is found to be highly non-exponential. In this range, the system can show stretched exponential ($ e^{-{(t/τ_s)}^β} $) and even logarithmic time dependence of energy relaxation over a limited range of time. Introduction of density exchange in the lattice markedly weakens this non-exponentiality of the relaxation function, irrespective of the nature of perturbation.

cond-mat.soft↗

arXiv2003

Simulation and theory of vibrational phase relaxation in the critical and supercritical nitrogen: Origin of observed anomalies

We present results of extensive computer simulations and theoretical analysis of vibrational phase relaxation of a nitrogen molecule along the critical isochore and also along the gas-liquid coexistence. The simulation includes all the different contributions [atom-atom (AA), vibration-rotation (VR) and resonant transfer] and their cross-correlations. Following Everitt and Skinner, we have included the vibrational coordinate ($q$) dependence of the interatomic potential. It is found that the latter makes an important contribution. The principal important results are: (a) a crossover from a Lorentzian-type to a Gaussian line shape is observed as the critical point is approached along the isochore (from above), (b) the root mean square frequency fluctuation shows nonmonotonic dependence on the temperature along critical isochore, (c) along the coexistence line and the critical isochore the temperature dependent linewidth shows a divergence-like $λ$-shape behavior, and (d) the value of the critical exponents along the coexistence and along the isochore are obtained by fitting. The origin of the anomalous temperature dependence of linewidth can be traced to simultaneous occurrence of several factors, (i) the enhancement of negative cross-correlations between AA and VR contributions and (ii) the large density fluctuations as the critical point (CP) is approached. The former makes the decay faster so that local density fluctuations are probed on a femtosecond time scale. A mode coupling theory (MCT) analysis shows the slow decay of the enhanced density fluctuations near critical point. The MCT analysis demonstrates that the large enhancement of VR coupling near CP arises from the non-Gaussian behavior of density fluctuation and this enters through a nonzero value of the triplet direct correlation function.

cond-mat.soft↗

arXiv2003

Anomalous Temperature Dependence of Heat Capacity During a Cooling-Heating Cycle in Glassy Systems

Anomalous temperature dependence of heat capacity of glassy systems during a cooling-heating cycle has remained an ill-understood problem for a long time. Most of the features observed in the experimental measurement of the heat capacity of a supercooled liquid are shown here to be adequately explained by a general model. The model that we propose is motivated by the success of landscape paradigm, and describes βrelaxation in terms of a collection of two-level systems and conceives αrelaxation as a βrelaxation mediated cooperative transition in a double-well. The anomalous sharp rise in the heat capacity observed during heating is shown to have a kinetic origin, being caused by delayed energy relaxation due to nonequilibrium effects.

cond-mat.soft↗

arXiv2003

Relationship between Entropic Bottleneck in Free Energy Landscape, Nonexponential Relaxation and Fragility of Glass-Forming Liquids

A mesoscopic model is proposed to explain the anomalous dynamics in a supercooled liquid as its glass transition temperature is approached from above. The model is based on the assumption of $β$ organized $α$ process, with the requirement of coherent excitation of a minimum critical number $N_{c}$ of $β$ processes in the surroundings of a total $N_β$. Numerical evaluation of the model shows that the growth in this critical number in the background of a modest $N_β$ can lead to a severe entropic bottleneck and slow down the dynamics to an extent observed near real glass transition. The fragility of the glass-forming liquid is shown to be correlated with the growth of the ratio $γ(= N_{c}/N_β)$.

cond-mat.soft↗

arXiv2003

Dynamics of Bound and Free Water in an Aqueous Micellar Solution : Analysis of the Lifetime and Vibrational Frequencies of Hydrogen Bonds at a Complex Interface

In order to understand the nature and dynamics of interfacial water molecules on the surface of complex systems, large scale molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate surfactant molecules have been carried out. The lifetime and the intermolecular vibrational frequencies of the hydrogen bonds that the water molecules form with the polar headgroups of the surfactants, are calculated. Our earlier classification of the interfacial water molecules, based on structural and energetic considerations, into bound and free type is further validated by their dynamics. Lifetime correlation functions of the water-surfactant hydrogen bonds show the long lived nature of the bound water species. The water molecules that are singly hydrogen bonded to the surfactants have longer lifetime than those that form two such hydrogen bonds. The free water molecules that do not form any such hydrogen bonds behave similar to bulk water in their reorientational dynamics. A few water molecules that form two such hydrogen bonds are orientationally locked in for durations of the order of few hundreds of picoseconds. The intermolecular vibrational frequencies of these interfacial water molecules shows a significant blue shift in the librational band apart from a similar shift in the near neighbor bending modes, relative to water molecules in bulk. These blue shifts suggest an increase in rigidity in the structure around interfacial water molecules. This is in good agreement with recent incoherent, inelastic neutron scattering data on macromolecular solutions. The results of the present simulations should be relevant to the understanding of dynamics of water near any hydrophilic surface.

cond-mat.soft↗

arXiv2003

Molecular Dynamics Simulation of Vibrational Phase Relaxation along the Critical Isochore of Nitrogen : The Role of Local Density Fluctuations

Vibrational dephasing of nitrogen molecule is known to show highly interesting anomalies near its gas-liquid critical point. Here we present theoretical and computational studies of the Raman linewidth of nitrogen along the critical isochore. The linewidth is found to have a lambda shaped temperature dependence near the critical point. As observed in experimental studies, the calculated lineshape becomes Gaussian as the critical temperature ($T_{c}$) is approached. Both the present simulation and a mode coupling theory (MCT) analysis show that the slow decay of the enhanced density fluctuations near the critical point (CP), probed at the sub-picosecond time scales by vibrational frequency modulation, along with an enhanced vibration-rotation coupling, are the main causes of the observed anomalies.

physics.chem-ph↗