arXiv subjects

Biman Bagchi

Publications and source records attributed to Biman Bagchi.

At least 109 records · Page 6Linked to original sources

arXiv2010

Correlation between inherent structures and phase separation mechanism in binary mixtures

Binary mixtures are known to phase separate via both nucleation and spinodal decomposition, depending on the initial composition and extent of the quench. Here we develop an energy landscape view of phase separation and non-ideality in binary mixtures by exploring their potential energy landscape (PEL) as functions of temperature and composition, by employing a molecular model that promotes structure breaking abilities of the solute-solvent parent binary liquid at low temperatures. PEL that provides the inherent structure (IS) of a system is obtained by removing the kinetic energy (including that of intermolecular vibrations). Broad Distribution of inherent structure energy demonstrates the larger role of entropy in stabilizing the parent liquid of the structure breaking type of binary mixtures. At high temperature, although the parent structure is homogenous, the corresponding inherent structure is found to be always phase separated, with a density pattern that exhibits marked correlation with the energy of inherent structure. Over broad range of intermediate inherent structure energy, bicontinuous phase separation prevails with interpenetrating stripes as signatures of spinodal decomposition. At low inherent structure energy, the structure is largely phase separated with one interface where as at high inherent structure energy, we find nucleation type growth. Interestingly, at low temperature, the average inherent structure energy ( ) exhibits a drop with temperature which signals onset of crystallization in one of the phases while the other remains in the liquid state. The non-ideal composition dependence of viscosity is anti-correlated with average inherent structure energy.

cond-mat.stat-mech↗

arXiv2010

Gas-liquid Nucleation at Large Metastability

Nucleation at large metastability is still largely an unsolved problem, although is a problem of tremendous current interest, with wide practical value. It is well-accepted that the classical nucleation theory (CNT) fails to provide a qualitative picture and gives incorrect quantitative values for such quantities as activation free energy barrier and supersaturation dependence of nucleation rate, especially at large metastability. In this article, we present a powerful alternative formalism to treat nucleation at large supersaturation. This formalism goes over to the classical picture at small supersaturation where CNT is expected to be valid. The new theory is based on an extended set of order parameters in terms of k-th largest liquid-like clusters where k=1 is the largest cluster in the system, k=2 is the second largest cluster and so on. We derive an analytic expression for the free energy of formation of the k-th largest cluster which shows that at large metastability the barrier of growth for the few largest liquid-like clusters disappear, the nucleation becomes collective and the approach to the critical size occurs by barrierless diffusion in the cluster size space. The expression for the rate of barrier crossing predicts a weaker supersaturation dependence than that of CNT at large metastability. Such a cross-over behavior has indeed been observed in recent experiments but eluded an explanation till now. In order to understand the large numerical difference between simulation predictions and experimental results, we carried out a study of the dependence on the range of intermolecular interaction of both the surface tension of an equilibrium planar gas-liquid interface and the free energy barrier of nucleation. Both are found to depend significantly on the range of interaction for a Lennard-Jones potential, both in two and three dimensions.

cond-mat.stat-mech↗

arXiv2010

Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a phosphate transfer, and then the release of two ADP molecules. We have computed a novel two dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, with explicit interactions with water. Our computed 2DCFES clearly reveals the existence of a stable half-open-half-closed (HOHC) intermediate state of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for the reaction by about 20 kJ/mol. We find that the stability of the half-open-half-closed state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

cond-mat.stat-mech↗

arXiv2010

A kinetic Ising model study of dynamical correlations in confined fluids: Emergence of both fast and slow time scales

Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation of molecules in confined systems such as water in reverse micelles, cyclodextrin cavities and nano-tubes. Here we introduce a novel finite length one dimensional Ising model to investigate the propagation and the annihilation of dynamical correlations in finite systems and to understand the intriguing shortening of the orientational relaxation time that has been reported for small sized reverse micelles. In our finite sized model, the two spins at the two end cells are oriented in the opposite directions, to mimic the effects of surface that in real system fixes water orientation in the opposite directions. This produces opposite polarizations to propagate inside from the surface and to produce bulk-like condition at the centre. This model can be solved analytically for short chains. For long chains we solve the model numerically with Glauber spin flip dynamics (and also with Metropolis single-spin flip Monte Carlo algorithm). We show that model nicely reproduces many of the features observed in experiments. Due to the destructive interference among correlations that propagate from the surface to the core, one of the rotational relaxation time components decays faster than the bulk. In general, the relaxation of spins is non-exponential due to the interplay between various interactions. In the limit of strong coupling between the spins or in the limit of low temperature, the nature of relaxation of the spins undergoes a qualitative change with the emergence of a homogeneous dynamics where decay is predominantly exponential, again in agreement with experiments.

cond-mat.stat-mech↗

arXiv2010

Propagating rotational jump events drive liquid-liquid transition in supercooled liquid water

We observe, at low temperature, the appearance of propagating events that originate from the inter-conversion between adjacent four and five coordinated water molecules in supercooled liquid water, resulting in the migration of the coordination number five in a string-like fashion, creating rotational jumps along the way. The length of the connected events increases with lowering temperature. Each propagation event is terminated by a 3-coordinated species, present in a small number at large supercooling, which interacts cooperatively with 5-coordinated molecules to annihilate both the species. We find that these growing dynamical correlations manifest in a divergent-like growth of a non-linear density response function, \times4(t), which is given by a four point time correlation function (FPTCF). The locus of the maximum of \times4(t), when plotted against the time t* of maximum, exhibits a sharp peak precisely at the temperature where the static response functions (specific heat, isothermal compressibility) also show similar sharp, divergent-like, peak. While the decay of population fluctuation time correlation function of both 4- and 5- coordinated species slows down dramatically and a step-like feature of the relaxation becomes evident, the lifetime itself of 5-corrdinated species remains short. These results suggest a new molecular mechanism of low temperature anomalies and of the liquid-liquid transition in terms of initiation, growth and termination of propagating jump and inter-conversion events.

cond-mat.stat-mech↗

arXiv2009

Wavenumber dependence of the structural relaxation time in the crossover regime of supercooled liquid dynamics

As a liquid is progressively supercooled an intriguing weakening of the wavenumber ($q$) dependence of the structural relaxation time $τ(q)$ in the large q limit is observed both in experiments and simulation studies. Neither the continuous Brownian diffusive dynamics nor the discontinuous activated events can alone explain the anomalous wavenumber dependence. Here we use our recently developed theory that unifies the mode coupling theory (MCT) for continuous dynamics and the random first order transition theory (RFOT) treatment of activated discontinuous motion as a nucleation (instanton) process, to understand the wavenumber dependence of density relaxation. The predicted smooth change in mechanism of relaxation from diffusive to activated, in the crossover regime, is wavevector dependent and is eventually responsible for sub-quadratic, almost linear, $q$ dependence of the relaxation time.

cond-mat.soft↗

arXiv2009

Vibrational dynamics and boson peak in a supercooled polydisperse liquid

Vibrational density of states (VDOS) in a supercooled polydisperse liquid is computed by diagonalizing the Hessian matrix evaluated at the potential energy minima for systems with different values of polydispersity. An increase of polydispersity leads to an increase in relative population of the localized high-frequency modes. At low frequencies, the density of states show an excess compared to the Debye squared-frequency law, which has been identified with the boson peak. The height of the boson peak increases with polydispersity. The values of the participation ratio as well as the level spacing statistics demonstrate that the modes comprising the boson peak are largely delocalized. Interestingly, the intensity of the boson peak shows a rather narrow sensitivity to changes in temperature and is seen to persist even at high temperatures. Study of the difference spectrum at two different polydispersity reveals that the increase in the height of boson peak is due to a population shift from modes with frequencies above the maximum in the VDOS to that below the maximum, indicating an increase in the fraction of the unstable modes in the system. The latter is further supported by the facilitation of the observed dynamics by polydispersity. Since the strength of the liquid increases with polydispersity, the present result provides an evidence that the intensity of boson peak correlates positively with the strength of the liquid, as observed earlier in many experimental systems.

cond-mat.other↗

arXiv2008

Suppression of the rate of growth of dynamic heterogeneities and its relation to the local structure in a supercooled polydisperse liquid

The relationship between the microscopic arrangement of molecules in a supercooled liquid and its slow dynamics at low temperature near glass transition is studied by Molecular Dynamics (MD) simulations. A Lennard-Jones liquid with polydispersity in size and mass of constituent particles is chosen as the model system. Our studies reveal that the local structure (that varies with polydispersity) plays a crucial role both in the slowing down of dynamics and in the growth of the dynamic heterogeneities, besides determining the glass forming ability (GFA) of the system. Increasing polydispersity at fixed volume fraction is found to suppress the rate of growth of dynamic correlations, as detected by the growth in the peak of the non-linear density response function. The growth in dynamical correlation is manifested in a stronger than usual breakdown of Stokes-Einstein relation at lower polydispersity at low temperatures and also leads to a decrease in the fragility of the system with polydispersity. We show that the suppression of the rate of growth of the dynamic heterogeneity can be attributed to the loss of structural correlations (as measured by the structure factor and the local bond orientational order) with polydispersity. While a critical polydispersity is required to avoid crystallization, we find that further increase in polydispersity lowers the glass forming ability (GFA).

cond-mat.soft↗

arXiv2008

Energy Landscape, Anti-Plasticization and Polydispersity Induced Crossover of Heterogeneity in Supercooled Polydisperse Liquids

Polydispersity is found to have a significant effect on the potential energy landscape; the the average inherent structure energy with temperature decreases with polydispersity. Increasing polydispersity at fixed volume fraction decreases the glass transition temperature and the fragility of glass formation analogous to the antiplasticization seen in some polymeric melts. An interesting temperature dependent crossover of heterogeneity with polydispersity is observed at low temperature due to the faster build-up of dynamic heterogeneity at lower polydispersity.

cond-mat.soft↗

arXiv2008

Dynamical transition in translational and rotational dynamics of water in the grooves of DNA duplex at low temperature

We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both the major and the minor grooves of a DNA duplex. The transition occurs at a slightly higher temperature ($T_{GL} \approx $ 255 K) than the temperature ($T_L\approx$ 247 K) where the bulk water is conjectured to undergo a dynamical transition. Groove water, however, exhibits markedly different temperature dependence of its properties from the bulk. Entropy calculations reveal that the minor groove water is ordered even at room temperature and the transition at $T \approx$ 255 K can be characterized as a {\em strong-to-strong} dynamical transition. The low temperature water is characterized by pronounced tetrahedral order, as manifested in the sharp rise near $109^{\circ}$ in the O-O-O angle distribution. We find that Adams-Gibbs relation between configurational entropy and translational diffusion holds quite well when the two quantities are plotted together in a master plot for different region of aqueous DNA duplex (bulk, major and minor grooves) at different temperatures. The activation energy for the transfer of water molecules between different regions of DNA is found to be independent of temperature.

cond-mat.soft↗

arXiv2008

Gas-Liquid Nucleation in Two Dimensional System

We study the nucleation of the liquid phase from a supersaturated vapor in two dimensions (2D). Using different Monte Carlo simulation methods, we calculate the free energy barrier for nucleation, the line tension and also investigate the size and shape of the critical nucleus. The study is carried out at an intermediate level of supersaturation(away from the spinodal limit). In 2D, a large cut-off in the truncation of the Lennard-Jones (LJ) potential is required to obtain converged results, whereas low cut-off (say, $2.5σ$ is generally sufficient in three dimensional studies, where $σ$ is the LJ diameter) leads to a substantial error in the values of line tension, nucleation barrier and characteristics of the critical cluster. It is found that in 2D, the classical nucleation theory (CNT) fails to provide a reliable estimate of the free energy barrier. It underestimates the barrier by as much as 70% at the saturation-ratio S=1.1 (defined as S=P/PC, where PC is the coexistence pressure at reduced temperature $T^{\star}= 0.427$). Interestingly, CNT has been found to overestimate the nucleation free energy barrier in three dimensional (3D)systems near the triple point. In fact, the agreement with CNT is worse in 2D than in 3D. Moreover, the existing theoretical estimate of the line tension overestimates the value significantly.

physics.chem-ph↗

arXiv2008

Hopping induced continuous diffusive dynamics below the non-ergodic transition

In low temperature supercooled liquid, below the ideal mode coupling theory transition temperature, hopping and continuous diffusion are seen to coexist. We present a theory which incorporates interaction between the two processes and shows that hopping can induce continuous diffusion in the otherwise frozen liquid. Several universal features arise from nonlinear interactions between the continuous diffusive dynamics (described here by the mode coupling theory (MCT)) and the activated hopping (described here by the random first order transition theory). We apply the theory to real systems (Salol) to show that the theory correctly predicts the temperature dependence of the non-exponential stretching parameter, $β$, and the primary $α$ relaxation timescale, $τ$. The study explains why, even below the ergodic to non-ergodic transition, the dynamics is well described by MCT. The non-linear coupling between the two dynamical processes modifies the relaxation behavior of the structural relaxation from what would be predicted by a theory with a complete static Gaussian barrier distribution in a manner that may be described as a facilitation effect. Furthermore, the theory explains the observed variation of the stretching exponent $β$ with the fragility parameter, $D$.

cond-mat.stat-mech↗

arXiv2008

Thermodynamic and transport anomalies near isotropic-nematic phase transition

A theoretical study of the variation of thermodynamic and transport properties of calamitic liquid crystals across the isotropic-nematic phase transition is carried out by calculating the {\it wavenumber (k) and time (t)} dependent intermediate scattering function of the liquid, via computer simulations of model nematogens. The objective is to understand the experimentally observed anomalies and sharp variation in many thermodynamic and transport properties, namely specific heat $C$, sound attenuation coefficient $Γ$, thermal diffusivity $D_T$ and sound velocity $c_s$ are as the I-N transition is approached from the isotropic side. The small wavelength limit of the calculated intermediate scattering function $F(k,t)$ is used to obtain the ratio of specific heats $γ$ and other properties mentioned above. We find that all of them show non-monotonic variations near the I-N transition, with $Γ$ showing a cusp-like behavior. We suggest that the observed anomalous features are a direct consequence of the existence of pseudo-nematic domains in the system near the phase boundary and the melting and formation of such domains give rise to sound attenuation and also to the observed specific heat anomaly. A theoretical description of these anomalies should invoke translation-rotation coupling at molecular level. While the heterogeneous dynamics observed here bear resemblance to that in deeply supercooled liquids near glass transition, the thermodynamic anomalies articulated here are largely absent in supercooled liquids.

cond-mat.soft↗

arXiv2007

Orientational relaxation in a discotic liquid crystal

We investigate orientational relaxation of a model discotic liquid crystal, consists of disc-like molecules, by molecular dynamics simulations along two isobars starting from the high temperature isotropic phase. The two isobars have been so chosen that (A) the phase sequence isotropic (I)-nematic (N)-columnar (C) appears upon cooling along one of them and (B) the sequence isotropic (I)-columnar (C) along the other. While the orientational relaxation in the isotropic phase near the I-N phase transition in system (A) shows a power law decay at short to intermediate times, such power law relaxation is not observed in the isotropic phase near the I-C phase boundary in system (B). In order to understand this difference (the existence or the absence of the power law decay), we calculated the the growth of the orientational pair distribution functions (OPDF) near the I-N phase boundary and also near the I-C phase boundary. We find that OPDF shows a marked growth in long range correlation as the I-N phase boundary is approached in the I-N-C system (A), but such a growth is absent in the I-C system, which appears to be consistent with the result that I-N phase transition in the former is weakly first order while the the I-C phase transition in the later is not weak. As the system settles into the nematic phase, the decay of the single-particle second-rank orientational OTCF follows a pattern that is similar to what is observed with calamitic liquid crystals and supercooled molecular liquids.

cond-mat.soft↗

arXiv2007

How glassy are orientational dynamics of rodlike molecules near the isotropic-nematic transition?

In an attempt to quantitatively characterize the recently observed slow dynamics in the isotropic and nematic phase of liquid crystals, we investigate the single-particle orientational dynamics of rodlike molecules across the isotropic-nematic transition in computer simulations of a family of model systems of thermotropic liquid crystals. Several remarkable features of glassy dynamics are on display including non-exponential relaxation, dynamical heterogeneity, and non-Arrhenius temperature dependence of the orientational relaxation time. In order to obtain a quantitative measure of glassy dynamics in line with the estbalished methods in supercooled liquids, we construct a relaxation time versus scaled inverse temperature plot, and demonstrate that one can indeed define a 'fragility index' for thermotropic liquid crystals, that depends on density and aspect ratio. The values of the fragility parameter are surprisingly in the range one observed for glass forming liquids. A plausible correlation between the energy landscape features and the observed fragility is discussed.

cond-mat.soft↗

arXiv2007

Dynamical Heterogeneity and the interplay between activated and mode coupling dynamics in supercooled liquids

We present a theoretical analysis of the dynamic structure factor (DSF) of a liquid at and below the mode coupling critical temperature $T_c$, by developing a self-consistent theoretical treatment which includes the contributions both from continuous diffusion, described using general two coupling parameter ($F_{12}$) mode coupling theory (MCT), and from the activated hopping, described using the random first order transition (RFOT) theory, incorporating the effect of dynamical heterogeneity. The theory is valid over the whole temperature plane and shows correct limiting MCT like behavior above $T_{c}$ and goes over to the RFOT theory near the glass transition temperature, $T_{g}$. Between $T_{c}$ and $T_{g}$, the theory predicts that neither the continuous diffusion, described by pure mode coupling theory, nor the hopping motion alone suffices but both contribute to the dynamics while interacting with each other. We show that the interplay between the two contributions conspires to modify the relaxation behavior of the DSF from what would be predicted by a theory with a complete static Gaussian barrier distribution in a manner that may be described as a facilitation effect. Close to $T_c$, coupling between the short time part of MCT dynamics and hopping reduces the stretching given by the F$_{12}$-MCT theory significantly and accelerates structural relaxation. As the temperature is progressively lowered below $T_c$, the equations yield a crossover from MCT dominated regime to the hopping dominated regime. In the combined theory the dynamical heterogeneity is modified because the low barrier components interact with the MCT dynamics to enhance the relaxation rate below $T_c$ and reduces the stretching that would otherwise arise from an input static barrier height distribution.

cond-mat.stat-mech↗

arXiv2007

Mechanism of nucleation and growth near the gas-liquid spinodal

Understanding the mechanism of nucleation of the stable phase inside the metastable parent phase during a first order phase transition has been a subject of outstanding interest in natural science. The problem becomes even more challenging as the spinodal is approached. In this work, we have undertaken extensive computer simulation studies to probe the molecular mechanism for the onset of instability. We have constructed the free energy surfaces of nucleation as a function of multiple reaction coordinates, both for supercooled Lennard-Jones fluid and for 2- and 3-dimensional Ising models. While the classical Becker-Doring (BD) picture of homogenous nucleation, that assumes the growth of a single nucleus by single particle addition, holds good at low to moderate supersaturation, the formation of the new stable phase becomes more collective and spread over the whole system at large supersaturation. As the spinodal curve is approached from the coexistence line, the free energy, as a function of the size of the largest liquid-like cluster, develops a minimum at a sub-critical cluster size. This minimum at intermediate size is responsible for the barrier towards further growth of the nucleus at large supersaturation. As the spinodal is approached closely, this minimum gradually disappears and so does the free energy barrier for the cluster growth. We find the emergence of an alternative free energy pathway (with a barrier less than that in the BD picture) that involves participation of many sub-critical liquid-like clusters and the growth of the stable phase is promoted by a coalescence mechanism. Very close to the spinodal the free energy surface becomes quite flat, the significance of a critical nucleus is lost and the classical Becker-Doring picture of nucleation breaks down.

cond-mat.soft↗

arXiv2006

Rate of Excitation Energy Transfer between Fluorescent Dyes and Nanoparticles

Long range resonance energy transfer (RET) between a donor and an acceptor molecule is increasingly being used in many areas of biological and material science. The phenomenon is used to monitor the in vivo separation between different (bio) polymers/units of (bio) polymers and hence the dynamics of various biomolecular processes. Because of the sensitivity of the rate on to the distance between the donor (D) and the acceptor (A), the technique is popularly termed as "spectroscopic ruler". In this work we examine the distance and orientation dependence of RET in three different systems: (i) between a conjugated polymer and a fluorescent dye, (ii) between a nanometal particle (NMP) and a fluorescent dye and (iii) between two NMP. We show that in all the three cases, the rate of RET follows a distance dependence of d^(- sigma) where exponent sigma approaches 6 at large d (F"orster type dependence) but has a value varying from 3-4 at short to intermediate distance. At short separation, the amplitude of rate is considerably smaller than predicted by the F"orster theory.

cond-mat.mtrl-sci↗