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Biman Bagchi

Publications and source records attributed to Biman Bagchi.

At least 37 records · Page 2Linked to original sources
PubMed2005

Hydration layer of a cationic micelle, C(10)TAB: structure, rigidity, slow reorientation, hydrogen bond lifetime, and solvation dynamics.

We report a theoretical study of the structure and dynamics of the water layer (the hydration layer) present at the surface of the cationic micelle decyltrimethylammonium bromide (DeTAB) by using atomistic molecular dynamics simulations. The simulated micelle consisted of 47 surfactant molecules (and an equal number of bromide ions), in good agreement with the pioneering light scattering experiments by Debye which found an aggregation number of 50. In this micelle, three partially positively charged methyl groups of each surfactant headgroup face the surrounding water. The nature of the cationic micellar surface is found to play an important role in determining the arrangement of water which is quite different from that in the bulk or on the surface of an anionic micelle, like cesium perfluorooctanoate. Water molecules present in the hydration layer are found to be preferentially distributed in the region between the three partially charged methyl headgroups. It is found that both the translational and rotational motions of water exhibit appreciably slower dynamics in the layer than those in the bulk. The solvation time correlation function (TCF) of bromide ions exhibits a long time component which is found to originate primarily from the interaction of the probe with the micellar headgroups. Thus, the decay of the solvation TCF is controlled largely by the residence time of the probe in the surface. The residence time distribution of the water molecules also exhibits a slow time component. We also calculate the collective number density fluctuation in the layer and find a prominent slow component compared to the similar quantity in the bulk. This slow component demonstrates that water structure in the hydration layer is more rigid than that in the bulk. These results demonstrate that the slow dynamics of hydration layer water is generic to macromolecular surfaces of either polarity.

Journal Article↗
PubMed2005

Orientation-dependent potential of mean force for protein folding.

We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model, the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other sites through an orientation-dependent interaction potential which we construct in the following fashion. First, the site-site potential of mean force (PMF) between heavy atoms is calculated [following F. Melo and E. Feytsman, J. Mol. Biol. 267, 207 (1997)] from statistics of their distance separation obtained from crystal structures. These site-site potentials are then used to calculate the distance and the orientation-dependent potential between side chains of all the amino acid residues (AAR). The distance and orientation dependencies show several interesting results. For example, we find that the PMF between two hydrophobic AARs, such as phenylalanine, is strongly attractive at short distances (after the obvious repulsive region at very short separation) and is characterized by a deep minimum, for specific orientations. For the interaction between two hydrophilic AARs, such a deep minimum is absent and in addition, the potential interestingly reveals the combined effect of polar (charge) and hydrophobic interactions among some of these AARs. The effectiveness of our potential has been tested by calculating the Z-scores for a large set of proteins. The calculated Z-scores show high negative values for most of them, signifying the success of the potential to identify the native structure from among a large number of its decoy states.

Arginine↗
PubMed2005

Nonmonotonic composition dependence of vibrational phase relaxation rate in binary mixtures.

We present here isothermal-isobaric N-P-T ensemble molecular dynamics simulations of vibrational phase relaxation in a model system to explore the unusual features arising due to concentration fluctuations which are absent in one component systems. The model studied consider strong attractive interaction between the dissimilar species to discourage phase separation. The model reproduces the experimentally observed nonmonotonic, nearly symmetric, composition dependence of the dephasing rate. In addition, several other experimentally observed features, such as the maximum of the frequency modulation correlation time tau(c) at mole fraction near 0.5 and the maximum rate enhancement by a factor of about 3 above the pure component value, are also reproduced. The product of mean square frequency modulation [ ] with tau(c) indicates that the present model is in the intermediate regime of inhomogeneous broadening. The nonmonotonic composition chi(A) dependence of the dephasing time tau(v) is found to be primarily due to the nonmonotonic chi dependence of tau(c), rather than due to a similar dependence in the amplitude of Delta omega(2)(0). The probability distribution of Delta omega shows a markedly non-Gaussian behavior at intermediate composition (chi(A) approximately =0.5). We have also calculated the composition dependence of the viscosity in order to explore the correlation between the composition dependence of viscosity eta(*) with that of tau(v) and tau(c). It is found that both the correlation time essentially follow the composition dependence of the viscosity. A mode coupling theory is presented to include the effects of composition fluctuations in binary mixture.

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PubMed2005

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 parameters (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 the glassy binary mixture. Localization of orientational motion near the I-N transition is found to be responsible for the observed anomalous orientational relaxation.

Journal Article↗
PubMed2005

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe.

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.

Binding Sites↗
PubMed2005

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 C(omega,T) 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 resembles a landscape picture, apparently first conceived by Stillinger [Science 267, 1935 (1995)], where an alpha-process is assumed to involve a concerted series of beta-processes. 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. The separation between the two peaks grows as the temperature drops, indicating the stringent constraint on the alpha-process due to the cooperativity requirement. The temperature dependence of the position of the low-frequency peak, due to the alpha-relaxation, shows a non-Arrhenius behavior as observed experimentally. The shape of the alpha-peak is, however, found to be temperature independent. 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. The relative amplitudes of the beta- and alpha-peaks in the present framework are found to depend on several characteristic features of the energy landscape, including the extent of cooperativity requirement for the alpha-relaxation and the asymmetry of the double well.

Journal Article↗
PubMed2004

Self-consistent mode-coupling theory for the viscosity of rodlike polyelectrolyte solutions.

A self-consistent mode-coupling theory is presented for the viscosity of solutions of charged rodlike polymers. The static structure factor used in the theory is obtained from polymer integral equation theory; the Debye-Huckel approximation is inadequate even at low concentrations. The theory predicts a nonmonotonic dependence of the reduced excess viscosity eta(R) on concentration from the behavior of the static structure factor in polyelectrolyte solutions. The theory predicts that the peak in eta(R) occurs at concentrations slightly lower than the overlap threshold concentration, c*. 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*, is independent of salt concentration or molecular weight. The predictions can be tested experimentally.

Journal Article↗
PubMed2004

Anomalous viscoelasticity near the isotropic-nematic phase transition in liquid crystals.

Recent optical Kerr effect experiments have shown that orientational relaxation of nematogens shows a pronounced slow down of the response function at intermediate times and also a power law decay near the isotropic-nematic (I-N) transition. In many aspects, this behavior appears to be rather similar to the ones observed in the supercooled liquid near-glass transition. We have performed molecular dynamics simulations of model nematogens (Gay-Berne with aspect ratio 3) to explore the viscoelasticity near the I-N transition and also investigated the correlation of viscoelasticity (if any) with orientational relaxation. It is found that although the viscosity indeed undergoes a somewhat sharper than normal change near the I-N transition, it is not characterized by any divergence-like behavior (like the ones observed in the supercooled liquid). The rotational friction, on the other hand, shows a much sharper rise as the I-N transition is approached. Interestingly, the probability distribution of the amplitude of the three components of the stress tensor shows anisotropy near the I-N transition-similar anisotropy has also been seen in the deeply supercooled liquid. Frequency dependence of viscosity shows several unusual behaviors: (a) There is a weak, power law dependence on frequency [eta(')(omega) approximately omega(-alpha)] at low frequencies and (b) there is a rapid increase in the sharp peak observed in eta(')(omega) in the intermediate frequency on approach to the I-N transition density. These features can be explained from the stress-stress time correlation function. The angular velocity correlation function also exhibits a power law decay in time. The reason for this is discussed.

Journal Article↗
PubMed2004

Nonmonotonic temperature dependence of heat capacity through the glass transition within a kinetic model.

The heat capacity of a supercooled liquid subjected to a temperature cycle through its glass transition is studied within a kinetic model. In this model, the beta process is assumed to be thermally activated and described by a two-level system. The alpha process is described as a beta relaxation mediated cooperative transition in a double well. The overshoot of the heat capacity during the heating scan is well reproduced and is shown to be directly related to delayed energy relaxation in the double well. In addition, the calculated scan rate dependencies of the glass transition temperature T(g) and the limiting fictive temperature T(f) (L) show qualitative agreement with the known results. Heterogeneity is found to significantly reduce the overshoot of heat capacity. Furthermore, the frequency dependent heat capacity has been calculated within the present framework and found to be rather similar to the experimentally observed behavior of supercooled liquids.

Journal Article↗
PubMed2004

In search of temporal power laws in the orientational relaxation near isotropic-nematic phase transition in model nematogens.

Recent Kerr relaxation experiments by Gottke et al. have revealed the existence of a pronounced temporal power law decay in the orientational relaxation near the isotropic-nematic phase transition (INPT) of nematogens of rather small aspect ratio, kappa (kappa approximately 3-4). We have carried out very long (50 ns) molecular dynamics simulations of model (Gay-Berne) prolate ellipsoids with aspect ratio 3 in order to investigate the origin of this power law. The model chosen is known to undergo an isotropic to nematic phase transition for a range of density and temperature. The distance dependence of the calculated angular pair correlation function correctly shows the emergence of a long range correlation as the INPT is approached along the density axis. In the vicinity of INPT, the single particle second rank orientational time correlation function exhibits power law decay, (t(-alpha)) with exponent alpha approximately 2/3. More importantly, we find the sudden appearance of a pronounced power-law decay in the collective part of the second rank orientational time correlation function at short times when the density is very close to the transition density. The power law has an exponent close to unity, that is, the correlation function decays almost linearly with time. At long times, the decay is exponential-like, as predicted by Landau-de Gennes mean field theory. Since Kerr relaxation experiments measure the time derivative of the collective second rank orientational pair correlation function, the simulations recover the near independence of the signal on time observed in experiments. In order to capture the microscopic essence of the dynamics of pseudonematic domains inside the isotropic phase, we introduce and calculate a dynamic orientational pair correlation function (DOPCF) obtained from the coefficients in the expansion of the distinct part of orientational van Hove time correlation function in terms of spherical harmonics. The DOPCF exhibits power law relaxation when the pair separation length is below certain critical length. The orientational relaxation of a local director, defined in terms of the sum of unit vectors of all the ellipsoidal molecules, is also found to show slow power law relaxation over a long time scale. These results have been interpreted in terms of a newly developed mode coupling theory of orientational dynamics near the INPT. In the present case, the difference between the single particle and the collective orientational relaxation is huge which can be explained by the frequency dependence of the memory kernel, calculated from the mode coupling theory. The relationship of this power law with the one observed in a supercooled liquid near its glass transition temperature is explored.

Journal Article↗
PubMed2004

Density and energy relaxation in an open one-dimensional system.

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 proportional, variant 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 proportional, 1/r6). 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 nonexponential. In this range, the system can show stretched exponential (e-(t/taus)beta) and even logarithmic time dependence of energy relaxation over a limited range of time. Introduction of density exchange in the lattice markedly weakens this nonexponentiality of the relaxation function, irrespective of the nature of perturbation.

Journal Article↗
PubMed2004

Anomalous dielectric relaxation of water molecules at the surface of an aqueous micelle.

Dielectric relaxation of aqueous solutions of micelles, proteins, and many complex systems shows an anomalous dispersion at frequencies intermediate between those corresponding to the rotational motion of bulk water and that of the organized assembly or macromolecule. The precise origin of this anomalous dispersion is not well-understood. In this work we employ large scale atomistic molecular dynamics simulations to investigate the dielectric relaxation (DR) of water molecules in an aqueous micellar solution of cesium pentadecafluorooctanoate. The simulations clearly show the presence of a slow component in the moment-moment time correlation function [PhiMW(t)] of water molecules, with a time constant of about 40 ps, in contrast to only 9 ps for bulk water. Interestingly, the orientational time correlation function [Cmu(t)] of individual water molecules at the surface exhibits a component with a time constant of about 19 ps. We show that these two time constants can be related by the well-known micro-macrorelations of statistical mechanics. In addition, the reorientation of surface water molecules exhibits a very slow component that decays with a time constant of about 500 ps. An analysis of hydrogen bond lifetime and of the rotational relaxation in the coordinate frame fixed on the micellar body seems to suggest that the 500 ps component owes its origin to the existence of an extended hydrogen bond network of water molecules at the surface. However, this ultraslow component is not found in the total moment-moment time correlation function of water molecules in the solution. The slow DR of hydration water is found to be well correlated with the slow solvation dynamics of cesium ions at the water-micelle interface.

Colloids↗
PubMed2004

Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.

The folding of an extended protein to its unique native state requires establishment of specific, predetermined, often distant, contacts between amino acid residue pairs. The dynamics of contact pair formation between various hydrophobic residues during folding of two different small proteins, the chicken villin head piece (HP-36) and the Alzheimer protein beta-amyloid (betaA-40), are investigated by Brownian dynamics (BD) simulations. These two proteins represent two very different classes-HP-36 being globular while betaA-40 is nonglobular, stringlike. Hydropathy scale and nonlocal helix propensity of amino acids are used to model the complex interaction potential among the various amino acid residues. The minimalistic model we use here employs a connected backbone chain of atoms of equal size while an amino acid is attached to each backbone atom as an additional atom of differing sizes and interaction parameters, determined by the characteristics of each amino acid. Even for such simple models, we find that the low-energy structures obtained by BD simulations of both the model proteins mimic the native state of the real protein rather well, with a best root-mean-square deviation of 4.5 A for HP-36. For betaA-40 (where a single well-defined structure is not available), the simulated structures resemble the reported ensemble rather well, with the well-known beta-bend correctly reproduced. We introduce and calculate a contact pair distance time correlation function, C(P) (ij)(t), to quantify the dynamical evolution of the pair contact formation between the amino acid residue pairs i and j. The contact pair time correlation function exhibits multistage dynamics, including a two stage fast collapse, followed by a slow (microsecond long) late stage dynamics for several specific pairs. The slow late stage dynamics is in accordance with the findings of Sali et al. Analysis of the individual trajectories shows that the slow decay is due to the attempt of the protein to form energetically more favorable pair contacts to replace the less favorable ones. This late stage contact formation is a highly cooperative process, involving participation of several pairs and thus entropically unfavorable and expected to face a large free energy barrier. This is because any new pair contact formation among hydrophobic pairs will require breaking of several contacts, before the favorable ones can be formed. This aspect of protein folding dynamics is similar to relaxation in glassy liquids, where also alpha relaxation requires highly cooperative process of hopping. The present analysis suggests that waiting time for the necessary pair contact formation may obey the Poissonian distribution. We also study the dynamics of Forster energy transfer during folding between two tagged amino acid pairs. This dynamics can be studied by fluorescence resonance energy transfer (FRET). It is found that suitably placed donor-acceptor pairs can capture the slow dynamics during folding. The dynamics probed by FRET is predicted to be nonexponential.

Alzheimer Disease↗
PubMed2003

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, fully atomistic molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate (CsPFO) surfactant molecules have been carried out. The lifetime and the intermolecular vibrational frequencies of the hydrogen bonds that the water molecules form with the hydrophilic, polar head groups (PHG) of the surfactants are calculated. Our earlier classification [S. Balasubramanian et al., Curr. Sci. 84, 428 (2003); e-print cond-mat/0212097] of the interfacial water molecules, based on structural and energetic considerations, into bound and free types 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. Surprisingly, the water molecules that are singly hydrogen bonded to the surfactants have a longer lifetime than those that form two such hydrogen bonds. The free water molecules that do not form any such hydrogen bonds behave similarly 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 a few hundreds of picoseconds; that is, much longer than their average lifetime. The intermolecular vibrational frequencies of these interfacial water molecules have been studied from the power spectra of their velocity autocorrelation function. We find a significant blue shift in the librational band of the interfacial water molecules, 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 [S. Ruffle et al., J. Am. Chem. Soc. 124, 565 (2002)]. The results of the present simulations appear to be rather general and should be relevant to the understanding of the dynamics of water near any hydrophilic surface.

Journal Article↗
PubMed2003

Diffusion and viscosity in a supercooled polydisperse system.

We have carried out extensive molecular dynamics simulations of a supercooled polydisperse Lennard-Jones liquid with large variations in temperature at a fixed pressure. The particles in the system are considered to be polydisperse in both size and mass. The temperature dependence of dynamical properties such as the viscosity (eta) and the self-diffusion coefficients (D(i)) of different size particles is studied. Both viscosity and diffusion coefficients show super-Arrhenius temperature dependence and fit well to the well-known Vogel-Fulcher-Tammann equation. Within the temperature range investigated, the value of Angell's fragility parameter (D approximately 1.4) classifies the present system as a very fragile liquid. The critical temperature for diffusion (T(D(i))(o)) increases with the size of the particles. The critical temperature for viscosity (T(eta)(o)) is larger than that for diffusion, and sizable deviations appear for the smaller size particles, implying a decoupling of translational diffusion from viscosity in deeply supercooled liquids. Indeed, the diffusion shows markedly non-Stokesian behavior at low temperatures where a highly nonlinear dependence on size is observed. An inspection of the trajectories of the particles shows that at low temperatures the motions of both the smallest and largest size particles are discontinuous (jump type). However, the crossover from continuous Brownian to large length hopping motion takes place at shorter time scales for the smaller size particles.

Journal Article↗
PubMed2003

Pair dynamics in a glass-forming binary mixture: simulations and theory.

We have carried out molecular dynamics simulations to understand the dynamics of a tagged pair of atoms in a strongly nonideal glass-forming binary Lennard-Jones mixture. Here atom B is smaller than atom A (sigma(BB)=0.88sigma(AA), where sigma(AA) is the molecular diameter of the A particles) and the AB interaction is stronger than that given by Lorentz-Berthelot mixing rule (epsilon(AB)=1.5epsilon(AA), where epsilon(AA) is the interaction energy strength between the A particles). The generalized time-dependent pair distribution function is calculated separately for the three pairs (AA, BB, and AB). The three pairs are found to behave differently. The relative diffusion constants are found to vary in the order D(BB)(R)>D(AB)(R)>D(AA)(R), with D(BB)(R) approximately 2D(AA)(R), showing the importance of the hopping process (B hops much more than A). We introduce a non-Gaussian parameter [alpha(P)(2)(t)] to monitor the relative motion of a pair of atoms and evaluate it for all the three pairs with initial separations chosen to be at the first peak of the corresponding partial radial distribution functions. At intermediate times, significant deviation from the Gaussian behavior of the pair distribution functions is observed with different degrees for the three pairs. A simple mean-field (MF) model, proposed originally by Haan [Phys. Rev. A 20, 2516 (1979)] for one-component liquid, is applied to the case of a binary mixture and compared with the simulation results. While the MF model successfully describes the dynamics of the AA and AB pairs, the agreement for the BB pair is less satisfactory. This is attributed to the large scale anharmonic motions of the B particles in a weak effective potential. Dynamics of the next nearest neighbor pairs is also investigated.

Journal Article↗
PubMed2003

Vibrational phase relaxation along the critical isochore of nitrogen: the role of local density fluctuations in the rate enhancement.

Vibrational dephasing of the 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 line shape becomes Gaussian as the critical temperature (T(c)) is approached. Both the present simulation and a mode coupling theory analysis show that the slow decay of the enhanced density fluctuations near the critical point, probed at the subpicosecond time scales by vibrational frequency modulation, along with an enhanced vibration-rotation coupling, are the main causes of the observed anomalies.

Journal Article↗