Dynamics of water at the interface of a small protein, enterotoxin

Fully atomistic molecular dynamics simulations have been carried out to investigate the correlation of biological activity with dynamics of water molecules in an aqueous protein solution of the toxic domain of enterotoxin (PDB ID: 1ETN). This is a small protein of 13 amino acid residues. Our study of this water soluble protein clearly reveals that water dynamics slows down in the hydration layer. Despite this general slowing down, water molecules in the vicinity of the second beta turn of this protein exhibit faster dynamics than those near other regions of the protein. Since this beta turn is believed to play a critical role in the receptor binding of this protein, the faster dynamics of water near the beta turn m ay have biological significance. The collective orientational dynamics of the water molecules in the protein solution exhibits a characteristic long time component of 27 ps, which agrees well with dielectric relaxation experiments.

Identity, energetics, dynamics and environment of interfacial water molecules in a micellar solution

The structure and energetics of interfacial water molecules in the aqueous micelle of cesium perfluorooctanoate have been investigated, using large-scale atomistic molecular dynamics simulations, with the primary objective of classifying them. The simulations show that the water molecules at the interface fall into two broad classes: bound and free, present in a ratio of 9:1. The bound water molecules can be further categorized on the basis of the number of hydrogen bonds (one or two) that they form with the surfactant headgroups. The hydrogen bonds of the doubly hydrogen-bonded species are found to be, on the average, slightly weaker than those in the singly bonded species. The environment around interfacial water molecules is more ordered than that in the bulk. The surface water molecules have substantially lower potential energy, because of interaction with the micelle. In particular, both forms of bound water have energies that are lower by �2.5-4.0 kcal/ mol. Entropy is found to play an important role in determining the relative concentration of the species.

Study of the dynamics of protein folding through minimalistic models

Starting with the Levinthal paradox, a brief introduction to the protein folding problem is presented. The existing theories of protein folding, including the folding funnel scenario, are discussed. After briefly discussing different simulation studies of model proteins, we discuss our recent work on the dynamics of folding of the model HP-36 (the chicken villin headpiece) protein by using a simplified hydropathy scale. Special attention has been paid to the statics and dynamics of contact formation among the hydrophobic residues. The results obtained from this simple model appear to be surprisingly similar to several features observed in the folding of real proteins. The account concludes with a discussion of future problems.

Vortex dynamics and upper critical fields in ultrathin Bi films

Current-voltage (I-V) characteristics of quench condensed, superconducting, ultrathin Bi films in a magnetic field are reported. These I-V's show hysteresis for all films, grown both with and without thin Ge underlayers. Films on Ge underlayers, close to superconductor-insulator transition, show a peak in the critical current, indicating a structural transformation of the vortex solid. These underlayers, used to make the films more homogeneous, are found to be more effective in pinning the vortices. The upper critical fields (B-c2) of these films are determined from the resistive transitions in perpendicular magnetic field. The temperature dependence of the upper critical field is found to differ significantly from Ginzburg-Landau theory, after modifications for disorder.

Procedural aspects of modeling the dynamics of a three wheeled vehicle using ADAMS-CAR

We describe in some detail the process of development of a dynamic model of a three wheeled vehicle using ADAMS-CAR. We first describe the rigid body model, and then the modeling of structural flexibilities. The aim of this report is to document procedural details of such modeling, with a view to presenting more research and development oriented investigations in the future. The contents of this report may also be of interest to practicing engineers engaged in multi-body dynamics modeling of wheeled vehicles.

Structural Rigidity of Paranemic Crossover and Juxtapose DNA Nanostructures

Crossover motifs are integral components for designing DNA-based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been investigated extensively using both experimental and theoretical tools, to date there is no quantitative information about structural rigidity and the mechanical strength of parallel crossover DNA motifs. We have used fully atomistic molecular dynamics simulations in explicit solvent to get the force-extension curve of parallel DNA nanostructures to characterize their mechanical rigidity. In the presence of monovalent Na(+) ions, we find that the stretch modulus (gamma(1)) of the paranemic crossover and its topoisomer JX DNA structure is significantly higher (similar to 30%) compared to normal B-DNA of the same sequence and length. However, this is in contrast to the original expectation that these motifs are almost twice as rigid compared to the double-stranded B-DNA. When the DNA motif is surrounded by a solvent with Mg(2+) counterions, we find an enhanced rigidity compared to Na(+) environment due to the electrostatic screening effects arising from the divalent nature of Mg(2+) ions. To our knowledge, this is the first direct determination of the mechanical strength of these crossover motifs, which can be useful for the design of suitable DNA for DNA-based nanostructures and nanomechanical devices with improved structural rigidity.

Brillouin Scattering Investigation of Solvation Dynamics in Succinonitrile-Lithium Salt Plastic Crystalline Electrolytes

Temperature dependent Brillouin scattering studies have been performed to ascertain the influence of solvent dynamics on ion-transport in succinonitrile-lithium salt plastic crystalline electrolytes. Though very rarely employed, we observe that Brillouin spectroscopy is an invaluable tool for investigation of solvent dynamics. Analysis of various acoustic (long wavelength) phonon modes observed in the Brillouin scattering spectra reveal the influence of trans-gauche isomerism and as well as ion-association effects on ion transport. Although pristine SN and dilute SN-LiClO(4) samples show only the bulk longitudinal-acoustic (LA) mode, concentrated SN-LiClO(4) (similar to 0.3-1 M) electrolytes display both the bulk LA mode as well as salt induced brillouin modes at ambient temperature. The appearance of more than one brillouin mode is attributed to the scattering of light from regions with different compressibilities (''compactness''). Correspondingly, these modes show a large decrease in the full width at half-maximum (abbreviated as nu(f)) as the temperature decreases. Anomalous temperature dependent behavior of nu(f) with addition of salt could be attributed to the presence of disorder or strong coupling with a neighbor. The shape of the spectrum was evaluated using a Lorentzian and Fano line shape function depending on the nature and behavior of the Brillouin modes.

Structure and dynamics of protein excited states with millisecond lifetimes

An in-depth understanding of biological processes often requires detailed atomic resolution structures of the molecules involved. However in solution where most of these processes occur the conformation of biomolecules like RNA, DNA and proteins is not static but fluctuates. Routinely used structural techniques like X-ray crystallography, NMR spectroscopy and cryo-electron microscopy have almost always been used to determine the structure of the dominant conformation or obtain an average structure of the biomolecule in solution with very little detailed information regarding the dynamics of these molecules in solution. Over the last few years, NMR based methods have been developed to study the dynamics of these biomolecules in solution in a site-specific manner with the aim of generating structures of the different conformations that these molecules can adopt in solution. One powerful technique is the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiment, which can be used to detect and characterize protein excited states that are populated for as less as 0.5% of the time with ∼0.5–10 millisecond lifetimes. Due to recent advances in NMR pulse sequences and labeling methodology, it is now possible to determine the structures of these transiently populated excited states with millisecond lifetimes by obtaining accurate chemical shifts, residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) of these excited states. In these excited states the dynamics of some methyl containing residues can also be studied.

Molecular Dynamics of Thermotropic Liquid Crystals: Anomalous relaxation dynamics of calamitic and discotic liquid crystals

Recent optical kerr effect (OKE) studies have demonstrated that orientational relaxation of rod-like nematogens exhibits temporal power law decay at intermediate times not only near the isotropic–nematic (I–N) phase boundary but also in the nematic phase. Such behaviour has drawn an intriguing analogy with supercooled liquids. We have investigated both collective and single-particle orientational dynamics of a family of model system of thermotropic liquid crystals using extensive computer simulations. 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. Over a temperature range near the I–N phase boundary, the system behaves remarkably like a fragile glass-forming liquid. Using proper scaling, we construct the usual relaxation time versus inverse temperature plot and explicitly demonstrate that one can successfully define a density dependent fragility of liquid crystals. The fragility of liquid crystals shows a temperature and density dependence which is remarkably similar to the fragility of glass forming supercooled liquids. Energy landscape analysis of inherent structures shows that the breakdown of the Arrhenius temperature dependence of relaxation rate occurs at a temperature that marks the onset of the growth of the depth of the potential energy minima explored by the system. A model liquid crystal, consisting of disk-like molecules, has also been investigated in molecular dynamics simulations for orientational relaxation along two isobars starting from the high temperature isotropic phase. The isobars have been so chosen that the phase sequence isotropic (I)–nematic (N)–columnar (C) appears upon cooling along one of them and the sequence isotropic (I)–columnar(C) along the other. While the orientational relaxation in the isotropic phase near the I–N phase transition 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. The origin of the power law decay in the single-particle second-rank orientational time correlation function (OTCF) is traced to the growth of the orientational pair distribution functions near the I–N phase boundary. 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.

Effect of dimerization on dynamics of spin-charge separation in Pariser-Parr-Pople model: A time-dependent density matrix renormalization group study

We investigate the effect of static electron-phonon coupling on real-time dynamics of spin and charge transport in pi-conjugated polyene chains. The polyene chain is modeled by the Pariser-Parr-Pople Hamiltonian with dimerized nearest-neighbor parameter t(0)(1 + delta) for short bonds and t(0)(1 - delta) for long bonds, and long-range electron-electron interactions. We follow the time evolution of the spin and charge using time-dependent density matrix renormalization group technique when a hole is injected at one end of the chain in its ground state. We find that spin and charge dynamics followed through spin and charge velocities depend both on chain length and extent of dimerization delta. Analysis of the results requires focusing on physical quantities such as average spin and charge polarizations, particularly in the large dimerization limit. In the dimerization range 0.0 <= delta <= 0.15, spin-charge dynamics is found to have a well-defined behavior, with spin-charge separation (measured as the ratio of charge velocity to spin velocity) as well as the total amount of charge and spin transported in a given time along the chain decreasing as dimerization increases. However, in the range 0.3 <= delta <= 0.5, it is observed that the dynamics of spin and charge transport becomes complicated. It is observed that, for large delta values, spin-charge separation is suppressed and the injected hole fails to travel the entire length of the chain.

Insights into the Substrate Specificity of a Thioesterase Rv0098 of Mycobacterium Tuberculosis through X-ray Crystallographic and Molecular Dynamics Studies

The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of substrate specificities of varying chain length. Molecular dynamics studies demonstrated that certain residues of the substrate binding tunnel are flexible and thus modulate the length of the tunnel. The flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. A combination of crystallographic and molecular dynamics studies thus explained the structural basis of accommodating long chain substrates by Rv0098 of M. tuberculosis.

Real-time density matrix renormalization group dynamics of spin and charge transport in push-pull polyenes and related systems

In this paper we investigate the effect of terminal substituents on the dynamics of spin and charge transport in donor-acceptor substituted polyenes [D-(CH)(x)-A] chains, also known as push-pull polyenes. We employ a long-range correlated model Hamiltonian for the D-(CH)(x)-A system, and time-dependent density matrix renormalization group technique for time propagating the wave packet obtained by injecting a hole at a terminal site, in the ground state of the system. Our studies reveal that the end groups do not affect spin and charge velocities in any significant way, but change the amount of charge transported. We have compared these push-pull systems with donor-acceptor substituted polymethine imine (PMI), D-(CHN)(x)-A, systems in which besides electron affinities, the nature of p(z) orbitals in conjugation also alternate from site to site. We note that spin and charge dynamics in the PMIs are very different from that observed in the case of push-pull polyenes, and within the time scale of our studies, transport of spin and charge leads to the formation of a ``quasi-static'' state.

From anomalies in neat liquid to structure, dynamics and function in the biological world

Water brings its remarkable thermodynamic and dynamic anomalies in the pure liquid state to biological world where water molecules face a multitude of additional interactions that frustrate its hydrogen bond network. Yet the water molecules participate and control enormous number of biological processes in manners which are yet to be understood at a molecular level. We discuss thermodynamics, structure, dynamics and properties of water around proteins and DNA, along with those in reverse micelles. We discuss the roles of water in enzyme kinetics, in drug-DNA intercalation and in kinetic-proof reading ( the theory of lack of errors in biosynthesis). We also discuss how water may play an important role in the natural selection of biomolecules. (C) 2011 Elsevier B. V. All rights reserved.

Dependence of diffusivity on density and solute diameter in liquid phase: A molecular dynamics study of Lennard-Jones system

Investigations into the variation of self-diffusivity with solute radius, density, and degree of disorder of the host medium is explored. The system consists of a binary mixture of a relatively smaller sized solute, whose size is varied and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8, and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, additional simulations were carried out in which the degree of disorder has been varied while keeping the density constant. The results show that the diffusivity maximum gradually disappears with increase in disorder. Disorder has been characterized by means of the minimal spanning tree. Simulations have also been carried out in which the degree of disorder is constant and only the density is altered. The results from these simulations show that the maximum in diffusivity now shifts to larger distances with decrease in density. This is in agreement with the changes in void and neck distribution with density of the host medium. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.3701619]

Variation of diffusivity with the cation radii in molten salts of superionic conductors containing iodine anion: A molecular dynamics study

A molecular dynamics study of the dependence of diffusivity of the cation on ionic radii in molten AgI is reported. We have employed modified Parinello-Rahman-Vashistha interionic pair potential proposed by Shimojo and Kobayashi.(1) Our results suggest that the diffusivity of the cation exhibits an increase followed by a decrease as the ionic radius is increased. Several structural and dynamical properties are reported.