Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations

Peanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its.. secondary structure but considerable loss of the tertiary structure at high temperature. e generation of a This observation impies the molten globule-like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal-binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal-ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein.

Melting of an Anchored Bilayer: Molecular Dynamics Simulations of the Structural Transition in (CnH2n+1NH3)(2)PbI4 (n=12, 14, 16, 18)

The thermally driven Structural phase transition in the organic-inorganic hybrid perovskite (CnH2n+1NH3)(2)PbI4 has been investigated using molecular dynamics (MD) simulations. This system consists of positively charged alkyl-amine chains anchored to a rigid negatively charged PbI4 sheet with the chains organized as bilayers with a herringbone arrangement. Atomistic simulations were performed using ail isothermal-isobaric ensemble over a wide temperature range from 65 to 665 K for different alkyl chain lengths, n = 12, 14, 16, and 18. The simulations are able to reproduce the essential Features of the experimental observations of this system, including the existence of a transition, the linear variation of the transition temperature with alkyl chain length, and the expansion of the bilayer thickness at the transition. By use of the distance fluctuation Criteria, it is Shown that the transition is associated With a Melting of the alkyl chains of the anchored bilayer. Ail analysis of the conformation of the alkyl chains shows increased disorder in the form of gauche defects above due melting transition. Simulations also show that the melting transition is characterized by the complete disappearance of all-trans alkyl chains in the anchored bilayer, in agreement with experimental observations. A conformationally disordered chain has a larger effective cross-sectional area, and above due transition a uniformly tilted arrangement of the anchored chains call no longer be Sustained. At the melt the angular distribution of the orientation of the chains are 110 longer uniform; the chains are splayed allowing for increased space for individual chains of the anchored bilayer. This is reflected in a sharp rise in the ratio of the mean head-to-head to tail-to-tail distance of the chains of the bilayer at the transition resulting in in expansion of the bilayer thickness. The present MD simulations provide a simple explanation as to how changes in conformation of individual alkyl-chains gives rise to the observed increase in the interlayer lattice spacing of (CnH2n+1NH3)(2)PbI4 at the melting transition.

Diffusion of Pure CH4 and Its Binary Mixture with CO2 in Faujasite NaY: A Combination of Neutron Scattering Experiments and Molecular Dynamics Simulations

The self-diffusion properties of pure CH4 and its binary mixture with CO2 within MY zeolite have been investigated by combining an experimental quasi-elastic neutron scattering (QENS) technique and classical Molecular dynamics simulations. The QENS measurements carried out at 200 K led to an unexpected self-diffusivity profile for Pure CH4 with the presence of a maximum for a loading of 32 CH4/unit cell, which was never observed before for the diffusion of apolar species in azeolite system With large windows. Molecular dynamics simulations were performed using two distinct microscopic models for representing the CH4/NaY interactions. Depending on the model, we are able to fairly reproduce either the magnitude or the profile of the self-diffusivity.Further analysis allowed LIS to provide some molecular insight into the diffusion mechanism in play. The QENS measurements report only a slight decrease of the self-diffusivity of CH4 in the presence of CO2 when the CO2 loading increases. Molecular dynamics simulations successfully capture this experimental trend and suggest a plausible microscopic diffusion mechanism in the case of this binary mixture.

Superplasticity in intermetallic NiAl nanowires via atomistic simulations

A novel superplastic deformation in an intermetallic B2-NiAl nanowire of cross-sectional dimensions of similar to 20 angstrom with failure strain as high as similar to 700% at 700 K temperature is reported. The minimum temperature under which the superplasticity has been observed is around 0.36 T-m, which is much lower than 0.5 T-m (T-m = melting temperature i.e. 1911 K for bulk B2-NiAl). Superplasticity is observed due to transformation from crystalline phase to amorphous phase after yielding of the nanowire. (C) 2010 Elsevier B.V. All rights reserved.

Stochastic simulations of the origins and implications of long-tailed distributions in gene expression

Gene expression noise results in protein number distributions ranging from long-tailed to Gaussian. We show how long-tailed distributions arise from a stochastic model of the constituent chemical reactions and suggest that, in conjunction with cooperative switches, they lead to more sensitive selection of a subpopulation of cells with high protein number than is possible with Gaussian distributions. Single-cell-tracking experiments are presented to validate some of the assumptions of the stochastic simulations. We also examine the effect of DNA looping on the shape of protein distributions. We further show that when switches are incorporated in the regulation of a gene via a feedback loop, the distributions can become bimodal. This might explain the bimodal distribution of certain morphogens during early embryogenesis.

Surface instability of confined elastic bilayers: Theory and simulations

The surface of a soft elastic film becomes unstable and forms a self-organized undulating pattern because of adhesive interactions when it comes in contact proximity with a rigid surface. For a single film, the pattern length scale lambda, which is governed by the minimization of the elastic stored energy, gives lambda similar to 3h, where h is the film thickness. Based on a linear stability analysis and simulations of adhesion and debonding, we consider the contact instability of an elastic bilayer, which provides greater flexibility in the morphological control of interfacial instability. Unlike the case of a single film, the morphology of the contact instability patterns, debonding distance, and debonding force in a bilayer can be controlled in a nonlinear way by varying the thicknesses and shear moduli of the films. Interestingly, the pattern wavelength in a bilayer can be greatly increased or decreased compared to a single film when the adhesive contact is formed by the stiffer or the softer of the two films, respectively. In particular, lambda as small as 0.5h can be obtained. This indicates a new strategy for pattern miniaturization in elastic contact lithography.

Comments on "Full-sphere simulations of circulation-dominated solar dynamo: Exploring the parity issue" - Reply

We respond to Dikpati et al.'s criticism of our recent solar dynamo model. A different treatment of the magnetic buoyancy is the most probable reason for their different results.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Numerical simulations of crack tip fields in polycrystalline plastic solids

In this paper, modes I and II crack tip fields in polycrystalline plastic solids are studied under plane strain, small scale yielding conditions. Two different initial textures of an Al–Mg alloy, viz., continuous cast AA5754 sheets in the recrystallized and cold rolled conditions, are considered. The former is nearly-isotropic, while the latter displays distinct anisotropy. Finite element simulations are performed by employing crystal plasticity constitutive equations along with a Taylor-type homogenization as well as by using the Hill quadratic yield theory. It is found that significant texture evolution occurs close to the notch tip which profoundly influences the stress and plastic strain distributions. Also, the cold rolling texture gives rise to higher magnitude of plastic strain near the tip.

Numerical simulations of crack tip fields in polycrystalline plastic solids

In this paper, modes I and II crack tip fields in polycrystalline plastic solids are studied under plane strain, small scale yielding conditions. Two different initial textures of an Al-Mg alloy, viz.,continuous cast AA5754 sheets in the recrystallized and cold rolled conditions, are considered. The former is nearly-isotropic, while the latter displays distinct anisotropy. Finite element simulations are performed by employing crystal plasticity constitutive equations along with a Taylor-type homogenization as well as by using the Hill quadratic yield theory. It is found that significant texture evolution occurs close to the notch tip which profoundly influences the stress and plastic strain distributions. Also, the cold rolling texture gives rise to higher magnitude of plastic strain near the tip. (C) 2010 Elsevier Ltd. All rights reserved.

Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naive to Nevirapine by Using Stochastic Simulations and a Mathematical Model

Nevirapine forms the mainstay of our efforts to curtail the pediatric AIDS epidemic through prevention of mother-to-child transmission of HIV-1. A key limitation, however, is the rapid selection of HIV-1 strains resistant to nevirapine following the administration of a single dose. This rapid selection of resistance suggests that nevirapine-resistant strains preexist in HIV-1 patients and may adversely affect outcomes of treatment. The frequencies of nevirapine-resistant strains in vivo, however, remain poorly estimated, possibly because they exist as a minority below current assay detection limits. Here, we employ stochastic simulations and a mathematical model to estimate the frequencies of strains carrying different combinations of the common nevirapine resistance mutations K103N, V106A, Y181C, Y188C, and G190A in chronically infected HIV-1 patients naive to nevirapine. We estimate the relative fitness of mutant strains from an independent analysis of previous competitive growth assays. We predict that single mutants are likely to preexist in patients at frequencies (similar to 0.01% to 0.001%) near or below current assay detection limits (>0.01%), emphasizing the need for more-sensitive assays. The existence of double mutants is subject to large stochastic variations. Triple and higher mutants are predicted not to exist. Our estimates are robust to variations in the recombination rate, cellular superinfection frequency, and the effective population size. Thus, with 10(7) to 10(8) infected cells in HIV-1 patients, even when undetected, nevirapine-resistant genomes may exist in substantial numbers and compromise efforts to prevent mother-to-child transmission of HIV-1, accelerate the failure of subsequent antiretroviral treatments, and facilitate the transmission of drug resistance.

Redundancy resolution using tractrix -- Simulations and Experiments

Hyper-redundant robots are characterized by the presence of a large number of actuated joints, many more than the number required to perform a given task. These robots have been proposed and used for many applications involving avoiding obstacles or, in general, to provide enhanced dexterity in performing tasks. Making effective use of the extra degrees of freedom or resolution of redundancy has been an extensive topic of research and several methods have been proposed in literature. In this paper, we compare three known methods and show that an algorithm based on a classical curve called the tractrix leads to a more 'natural' motion of the hyper-redundant robot, with the displacements diminishing from the end-effector to the fixed base. In addition, since the actuators nearer the base 'see' a greater inertia due to the links farther away, smaller motion of the actuators nearer the base results in better motion of the end-effector as compared to other two approaches. We present simulation and experimental results performed on a prototype eight link planar hyper-redundant manipulator.

Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Dense granular flow down an inclined plane A comparison between the hard particle model and soft particle simulations

The granular flow down an inclined plane is simulated using the discrete element (DE) technique to examine the extent to which the dynamics of an unconfined dense granular flow can be well described by a hard particle model First, we examine the average coordination number for the particles in the flow down an inclined plane using the DE technique using the linear contact model with and without friction, and the Hertzian contact model with friction The simulations show that the average coordination number decreases below 1 for values of the spring stiffness corresponding to real materials, such as sand and glass, even when the angle of inclination is only 10 larger than the angle of repose Additional measures of correlations in the system, such as the fraction of particles with multibody contact, the force ratio (average ratio of the magnitudes of the largest and the second largest force on a particle), and the angle between the two largest forces on the particle, show no evidence of force chains or other correlated motions in the system An analysis of the bond-orientational order parameter indicates that the flow is in the random state, as in event-driven (ED) simulations V Kumaran, J Fluid Mech 632, 107 (2009), J Fluid Mech 632, 145 (2009)] The results of the two simulation techniques for the Bagnold coefficients (ratio of stress and square of the strain rate) and the granular temperature (mean square of the fluctuating velocity) are compared with the theory V Kumaran, J Fluid Mech 632, 107 (2009), J Fluid Mech 632, 145 (2009)] and are found to be in quantitative agreement In addition, we also conduct a comparison of the collision frequency and the distribution of the precollisional relative velocities of particles in contact The strong correlation effects exhibited by these two quantities in event-driven simulations V Kumaran, J Fluid Mech 632, 145 (2009)] are also found in the DE simulations (C) 2010 American Institute of Physics doi 10 1063/1 3504660]