Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations

Banana lectin (Banlec) is a homodimeric non-glycosylated protein. It exhibits the b-prism I structure. High-temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter- and intra-subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high-temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability.

CMC simulations of lifted turbulent jet flame in a vitiated coflow

Lifted turbulent jet diffusion flame is simulated using Conditional Moment Closure (CMC). Specifically, the burner configuration of Cabra et al. [R. Cabra, T. Myhrvold, J.Y. Chen. R.W. Dibble, A.N. Karpetis, R.S. Barlow, Proc. Combust. Inst. 29 (2002) 1881-1887] is chosen to investigate H-2/N-2 jet flame supported by a vitiated coflow of products of lean H-2/air combustion. A 2D, axisymmetric flow-model fully coupled with the scalar fields, is employed. A detailed chemical kinetic scheme is included, and first order CIVIC is applied. Simulations are carried out for different jet velocities and coflow temperatures (T-c) The predicted liftoff generally agrees with experimental data, as well as joint-PDF results. Profiles of mean scalar fluxes in the mixture fraction space, for T-c = 1025 and 1080 K reveal that (1) Inside the flame zone, the chemical term balances the molecular diffusion term, and hence the Structure is of a diffusion flamelet for both cases. (2) In the pre-flame zone, the structure depends on the coflow temperature: for the 1025 K case, the chemical term being small, the advective term balances the axial turbulent diffusion term. However, for the 1080 K case. the chemical term is large and balances the advective term, the axial turbulent diffusion term being small. It is concluded that, lift-off is controlled (a) by turbulent premixed flame propagation for low coflow temperature while (b) by autoignition for high coflow temperature. (C) 2009 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Numerical simulations of void growth near a notch tip in ductile single crystals

The objective of this work is to study the growth of a cylindrical void ahead of a notch tip in ductile FCC single crystals under mode I, plane strain, small scale yielding (SSY) conditions. To this end, finite element simulations are performed within crystal plasticity framework neglecting elastic anisotropy. Attention is focussed on the effects of crystal hardening, ratio of void diameter to spacing from the notch and crystal orientation on plastic flow localization in the ligament connecting the notch and the void as well as their growth. The results show strong interaction between shear bands emanating from the notch and angular sectors of single slip forming around the void leading to intense plastic strain development in the ligament. Further, the ductile fracture processes are retarded by increase in hardening of the single crystal and decrease in ratio of void diameter to spacing from the notch. Also, a strong influence of crystal orientation on near-tip void growth and plastic slip band development is observed. Finally, the synergistic, cooperative growth of multiple voids ahead of the notch tip is examined.

Allostery in tRNA Synthetases Elucidated from MD Simulations and Protein Structure Networks

tRNA synthetases (aaRS) are enzymes crucial in the translation of genetic code. The enzyme accylates the acceptor stem of tRNA by the congnate amino acid bound at the active site, when the anti-codon is recognized by the anti-codon site of aaRS. In a typical aaRS, the distance between the anti-codon region and the amino accylation site is approximately 70 Å. We have investigated this allosteric phenomenon at molecular level by MD simulations followed by the analysis of protein structure networks (PSN) of non-covalent interactions. Specifically, we have generated conformational ensembles by performing MD simulations on different liganded states of methionyl tRNA synthetase (MetRS) from Escherichia coli and tryptophenyl tRNA synthetase (TrpRS) from Human. The correlated residues during the MD simulations are identified by cross correlation maps. We have identified the amino acids connecting the correlated residues by the shortest path between the two selected members of the PSN. The frequencies of paths have been evaluated from the MD snapshots[1]. The conformational populations in different liganded states of the protein have been beautifully captured in terms of network parameters such as hubs, cliques and communities[2]. These parameters have been associated with the rigidity and plasticity of the protein conformations and can be associated with free energy landscape. A comparison of allosteric communication in MetRS and TrpRS [3] elucidated in this study highlights diverse means adopted by different enzymes to perform a similar function. The computational method described for these two enzymes can be applied to the investigation of allostery in other systems.

Fast Accurate Transient Stability Simulations

The paper describes a Simultaneous Implicit (SI) approach for transient stability simulations based on an iterative technique using traingularised admittance matrix [1]. The reduced saliency of generator in the subtransient state is taken advantage of to speed up the algorithm. Accordingly, generator differential equations, except rotor swing, contain voltage proportional to fluxes in the main field, dampers and a hypothetical winding representing deep flowing eddy currents, as state variables. The simulation results are validated by comparison with two independent methods viz. Runge-Kutta simulation for a simplified system and a method based on modelling damper windings using conventional induction motor theory.

Indentation strength of a piezoelectric ceramic: Experiments and simulations

The spherical indentation strength of a lead zirconate titanate (PZT) piezoelectric ceramic was investigated under poled and unpoled conditions and with different electrical boundary conditions (arising through the use of insulating or conducting indenters). Experimental results show that the indentation strength of the poled PZT is higher than that of the unpoled PZT. The strength of a poled PZT under a conducting indenter is higher than that under an insulating indenter. Poling direction (with respect to the direction of indentation loading) did not significantly affect the strength of material. Complementary finite element analysis (FEA) of spherical indentation of an elastic, linearly coupled piezoelectric half-space is conducted for rationalizing the experimental observations. Simulations show marked dependency of the contact stress on the boundary conditions. In particular, contact stress redistribution in the Coupled problem leads to a change in the fracture initiation, from Hertzian cracking in the unpoled material to Subsurface damage initiation in poled PZT. These observations help explain the experimental ranking of strength the PZT in different material conditions or under different boundary conditions.

Molecular dynamics simulations of sliding in an Fe-Cu tribopair system

Experimental evidence suggests that high strain rates, stresses, strains and temperatures are experienced near sliding interfaces. The associated microstructural changes are due to several dynamic an interacting phenomena. 3D non-equilibrium molecular dynamics (MD) simulations of sliding were conducted with the aim of understanding the dynamic processes taking place in crystalline tribopairs, with a focus on plastic deformation and microstructural evolution. Embedded atom potentials were employed for simulating sliding of an Fe-Cu tribopair. Sliding velocity, crystal orientation and presence of lattice defects were some of the variables in these simulations. Extensive plastic deformation involving dislocation and twin activity, dynamic recrystallization, amorphization and/or nanocrystallization, mechanical mixing and material transfer were observed. Mechanical mixing in the vicinity of the sliding interface was observed even in the Fe-Cu system, which would cluster under equilibrium conditions, hinting at the ballistic nature of the process. Flow localization was observed at high velocities implying the possible role of adiabatic heating. The presence of preexisting defects (such as dislocations and interfaces) played a pivotal role in determining friction and microstructural evolution. The study also shed light on the relationship between adhesion and plastic deformation, and friction. Comparisons with experiments suggest that such simulations can indeed provide valuable insights that are difficult to obtain from experiments.

Statistically steady turbulence in thin films: direct numerical simulations with Ekman friction

We present a detailed direct numerical simulation (DNS) of the two-dimensional Navier-Stokes equation with the incompressibility constraint and air-drag-induced Ekman friction; our DNS has been designed to investigate the combined effects of walls and such a friction on turbulence in forced thin films. We concentrate on the forward-cascade regime and show how to extract the isotropic parts of velocity and vorticity structure functions and hence the ratios of multiscaling exponents. We find that velocity structure functions display simple scaling, whereas their vorticity counterparts show multiscaling, and the probability distribution function of the Weiss parameter 3, which distinguishes between regions with centers and saddles, is in quantitative agreement with experiments.

Evolution of texture during equal channel angular extrusion of commercially pure aluminum: Experiments and simulations

The evolution of crystallographic texture has been comprehensively studied for commercially pure Al as a function of amount of ECAE deformation for the three major routes of ECAE processing. It has been observed that processing through different routes leads to different type of texture, in both qualitative as well as quantitative sense. The results have been analyzed on the basis of existing concepts on ECAE deformation and simulations have been carried out using the simple shear model of ECAE implemented into the Viscoplastic Self Consistent model of polycrystal plasticity. The simulations revealed that non-octahedral slip is needed to reproduce the experimental texture development.

Stationary crack tip fields in elastic-plastic solids: an overview of recent numerical simulations

In this paper, an overview of some recent numerical simulations of stationary crack tip fields in elastic-plastic solids is presented. First, asymptotic analyses carried out within the framework of 2D plane strain or plane stress conditions in both pressure insensitive and pressure sensitive plastic solids are reviewed. This is followed by discussion of salient results obtained from recent computational studies. These pertain to 3D characteristics of elastic-plastic near-front fields under mixed mode loading, mechanics of fracture and simulation of near-tip shear banding process of amorphous alloys and influence of crack tip constraint on the structure of near-tip fields in ductile single crystals. These results serve to illustrate several important features associated with stress and strain distributions near the crack tip and provide the foundation for understanding the operative failure mechanisms. The paper concludes by highlighting some of the future prospects for this field of study.

Ab initio molecular dynamics simulations of excited hydrogen halides and methyl halides

Using excited-state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field approach, we study the mechanism of photodissociation in terms of time evolution of structure, kinetic energy, charges and potential energy for the first excited state of hydrogen halides and methyl halides. Although the hydrogen halides and methyl halides are similar in the photodissociation mechanism, their dynamics are slightly different. The presence of the methyl group causes delay in photodissociation as compared to hydrogen halides.

Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies

Molecular dynamics simulations have been carried out on all the jacalin-carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X-ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin-carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations, and the scatter of the locations of carbohydrate and carbohydrate-binding residues are consistent with the known thermodynamic parameters of jacalin-carbohydrate interactions. The simulations, along with X-ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin-carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands, and the complexes indicate a combination of conformational selection and induced fit. Proteins 2009; 77:760-777.

Post-liquefaction undrained monotonic behaviour of sands: experiments and DEM simulations

This paper presents the results of a series of servo-controlled cyclic triaxial tests and numerical simulations using the three- dimensional discrete element method (DEM) on post-liquefaction undrained monotonic strength of granular materials. In a first test series,undrained monotonic tests were carried out after dissipating the excess pore water pressure developed during liquefaction. The influence of different parameters such as amplitude of axial strain,relative density and confining pressure prior to liquefaction on the post-liquefaction undrained response have been investigated.The results obtained highlight an insignificant influence of amplitude of axial strain, confining pressure and a significant influence of relative density on the post-liquefaction undrained monotonic stress-strain response.In the second series, undrained monotonic tests were carried out on similar triaxial samples without dissipating the excess pore water pressure developed during liquefaction. The results highlight that the amplitude of axial strain prior to liquefaction has a significant influence on the post-liquefaction undrained monotonic response.In addition,DEM simulations have been carried out on an assembly of spheres to simulate post-liquefaction behaviour.The simulations were very similar to the experiments with an objective to understand the behaviour of monotonic strength of liquefied samples from the grain scale. The numerical simulations using DEM have captured qualitatively all the features of the post-liquefaction undrained monotonic response in a manner similar to that of the experiments.In addition,a detailed study on the evolution of micromechanical parameters such as the average coordination number and induced anisotropic coefficients has been reported during the post-liquefaction undrained monotonic loading.

Precipitate growth with composition-dependent diffusivity: Comparison between theory and phase field simulations

We consider the growth of an isolated precipitate when the matrix diffusivity depends on the composition. We have simulated precipitate growth using the Cahn-Hilliard model, and find good agreement between our results and those from a sharp interface theory for systems with and without a dilatational misfit. With misfit, we report (and rationalize) an interesting difference between systems with a constant diffusivity and those with a variable diffusivity in the matrix.

Extending temporal simulations

Direct numerical simulations (DNS) of spatially growing turbulent shear layers may be performed as temporal simulations by solving the governing equations with some additional terms while imposing streamwise periodicity. These terms are functions of the means whose spatial growth is calculated easily and accurately from statistics of the temporal DNS. Equations for such simulations are derived.