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]

Direct numerical simulations of statistically steady, homogeneous, isotropic fluid turbulence with polymer additives

We carry out a direct numerical simulation (DNS) study that reveals the effects of polymers on statistically steady, forced, homogeneous, and isotropic fluid turbulence. We find clear manifestations of dissipation-reduction phenomena: on the addition of polymers to the turbulent fluid, we obtain a reduction in the energy dissipation rate; a significant modification of the fluid-energy spectrum, especially in the deep-dissipation range; and signatures of the suppression of small-scale structures, including a decrease in small-scale vorticity filaments. We also compare our results with recent experiments and earlier DNS studies of decaying fluid turbulence with polymer additives.

Microstructure evolution and hardness variation during annealing of equal channel angular pressed ultra-fine grained nickel subjected to 12 passes

The microstructure, thermal stability and hardness of ultra-fine grained (UFG) Ni produced by 12 passes of equal channel angular pressing (ECAP) through the route Bc were studied. Comparing the microstructure and hardness of the as-ECAPed samples with the published data on UFG Ni obtained after 8 passes of ECAP through the route Bc reveals a smaller average grain size (230 nm in the present case compared with 270 nm in 8-pass Ni), significantly lower dislocation density (1.08 x 10(14) m(-2) compared with 9 x 10(14) m(-2) in 8-pass Ni) and lower hardness (2 GPa compared with 2.45 GPa for 8-pass Ni). Study of the thermal stability of the 12-pass UFG Ni revealed that recovery is dominant in the temperature range 150-250A degrees C and recrystallisation occurred at temperatures > 250 A degrees C. The UFG microstructure is relatively stable up to about 400 A degrees C. Due to the lower dislocation density and consequently a lower stored energy, the recrystallisation of 12-pass ECAP Ni occurred at a higher temperature (similar to 250 A degrees C) compared with the 8-pass Ni (similar to 200 A degrees C). In the 12-pass Nickel, hardness variation shows that its dependence on grain size is inversely linear rather than the common grain size(-0.5) dependence.

Parallel Tempering Simulations of Liquid-Phase Adsorption of n-Alkane Mixtures in Zeolite LTA-5A

Adsorption of n-alkane mixtures in the zeolite LTA-5A under liquid-phase conditions has been studied using grand canonical Monte Carlo (GCMC) simulations combined with parallel tempering. Normal GCMC techniques fail for some of these systems due to the preference of linear molecules to coil within a single cage in the zeolite. The narrow zeolite windows severerly restrict interactions of the molecules, making it difficult to simulate cooperative rearrangements necessary to explore configuration space. Because of these reasons, normal GCMC simulations results show poor reproducibility in some cases. These problems were overcome with parallel tempering techniques. Even with parallel tempering, these are very challenging systems for molecular simulation. Similar problems may arise for other zeolites such as CHA, AFX, ERI, KFI, and RHO having cages connected by narrow windows. The simulations capture the complex selectivity behavior observed in experiments such as selectivity inversion and azeotrope formation.

Hydrogen Storage Capacity of Carbon-Foams: Grand Canonical Monte Carlo Simulations

Hydrogen storage in the three-dimensional carbon foams is analyzed using classical grand canonical Monte Carlo simulations. The calculated storage capacities of the foams meet the material-based DOE targets and are comparable to the capacities of a bundle of well-separated similar diameter open nanotubes. The pore sizes in the foams are optimized for the best hydrogen uptake. The capacity depends sensitively on the C-H-2 interaction potential, and therefore, the results are presented for its ``weak'' and ``strong'' choices, to offer the lower and upper bounds for the expected capacities. Furthermore, quantum effects on the effective C-H-2 as well as H-2-H-2 interaction potentials are considered. We find that the quantum effects noticeably change the adsorption properties of foams and must be accounted for even at room temperature.

Molecular Dynamics Simulations of Orientational Relaxation in Dipolar Lattice: Lack of Diffusive Decay for Second and Higher Rank Correlation Functions

Extensive molecular dynamics simulations have been carried out to calculate the orientational correlation functions Cl(t), G(t) = [4n/(21 + l)]Ci=-l (Y*lm(sZ(0)) Ylm(Q(t))) (where Y,,(Q) are the spherical harmonics) of point dipoles in a cubic lattice. The decay of Cl(t) is found to be strikingly different from higher l-correlation functions-the latter do not exhibit diffusive dynamics even in the long time. Both the cumulant expansion expression of Lynden-Bell and the conventional memory function equation provide very good description of the Cl(t) in the short time but fail to reproduce the observed slow, long time decay of c1 (t) .

Diffusion Anomaly in Silicalite and VPI-5 from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations on rigid and flexible framework models of silicalite and a rigid framework model of the aluminophosphate VPI-5 for different sorbate diameters are reported. The sorbate-host interactions are modeled in terms of simple atom-atom Lennard-Jones interactions. The results suggest that the diffusion coefficient exhibits an anomaly as gamma approaches unity. The MD results confirm the existence of a linear regime for sorbate diameters significantly smaller than the channel diameter and an anomalous regime observed for sorbate diameters comparable to the channel diameter. The power spectra obtained by Fourier transformation of the velocity autocorrelation function indicate that there is an increase in the intensity of the low-frequency component for the velocity component parallel to the direction of motion for the sorbate diameter in the anomalous regime. The present results suggest that the diffusion anomaly is observed irrespective of (1) the geometry and topology of the pore structure and (2) the nature of the host material. The results are compared with the work of Derouane and co-workers, who have suggested the existence of ''floating molecules'' on the basis of earlier theoretical and computational approaches.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Finite element simulations of ductile rupture in a constrained metal foil

A numerical study of the ductile rupture in a metal foil constrained between two stiff ceramic blocks is performed. The finite element analysis is carried out under the conditions of mode I, plane strain, small-scale yielding. The rate-independent version of the Gurson model that accounts for the ductile failure mechanisms of microvoid nucleation, growth and coalescence is employed to represent the behavior of the metal foil. Different distributions of void nucleating sites in the metal foil are considered for triggering the initiation of discrete voids. The results clearly show that far-field triaxiality-induced cavitation is the dominant failure mode when the spacing of the void nucleating sites is large. On the contrary, void coalescence near the notch tip is found to be the operative failure mechanism when closely spaced void nucleating sites are considered.

On the spurious increase in particle volume fraction during coarsening simulations

The problem of spurious increase in volume fraction of second-phase particles during computer simulations of coarsening is examined. The origin of this problem is traced to the use of too long a time step (used for numerical integration of growth rates with respect to time) which leads to small particles with large negative growth rates shrinking to negative radii at the end of the time step. Such a shrinkage to negative sizes has the effect of pumping solute into the system. It is therefore suggested that the length of the time step be chosen in accordance with the size of the smallest particle present in the system. It is shown that spurious increase in particle Volume has a significant effect on the particle size distributions in the scaling regime (making them broader and more skewed in the Lifshitz-Slyozov-Wagner model). Its effect on coarsening kinetics, however, is found to be small.

Characteristic water contents of a fine-grained soil-water system

This paper critically appraises the limitations of the liquid-limit water content of clayey soils determined conventionally either by percussion cup or by the cone penetration method. It is shown that the conventional liquid limit and plastic limit are arbitrary, strength-based water contents and that they cannot represent the plasticity limits, and that the state of the soil-water system at the conventional liquid limit does not correspond to a stress-free reference state. The present investigation identifies three characteristic limiting water contents for a soil-water system which have well-defined, unique mechanisms controlling them, namely the free swell limit, settling limit and shrinkage limit. Simple procedures for the determination of the free swell limit and settling limit of natural soils are presented. The settling limit is shown to be the 'real liquid limit' of any clayey soil. With a number of experimental illustrations, it is clearly shown that the settling limit represents the maximum water-holding capacity of clayey soils and that it corresponds to the stress-free reference state.

Numerical simulations of fracture initiation in ductile solids under mode I, dynamic loading

In this paper, an overview of some recent computational studies by the authors on ductile crack initiation under mode I, dynamic loading is presented. In these studies, a large deformation finite element procedure is employed along with the viscoplastic version of the Gurson constitutive model that accounts for the micro-mechanical processes of void nucleation, growth and coalescence. A three-point bend fracture specimen subjected to impact, and a single edge notched specimen loaded by a tensile stress pulse are analysed. Several loading rates are simulated by varying the impact speed or the rise time and magnitude of the stress pulse. A simple model involving a semi-circular notch with a pre-nucleated circular hole situated ahead of it is considered. The growth of the hole and its interaction with the notch tip, which leads to plastic strain and porosity localization in the ligament connecting them, is simulated. The role of strain-rate dependence on ductile crack initiation at high loading rates, and the specimen geometry effect on the variation of dynamic fracture toughness with loading rate are Investigated.