Molecular Dynamics Investigation of Structure and Transport in the K2O-2SiO2 System Using a Partial Charge Based Model Potential

Potassium disilicate glass and melt have been investigated by using a new partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygenrich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Molecular dynamics Investigation of structure and transport in the K2O-2SiO2 system using a partial charge based model potential

Potassium disilicate glass and melt have been investigated by using anew partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygen-rich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Topological phases, Majorana modes and quench dynamics in a spin ladder system

We explore the salient features of the `Kitaev ladder', a two-legged ladder version of the spin-1/2 Kitaev model on a honeycomb lattice, by mapping it to a one-dimensional fermionic p-wave superconducting system. We examine the connections between spin phases and topologically non-trivial phases of non-interacting fermionic systems, demonstrating the equivalence between the spontaneous breaking of global Z(2) symmetry in spin systems and the existence of isolated Majorana modes. In the Kitaev ladder, we investigate topological properties of the system in different sectors characterized by the presence or absence of a vortex in each plaquette of the ladder. We show that vortex patterns can yield a rich parameter space for tuning into topologically non-trivial phases. We introduce and employ a new topological invariant for explicitly determining the presence of zero energy Majorana modes at the boundaries of such phases. Finally, we discuss dynamic quenching between topologically non-trivial phases in the Kitaev ladder and, in particular, the post-quench dynamics governed by tuning through a quantum critical point.

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]

Influence of system size on spatiotemporal dynamics of a model for plastic instability: Projecting low-dimensional and extensive chaos

This work is a continuation of our efforts to quantify the irregular scalar stress signals from the Ananthakrishna model for the Portevin-Le Chatelier instability observed under constant strain rate deformation conditions. Stress related to the spatial average of the dislocation activity is a dynamical variable that also determines the time evolution of dislocation densities. We carry out detailed investigations on the nature of spatiotemporal patterns of the model realized in the form of different types of dislocation bands seen in the entire instability domain and establish their connection to the nature of stress serrations. We then characterize the spatiotemporal dynamics of the model equations by computing the Lyapunov dimension as a function of the drive parameter. The latter scales with the system size only for low strain rates, where isolated dislocation bands are seen, and at high strain rates, where fully propagating bands are seen. At intermediate applied strain rates corresponding to the partially propagating bands, the Lyapunov dimension exhibits two distinct slopes, one for small system sizes and another for large. This feature is rationalized by demonstrating that the spatiotemporal patterns for small system sizes are altered from the partially propagating band types to isolated burst type. This in turn allows us to reconfirm that low-dimensional chaos is projected from the stress signals as long as there is a one-to-one correspondence between the bursts of dislocation bands and the stress drops. We then show that the stress signals in the regime of partially to fully propagative bands have features of extensive chaos by calculating the correlation dimension density. We also show that the correlation dimension density also depends on the system size. A number of issues related to the system size dependence of the Lyapunov dimension density and the correlation dimension density are discussed.

Current kinematics and dynamics of Africa and the East African Rift System

Although the East African Rift System (EARS) is an archetype continental rift, the forces driving its evolution remain debated. Some contend buoyancy forces arising from gravitational potential energy (GPE) gradients within the lithosphere drive rifting. Others argue for a major role of the diverging mantle flow associated with the African Superplume. Here we quantify the forces driving present-day continental rifting in East Africa by (1) solving the depth averaged 3-D force balance equations for 3-D deviatoric stress associated with GPE, (2) inverting for a stress field boundary condition that we interpret as originating from large-scale mantle tractions, (3) calculating dynamic velocities due to lithospheric buoyancy forces, lateral viscosity variations, and velocity boundary conditions, and (4) calculating dynamic velocities that result from the stress response of horizontal mantle tractions acting on a viscous lithosphere in Africa and surroundings. We find deviatoric stress associated with lithospheric GPE gradients are similar to 8-20 MPa in EARS, and the minimum deviatoric stress resulting from basal shear is similar to 1.6 MPa along the EARS. Our dynamic velocity calculations confirm that a force contribution from GPE gradients alone is sufficient to drive Nubia-Somalia divergence and that additional forcing from horizontal mantle tractions overestimates surface kinematics. Stresses from GPE gradients appear sufficient to sustain present-day rifting in East Africa; however, they are lower than the vertically integrated strength of the lithosphere along most of the EARS. This indicates additional processes are required to initiate rupture of continental lithosphere, but once it is initiated, lithospheric buoyancy forces are enough to maintain rifting.

Self-organized criticality in dynamics without branching

We demonstrate the phenomenon of self-organized criticality (SOC) in a simple random walk model described by a random walk of a myopic ant, i.e., a walker who can see only nearest neighbors. The ant acts on the underlying lattice aiming at uniform digging, i.e., reduction of the height profile of the surface but is unaffected by the underlying lattice. In one, two, and three dimensions we have explored this model and have obtained power laws in the time intervals between consecutive events of "digging." Being a simple random walk, the power laws in space translate to power laws in time. We also study the finite size scaling of asymptotic scale invariant process as well as dynamic scaling in this system. This model differs qualitatively from the cascade models of SOC.

Shock propagation in gas dynamics: explicit form of higher order compatibility conditions

With the use of tensor analysis and the method of singular surfaces, an infinite system of equations can be derived to study the propagation of curved shocks of arbitrary strength in gas dynamics. The first three of these have been explicitly given here. This system is further reduced to one involving scalars only. The choice of dependent variables in the infinite system is quite important, it leads to coefficients free from singularities for all values of the shock strength.

Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNaseS and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model, According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Intermittent Dynamics, Stochastic Resonance and Dynamical Heterogeneity in Supercooled Liquid Water

Here we find through computer simulations and theoretical analysis that the low temperature thermodynamic anomalies of liquid water arises from the intermittent fluctuation between its high density and low density forms, consisting largely of 5-coordinated and 4-coordinated water molecules, respectively. The fluctuations exhibit strong dynamic heterogeneity (defined by the four point time correlation function), accompanied by a divergence like growth of the dynamic correlation length, of the type encountered in fragile supercooled liquids. The intermittency has been explained by invoking a two state model often employed to understand stochastic resonance, with the relevant periodic perturbation provided here by the fluctuation of the total volume of the system.

Separability in relativistic Hamiltonian particle dynamics

The problem of separability in recent models of classical relativistic interacting particles is examined. This physical requirement is shown to be more subtle than naive separability of all the constraints defining the system: it is adequate to be able to canonically transform the time-fixing constraints from an unseparated to a separated form when clusters emerge. Viewing separability in this way, and within a specific framework, we are led to a new no-interaction theorem which states the incompatibility of nontrivial interaction with relativistic invariance, separability, and invariant world lines for more than two particles.

Quantum entanglement in a noncommutative system

We explore the effect of two-dimensional position-space noncommutativity on the bipartite entanglement of continuous-variable systems. We first extend the standard symplectic framework for studying entanglement of Gaussian states of commutative systems to the case of noncommutative systems residing in two dimensions. Using the positive partial transpose criterion for separability of bipartite states, we derive a condition on the separability of a noncommutative system that is dependent on the noncommutative parameter theta. We then consider the specific example of a bipartite Gaussian state and show the quantitative reduction in entanglement originating from noncommutative dynamics. We show that such a reduction in entanglement for a noncommutative system arising from the modification of the variances of the phase-space variables (uncertainty relations) is clearly manifested between two particles that are separated by small distances.

Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study

Molecular dynamics (MD) simulations are reported for an anchored bilayer formed by the intercalation of cetyl trimethyl ammonium (CTA) and CH3(CH2)15N+(CH3) ions in a layered solid, CdPS3. The intercalated CTA ions are organized with the cationic headgroups tethered to the inorganic sheet and the hydrocarbon tails arranged as bilayers. Simulations were performed at three temperatures, 65, 180, and 298 K, using an isothermal−isobaric ensemble that was subsequently switched once macroscopic parameters had converged to a canonical isothermal−isochoric ensemble. The simulations are able to reproduce the experimental features of this system, including the formation of the bilayer and layer-to-layer separation distance. An analysis of the conformation of the chains showed that at all three temperatures a fraction of the alkyl chains retained a planar all-trans conformation, and that gauche bonds occurred as part of a “kink” (gauche+−trans−gauche−) sequence and not as isolated gauche bonds. Trans−gauche isomerization rates for the alkyl chains in the anchored bilayer are slower than those in lipid bilayers at the same temperature and show a progressive increase as the torsion numbers approach the tail. A two-dimensional periodic Voronoi tessellation analysis was performed to obtain the single-molecular area of an alkyl chain in the bilayer. The single-molecular area relaxation times are an order of magnitude longer than the trans−gauche isomerization times. The results indicate that the trans−gauche isomerization is associated with the creation and annihilation of a kink defect sequence. The results of the present MD simulation explain the apparent conflicting estimates of the gauche disorder in this system as obtained from infrared and 13C nuclear magnetic resonance measurements.

NMR relaxation study of disorder in the mixed system BP x GPI(1-x) and the low temperature transition from classical to quantum rotation

1H NMR spin-lattice relaxation time (T1) studies have been carried out in the temperature range 100 K to 4 K, at two Larmor frequencies 11.4 and 23.3 MHz, in the mixed system of betaine phosphate and glycine phosphite (BPxGPI(1-x)), to study the effects of disorder on the proton group dynamics. Analysis of T1 data indicates the presence of a number of inequivalent methyl groups and a gradual transition from classical reorientations to quantum tunneling rotations. At lower temperatures, microstructural disorder in the local environments of the methyl groups, result in a distribution in the activation energy (Ea) and the torsional energy gap (E01). For certain values of x, the magnetisation recovery shows biexponential behaviour at lower temperatures.

Classical Langevin dynamics of a charged particle moving on a sphere and diamagnetism: A surprise

It is generally known that the orbital diamagnetism of a classical system of charged particles in thermal equilibrium is identically zero —the Bohr-van Leeuwen theorem. Physically, this null result derives from the exact cancellation of the orbital diamagnetic moment associated with the complete cyclotron orbits of the charged particles by the paramagnetic moment subtended by the incomplete orbits skipping the boundary in the opposite sense. Motivated by this crucial but subtle role of the boundary, we have simulated here the case of a finite but unbounded system, namely that of a charged particle moving on the surface of a sphere in the presence of an externally applied uniform magnetic field. Following a real space-time approach based on the classical Langevin equation, we have computed the orbital magnetic moment that now indeed turns out to be non-zero and has the diamagnetic sign. To the best of our knowledge, this is the first report of the possibility of finite classical diamagnetism in principle, and it is due to the avoided cancellation.