Onset of Patterns in an Ocillated Granular Layer: Continuum and Molecular Dynamics Simulations

We study the onset of patterns in vertically oscillated layers of frictionless dissipative particles. Using both numerical solutions of continuum equations to Navier-Stokes order and molecular dynamics (MD) simulations, we find that standing waves form stripe patterns above a critical acceleration of the cell. Changing the frequency of oscillation of the cell changes the wavelength of the resulting pattern; MD and continuum simulations both yield wavelengths in accord with previous experimental results. The value of the critical acceleration for ordered standing waves is approximately 10% higher in molecular dynamics simulations than in the continuum simulations, and the amplitude of the waves differs significantly between the models. The delay in the onset of order in molecular dynamics simulations and the amplitude of noise below this onset are consistent with the presence of fluctuations which are absent in the continuum theory. The strength of the noise obtained by fit to Swift-Hohenberg theory is orders of magnitude larger than the thermal noise in fluid convection experiments, and is comparable to the noise found in experiments with oscillated granular layers and in recent fluid experiments on fluids near the critical point. Good agreement is found between the mean field value of onset from the Swift-Hohenberg fit and the onset in continuum simulations. Patterns are compared in cells oscillated at two different frequencies in MD; the layer with larger wavelength patterns has less noise than the layer with smaller wavelength patterns.Comment: Published in Physical Review

Persistent holes in a fluid

We observe stable holes in a vertically oscillated 0.5 cm deep aqueous suspension of cornstarch for accelerations a above 10g. Holes appear only if a finite perturbation is applied to the layer. Holes are circular and approximately 0.5 cm wide, and can persist for more than 10^5 cycles. Above a = 17g the rim of the hole becomes unstable producing finger-like protrusions or hole division. At higher acceleration, the hole delocalizes, growing to cover the entire surface with erratic undulations. We find similar behavior in an aqueous suspension of glass microspheres.Comment: 4 pages, 6 figure

Fluctuations in viscous fingering

Our experiments on viscous (Saffman-Taylor) fingering in Hele-Shaw channels reveal finger width fluctuations that were not observed in previous experiments, which had lower aspect ratios and higher capillary numbers Ca. These fluctuations intermittently narrow the finger from its expected width. The magnitude of these fluctuations is described by a power law, Ca^{-0.64}, which holds for all aspect ratios studied up to the onset of tip instabilities. Further, for large aspect ratios, the mean finger width exhibits a maximum as Ca is decreased instead of the predicted monotonic increase.Comment: Revised introduction, smoothed transitions in paper body, and added a few additional minor results. (Figures unchanged.) 4 pages, 3 figures. Submitted to PRE Rapi

Oscillating Fracture in Rubber

We have found an oscillating instability of fast-running cracks in thin rubber sheets. A well-defined transition from straight to oscillating cracks occurs as the amount of biaxial strain increases. Measurements of the amplitude and wavelength of the oscillation near the onset of this instability indicate that the instability is a Hopf bifurcation

Breathing Spots in a Reaction-Diffusion System

A quasi-2-dimensional stationary spot in a disk-shaped chemical reactor is observed to bifurcate to an oscillating spot when a control parameter is increased beyond a critical value. Further increase of the control parameter leads to the collapse and disappearance of the spot. Analysis of a bistable activator-inhibitor model indicates that the observed behavior is a consequence of interaction of the front with the boundary near a parity breaking front bifurcation.Comment: 4 pages RevTeX, see also http://chaos.ph.utexas.edu/ and http://t7.lanl.gov/People/Aric

Continuum-type stability balloon in oscillated granular layers

The stability of convection rolls in a fluid heated from below is limited by secondary instabilities, including the skew-varicose and crossroll instabilities. We observe a stability boundary defined by the same instabilities in stripe patterns in a vertically oscillated granular layer. Molecular dynamics simulations show that the mechanism of the skew-varicose instability in granular patterns is similar to that in convection. These results suggest that pattern formation in granular media can be described by continuum models analogous to those used in fluid systems.Comment: 4 pages, 6 ps figs, submitted to PR

Shocks in supersonic sand

We measure time-averaged velocity, density, and temperature fields for steady granular flow past a wedge and calculate a speed of granular pressure disturbances (sound speed) equal to 10% of the flow speed. The flow is supersonic, forming shocks nearly identical to those in a supersonic gas. Molecular dynamics simulations of Newton's laws and Monte Carlo simulations of the Boltzmann equation yield fields in quantitative agreement with experiment. A numerical solution of Navier-Stokes-like equations agrees with a molecular dynamics simulation for experimental conditions excluding wall friction.Comment: 4 pages, 5 figure

Transport Coefficients for Granular Media from Molecular Dynamics Simulations

Under many conditions, macroscopic grains flow like a fluid; kinetic theory pred icts continuum equations of motion for this granular fluid. In order to test the theory, we perform event driven molecular simulations of a two-dimensional gas of inelastic hard disks, driven by contact with a heat bath. Even for strong dissipation, high densities, and small numbers of particles, we find that continuum theory describes the system well. With a bath that heats the gas homogeneously, strong velocity correlations produce a slightly smaller energy loss due to inelastic collisions than that predicted by kinetic theory. With an inhomogeneous heat bath, thermal or velocity gradients are induced. Determination of the resulting fluxes allows calculation of the thermal conductivity and shear viscosity, which are compared to the predictions of granular kinetic theory, and which can be used in continuum modeling of granular flows. The shear viscosity is close to the prediction of kinetic theory, while the thermal conductivity can be overestimated by a factor of 2; in each case, transport is lowered with increasing inelasticity.Comment: 14 pages, 17 figures, 39 references, submitted to PRE feb 199

Contrasting Roles of Mitogen-Activated Protein Kinases in Cellular Entry and Replication of Hepatitis C Virus: MKNK1 Facilitates Cell Entry

The human kinome comprises over 800 individual kinases. These contribute in multiple ways to regulation of cellular metabolism and may have direct and indirect effects on virus replication. Kinases are tempting therapeutic targets for drug development, but achieving sufficient specificity is often a challenge for chemical inhibitors. While using inhibitors to assess whether c-Jun N-terminal (JNK) kinases regulate hepatitis C virus (HCV) replication, we encountered unexpected off-target effects that led us to discover a role for a mitogen-activated protein kinase (MAPK)-related kinase, MAPK interacting serine/threonine kinase 1 (MKNK1), in viral entry. Two JNK inhibitors, AS601245 and SP600125, as well as RNA interference (RNAi)-mediated knockdown of JNK1 and JNK2, enhanced replication of HCV replicon RNAs as well as infectious genome-length RNA transfected into Huh-7 cells. JNK knockdown also enhanced replication following infection with cell-free virus, suggesting that JNK actively restricts HCV replication. Despite this, AS601245 and SP600125 both inhibited viral entry. Screening of a panel of inhibitors targeting kinases that may be modulated by off-target effects of AS601245 and SP600125 led us to identify MKNK1 as a host factor involved in HCV entry. Chemical inhibition or siRNA knockdown of MKNK1 significantly impaired entry of genotype 1a HCV and HCV-pseudotyped lentiviral particles (HCVpp) in Huh-7 cells but had only minimal impact on viral RNA replication or cell proliferation and viability. We propose a model by which MKNK1 acts to facilitate viral entry downstream of the epidermal growth factor receptor (EGFR) and extracellular signal-regulated kinase (ERK), both of which have been implicated in the entry process

Phase Bubbles and Spatiotemporal Chaos in Granular Patterns

We use inelastic hard sphere molecular dynamics simulations and laboratory experiments to study patterns in vertically oscillated granular layers. The simulations and experiments reveal that {\em phase bubbles} spontaneously nucleate in the patterns when the container acceleration amplitude exceeds a critical value, about $7g$, where the pattern is approximately hexagonal, oscillating at one-fourth the driving frequency ($f/4$). A phase bubble is a localized region that oscillates with a phase opposite (differing by $\pi$) to that of the surrounding pattern; a localized phase shift is often called an {\em arching} in studies of two-dimensional systems. The simulations show that the formation of phase bubbles is triggered by undulation at the bottom of the layer on a large length scale compared to the wavelength of the pattern. Once formed, a phase bubble shrinks as if it had a surface tension, and disappears in tens to hundreds of cycles. We find that there is an oscillatory momentum transfer across a kink, and this shrinking is caused by a net collisional momentum inward across the boundary enclosing the bubble. At increasing acceleration amplitudes, the patterns evolve into randomly moving labyrinthian kinks (spatiotemporal chaos). We observe in the simulations that $f/3$ and $f/6$ subharmonic patterns emerge as primary instabilities, but that they are unstable to the undulation of the layer. Our experiments confirm the existence of transient $f/3$ and $f/6$ patterns.Comment: 6 pages, 12 figures, submitted to Phys. Rev. E on July 1st, 2001. for better quality figures, visit http://chaos.ph.utexas.edu/research/moo