Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

Using computer simulations of over 100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain is obtained. This is done by coarse-graining the atomistic water molecule positions over 129,000 collective variables that represent the water density field and then using the string method in these variables to compute the minimum free energy pathway (MFEP) for the collapsing chain. The dynamical relevance of the MFEP (i.e. its coincidence with the mechanism of collapse) is validated a posteriori using conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, it is shown that lengthscale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.Comment: 11 pages, 7 figures, including supporting informatio

Pressure-induced enhancement of superconductivity and suppression of semiconducting behavior in Ln(O0.5F0.5)BiS2 (Ln = La, Ce) compounds

Electrical resistivity measurements as a function of temperature between 1 K and 300 K were performed at various pressures up to 3 GPa on the superconducting layered compounds Ln(O0.5F0.5)BiS2 (Ln = La, Ce). At atmospheric pressure, La(O0.5F0.5)BiS2 and Ce(O0.5F0.5)BiS2 have superconducting critical temperatures, Tc, of 3.3 K and 2.3 K, respectively. For both compounds, the superconducting critical temperature Tc initially increases, reaches a maximum value of 10.1 K for La(O0.5F0.5)BiS2 and 6.7 K for CeO(0.5F0.5)BiS2, and then gradually decreases with increasing pressure. Both samples also exhibit transient behavior in the region between the lower Tc phase near atmospheric pressure and the higher Tc phase. This region is characterized by a broadening of the superconducting transition, in which Tc and the transition width, delta Tc, are reversible with increasing and decreasing pressure. There is also an appreciable pressure-induced and hysteretic suppression of semiconducting behavior up to the pressure at which the maximum value of Tc is found. At pressures above the value at which the maximum in Tc occurs, there is a gradual decrease of Tc and further suppression of the semiconducting behavior with pressure, both of which are reversible.Comment: 9 pages, 6 figures. Phys. Rev. B accepte

Evidence of discrete scale invariance in DLA and time-to-failure by canonical averaging

Discrete scale invariance, which corresponds to a partial breaking of the scaling symmetry, is reflected in the existence of a hierarchy of characteristic scales l0, c l0, c^2 l0,... where c is a preferred scaling ratio and l0 a microscopic cut-off. Signatures of discrete scale invariance have recently been found in a variety of systems ranging from rupture, earthquakes, Laplacian growth phenomena, ``animals'' in percolation to financial market crashes. We believe it to be a quite general, albeit subtle phenomenon. Indeed, the practical problem in uncovering an underlying discrete scale invariance is that standard ensemble averaging procedures destroy it as if it was pure noise. This is due to the fact, that while c only depends on the underlying physics, l0 on the contrary is realisation-dependent. Here, we adapt and implement a novel so-called ``canonical'' averaging scheme which re-sets the l0 of different realizations to approximately the same value. The method is based on the determination of a realization-dependent effective critical point obtained from, e.g., a maximum susceptibility criterion. We demonstrate the method on diffusion limited aggregation and a model of rupture.Comment: 14 pages, 6 figures, in press in Int. J. Mod. Phys.

Deterministic spatio-temporal control of nano-optical fields in optical antennas and nano transmission lines

We show that pulse shaping techniques can be applied to tailor the ultrafast temporal response of the strongly confined and enhanced optical near fields in the feed gap of resonant optical antennas (ROAs). Using finite-difference time-domain (FDTD) simulations followed by Fourier transformation, we obtain the impulse response of a nano structure in the frequency domain, which allows obtaining its temporal response to any arbitrary pulse shape. We apply the method to achieve deterministic optimal temporal field compression in ROAs with reduced symmetry and in a two-wire transmission line connected to a symmetric dipole antenna. The method described here will be of importance for experiments involving coherent control of field propagation in nanophotonic structures and of light-induced processes in nanometer scale volumes.Comment: 5 pages, 5 figure

Gamma-ray bursts: postburst evolution of fireballs

The postburst evolution of fireballs that produce $\gamma$-ray bursts is studied, assuming the expansion of fireballs to be adiabatic and relativistic. Numerical results as well as an approximate analytic solution for the evolution are presented. Due to adoption of a new relation among $t$, $R$ and $\gamma$ (see the text), our results differ markedly from the previous studies. Synchrotron radiation from the shocked interstellar medium is attentively calculated, using a convenient set of equations. The observed X-ray flux of GRB afterglows can be reproduced easily. Although the optical afterglows seem much more complicated, our results can still present a rather satisfactory approach to observations. It is also found that the expansion will no longer be highly relativistic about 4 days after the main GRB. We thus suggest that the marginally relativistic phase of the expansion should be investigated so as to check the afterglows observed a week or more later.Comment: 17 pages, 4 figures, MNRAS in pres

Modeling Vacuum Arcs

We are developing a model of vacuum arcs. This model assumes that arcs develop as a result of mechanical failure of the surface due to Coulomb explosions, followed by ionization of fragments by field emission and the development of a small, dense plasma that interacts with the surface primarily through self sputtering and terminates as a unipolar arc capable of producing breakdown sites with high enhancement factors. We have attempted to produce a self consistent picture of triggering, arc evolution and surface damage. We are modeling these mechanisms using Molecular Dynamics (mechanical failure, Coulomb explosions, self sputtering), Particle-In-Cell (PIC) codes (plasma evolution), mesoscale surface thermodynamics (surface evolution), and finite element electrostatic modeling (field enhancements). We can present a variety of numerical results. We identify where our model differs from other descriptions of this phenomenon.Comment: 4 pages, 5 figure

Jamming Transition of Point-to-Point Traffic Through Cooperative Mechanisms

We study the jamming transition of two-dimensional point-to-point traffic through cooperative mechanisms using computer simulation. We propose two decentralized cooperative mechanisms which are incorporated into the point-to-point traffic models: stepping aside (CM-SA) and choosing alternative routes (CM-CAR). Incorporating CM-SA is to prevent a type of ping-pong jumps from happening when two objects standing face-to-face want to move in opposite directions. Incorporating CM-CAR is to handle the conflict when more than one object competes for the same point in parallel update. We investigate and compare four models mainly from fundamental diagrams, jam patterns and the distribution of cooperation probability. It is found that although it decreases the average velocity a little, the CM-SA increases the critical density and the average flow. Despite increasing the average velocity, the CM-CAR decreases the average flow by creating substantially vacant areas inside jam clusters. We investigate the jam patterns of four models carefully and explain this result qualitatively. In addition, we discuss the advantage and applicability of decentralized cooperation modeling.Comment: 17 pages, 14 figure

Modeling the Optical Afterglow of GRB 030329

The best-sampled afterglow light curves are available for GRB 030329. A distinguishing feature of this event is the obvious rebrightening at around 1.6 days after the burst. Proposed explanations for the rebrightening mainly include the two-component jet model and the refreshed shock model, although a sudden density-jump in the circumburst environment is also a potential choice. Here we re-examine the optical afterglow of GRB 030329 numerically in light of the three models. In the density-jump model, no obvious rebrightening can be produced at the jump moment. Additionally, after the density jump, the predicted flux density decreases rapidly to a level that is significantly below observations. A simple density-jump model thus can be excluded. In the two-component jet model, although the observed late afterglow (after 1.6 days) can potentially be explained as emission from the wide-component, the emergence of this emission actually is too slow and it does not manifest as a rebrightening as previously expected. The energy-injection model seems to be the most preferred choice. By engaging a sequence of energy-injection events, it provides an acceptable fit to the rebrightening at $\sim 1.6$ d, as well as the whole observed light curve that extends to $\sim 80$ d. Further studies on these multiple energy-injection processes may provide a valuable insight into the nature of the central engines of gamma-ray bursts.Comment: 18 pages, 3 figures; a few references added and minor word changes; now accepted for publication in Ap