Make life simple: unleash the full power of the parallel tempering algorithm

We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average round-trip time of a replica in temperature space can be significantly decreased. The temperatures are not dynamically adjusted as in previous attempts but chosen to yield a 50% exchange rate of adjacent replicas. We illustrate the new algorithm with results for the Ising model in two and the Edwards-Anderson Ising spin glass in three dimensionsComment: 4 pages, 5 figure

General approach for studying first-order phase transitions at low temperatures

By combining different ideas, a general and efficient protocol to deal with discontinuous phase transitions at low temperatures is proposed. For small $T$'s, it is possible to derive a generic analytic expression for appropriate order parameters, whose coefficients are obtained from simple simulations. Once in such regimes simulations by standard algorithms are not reliable, an enhanced tempering method, the parallel tempering -- accurate for small and intermediate system sizes with rather low computational cost -- is used. Finally, from finite size analysis, one can obtain the thermodynamic limit. The procedure is illustrated for four distinct models, demonstrating its power, e.g., to locate coexistence lines and the phases density at the coexistence.Comment: 5 page

The role of advection, straining, and mixing on the tidal variability of estuarine stratification

Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 855–868, doi:10.1175/JPO-D-10-05010.1.Data from the Hudson River estuary demonstrate that the tidal variations in vertical salinity stratification are not consistent with the patterns associated with along-channel tidal straining. These observations result from three additional processes not accounted for in the traditional tidal straining model: 1) along-channel and 2) lateral advection of horizontal gradients in the vertical salinity gradient and 3) tidal asymmetries in the strength of vertical mixing. As a result, cross-sectionally averaged values of the vertical salinity gradient are shown to increase during the flood tide and decrease during the ebb. Only over a limited portion of the cross section does the observed stratification increase during the ebb and decrease during the flood. These observations highlight the three-dimensional nature of estuarine flows and demonstrate that lateral circulation provides an alternate mechanism that allows for the exchange of materials between surface and bottom waters, even when direct turbulent mixing through the pycnocline is prohibited by strong stratification.The funding for this research was obtained from NSF Grant OCE-08-25226.2012-11-0

Broadband acoustic quantification of stratified turbulence

Author Posting. © Acoustical Society of America, 2013. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 134 (2013): 40-54, doi:10.1121/1.4807780.High-frequency broadband acoustic scattering techniques have enabled the remote, high-resolution imaging and quantification of highly salt-stratified turbulence in an estuary. Turbulent salinity spectra in the stratified shear layer have been measured acoustically and by in situ turbulence sensors. The acoustic frequencies used span 120–600 kHz, which, for the highly stratified and dynamic estuarine environment, correspond to wavenumbers in the viscous-convective subrange (500–2500 m−1). The acoustically measured spectral levels are in close agreement with spectral levels measured with closely co-located micro-conductivity probes. The acoustically measured spectral shapes allow discrimination between scattering dominated by turbulent salinity microstructure and suspended sediments or swim-bladdered fish, the two primary sources of scattering observed in the estuary in addition to turbulent salinity microstructure. The direct comparison of salinity spectra inferred acoustically and by the in situ turbulence sensors provides a test of both the acoustic scattering model and the quantitative skill of acoustical remote sensing of turbulence dissipation in a strongly sheared and salt-stratified estuary.This work was supported by NSF grant OCE- 0824871, ONR grant N00014-0810495, and WHOI internal funds

The influence of stratification and nonlocal turbulent production on estuarine turbulence : an assessment of turbulence closure with field observations

Author Posting. © American Meteorological Society, 2011. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 41 (2011): 166-185, doi:10.1175/2010JPO4470.1.Field observations of turbulent kinetic energy (TKE), dissipation rate ε, and turbulent length scale demonstrate the impact of both density stratification and nonlocal turbulent production on turbulent momentum flux. The data were collected in a highly stratified salt wedge estuary using the Mobile Array for Sensing Turbulence (MAST). Estimates of the dominant length scale of turbulent motions obtained from the vertical velocity spectra provide field confirmation of the theoretical limitation imposed by either the distance to the boundary or the Ozmidov scale, whichever is smaller. Under boundary-limited conditions, anisotropy generally increases with increasing shear and decreased distance to the boundary. Under Ozmidov-limited conditions, anisotropy increases rapidly when the gradient Richardson number exceeds 0.25. Both boundary-limited and Ozmidov-limited conditions demonstrate significant deviations from a local production–dissipation balance that are largely consistent with simple scaling relationships for the vertical divergence in TKE flux. Both the impact of stratification and deviation from equilibrium turbulence observed in the data are largely consistent with commonly used turbulence closure models that employ “nonequilibrium” stability functions. The data compare most favorably with the nonequilibrium version of the L. H. Kantha and C. A. Clayson stability functions. Not only is this approach more consistent with the observed critical gradient Richardson number of 0.25, but it also accounts for the large deviations from equilibrium turbulence in a manner consistent with the observations.The funding for this research was obtained from ONR Grant N00014-06-1-0292 and NSF Grants and OCE-08-25226 and OCE-08-24871

Ground-state topology of the Edwards-Anderson +/-J spin glass model

In the Edwards-Anderson model of spin glasses with a bimodal distribution of bonds, the degeneracy of the ground state allows one to define a structure called backbone, which can be characterized by the rigid lattice (RL), consisting of the bonds that retain their frustration (or lack of it) in all ground states. In this work we have performed a detailed numerical study of the properties of the RL, both in two-dimensional (2D) and three-dimensional (3D) lattices. Whereas in 3D we find strong evidence for percolation in the thermodynamic limit, in 2D our results indicate that the most probable scenario is that the RL does not percolate. On the other hand, both in 2D and 3D we find that frustration is very unevenly distributed. Frustration is much lower in the RL than in its complement. Using equilibrium simulations we observe that this property can be found even above the critical temperature. This leads us to propose that the RL should share many properties of ferromagnetic models, an idea that recently has also been proposed in other contexts. We also suggest a preliminary generalization of the definition of backbone for systems with continuous distributions of bonds, and we argue that the study of this structure could be useful for a better understanding of the low temperature phase of those frustrated models.Comment: 16 pages and 21 figure

Retinoic Acid-Binding Protein in Human Breast Cancer and Dysplasia

Seventy-five specimens of human breast tissue were checked for the presence of cellular retinoic acid-binding protein (cRABP). Fifty-two percent of the primary carcinomas and 43% of the dysplastic breast lesions (stage MIl) contained detectable amounts of cRABP, whereas no cRABP was found in normal tissue. Sucrose gradient centrifugation and electrophoresis on agarose were used for analysis of the presence of cRABP. The cRABP of human origin (normal uterus and neoplastic mammary tissue) differed in its mobility in agarose electrophoresis from that of rat testis cRA

Possibility to measure thermal effects in the Casimir force

We analyze the possibility to measure small thermal effects in the Casimir force between metal test bodies in configurations of a sphere above a plate and two parallel plates. For sphere-plate geometry used in many experiments we investigate the applicability of the proximity force approximation (PFA) to calculate thermal effects in the Casimir force and its gradient. It is shown that for real metals the two formulations of the PFA used in the literature lead to relative differences in the obtained results being less than a small parameter equal to the ratio of separation distance to sphere radius. For ideal metals the PFA results for the thermal correction are obtained and compared with available exact results. It is emphasized that in the experimental region in the zeroth order of the small parameter mentioned above the thermal Casimir force and its gradient calculated using the PFA (and thermal corrections in their own right) coincide with respective exact results. For real metals available exact results are outside the application region of the PFA. However, the exact results are shown to converge to the PFA results when the small parameter goes down to the experimental values. We arrive at the conclusion that large thermal effects predicted by the Drude model approach, if existing at all, could be measured in both static and dynamic experiments in sphere-plate and plate-plate configurations. As to the small thermal effects predicted by the plasma model approach, the static experiment in the configuration of two parallel plates is found to be the best for its observation.Comment: 35 pages, 9 figures; Phys. Rev. A, to appea

Electron impact double ionization of helium from classical trajectory calculations

With a recently proposed quasiclassical ansatz [Geyer and Rost, J. Phys. B 35 (2002) 1479] it is possible to perform classical trajectory ionization calculations on many electron targets. The autoionization of the target is prevented by a M\o{}ller type backward--forward propagation scheme and allows to consider all interactions between all particles without additional stabilization. The application of the quasiclassical ansatz for helium targets is explained and total and partially differential cross sections for electron impact double ionization are calculated. In the high energy regime the classical description fails to describe the dominant TS1 process, which leads to big deviations, whereas for low energies the total cross section is reproduced well. Differential cross sections calculated at 250 eV await their experimental confirmation.Comment: LaTeX, 22 pages, 10 figures, submitted to J. Phys.

Factor analysis of attentional set-shifting performance in young and aged mice

<p>Abstract</p> <p>Background</p> <p>Executive dysfunction may play a major role in cognitive decline with aging because frontal lobe structures are particularly vulnerable to advancing age. Lesion studies in rats and mice have suggested that intradimensional shifts (IDSs), extradimensional shifts (EDSs), and reversal learning are mediated by the anterior cingulate cortex, the medial prefrontal cortex, and the orbitofrontal cortex, respectively. We hypothesized that the latent structure of cognitive performance would reflect functional localization in the brain and would be altered by aging.</p> <p>Methods</p> <p>Young (4 months, n = 16) and aged (23 months, n = 18) C57BL/6N mice performed an attentional set-shifting task (ASST) that evaluates simple discrimination (SD), compound discrimination (CD), IDS, EDS, and reversal learning. The performance data were subjected to an exploratory factor analysis to extract the latent structures of ASST performance in young and aged mice.</p> <p>Results</p> <p>The factor analysis extracted two- and three-factor models. In the two-factor model, the factor associated with SD and CD was clearly separated from the factor associated with the rest of the ASST stages in the young mice only. In the three-factor model, the SD and CD loaded on distinct factors. The three-factor model also showed a separation of factors associated with IDS, EDS, and CD reversal. However, the other reversal learning variables, ID reversal and ED reversal, had somewhat inconsistent factor loadings.</p> <p>Conclusions</p> <p>The separation of performance factors in aged mice was less clear than in young mice, which suggests that aged mice utilize neuronal networks more broadly for specific cognitive functions. The result that the factors associated with SD and CD were separated in the three-factor model may suggest that the introduction of an irrelevant or distracting dimension results in the use of a new/orthogonal strategy for better discrimination.</p