Potential energy landscape-based extended van der Waals equation

The inherent structures ({\it IS}) are the local minima of the potential energy surface or landscape, $U({\bf r})$, of an {\it N} atom system. Stillinger has given an exact {\it IS} formulation of thermodynamics. Here the implications for the equation of state are investigated. It is shown that the van der Waals ({\it vdW}) equation, with density-dependent $a$ and $b$ coefficients, holds on the high-temperature plateau of the averaged {\it IS} energy. However, an additional ``landscape'' contribution to the pressure is found at lower $T$. The resulting extended {\it vdW} equation, unlike the original, is capable of yielding a water-like density anomaly, flat isotherms in the coexistence region {\it vs} {\it vdW} loops, and several other desirable features. The plateau energy, the width of the distribution of {\it IS}, and the ``top of the landscape'' temperature are simulated over a broad reduced density range, $2.0 \ge \rho \ge 0.20$, in the Lennard-Jones fluid. Fits to the data yield an explicit equation of state, which is argued to be useful at high density; it nevertheless reproduces the known values of $a$ and $b$ at the critical point

Inherent-Structure Dynamics and Diffusion in Liquids

The self-diffusion constant D is expressed in terms of transitions among the local minima of the potential (inherent structure, IS) and their correlations. The formulae are evaluated and tested against simulation in the supercooled, unit-density Lennard-Jones liquid. The approximation of uncorrelated IS-transition (IST) vectors, D_{0}, greatly exceeds D in the upper temperature range, but merges with simulation at reduced T ~ 0.50. Since uncorrelated IST are associated with a hopping mechanism, the condition D ~ D_{0} provides a new way to identify the crossover to hopping. The results suggest that theories of diffusion in deeply supercooled liquids may be based on weakly correlated IST.Comment: submitted to PR

The Potential Energy Landscape and Mechanisms of Diffusion in Liquids

The mechanism of diffusion in supercooled liquids is investigated from the potential energy landscape point of view, with emphasis on the crossover from high- to low-T dynamics. Molecular dynamics simulations with a time dependent mapping to the associated local mininum or inherent structure (IS) are performed on unit-density Lennard-Jones (LJ). New dynamical quantities introduced include r2_{is}(t), the mean-square displacement (MSD) within a basin of attraction of an IS, R2(t), the MSD of the IS itself, and g_{loc}(t) the mean waiting time in a cooperative region. At intermediate T, r2_{is}(t) posesses an interval of linear t-dependence allowing calculation of an intrabasin diffusion constant D_{is}. Near T_{c} diffusion is intrabasin dominated with D = D_{is}. Below T_{c} the local waiting time tau_{loc} exceeds the time, tau_{pl}, needed for the system to explore the basin, indicating the action of barriers. The distinction between motion among the IS below T_{c} and saddle, or border dynamics above T_{c} is discussed.Comment: submitted to pr

Mean-atom-trajectory model for the velocity autocorrelation function of monatomic liquids

We present a model for the motion of an average atom in a liquid or supercooled liquid state and apply it to calculations of the velocity autocorrelation function $Z(t)$ and diffusion coefficient $D$. The model trajectory consists of oscillations at a distribution of frequencies characteristic of the normal modes of a single potential valley, interspersed with position- and velocity-conserving transits to similar adjacent valleys. The resulting predictions for $Z(t)$ and $D$ agree remarkably well with MD simulations of Na at up to almost three times its melting temperature. Two independent processes in the model relax velocity autocorrelations: (a) dephasing due to the presence of many frequency components, which operates at all temperatures but which produces no diffusion, and (b) the transit process, which increases with increasing temperature and which produces diffusion. Because the model provides a single-atom trajectory in real space and time, including transits, it may be used to calculate all single-atom correlation functions.Comment: LaTeX, 8 figs. This is an updated version of cond-mat/0002057 and cond-mat/0002058 combined Minor changes made to coincide with published versio

Structural Probe of a Glass Forming Liquid: Generalized Compressibility

We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming liquid consisting of a two component mixture of soft spheres in three dimensions. As the temperature is lowered (or as the density is increased), the generalized compressibility drops sharply at the glass transition, with the drop becoming more and more abrupt as the measurement time increases. At our longest measurement times, the drop occurs approximately at the mode coupling temperature $T_C$. The drop in the linear generalized compressibility occurs at the same temperature as the peak in the specific heat. By examining the inherent structure energy as a function of temperature, we find that our results are consistent with the kinetic view of the glass transition in which the system falls out of equilibrium. We find no size dependence and no evidence for a second order phase transition though this does not exclude the possibility of a phase transition below the observed glass transition temperature. We discuss the relation between the linear generalized compressibility and the ordinary isothermal compressibility as well as the static structure factor.Comment: 18 pages, Latex, 26 encapsulated postscript figures, revised paper is shorter, to appear in Phys. Rev.

Design and modeling of electrolyte pumping power reduction in redox flow cells

Because of flexible design, long life, and low-cost maintenance, redox flow cell has been recognized as one of the reliable energy storage techniques in remote power systems. In redox flow cells, electrolyte circulation through carbon felt is necessary in order to produce effective ion exchange during the charge and discharge operations. Pumping power required for electrolyte circulation could be significant, especially for multi-stack cell, due to low permeability of the porous carbon felt. Moreover, effective method for transporting bubbles formed inside the electrode is necessary for increasing the effective area of reaction of the electrodes. To further improve the overall performance of the redox flow cells, we proposed several novel designs of electrolyte inlet/outlet port and flow passage in carbon felt intending to reduce the electrolyte pumping power and to increase the effective area. Based on our numerical modeling, it is found that pumping power can be reduced by appropriate inlet/outlet port design and carbon felt with flow channel. The non-uniform flow pattern may cause the bubbles to be carried away from the electrodes effectively. The proposed designs can be applied not only for the single-stack cell but also applicable for the multiple-stacked cells

Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

<p>Abstract</p> <p>Background</p> <p>Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as <it>Arabidopsis thaliana </it>do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied.</p> <p>Results</p> <p>Several molecular biology tools were used to isolate flower-specific gene promoters from <it>Oncidium </it>'Gower Ramsey' (<it>Onc</it>. GR). A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in <it>Onc</it>. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (<it>TI</it>) genes (<it>OnTI1</it>, <it>OnTI2 </it>and <it>OnTI3</it>), which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable <it>A. thaliana </it>transformation analyses.</p> <p>Conclusions</p> <p>By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.</p

BK polyomavirus microRNA levels in exosomes are modulated by non-coding control region activity and down-regulate viral replication when delivered to non-infected cells prior to infection

In immunosuppressed patients, BKPyV-variants emerge carrying rearranged non-coding control-regions (rr-NCCRs) that increase early viral gene region (EVGR) expression and replication capacity. BKPyV also encodes microRNAs, which have been reported to downregulate EVGR-encoded large T-antigen transcripts, to decrease viral replication in infected cells and to be secreted in exosomes. To investigate the interplay of NCCR and microRNAs, we compared archetype- and rr-NCCR-BKPyV infection in cell culture. We found that laboratory and clinical rr-NCCR-BKPyV-strains show higher replication rates but significantly lower microRNA levels than archetype virus intracellularly and in exosomes. To investigate whether rr-NCCR or increased EVGR activity modulated microRNA levels, we examined the (sp1-4)NCCR-BKPyV, which has an archetype NCCR-architecture but shows increased EVGR expression due to point mutations inactivating one Sp1 binding site. We found that microRNA levels following (sp1-4)NCCR-BKPyV infection were as low as in rr-NCCR-variants. Thus, NCCR rearrangements are not required for lower miRNA levels. Accordingly, Sp1 siRNA knock-down decreased microRNA levels in archetype BKPyV infection but had no effect on (sp1-4)- or rr-NCCR-BKPyV. However, rr-NCCR-BKPyV replication was downregulated by exosome preparations carrying BKPyV-microRNA prior to infection. To explore the potential relevance in humans, urine samples from 12 natalizumab-treated multiple sclerosis patients were analysed. In 7 patients, rr-NCCR-BKPyV were detected showing high urine BKPyV loads but low microRNAs levels, whereas the opposite was seen in 5 patients with archetype BKPyV. We discuss the results in a dynamic model of BKPyV replication according to NCCR activity and exosome regulation, which integrates immune selection pressure, spread to new host cells and rr-NCCR emergence

Effects of the field modulation on the Hofstadter's spectrum

We study the effect of spatially modulated magnetic fields on the energy spectrum of a two-dimensional (2D) Bloch electron. Taking into account four kinds of modulated fields and using the method of direct diagonalization of the Hamiltonian matrix, we calculate energy spectra with varying system parameters (i.e., the kind of the modulation, the relative strength of the modulated field to the uniform background field, and the period of the modulation) to elucidate that the energy band structure sensitively depends on such parameters: Inclusion of spatially modulated fields into a uniform field leads occurrence of gap opening, gap closing, band crossing, and band broadening, resulting distinctive energy band structure from the Hofstadter's spectrum. We also discuss the effect of the field modulation on the symmetries appeared in the Hofstadter's spectrum in detail.Comment: 7 pages (in two-column), 10 figures (including 2 tables

Dynamics of fluctuations in a fluid below the onset of Rayleigh-B\'enard convection

We present experimental data and their theoretical interpretation for the decay rates of temperature fluctuations in a thin layer of a fluid heated from below and confined between parallel horizontal plates. The measurements were made with the mean temperature of the layer corresponding to the critical isochore of sulfur hexafluoride above but near the critical point where fluctuations are exceptionally strong. They cover a wide range of temperature gradients below the onset of Rayleigh-B\'enard convection, and span wave numbers on both sides of the critical value for this onset. The decay rates were determined from experimental shadowgraph images of the fluctuations at several camera exposure times. We present a theoretical expression for an exposure-time-dependent structure factor which is needed for the data analysis. As the onset of convection is approached, the data reveal the critical slowing-down associated with the bifurcation. Theoretical predictions for the decay rates as a function of the wave number and temperature gradient are presented and compared with the experimental data. Quantitative agreement is obtained if allowance is made for some uncertainty in the small spacing between the plates, and when an empirical estimate is employed for the influence of symmetric deviations from the Oberbeck-Boussinesq approximation which are to be expected in a fluid with its density at the mean temperature located on the critical isochore.Comment: 13 pages, 10 figures, 52 reference