High pressure diamond-like liquid carbon

We report density-functional based molecular dynamics simulations, that show that, with increasing pressure, liquid carbon undergoes a gradual transformation from a liquid with local three-fold coordination to a 'diamond-like' liquid. We demonstrate that this unusual structural change is well reproduced by an empirical bond order potential with isotropic long range interactions, supplemented by torsional terms. In contrast, state-of-the-art short-range bond-order potentials do not reproduce this diamond structure. This suggests that a correct description of long-range interactions is crucial for a unified description of the solid and liquid phases of carbon.Comment: 4 pages, 5 figure

Ozone database in support of CMIP5 simulations: results and corresponding radiative forcing

A continuous tropospheric and stratospheric vertically resolved ozone time series, from 1850 to 2099, has been generated to be used as forcing in global climate models that do not include interactive chemistry. A multiple linear regression analysis of SAGE I+II satellite observations and polar ozonesonde measurements is used for the stratospheric zonal mean dataset during the well-observed period from 1979 to 2009. In addition to terms describing the mean annual cycle, the regression includes terms representing equivalent effective stratospheric chlorine (EESC) and the 11-yr solar cycle variability. The EESC regression fit coefficients, together with pre-1979 EESC values, are used to extrapolate the stratospheric ozone time series backward to 1850. While a similar procedure could be used to extrapolate into the future, coupled chemistry climate model (CCM) simulations indicate that future stratospheric ozone abundances are likely to be significantly affected by climate change, and capturing such effects through a regression model approach is not feasible. Therefore, the stratospheric ozone dataset is extended into the future (merged in 2009) with multimodel mean projections from 13 CCMs that performed a simulation until 2099 under the SRES (Special Report on Emission Scenarios) A1B greenhouse gas scenario and the A1 adjusted halogen scenario in the second round of the Chemistry-Climate Model Validation (CCMVal-2) Activity. The stratospheric zonal mean ozone time series is merged with a three-dimensional tropospheric data set extracted from simulations of the past by two CCMs (CAM3.5 and GISSPUCCINI)and of the future by one CCM (CAM3.5). The future tropospheric ozone time series continues the historical CAM3.5 simulation until 2099 following the four different Representative Concentration Pathways (RCPs). Generally good agreement is found between the historical segment of the ozone database and satellite observations, although it should be noted that total column ozone is overestimated in the southern polar latitudes during spring and tropospheric column ozone is slightly underestimated. Vertical profiles of tropospheric ozone are broadly consistent with ozonesondes and in-situ measurements, with some deviations in regions of biomass burning. The tropospheric ozone radiative forcing (RF) from the 1850s to the 2000s is 0.23Wm−2, lower than previous results. The lower value is mainly due to (i) a smaller increase in biomass burning emissions; (ii) a larger influence of stratospheric ozone depletion on upper tropospheric ozone at high southern latitudes; and possibly (iii) a larger influence of clouds (which act to reduce the net forcing) compared to previous radiative forcing calculations. Over the same period, decreases in stratospheric ozone, mainly at high latitudes, produce a RF of −0.08Wm−2, which is more negative than the central Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) value of −0.05Wm−2, but which is within the stated range of −0.15 to +0.05Wm−2. The more negative value is explained by the fact that the regression model simulates significant ozone depletion prior to 1979, in line with the increase in EESC and as confirmed by CCMs, while the AR4 assumed no change in stratospheric RF prior to 1979. A negative RF of similar magnitude persists into the future, although its location shifts from high latitudes to the tropics. This shift is due to increases in polar stratospheric ozone, but decreases in tropical lower stratospheric ozone, related to a strengthening of the Brewer-Dobson circulation, particularly through the latter half of the 21st century. Differences in trends in tropospheric ozone among the four RCPs are mainly driven by different methane concentrations, resulting in a range of tropospheric ozone RFs between 0.4 and 0.1Wm−2 by 2100. The ozone dataset described here has been released for the Coupled Model Intercomparison Project (CMIP5) model simulations in netCDF Climate and Forecast (CF) Metadata Convention at the PCMDI website (http://cmip-pcmdi.llnl.gov/)

Quantitative investigation of two metallohydrolases by X-ray absorption spectroscopy near-edge spectroscopy

The last several years have witnessed a tremendous increase in biological applications using X-ray absorption spectroscopy (BioXAS), thanks to continuous advancements in synchrotron radiation (SR) sources and detector technology. However, XAS applications in many biological systems have been limited by the intrinsic limitations of the Extended X-ray Absorption Fine Structure (EXAFS) technique e.g., the lack of sensitivity to bond angles. As a consequence, the application of the X-ray absorption near-edge structure (XANES) spectroscopy changed this scenario that is now continuously changing with the introduction of the first quantitative XANES packages such as Minut XANES (MXAN). Here we present and discuss the XANES code MXAN, a novel XANES-fitting package that allows a quantitative analysis of experimental data applied to Zn K-edge spectra of two metalloproteins: Leptospira interrogans Peptide deformylase (LiPDF) and acutolysin-C, a representative of snake venom metalloproteinases (SVMPs) from Agkistrodon acutus venom. The analysis on these two metallohydrolases reveals that proteolytic activities are correlated to subtle conformation changes around the zinc ion. In particular, this quantitative study clarifies the occurrence of the LiPDF catalytic mechanism via a two-water-molecules model, whereas in the acutolysin-C we have observed a different proteolytic activity correlated to structural changes around the zinc ion induced by pH variations

Large Thermoelectric Power Factor in TiS2 Crystal with Nearly Stoichiometric Composition

A TiS$_{2}$ crystal with a layered structure was found to have a large thermoelectric power factor.The in-plane power factor $S^{2}/ \rho$ at 300 K is 37.1~$\mu$W/K$^{2}$cm with resistivity ($\rho$) of 1.7 m$\Omega$cm and thermopower ($S$) of -251~$\mu$V/K, and this value is comparable to that of the best thermoelectric material, Bi$_{2}$Te$_{3}$ alloy. The electrical resistivity shows both metallic and highly anisotropic behaviors, suggesting that the electronic structure of this TiS$_{2}$ crystal has a quasi-two-dimensional nature. The large thermoelectric response can be ascribed to the large density of state just above the Fermi energy and inter-valley scattering. In spite of the large power factor, the figure of merit, $ZT$ of TiS$_{2}$ is 0.16 at 300 K, because of relatively large thermal conductivity, 68~mW/Kcm. However, most of this value comes from reducible lattice contribution. Thus, $ZT$ can be improved by reducing lattice thermal conductivity, e.g., by introducing a rattling unit into the inter-layer sites.Comment: 11 pages, 4 figures, to be published in Physical Review

Large deviations of lattice Hamiltonian dynamics coupled to stochastic thermostats

We discuss the Donsker-Varadhan theory of large deviations in the framework of Hamiltonian systems thermostated by a Gaussian stochastic coupling. We derive a general formula for the Donsker-Varadhan large deviation functional for dynamics which satisfy natural properties under time reversal. Next, we discuss the characterization of the stationary state as the solution of a variational principle and its relation to the minimum entropy production principle. Finally, we compute the large deviation functional of the current in the case of a harmonic chain thermostated by a Gaussian stochastic coupling.Comment: Revised version, published in Journal of Statistical Physic

Emergence of Anti-Cancer Drug Resistance: Exploring the Importance of the Microenvironmental Niche via a Spatial Model

Practically, all chemotherapeutic agents lead to drug resistance. Clinically, it is a challenge to determine whether resistance arises prior to, or as a result of, cancer therapy. Further, a number of different intracellular and microenvironmental factors have been correlated with the emergence of drug resistance. With the goal of better understanding drug resistance and its connection with the tumor microenvironment, we have developed a hybrid discrete-continuous mathematical model. In this model, cancer cells described through a particle-spring approach respond to dynamically changing oxygen and DNA damaging drug concentrations described through partial differential equations. We thoroughly explored the behavior of our self-calibrated model under the following common conditions: a fixed layout of the vasculature, an identical initial configuration of cancer cells, the same mechanism of drug action, and one mechanism of cellular response to the drug. We considered one set of simulations in which drug resistance existed prior to the start of treatment, and another set in which drug resistance is acquired in response to treatment. This allows us to compare how both kinds of resistance influence the spatial and temporal dynamics of the developing tumor, and its clonal diversity. We show that both pre-existing and acquired resistance can give rise to three biologically distinct parameter regimes: successful tumor eradication, reduced effectiveness of drug during the course of treatment (resistance), and complete treatment failure

Large Deviations for Stochastic Evolution Equations with Small Multiplicative Noise

The Freidlin-Wentzell large deviation principle is established for the distributions of stochastic evolution equations with general monotone drift and small multiplicative noise. As examples, the main results are applied to derive the large deviation principle for different types of SPDE such as stochastic reaction-diffusion equations, stochastic porous media equations and fast diffusion equations, and the stochastic p-Laplace equation in Hilbert space. The weak convergence approach is employed in the proof to establish the Laplace principle, which is equivalent to the large deviation principle in our framework.Comment: 31 pages, published in Appl. Math. Opti

Nanofabrication by magnetic focusing of supersonic beams

We present a new method for nanoscale atom lithography. We propose the use of a supersonic atomic beam, which provides an extremely high-brightness and cold source of fast atoms. The atoms are to be focused onto a substrate using a thin magnetic film, into which apertures with widths on the order of 100 nm have been etched. Focused spot sizes near or below 10 nm, with focal lengths on the order of 10 microns, are predicted. This scheme is applicable both to precision patterning of surfaces with metastable atomic beams and to direct deposition of material.Comment: 4 pages, 3 figure

New Quantum Theory of Laser Cooling Mechanisms

In this paper, we study the laser cooling mechanisms with a new quantum theory approach by applying a new Schrodinger equation, which can describe a particle in conservative and non-conservative force field. With the new theory, we prove the atom in laser field can be cooled, and give the atom cooling temperature, which is accordance with experiment result. Otherwise, we give new prediction that the atom cooling temperature is directly proportional to the atom vibration frequency. By calculation, we find they are: $T=0.4334\omega$.Comment: arXiv admin note: text overlap with arXiv:physics/0601097, arXiv:0710.5078, arXiv:0707.2280 by other authors without attributio

Properties of the Lambda(1520) Resonance from High-Precision Electroproduction Data

High-resolution spectrometer measurements of the reaction H(e,e'K+)X at small Q2 are used to extract the mass and width of the Lambda(1520). We investigate the influence of various assumptions used in the extraction. The width appears to be more sensitive to the assumptions than the mass. To reach a width uncertainty about 1 MeV or better, one needs to know the structure of the non-resonant background. Based on the new Jefferson Lab Hall A data, our final values for the Breit-Wigner parameters are M = 1520.4 +- 0.6 (stat) +- 1.5 (syst) MeV, Gamma = 18.6 +- 1.9 (stat) +- 1 (syst) MeV. For the first time, we also estimate the pole position for this resonance and find that both the pole mass and width seem to be smaller than the Breit-Wigner values.Comment: 7 pages, 3 figures; corresponds to the published versio