Non-equilibrium thermodynamics in sheared hard-sphere materials

We combine the shear-transformation-zone (STZ) theory of amorphous plasticity with Edwards' statistical theory of granular materials to describe shear flow in a disordered system of thermalized hard spheres. The equations of motion for this system are developed within a statistical thermodynamic framework analogous to that which has been used in the analysis of molecular glasses. For hard spheres, the system volume $V$ replaces the internal energy $U$ as a function of entropy $S$ in conventional statistical mechanics. In place of the effective temperature, the compactivity $X = \partial V / \partial S$ characterizes the internal state of disorder. We derive the STZ equations of motion for a granular material accordingly, and predict the strain rate as a function of the ratio of the shear stress to the pressure for different values of a dimensionless, temperature-like variable near a jamming transition. We use a simplified version of our theory to interpret numerical simulations by Haxton, Schmiedeberg and Liu, and in this way are able to obtain useful insights about internal rate factors and relations between jamming and glass transitions.Comment: 9 pages, 6 figure

The Construction and Related Industries in a Changing Socio-Economic Environment: The Case of Hong Kong

Hong Kong is well known for its “housing market bubble”. Both theoretical and empirical studies point to the supply side being the “root of all evil”. This paper takes a preliminary step in understanding the supply side of the Hong Kong market by investigating the construction and related industries. After taking into consideration of the unusual public expenditure, the construction industry seems to be “normal” in international standard. Its relationship with the aggregate economy is also examined. Directions for future research are also suggested.housing, construction, government policy, employment, investment

Computational Methods for Parameter Estimation in Climate Models

Intensive computational methods have been used by Earth scientists in a wide range of problems in data inversion and uncertainty quantification such as earthquake epicenter location and climate projections. To quantify the uncertainties resulting from a range of plausible model configurations it is necessary to estimate a multidimensional probability distribution. The computational cost of estimating these distributions for geoscience applications is impractical using traditional methods such as Metropolis/Gibbs algorithms as simulation costs limit the number of experiments that can be obtained reasonably. Several alternate sampling strategies have been proposed that could improve on the sampling efficiency including Multiple Very Fast Simulated Annealing (MVFSA) and Adaptive Metropolis algorithms. The performance of these proposed sampling strategies are evaluated with a surrogate climate model that is able to approximate the noise and response behavior of a realistic atmospheric general circulation model (AGCM). The surrogate model is fast enough that its evaluation can be embedded in these Monte Carlo algorithms. We show that adaptive methods can be superior to MVFSA to approximate the known posterior distribution with fewer forward evaluations. However the adaptive methods can also be limited by inadequate sample mixing. The Single Component and Delayed Rejection Adaptive Metropolis algorithms were found to resolve these limitations, although challenges remain to approximating multi-modal distributions. The results show that these advanced methods of statistical inference can provide practical solutions to the climate model calibration problem and challenges in quantifying climate projection uncertainties. The computational methods would also be useful to problems outside climate prediction, particularly those where sampling is limited by availability of computational resources.National Science Foundation OCE-0415251CONACyT-Mexico 159764Institute for Geophysic

Pathway of human AS3MT arsenic methylation

A synthetic gene encoding human As(III) S-adenosylmethionine (SAM) methyltransferase (hAS3MT) was expressed, and the purified enzyme was characterized. The synthetic enzyme is considerably more active than a cDNA-expressed enzyme using endogenous reductants thioredoxin (Trx), thioredoxin reductase (TR), NADPH, and reduced glutathione (GSH). Each of the seven cysteines (the four conserved residues, Cys32, Cys61, Cys156, and Cys206, and nonconserved, Cys72, Cys85, and Cys250) was individually changed to serine. The nonconserved cysteine derivates were still active. None of the individual C32S, C61S, C156S, and C206S derivates were able to methylate As(III). However, the C32S and C61S enzymes retained the ability to methylate MAs(III). These observations suggest that Cys156 and Cys206 play a different role in catalysis than that of Cys32 and Cys61. A homology model built on the structure of a thermophilic orthologue indicates that Cys156 and Cys206 form the As(III) binding site, whereas Cys32 and Cys61 form a disulfide bond. Two observations shed light on the pathway of methylation. First, binding assays using the fluorescence of a single-tryptophan derivative indicate that As(GS)3 binds to the enzyme much faster than inorganic As(III). Second, the major product of the first round of methylation is MAs(III), not MAs(V), and remains enzyme-bound until it is methylated a second time. We propose a new pathway for hAS3MT catalysis that reconciles the hypothesis of Challenger ((1947) Sci. Prog., 35, 396-416) with the pathway proposed by Hayakawa et al. ((2005) Arch. Toxicol., 79, 183-191). The products are the more toxic and more carcinogenic trivalent methylarsenicals, but arsenic undergoes oxidation and reduction as enzyme-bound intermediates

Gravitational waves from pulsations of neutron stars described by realistic Equations of State

In this work we discuss the time-evolution of nonspherical perturbations of a nonrotating neutron star described by a realistic Equation of State (EOS). We analyze 10 different EOS for a large sample of neutron star models. Various kind of generic initial data are evolved and the corresponding gravitational wave signals are computed. We focus on the dynamical excitation of fluid and spacetime modes and extract the corresponding frequencies. We employ a constrained numerical algorithm based on standard finite differencing schemes which permits stable and long term evolutions. Our code provides accurate waveforms and allows to capture, via Fourier analysis of the energy spectra, the frequencies of the fluid modes with an accuracy comparable to that of frequency domain calculations. The results we present here are useful for provindig comparisons with simulations of nonlinear oscillations of (rotating) neutron star models as well as testbeds for 3D nonlinear codes.Comment: 17 pages, 9 figures. Small changes. Version published in Phys. Rev.

Shear flow of angular grains: acoustic effects and non-monotonic rate dependence of volume

Naturally-occurring granular materials often consist of angular particles whose shape and frictional characteristics may have important implications on macroscopic flow rheology. In this paper, we provide a theoretical account for the peculiar phenomenon of auto-acoustic compaction -- non-monotonic variation of shear band volume with shear rate in angular particles -- recently observed in experiments. Our approach is based on the notion that the volume of a granular material is determined by an effective-disorder temperature known as the compactivity. Noise sources in a driven granular material couple its various degrees of freedom and the environment, causing the flow of entropy between them. The grain-scale dynamics is described by the shear-transformation-zone (STZ) theory of granular flow, which accounts for irreversible plastic deformation in terms of localized flow defects whose density is governed by the state of configurational disorder. To model the effects of grain shape and frictional characteristics, we propose an Ising-like internal variable to account for nearest-neighbor grain interlocking and geometric frustration, and interpret the effect of friction as an acoustic noise strength. We show quantitative agreement between experimental measurements and theoretical predictions, and propose additional experiments that provide stringent tests on the new theoretical elements.Comment: 12 pages, 3 figure

The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints

Stick-slip instabilities in sheared granular flow: the role of friction and acoustic vibrations

We propose a theory of shear flow in dense granular materials. A key ingredient of the theory is an effective temperature that determines how the material responds to external driving forces such as shear stresses and vibrations. We show that, within our model, friction between grains produces stick-slip behavior at intermediate shear rates, even if the material is rate-strengthening at larger rates. In addition, externally generated acoustic vibrations alter the stick-slip amplitude, or suppress stick-slip altogether, depending on the pressure and shear rate. We construct a phase diagram that indicates the parameter regimes for which stick-slip occurs in the presence and absence of acoustic vibrations of a fixed amplitude and frequency. These results connect the microscopic physics to macroscopic dynamics, and thus produce useful information about a variety of granular phenomena including rupture and slip along earthquake faults, the remote triggering of instabilities, and the control of friction in material processing.Comment: 12 pages, 8 figure

Spacelab 3 Mission Science Review

Papers and abstracts of the presentations made at the symposium are given as the scientific report for the Spacelab 3 mission. Spacelab 3, the second flight of the National Aeronautics and Space Administration's (NASA) orbital laboratory, signified a new era of research in space. The primary objective of the mission was to conduct applications, science, and technology experiments requiring the low-gravity environment of Earth orbit and stable vehicle attitude over an extended period (e.g., 6 days) with emphasis on materials processing. The mission was launched on April 29, 1985, aboard the Space Shuttle Challenger which landed a week later on May 6. The multidisciplinary payload included 15 investigations in five scientific fields: material science, fluid dynamics, life sciences, astrophysics, and atmospheric science