Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements

We present a new strategy for protein side-chain placement that uses flat-bottom potentials for rotamer scoring. The extent of the flat bottom depends on the coarseness of the rotamer library and is optimized for libraries ranging from diversities of 0.2 Å to 5.0 Å. The parameters reported here were optimized for forcefields using Lennard-Jones 12−6 van der Waals potential with DREIDING parameters but are expected to be similar for AMBER, CHARMM, and other forcefields. This Side-Chain Rotamer Excitation Analysis Method is implemented in the SCREAM software package. Similar scoring function strategies should be useful for ligand docking, virtual ligand screening, and protein folding applications

A Repelling-Attracting Metropolis Algorithm for Multimodality

Although the Metropolis algorithm is simple to implement, it often has difficulties exploring multimodal distributions. We propose the repelling-attracting Metropolis (RAM) algorithm that maintains the simple-to-implement nature of the Metropolis algorithm, but is more likely to jump between modes. The RAM algorithm is a Metropolis-Hastings algorithm with a proposal that consists of a downhill move in density that aims to make local modes repelling, followed by an uphill move in density that aims to make local modes attracting. The downhill move is achieved via a reciprocal Metropolis ratio so that the algorithm prefers downward movement. The uphill move does the opposite using the standard Metropolis ratio which prefers upward movement. This down-up movement in density increases the probability of a proposed move to a different mode. Because the acceptance probability of the proposal involves a ratio of intractable integrals, we introduce an auxiliary variable which creates a term in the acceptance probability that cancels with the intractable ratio. Using several examples, we demonstrate the potential for the RAM algorithm to explore a multimodal distribution more efficiently than a Metropolis algorithm and with less tuning than is commonly required by tempering-based methods

Energetic radiation and the sulfur chemistry of protostellar envelopes: Submillimeter interferometry of AFGL 2591

CONTEXT: The chemistry in the inner few thousand AU of accreting envelopes around young stellar objects is predicted to vary greatly with far-UV and X-ray irradiation by the central star. Aim We search for molecular tracers of high-energy irradiation by the protostar in the hot inner envelope. METHODS: The Submillimeter Array (SMA) has observed the high-mass star forming region AFGL 2591 in lines of CS, SO, HCN, HCN(v2=1), and HC15N with 0.6" resolution at 350 GHz probing radial scales of 600-3500 AU for an assumed distance of 1 kpc. The SMA observations are compared with the predictions of a chemical model fitted to previous single-dish observations. RESULTS: The CS and SO main peaks are extended in space at the FWHM level, as predicted in the model assuming protostellar X-rays. However, the main peak sizes are found smaller than modeled by nearly a factor of 2. On the other hand, the lines of CS, HCN, and HC15N, but not SO and HCN(v2=1), show pedestal emissions at radii of about 3500 AU that are not predicted. All lines except SO show a secondary peak within the approaching outflow cone. A dip or null in the visibilities caused by a sharp decrease in abundance with increasing radius is not observed in CS and only tentatively in SO. CONCLUSIONS: The emission of protostellar X-rays is supported by the good fit of the modeled SO and CS amplitude visibilities including an extended main peak in CS. The broad pedestals can be interpreted by far-UV irradiation in a spherically non-symmetric geometry, possibly comprising outflow walls on scales of 3500 -- 7000 AU. The extended CS and SO main peaks suggest sulfur evaporation near the 100 K temperature radius.Comment: Astronomy and Astrophysics, in pres

Residual stress development and evolution in two-phase crystalline material: a discrete dislocation study

Crystalline materials undergo heterogeneous deformation upon the application of external load, which results in the development of incompatible elastic strains in the material as soon as the load is removed. The presence of heterogeneous distribution of elastic strains in the absence of any form of external load results in the building up of stresses referred to as residual stresses. The heterogeneity of strain is attributed either to the presence of multiple phases or to the orientation gradients across the sample volume. This paper is an endeavour to model the presence of second phase in a two-dimensional discrete dislocation dynamics framework, which already contains constitutive rules to include three-dimensional mechanisms, such as line tension and dynamic junction formation. The model is used to investigate residual stress development in single crystals subjected to plane strain loading and then subsequently unloaded to study residual stresses. The dislocation accumulation around the second phase and its effect on the mechanical properties is studied. The orientation dependence of residual stresses as a function of the underlying defect substructure has also been explored. A variety of results are obtained. In particular, the development of stresses as a function of underlying defect substructure is also presented and found to depend upon the orientation of the crystal

A 100-MIPS GaAs asynchronous microprocessor

The authors describe how they ported an asynchronous microprocessor previously implemented in CMOS to gallium arsenide, using a technology-independent asynchronous design technique. They introduce new circuits including a sense-amplifier, a completion detection circuit, and a general circuit structure for operators specified by production rules. The authors used and tested these circuits in a variety of designs

Simulation studies on vapor phase condensation of magnesium and computations of nucleation rates using Discrete-Section model

Capacity of discrete section models as a reliable tool to analyze and predict the data in particle nucleation and growth experiments has been demonstrated through comparisons of simulated and experimental data. A computer code based on this model is developed and homogenous nucleation of particles and growth is simulated. The results have been benchmarked against the published data on nucleation and growth in iron vapors. The published experimental results of condensation of magnesium vapors through homogenous nucleation are then analyzed using the results of simulations. The predicted values of magnesium vapors super saturation ratio and temperature at the point of nucleation are in excellent agreement with the experimental data. The code is used to compute the particle nucleation rate and computed values are compared with the values predicted by analytical expressions based on different theories. It is demonstrated that the model is able to predict values which are close to experimental values and thus can be used to predict nucleation rate.

Chemical Modelling of Young Stellar Objects, I. Method and Benchmarks

Upcoming facilities such as the Herschel Space Observatory or ALMA will deliver a wealth of molecular line observations of young stellar objects (YSOs). Based on line fluxes, chemical abundances can then be estimated by radiative transfer calculations. To derive physical properties from abundances, the chemical network needs to be modeled and fitted to the observations. This modeling process is however computationally exceedingly demanding, particularly if in addition to density and temperature, far UV (FUV) irradiation, X-rays, and multi-dimensional geometry have to be considered. We develop a fast tool, suitable for various applications of chemical modeling in YSOs. A grid of the chemical composition of the gas having a density, temperature, FUV irradiation and X-ray flux is pre-calculated as a function of time. A specific interpolation approach is developed to reduce the database to a feasible size. Published models of AFGL 2591 are used to verify the accuracy of the method. A second benchmark test is carried out for FUV sensitive molecules. The novel method for chemical modeling is more than 250,000 times faster than direct modeling and agrees within a mean factor of 1.35. The tool is distributed for public use. In the course of devloping the method, the chemical evolution is explored: We find that X-ray chemistry in envelopes of YSOs can be reproduced by means of an enhanced cosmic-ray ionization rate. We further find that the abundance of CH+ in low-density gas with high ionization can be enhanced by the recombination of doubly ionized carbon (C++) and suggest a new value for the initial abundance of the main sulphur carrier in the hot-core.Comment: Accepted by ApJS. 24 pages, 15 figures. A version with higher resolution images is available from http://www.astro.phys.ethz.ch/staff/simonbr/papgridI.pdf . Online data available at http://www.astro.phys.ethz.ch/chemgrid.html . Second paper of this series of papers available at arXiv:0906.058

A non-equilibrium ortho-to-para ratio of water in the Orion PDR

The ortho-to-para ratio (OPR) of H$_2$O is thought to be sensitive to the temperature of water formation. The OPR of H$_2$O is thus useful to study the formation mechanism of water. We investigate the OPR of water in the Orion PDR (Photon-dominated region), at the Orion Bar and Orion S positions, using data from {\it Herschel}/HIFI. We detect the ground-state lines of ortho- and para-H$_2$$^{18}$O in the Orion Bar and Orion S and we estimate the column densities using LTE and non-LTE methods. Based on our calculations, the ortho-to-para ratio (OPR) in the Orion Bar is 0.1 $-$ 0.5, which is unexpectedly low given the gas temperature of $\sim$ 85 K, and also lower than the values measured for other interstellar clouds and protoplanetary disks. Toward Orion S, our OPR estimate is below 2. This low OPR at 2 positions in the Orion PDR is inconsistent with gas phase formation and with thermal evaporation from dust grains, but it may be explained by photodesorption