Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here, we alter the solvent environment in a controlled manner by choosing two different cosolvents of water, urea, and dimethyl sulfoxide (DMSO) and study unfolding of four different proteins to understand the respective sequence of melting by computer simulation methods. We indeed find interesting differences in the sequence of melting of alpha helices and beta sheets in these two solvents. For example, in 8 M urea solution, beta-sheet parts of a protein are found to unfold preferentially, followed by the unfolding of alpha helices. In contrast, 8 M DMSO solution unfolds alpha helices first, followed by the separation of beta sheets for the majority of proteins. Sequence of unfolding events in four different alpha/beta proteins and also in chicken villin head piece (HP-36) both in urea and DMSO solutions demonstrate that the unfolding pathways are determined jointly by relative exposure of polar and nonpolar residues of a protein and the mode of molecular action of a solvent on that protein.

Smoothed Functional Algorithms for Stochastic Optimization Using q-Gaussian Distributions

Smoothed functional (SF) schemes for gradient estimation are known to be efficient in stochastic optimization algorithms, especially when the objective is to improve the performance of a stochastic system However, the performance of these methods depends on several parameters, such as the choice of a suitable smoothing kernel. Different kernels have been studied in the literature, which include Gaussian, Cauchy, and uniform distributions, among others. This article studies a new class of kernels based on the q-Gaussian distribution, which has gained popularity in statistical physics over the last decade. Though the importance of this family of distributions is attributed to its ability to generalize the Gaussian distribution, we observe that this class encompasses almost all existing smoothing kernels. This motivates us to study SF schemes for gradient estimation using the q-Gaussian distribution. Using the derived gradient estimates, we propose two-timescale algorithms for optimization of a stochastic objective function in a constrained setting with a projected gradient search approach. We prove the convergence of our algorithms to the set of stationary points of an associated ODE. We also demonstrate their performance numerically through simulations on a queuing model.

Phase Diagram Study of Succinonitrile-Vanillin Organic Alloy System

Phase diagram studies of succinonitrile-vanillin system show the formation of 2:1 congruent melting type compound. Crystallization velocities of pure components, succinonitrile-vanillin complex, and two eutectics have been determined at different undercoolings. On the basis of heat of fusion measurements, excess thermodynamic functions have been calculated. Microstructural studies revealed that impurities modify the morphology. FTIR spectral studies and computer simulation have shown the existence of hydrogen bonding in the eutectics and the congruent melting compound. On the basis of experimental results, the mechanism of formation of eutectics and its solidification behavior are discussed.

The effect of thermal-activation on dislocation processes at an atomistic crack-tip

The effects of thermal activation on the dislocation emission from an atomistic crack tip are discussed, Molecular dynamics simulations at different constant temperatures are carried out to investigate the thermal effects. The simulated results show that the processes of the partial dislocation generation and emission are temperature dependent. As the temperature increases, the incipient duration of the partial dislocation nucleation becomes longer, the critical stress intensity factor for partial dislocation emission is reduced and, at the same loading level, more dislocations are emitted. The dislocation velocity moving away from the crack tip and the separations of partial dislocations are apparently not temperature dependent. The simulated results also show that, as the temperature increases, the stress distribution along the crack increases slightly. Therefore stress softening at the crack tip induced by thermal activation does not exist in the present simulation. A simple model is proposed to evaluate the relation of the critical stress intensity factor versus temperature. The obtained relation is in good agreement with our molecular dynamics results.

Crack tip behavior and crack-propagation in ductile materials

Dilatational plastic equations, which can include the effects of ductile damage, are derived based on the equivalency in expressions for dissipated plastic work. Void damage developed internally at the large-strain stage is represented by an effective continuum being strain-softened and plastically dilated. Accumulation of this local damage leads to progressive failure in materials. With regard to this microstructural background, the constitutive parameters included for characterizing material behaviour have the sense of internal variables. They are not able to be determined explicitly by macroscopic testing but rather through computer simulation of experimental curves and data. Application of this constitutive model to mode-I cracking examples demonstrates that a huge strain concentration accompanied by a substantial drop of stress does occur near the crack tip. Eventually, crack propagation is simulated by using finite elements in computations. Two numerical examples show good accordance with experimental data. The whole procedure of study serves as a justification of the constitutive formulation proposed in the text.

A Model of Ischemia-Induced Neuroblast Activation in the Adult Subventricular Zone

12 p.

Generation of periodic ultrashort electron bunches and strongly asymmetric ion Coulomb explosion in nanometer foils interacting with ultra-intense laser pulse

The interaction of a linearly polarized intense laser pulse with an ultrathin nanometer plasma layer is investigated to understand the physics of the ion acceleration. It is shown by the computer simulation that the plasma response to the laser pulse comprises two steps. First, due to the vxB effect, electrons in the plasma layer are extracted and periodic ultrashort relativistic electron bunches are generated every half of a laser period. Second, strongly asymmetric Coulomb explosion of ions in the foil occurs due to the strong electrostatic charge separation, once the foil is burnt through. Followed by the laser accelerated electron bunch, the ion expansion in the forward direction occurs along the laser beam that is much stronger as compared to the backward direction. (c) 2008 American Institute of Physics.

Attosecond X-ray pulse obtained from linear Thomson scattering

Linear Thomson scattering by a relativistic electron of a short pulse laser has been investigated by computer simulation. Under a laser field with a pulse of 33.3-fs full-width at half-maximum, and the initial energy of an electron of gamma(0) = 10, the motion of the electron is relativistic and generates an ultrashort radiation of 76-as with a photon wave length of 2.5-nm in the backward scattering. The radiation under a high relativistic energy electron has better characteristic than under a low relativistic energy electron in terms of the pulse width and the angular distribution. (c) 2005 Elsevier GrnbH. All rights reserved.

Digested sludge: delineation and modeling for ocean disposal

Experimental work was performed to delineate the system of digested sludge particles and associated trace metals and also to measure the interactions of sludge with seawater. Particle-size and particle number distributions were measured with a Coulter Counter. Number counts in excess of 10¹² particles per liter were found in both the City of Los Angeles Hyperion mesophilic digested sludge and the Los Angeles County Sanitation Districts (LACSD) digested primary sludge. More than 90 percent of the particles had diameters less than 10 microns.

Total and dissolved trace metals (Ag, Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) were measured in LACSD sludge. Manganese was the only metal whose dissolved fraction exceeded one percent of the total metal. Sedimentation experiments for several dilutions of LACSD sludge in seawater showed that the sedimentation velocities of the sludge particles decreased as the dilution factor increased. A tenfold increase in dilution shifted the sedimentation velocity distribution by an order of magnitude. Chromium, Cu, Fe, Ni, Pb, and Zn were also followed during sedimentation. To a first approximation these metals behaved like the particles.

Solids and selected trace metals (Cr, Cu, Fe, Ni, Pb, and Zn) were monitored in oxic mixtures of both Hyperion and LACSD sludges for periods of 10 to 28 days. Less than 10 percent of the filterable solids dissolved or were oxidized. Only Ni was mobilized away from the particles. The majority of the mobilization was complete in less than one day.

The experimental data of this work were combined with oceanographic, biological, and geochemical information to propose and model the discharge of digested sludge to the San Pedro and Santa Monica Basins. A hydraulic computer simulation for a round buoyant jet in a density stratified medium showed that discharges of sludge effluent mixture at depths of 730 m would rise no more than 120 m. Initial jet mixing provided dilution estimates of 450 to 2600. Sedimentation analyses indicated that the solids would reach the sediments within 10 km of the point discharge.

Mass balances on the oxidizable chemical constituents in sludge indicated that the nearly anoxic waters of the basins would become wholly anoxic as a result of proposed discharges. From chemical-equilibrium computer modeling of the sludge digester and dilutions of sludge in anoxic seawater, it was predicted that the chemistry of all trace metals except Cr and Mn will be controlled by the precipitation of metal sulfide solids. This metal speciation held for dilutions up to 3000.

The net environmental impacts of this scheme should be salutary. The trace metals in the sludge should be immobilized in the anaerobic bottom sediments of the basins. Apparently no lifeforms higher than bacteria are there to be disrupted. The proposed deep-water discharges would remove the need for potentially expensive and energy-intensive land disposal alternatives and would end the discharge to the highly productive water near the ocean surface.

Phase unwrapping based on branch cut placing and reliability ordering

A new 2-D quality-guided phase-unwrapping algorithm, based on the placement of the branch cuts, is presented. Its framework consists of branch cut placing guided by an original quality map and reliability ordering performed on a final quality map. To improve the noise immunity of the new algorithm, a new quality map, which is used as the original quality map to guide the placement of the branch cuts, is proposed. After a complete description of the algorithm and the quality map, several wrapped images are used to examine the effectiveness of the algorithm. Computer simulation and experimental results make it clear that the proposed algorithm works effectively even when a wrapped phase map contains error sources, such as phase discontinuities, noise, and undersampling. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Phase unwrapping based on branch cut placing and reliability ordering

A new 2-D quality-guided phase-unwrapping algorithm, based on the placement of the branch cuts, is presented. Its framework consists of branch cut placing guided by an original quality map and reliability ordering performed on a final quality map. To improve the noise immunity of the new algorithm, a new quality map, which is used as the original quality map to guide the placement of the branch cuts, is proposed. After a complete description of the algorithm and the quality map, several wrapped images are used to examine the effectiveness of the algorithm. Computer simulation and experimental results make it clear that the proposed algorithm works effectively even when a wrapped phase map contains error sources, such as phase discontinuities, noise, and undersampling. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

基于分支设置的质量导引相位展开算法

二维相位展开方法是近年来较为活跃、引起关注的一个研究课题，它在许多测量应用中有着重要的作用。尽管掩膜阻断算法在多个领域都有成功应用实例，该算法存在着固有的缺陷。为了克服掩膜阻断算法的缺陷，综合分支阻断方法和质量导引方法的优点，提出一种基于分支设置的质量导引相位展开新算法。它先以一个初始质量图来引导分支的设置，然后把分支对应的相位质量设置为最低，从而产生一个新的质量图，最后按新质量图来引导相位展开，并使用几个包裹相位图来验证此方法的有效性。计算机模拟相位图和实际相位图的相位展开结果表明，在存在复杂轮廓不连续

Coma measurement of projection optics in lithographic tools based on relative image displacements at multiple illumination settings

In this paper, we propose a novel method for measuring the coma aberrations of lithographic projection optics based on relative image displacements at multiple illumination settings. The measurement accuracy of coma can be improved because the phase-shifting gratings are more sensitive to the aberrations than the binary gratings used in the TAMIS technique, and the impact of distortion on displacements of aerial image can be eliminated when the relative image displacements are measured. The PROLITH simulation results show that, the measurement accuracy of coma increases by more than 25% under conventional illumination, and the measurement accuracy of primary coma increases by more than 20% under annular illumination, compared with the TAMIS technique. (c) 2007 Optical Society of America.

Weighted least-squares phase unwrapping algorithm based on derivative variance correlation map

Among different phase unwrapping approaches, the weighted least-squares minimization methods are gaining attention. In these algorithms, weighting coefficient is generated from a quality map. The intrinsic drawbacks of existing quality maps constrain the application of these algorithms. They often fail to handle wrapped phase data contains error sources, such as phase discontinuities, noise and undersampling. In order to deal with those intractable wrapped phase data, a new weighted least-squares phase unwrapping algorithm based on derivative variance correlation map is proposed. In the algorithm, derivative variance correlation map, a novel quality map, can truly reflect wrapped phase quality, ensuring a more reliable unwrapped result. The definition of the derivative variance correlation map and the principle of the proposed algorithm are present in detail. The performance of the new algorithm has been tested by use of a simulated spherical surface wrapped data and an experimental interferometric synthetic aperture radar (IFSAR) wrapped data. Computer simulation and experimental results have verified that the proposed algorithm can work effectively even when a wrapped phase map contains intractable error sources. (c) 2006 Elsevier GmbH. All rights reserved.

Near-field hexagonal array illumination based on fractional Talbot effect

Hexagonal array is a basic structure widely exists in nature and adopted by optoclectronic device. A phase plate based on the fractional Talbot effect that converts a single expanded laser beam into a regular hexagonal array of uniformly illuminated apertures with virtually 100% efficiency is presented. The uniform hexagonal array illumination with a fill factor of 1/12 is demonstrated by the computer simulation. (C) 2006 Elsevier GmbH. All rights reserved.