Optimal synthesis of three-dimensional complex amplitude distributions

The synthesis of three-dimensional (3-D) light distributions is important for many applications. For example, in scanning applications it is preferable that the scanning beam preserve its characteristics over a large distance to yield elongated scanning range. It is evident that any 3-D light distribution must satisfy the wave equation or, in second-order approximation, the Fresnel diffraction formula. Thus many desirable 3-D light distributions may not be realizable. We propose a single optical element (OE) that synthesizes a physical beam within a certain 3-D region. The OE provides the optimal physical beam in comparison with a desired one in the sense of minimal mean-square error.     

Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes

Flavin-dependent halogenases are potentially valuable biocatalysts for the regioselective halogenation of aromatic compounds. These enzymes, utilising benign inorganic halides, offer potential advantages over traditional non-enzymatic halogenation chemistry that often lacks regiocontrol and requires deleterious reagents. Here we extend the biocatalytic repertoire of the tryptophan halogenases, demonstrating how these enzymes can halogenate a range of alternative aryl substrates. Using structure guided mutagenesis we also show that it is possible to alter the regioselectivity as well as increase the activity of the halogenases with non-native substrates including anthranilic acid; an important intermediate in the synthesis and biosynthesis of pharmaceuticals and other valuable products.     

Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer

Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics‐molecular mechanics approach with a recently developed semiempirical AM1‐SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C? H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important. © 2014 Wiley Periodicals, Inc.     

Simple continuous and discrete models for simulating replica exchange simulations of protein folding

The efficiency of temperature replica exchange (RE) simulations hinge on their ability to enhance conformational sampling at physiological temperatures by taking advantage of more rapid conformational interconversions at higher temperatures. While temperature RE is a parallel simulation technique that is relatively straightforward to implement, kinetics in the RE ensemble is complicated, and there is much to learn about how best to employ RE simulations in computational biophysics. Protein folding rates often slow down above a certain temperature due to entropic bottlenecks. This "anti-Arrhenius" behavior represents a challenge for RE. However, it is far from straightforward to systematically explore the impact of this on RE by brute force molecular simulations, since RE simulations of protein folding are very difficult to converge. To understand some of the basic mechanisms that determine the efficiency of RE, it is useful to study simplified low dimensionality systems that share some of the key characteristics of molecular systems. Results are presented concerning the efficiency of temperature RE on a continuous two-dimensional potential that contains an entropic bottleneck. Optimal efficiency was obtained when the temperatures of the replicas did not exceed the temperature at which the harmonic mean of the folding and unfolding rates is maximized. This confirms a result we previously obtained using a discrete network model of RE. Comparison of the efficiencies obtained using the continuous and discrete models makes it possible to identify non-Markovian effects, which slow down equilibration of the RE ensemble on the more complex continuous potential. In particular, the rate of temperature diffusion and also the efficiency of RE is limited by the time scale of conformational rearrangements within free energy basins.     

Qualitative supercritical fluid extraction coupled to capillary gas chromatography

The usefulness and ease of utilizing supercritical fluid extraction (SFE) directly coupled to capillary gas chromatography (GC) as quantitative or qualitative analytical problem-solving tools will be demonstrated. As an alternative to conventional liquid solvent extractions, SFE presents itself as a means to achieve high extraction efficiencies of different compounds in complex solid matrices in very rapid tims frames. Moreover, SFE has an additional advantage of being able to achieve distinct extraction selectivities as a function of the solubilizing power of the supercritical fluid extracting phase. For on-line SFE/GC, the extraction effluent is directly transferred to the analytical chromatograph. On-line SFE/GC involves the decompression of pressurized extraction effluent directly into a heated, unmodified capillary split injection port of the GC. In this respect, SFE introduction into GC can be used as an alternative means of GC injection, comparable to such modes of injection as pyrolysis and thermal desorption. This paper will show applications of SFE/GC where mass spectrometric detection together with flame ionization detection was used for component identification from environmental, tobacco, and petroleum matrices.     

Iron(II) and zinc(II) monohelical binaphthyl salen complexes

A new chiral binaphthyl salen ligand with rigid polyaromatic sidearms gives monohelical complexes (Fe(II) and Zn(II)) of predetermined handedness.     

Jump conditions across strong compaction waves in gas saturated rigid porous media

Based on experimental results and some additional simplifying assumptions, the general macroscopic two phase equations governing the flow field which is developed in a gas saturated rigid porous medium domain were simplified to a form which enab led us to develop two analytical models for calculating the jump conditions across strong compaction waves.Predictions obtained by these two simplified analytical models are compared to the experimental results of Sandusky and Liddiard (1985) and to predictions of another more complicated model which was proposed by Powers et al. (1989). Fairly good to excelle nt agreements are evident.This article was processed using Springer-Verlag T_EX Shock Waves macro package 1.0 and the AMS fonts, developed by the American Mathematical Society.     

Accelerating CFD–DEM simulation of processes with wide particle size distributions

Size-reduction systems have been extensively used in industry for many years. Nevertheless, reliable engineering tools to be used to predict the comminution of particles are scarce. Computational fluid dynamics(CFD)–discrete element model(DEM) numerical simulation may be used to predict such a complex phenomenon and therefore establish a proper design and optimization model for comminution systems.They may also be used to predict attrition in systems where particle attrition is significant. Therefore,empirical comminution functions(which are applicable for any attrition/comminution process), such as:strength distribution, selection, equivalence, breakage, and fatigue, have been integrated into the threedimensional CFD–DEM simulation tool. The main drawback of such a design tool is the long computational time required owing to the large number of particles and the minute time-step required to maintain a steady solution while simulating the flow of particulate materials with very fine particles.The present study developed several methods to accelerate CFD–DEM simulations: reducing the number of operations carried out at the single-particle level, constructing a DEM grid detached from the CFD grid enabling a no binary search, generating a sub-grid within the DEM grid to enable a no binary search for fine particles, and increasing the computational time-step and eliminating the finest particles in the simulation while still tracking their contribution to the process.The total speedup of the simulation process without the elimination of the finest particles was a factor of about 17. The elimination of the finest particles gave additional speedup of a factor of at least 18.Therefore, the simulation of a grinding process can run at least 300 times faster than the conventional method in which a standard no binary search is employed and the smallest particles are tracked.     

Microscopic evidence for the modification of the electronic structure at grain boundaries of Cu(In(1-x),Ga(x))Se2 films

We investigated the electronic properties around grain boundaries of polycrystalline Cu(In(1-x),Ga(x)Se(2)) films as a function of Ga content, using scanning tunneling spectroscopy. Spectra acquired on samples with low Ga content (x=0 and 0.33) reveal downward band bending with respect to adjacent p-type grains, suggesting type inversion at the surface of grain boundaries. Such a behavior was not observed for samples with high Ga contents. These results are consistent with our atomic force microscopy data and may shed light on the origin of the x-dependent efficiency for polycrystalline Cu(In(1-x),Ga(x)Se(2))-based solar cells.