Parameter optimization for the Gaussian model of protein folding

Computational models of protein folding and ligand docking are large and complex. Few systematic methods have yet been developed to optimize the parameters in such models. We describe here an iterative parameter optimization strategy that is based on minimizing a structural error measure by descent in parameter space. At the start, we know the ‘correct’ native structure that we want the model to produce, and an initial set of parameters representing the relative strengths of interactions between the amino acids. The parameters are changed systematically until the model native structure converges as closely as possible to the correct native structure. As a test, we apply this parameter optimization method to the recently developed Gaussian model of protein folding: each amino acid is represented as a bead and all bonds, covalent and noncovalent, are represented by Hooke's law springs. We show that even though the Gaussian model has continuous degrees of freedom, parameters can be chosen to cause its ground state to be identical to that of Go-type lattice models, for which the global ground states are known. Parameters for a more realistic protein model can also be obtained to produce structures close to the real native structures in the protein database.     

The beat goes on: Rhythmic modulation of cortical potentials by imagined tapping.

A frequency analysis was used to tag cortical activity from imagined rhythmic movements. Participants synchronized overt and imagined taps with brief visual stimuli presented at a constant rate, alternating between left and right index fingers. Brain potentials were recorded from across the scalp and topographic maps made of their power at the alternation frequency between left and right taps. Two prominent power foci occurred in each hemisphere for both overt and imagined taps, one over sensorimotor cortex and the other over posterior parietal cortex, with homologous foci in opposite hemispheres arising from oscillations 180° out of phase. These findings demonstrate temporal isomorphism at a neural level between overt and imagined movements and illustrate a new approach to studying covert actions. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Electrokinetic Remediation of Cadmium-Contaminated Clay

Electrokinetic extraction has been demonstrated to be very effective in removing heavy metals from Georgia kaolinite. The relatively high removal efficiency depends on the extremely acidic soil environment generated by the electrokinetic process. However, the efficiency observed in Georgia kaolinite cannot be achieved in soils of high acid/base buffer capacity without enhancement. In this study, the effect of ethylenediaminetetraacetic acid (EDTA) to enhance electrokinetic extraction of cadmium from Milwhite kaolinite was examined. The influence of electro-osmotic flow direction on the migration of cadmium, EDTA, and their complexes were also investigated. It was observed that injection of EDTA from the cathode reservoir by a reverse electro-osmotic flow could mobilize the cadmium in the specimen effectively. A less significant mobilization of cadmium was observed when the electro-osmotic flow was directed toward the cathode. However, accumulation of cadmium near the anode was observed regardless of the electro-osmotic flow direction.     

A residualizing semantics for the partial evaluation of functional logic programs

Recent proposals for multi-paradigm declarative programming combine the most important features of functional, logic and concurrent programming into a single framework. The operational semantics of these languages is usually based on a combination of narrowing and residuation. In this paper, we introduce a non-standard, residualizing semantics for multi-paradigm declarative programs and prove its equivalence with a standard operational semantics. Our residualizing semantics is particularly relevant within the area of program transformation where it is useful, e.g., to perform computations during partial evaluation. Thus, the proof of equivalence is a crucial result to demonstrate the correctness of (existing) partial evaluation schemes.     

Prosody Evaluation as a Diagnostic Process: Subjective vs. Objective Measurements

A set of perception experiments, using reiterant and lexicalised speech, was designed to perform a diagnostic of the relative implication of prosody in the segmentation and hierarchisation of speech. Both natural and synthetic intonation were evaluated. Then, two distance measures—correlation and root-mean-square distance on the acoustic parameters (F0, syllabic duration and intensity)—were applied to match the perception results. This objective vs. subjective comparison underlines which acoustic cues are used by listeners to judge the adequacy of prosody in performing a given function such as demarcation. Results can be summarized by a scale of the perceptual distance between two demarcation functions. This study also points out the ability of listeners to retrieve pertinent information on the basis of pure prosodic stimuli.     

Dissymmetric warfare versus asymmetric warfare

This paper presents two concepts: asymmetric warfare and dissymmetric warfare. NATO and US Military operations in recent wars in Kosovo and Afghanistan are analysed by means of comparison with old Chinese strategic thinking. No‐Loss‐Strategy and virtual warfare as well as the transformation from asymmetric to dissymmetric and from dissymmetric to asymmetric warfare are reflected upon.     

Laser Doppler velocimetry with polarization-bistable VCSELs

We present a rate equation model of a single mode vertical-cavity surface-emitting laser (VCSEL) with two states of linear polarization, subject to Doppler-shifted optical feedback. Recent experimental work has shown that the polarization bistability often observed in VCSELs can be exploited to enhance the responsivity of these semiconductor lasers in speed-sensing applications. We review these experimental results briefly and use the rate equation model to explain the increased signal-to-noise ratio.     

Oil Spill Dispersant Effectiveness Protocol. I: Impact of Operational Variables

The current U.S. Environmental Protection Agency protocol for testing the effectiveness of dispersants, the swirling flask test, has been found to give widely varying results in the hands of different testing laboratories. The sources of the ambiguities in the test were determined by considering several options in a rigorous systematic fashion. Options considered were variability among three operators and the variability and limitations of three analytical instruments in establishing a calibration curve for oil/dispersant mixtures. Other options included flask type, impact of operational variables (rotational speed, mixing time, settling time, and oil:dispersant ratio), development of a revised procedure for dispersant effectiveness, reproducibility and repeatability of the revised procedure, and development of selection criteria for screening of dispersants. A redesign of the test flask, which is characterized by having baffles with a stopcock at the bottom for sample collection, was deemed necessary to accomplish reproducibility within operator and between operators. The results indicated that the baffled flask provided a total coefficient of variation (variations within operator and between operators) less than 11% compared to above 100% in some cases for the swirling flask.     

Oil Spill Dispersant Effectiveness Protocol. II: Performance of Revised Protocol

The current U.S. Environmental Protection Agency (EPA) protocol for testing the effectiveness of dispersants for use in treating oil spills on the open water, the swirling flask test (SFT), has been found to give widely varying results in the hands of different testing laboratories. Part I addressed the sources of the ambiguities in the EPA SFT and the development of a new test referred to as the baffled flask test (BFT). In this part of the series, further experiments were conducted for estimating the repeatability of three operators in determining the effectiveness of 18 dispersants by both the EPA SFT and the BFT methods. Overall statistical analysis of the results indicated that the coefficient of variation by the BFT was only 7.8% compared to 21.9% for the EPA SFT. The mean percent effectiveness of the EPA SFT was only 19.7% as compared to 64.6% for the BFT. Proposed selection criteria for screening of dispersants for listing on the National Contingency Plan Product Schedule have been developed.     

Wedged multilayer Laue lens

A multilayer Laue lens (MLL) is an x-ray focusing optic fabricated from a multilayer structure consisting of thousands of layers of two different materials produced by thin-film deposition. The sequence of layer thicknesses is controlled to satisfy the Fresnel zone plate law and the multilayer is sectioned to form the optic. An improved MLL geometry can be created by growing each layer with an in-plane thickness gradient to form a wedge, so that every interface makes the correct angle with the incident beam for symmetric Bragg diffraction. The ultimate hard x-ray focusing performance of a wedged MLL has been predicted to be significantly better than that of a nonwedged MLL, giving subnanometer resolution with high efficiency. Here, we describe a method to deposit the multilayer structure needed for an ideal wedged MLL and report our initial deposition results to produce these structures.