Taking Multiple Infections of Cells and Recombination into Account Leads to Small Within-Host Effective-Population-Size Estimates of HIV-1

Whether HIV-1 evolution in infected individuals is dominated by deterministic or stochastic effects remains unclear because current estimates of the effective population size of HIV-1 in vivo, N-e, are widely varying. Models assuming HIV-1 evolution to be neutral estimate N-e similar to 10(2)-10(4), smaller than the inverse mutation rate of HIV-1 (similar to 10(5)), implying the predominance of stochastic forces. In contrast, a model that includes selection estimates N-e>10(5), suggesting that deterministic forces would hold sway. The consequent uncertainty in the nature of HIV-1 evolution compromises our ability to describe disease progression and outcomes of therapy. We perform detailed bit-string simulations of viral evolution that consider large genome lengths and incorporate the key evolutionary processes underlying the genomic diversification of HIV-1 in infected individuals, namely, mutation, multiple infections of cells, recombination, selection, and epistatic interactions between multiple loci. Our simulations describe quantitatively the evolution of HIV-1 diversity and divergence in patients. From comparisons of our simulations with patient data, we estimate N-e similar to 10(3)-10(4), implying predominantly stochastic evolution. Interestingly, we find that N-e and the viral generation time are correlated with the disease progression time, presenting a route to a priori prediction of disease progression in patients. Further, we show that the previous estimate of N-e>10(5) reduces as the frequencies of multiple infections of cells and recombination assumed increase. Our simulations with N-e similar to 10(3)-10(4) may be employed to estimate markers of disease progression and outcomes of therapy that depend on the evolution of viral diversity and divergence.

Investigations on the Corona performance of a Ceramic disc Insulators integrated with Field Reduction Electrode

This paper presents laboratory investigations on the visible corona and discharge radio noise. Experimental investigations are carried on various types of normal and anti-fog types of ceramic disc insulator at the recently established artificial pollution experimental facility. The results obtained from the experimental investigations show better performance for the disc insulators fitted with field reduction electrodes. In addition to the corona and radio noise investigations the comparisons are also made for the experimental results of the potential distribution across the insulator string (with and without filed reduction electrode) with the simulation results obtained by using Surface Charge Simulation Method.

Crystal structure of Salmonella typhimurium 2-methylcitrate synthase: Insights on domain movement and substrate specificity

2-Methylcitric acid (2-MCA) cycle is one of the well studied pathways for the utilization of propionate as a source of carbon and energy in bacteria such as Salmonella typhimurium and Escherichia coli. 2-Methylcitrate synthase (2-MCS) catalyzes the conversion of oxaloacetate and propionyl-CoA to 2-methylcitrate and CoA in the second step of 2-MCA cycle. Here, we report the X-ray crystal structure of S. typhimurium 2-MCS (StPrpC) at 2.4 A resolution and its functional characterization. StPrpC was found to utilize propionyl-CoA more efficiently than acetyl-CoA or butyryl-CoA. The polypeptide fold and the catalytic residues of StPrpC are conserved in citrate synthases (CSs) suggesting similarities in their functional mechanisms. In the triclinic P1 cell, StPrpC molecules were organized as decamers composed of five identical dimer units. In solution, StPrpC was in a dimeric form at low concentrations and was converted to larger oligomers at higher concentrations. CSs are usually dimeric proteins. In Gram-negative bacteria, a hexameric form, believed to be important for regulation of activity by NADH, is also observed. Structural comparisons with hexameric E. coil CS suggested that the key residues involved in NADH binding are not conserved in StPrpC. Structural comparison with the ligand free and bound states of CSs showed that StPrpC is in a nearly closed conformation despite the absence of bound ligands. It was found that the Tyr197 and Leu324 of StPrpC are structurally equivalent to the ligand binding residues His and Val, respectively, of CSs. These substitutions might determine the specificities for acyl-CoAs of these enzymes. (C) 2010 Elsevier Inc. All rights reserved.

Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys

A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein-protein interface. In this work, we describe a novel method combining an interface-size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein-protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having <= 10 angstrom backbone root mean square deviation from true binding geometry. Comparisons with other state-of-art methods confirm the improved ranking power of our method without the use of any experiment-guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less-difficult bound binary protein-protein complexes with <= 35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with <= 5 angstrom backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 787-796, 2011.

Stretch effects extracted from propagating spherical premixed flames with detailed chemistry

This paper is concerned with extracting stretch effects from outward propagating spherical flames with full chemistry. It is a continuation of a recently published study from this laboratory where it is shown that single-step chemistry is insufficient to explain the experimental results on methane, propane and hydrogen-air systems. Comparisons of the present full chemistry calculations with the experimental results for several fuel/air systems are good/excellent, with the exception of rich propane-air for which it is argued that soot chemistry with attendant radiation loss need to be invoked. The reversal in trends of stretch effects due to change in pressure, initial temperature and N-2 dilution (observed in experiments) can be predicted well by full chemistry but not with simple single-step chemistry. Analysis of the results shows the important role played by many intermediate species and explains why full chemistry is needed to predict stretch effects.

Vertical uplift capacity of horizontal anchors

The method of characteristics coupled with a log-spiral failure surface was used to develop a theory for vertical uplift capacity of shallow horizontal strip anchors in a general c-phi soil. Uplift-capacity factors F(c), F(q) and F(gamma), for the effects of cohesion, surcharge, and density, respectively, have been established as functions of embedment ratio lambda and angle of friction phi. The extent of the failure surface at the ground has also been determined. Comparisons made with existing test results support the predictive capability of the theory, and comparisons with the analysis proposed by Meyerhof and Adams show the proposed analysis provides slightly more conservative predictions of pullout capacity.

Solution structure of BTK-2, a novel hK(v)1.1 inhibiting scorpion toxin, from the eastern Indian scorpion Mesobuthus tamulus

The three dimensional structure of a 32 residue three disulfide scorpion toxin, BTK-2, from the Indian red scorpion Mesobuthus tamulus has been determined using isotope edited solution NMR methods. Samples for structural and electrophysiological studies were prepared using recombinant DNA methods. Electrophysiological studies show that the peptide is active against hK(v)1.1 channels. The structure of BTK-2 was determined using 373 distance restraints from NOE data, 66 dihedral angle restraints from NOE, chemical shift and scalar coupling data, 6 constraints based on disulfide linkages and 8 constraints based on hydrogen bonds. The root mean square deviation (r.m.s.d) about the averaged co-ordinates of the backbone (N, C-alpha, C') and all heavy atoms are 0.81 +/- 0.23 angstrom and 1.51 +/- 0.29 angstrom respectively. The backbone dihedral angles (phi and psi) for all residues occupy the favorable and allowed regions of the Ramachandran map. The three dimensional structure of BTK-2 is composed of three well defined secondary structural regions that constitute the alpha-beta-beta, structural motif. Comparisons between the structure of BTK-2 and other closely related scorpion toxins pointed towards distinct differences in surface properties that provide insights into the structure-function relationships among this important class of voltage-gated potassium channel inhibiting peptides. (C) 2011 Elsevier B.V. All rights reserved.

Brownian dynamics simulation of dense binary colloidal mixtures. II. Translational and bond-orientational order

We report the Brownian dynamics simulation results on the translational and bond-angle-orientational correlations for charged colloidal binary suspensions as the interparticle interactions are increased to form a crystalline (for a volume fraction phi = 0.2) or a glassy (phi = 0.3) state. The translational order is quantified in terms of the two- and four-point density autocorrelation functions whose comparisons show that there is no growing correlation length near the glass transition. The nearest-neighbor orientational order is determined in terms of the quadratic rotational invariant Q(l) and the bond-orientational correlation functions g(l)(t). The l dependence of Q(l) indicates that icosahedral (l = 6) order predominates at the cost of the cubic order (l = 4) near the glass as well as the crystal transition. The density and orientational correlation functions for a supercooled liquid freezing towards a glass fit well to the streched-exponential form exp[-(t/tau)(beta)]. The average relaxation times extracted from the fitted stretched-exponential functions as a function of effective temperatures T* obey the Arrhenius law for liquids freezing to a crystal whereas these obey the Vogel-Tamman-Fulcher law exp[AT(0)*/(T* - T-0*)] for supercooled Liquids tending towards a glassy state. The value of the parameter A suggests that the colloidal suspensions are ''fragile'' glass formers like the organic and molecular liquids.

Generation of an eight node brick element using Papcovitch-Neuber functions

Some conventional finite elements suffer from drawbacks, such as shear locking, membrane locking, etc. To overcome them researchers have developed various techniques, termed as tricks by some and variational crimes by others. Many attempts have been made, but satisfactory explanations for why some of these techniques work have not been obtained, especially in the case of solid elements. This paper attempts a simple non-conforming solid element using assumed displacement fields which satisfy the Navier equation exactly. Its behaviour under simple loadings like bending, torsion and tension is examined and comparisons are made with existing elements.

Modelling plane mixing layers using vortex points and sheets

We present here a critical assessment of two vortex approaches (both two-dimensional) to the modelling of turbulent mixing layers. In the first approach the flow is represented by point vortices, and in the second it is simulated as the evolution of a continuous vortex sheet composed of short linear elements or ''panels''. The comparison is based on fresh simulations using approximately the same number of elements in either model, paying due attention in both to the boundary conditions far downstream as well as those on the splitter plate from which the mixing layer issues. The comparisons show that, while both models satisfy the well-known invariants of vortex dynamics approximately to the same accuracy, the vortex panel model, although ultimately not convergent, leads to smoother roll-up and values of stresses and moments that are in closer agreement with the experiment, and has a higher computational efficiency for a given degree of convergence on moments. The point vortex model, while faster for a given number of elements, produces an unsatisfactory roll-up which (for the number of elements used) is rendered worse by the incorporation of the Van der Vooren correction for sheet curvature.

Evaluation of strain-rate effects in transitional round jets using direct numerical simulation

The coherent flame model uses the strain rate to predict reaction rate per unit flame surface area and some procedure that solves for the dynamics of flame surfaces to predict species distributions. The strainrate formula for the reaction rate is obtained from the analytical solution for a flame in a laminar, plane stagnation point flow. Here, the formula's effectiveness is examined by comparisons with data from a direct numerical simulation (DNS) of a round jetlike flow that undergoes transition to turbulence. Significant differences due to general flow features can be understood qualitatively: Model predictions are good in the braids between vortex rings, which are present in the near field of round jets, as the strain rate is extensional and reaction surfaces are isolated. In several other regions, the strain rate is compressive or flame surfaces are folded close together. There, the predictions are poor as the local flow no longer resembles the model flow. Quantitative comparisons showed some discrepancies. A modified, consistent application of the strain-rate solution did not show significant changes in the prediction of mean reaction rate distributions.

Reinforcement Learning With Function Approximation for Traffic Signal Control

We propose, for the first time, a reinforcement learning (RL) algorithm with function approximation for traffic signal control. Our algorithm incorporates state-action features and is easily implementable in high-dimensional settings. Prior work, e. g., the work of Abdulhai et al., on the application of RL to traffic signal control requires full-state representations and cannot be implemented, even in moderate-sized road networks, because the computational complexity exponentially grows in the numbers of lanes and junctions. We tackle this problem of the curse of dimensionality by effectively using feature-based state representations that use a broad characterization of the level of congestion as low, medium, or high. One advantage of our algorithm is that, unlike prior work based on RL, it does not require precise information on queue lengths and elapsed times at each lane but instead works with the aforementioned described features. The number of features that our algorithm requires is linear to the number of signaled lanes, thereby leading to several orders of magnitude reduction in the computational complexity. We perform implementations of our algorithm on various settings and show performance comparisons with other algorithms in the literature, including the works of Abdulhai et al. and Cools et al., as well as the fixed-timing and the longest queue algorithms. For comparison, we also develop an RL algorithm that uses full-state representation and incorporates prioritization of traffic, unlike the work of Abdulhai et al. We observe that our algorithm outperforms all the other algorithms on all the road network settings that we consider.

Statistical thermodynamics of lattice models in zeolites: Implications of local versus global mean field interactions

The statistical thermodynamics of adsorption in caged zeolites is developed by treating the zeolite as an ensemble of M identical cages or subsystems. Within each cage adsorption is assumed to occur onto a lattice of n identical sites. Expressions for the average occupancy per cage are obtained by minimizing the Helmholtz free energy in the canonical ensemble subject to the constraints of constant M and constant number of adsorbates N. Adsorbate-adsorbate interactions in the Brag-Williams or mean field approximation are treated in two ways. The local mean field approximation (LMFA) is based on the local cage occupancy and the global mean field approximation (GMFA) is based on the average coverage of the ensemble. The GMFA is shown to be equivalent in formulation to treating the zeolite as a collection of interacting single site subsystems. In contrast, the treatment in the LMFA retains the description of the zeolite as an ensemble of identical cages, whose thermodynamic properties are conveniently derived in the grand canonical ensemble. For a z coordinated lattice within the zeolite cage, with epsilon(aa) as the adsorbate-adsorbate interaction parameter, the comparisons for different values of epsilon(aa)(*)=epsilon(aa)z/2kT, and number of sites per cage, n, illustrate that for -1 0. We compare the isotherms predicted with the LMFA with previous GMFA predictions [K. G. Ayappa, C. R. Kamala, and T. A. Abinandanan, J. Chem. Phys. 110, 8714 (1999)] (which incorporates both the site volume reduction and a coverage-dependent epsilon(aa)) for xenon and methane in zeolite NaA. In all cases the predicted isotherms are very similar, with the exception of a small steplike feature present in the LMFA for xenon at higher coverages. (C) 1999 American Institute of Physics. [S0021-9606(99)70333-8].

A checking method for probabilistic seismic-hazard assessment: case studies on three cities

The conventional Cornell's source-based approach of probabilistic seismic-hazard assessment (PSHA) has been employed all around the world, whilst many studies often rely on the use of computer packages such as FRISK (McGuire FRISK-a computer program for seismic risk analysis. Open-File Report 78-1007, United States Geological Survey, Department of Interior, Washington 1978) and SEISRISK III (Bender and Perkins SEISRISK III-a computer program for seismic hazard estimation, Bulletin 1772. United States Geological Survey, Department of Interior, Washington 1987). A ``black-box'' syndrome may be resulted if the user of the software does not have another simple and robust PSHA method that can be used to make comparisons. An alternative method for PSHA, namely direct amplitude-based (DAB) approach, has been developed as a heuristic and efficient method enabling users to undertake their own sanity checks on outputs from computer packages. This paper experiments the application of the DAB approach for three cities in China, Iran, and India, respectively, and compares with documented results computed by the source-based approach. Several insights regarding the procedure of conducting PSHA have also been obtained, which could be useful for future seismic-hazard studies.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.