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.

Role of population transfer under strong probe conditions in electromagnetically induced transparency

We analyze theoretically the phenomenon of electromagnetically induced transparency (UT) under conditions where the probe laser is not in the usual weak limit. We consider the effects in both three-level and four-level systems, which are either closed or open (due to losses to an external metastable level). We find that the EIT dip almost disappears in a closed three-level system but survives in an open system. In four-level systems, there is a narrow enhanced-absorption peak (EITA) at line center, which has applications as an optical clock. The peak converts to an EIT dip in a closed system, but again survives in an open system. (C) 2010 Elsevier B.V. All rights reserved.

Impact of climate change on Indian forests: a dynamic vegetation modeling approach

We make an assessment of the impact of projected climate change on forest ecosystems in India. This assessment is based on climate projections of the Regional Climate Model of the Hadley Centre (HadRM3) and the dynamic global vegetation model IBIS for A2 and B2 scenarios. According to the model projections, 39% of forest grids are likely to undergo vegetation type change under the A2 scenario and 34% under the B2 scenario by the end of this century. However, in many forest dominant states such as Chattisgarh, Karnataka and Andhra Pradesh up to 73%, 67% and 62% of forested grids are projected to undergo change. Net Primary Productivity (NPP) is projected to increase by 68.8% and 51.2% under the A2 and B2 scenarios, respectively, and soil organic carbon (SOC) by 37.5% for A2 and 30.2% for B2 scenario. Based on the dynamic global vegetation modeling, we present a forest vulnerability index for India which is based on the observed datasets of forest density, forest biodiversity as well as model predicted vegetation type shift estimates for forested grids. The vulnerability index suggests that upper Himalayas, northern and central parts of Western Ghats and parts of central India are most vulnerable to projected impacts of climate change, while Northeastern forests are more resilient. Thus our study points to the need for developing and implementing adaptation strategies to reduce vulnerability of forests to projected climate change.

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations. (C) 2011 American Institute of Physics. doi:10.1063/1.3516588]

Adaptive Keeper Design for Dynamic Logic Circuits Using Rate Sensing Technique

The increasing variability in device leakage has made the design of keepers for wide OR structures a challenging task. The conventional feedback keepers (CONV) can no longer improve the performance of wide dynamic gates for the future technologies. In this paper, we propose an adaptive keeper technique called rate sensing keeper (RSK) that enables faster switching and tracks the variation across different process corners. It can switch upto 1.9x faster (for 20 legs) than CONV and can scale upto 32 legs as against 20 legs for CONV in a 130-nm 1.2-V process. The delay tracking is within 8% across the different process corners. We demonstrate the circuit operation of RSK using a 32 x 8 register file implemented in an industrial 130-nm 1.2-V CMOS process. The performance of individual dynamic logic gates are also evaluated on chip for various keeper techniques. We show that the RSK technique gives superior performance compared to the other alternatives such as Conditional Keeper (CKP) and current mirror-based keeper (LCR).

Theoretical and Computational Analysis of Static and Dynamic Anomalies in Water-DMSO Binary Mixture at Low DMSO Concentrations

Experiments have repeatedly observed both thermodynamic and dynamic anomalies in aqueous binary mixtures, surprisingly at low solute concentration. Examples of such binary mixtures include water-DMSO, water-ethanol, water-tertiary butyl alcohol (TBA), and water-dioxane, to name a few. The anomalies have often been attributed to the onset of a structural transition, whose nature, however, has been left rather unclear. Here we study the origin of such anomalies using large scale computer simulations and theoretical analysis in water-DMSO binary mixture. At very low DMSO concentration (below 10%), small aggregates of DMSO are solvated by water through the formation of DMSO-(H2O)(2) moieties. As the concentration is increased beyond 10-12% of DMSO, spanning clusters comprising the same moieties appear in the system. Those clusters are formed and stabilized not only through H-bonding but also through the association of CH3 groups of DMSO. We attribute the experimentally observed anomalies to a continuum percolation-like transition at DMSO concentration X-DMSO approximate to 12-15%. The largest cluster size of CH3-CH3 aggregation clearly indicates the formation of such percolating clusters. As a result, a significant slowing down is observed in the decay of associated rotational auto time correlation functions (of the S = O bond vector of DMSO and O-H bond vector of water). Markedly unusual behavior in the mean square fluctuation of total dipole moment again suggests a structural transition around the same concentration range. Furthermore, we map our findings to an interacting lattice model which substantiates the continuum percolation model as the reason for low concentration anomalies in binary mixtures where the solutes involved have both hydrophilic and hydrophobic moieties.

An unusual distribution of glucose-6-phosphate dehydrogenase deficiency of south Indian newborn population.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is seen at a higher frequency in many national and ethnic groups in areas of current or former malaria endemicity. A screening programme undertaken to evaluate the gene frequencies for this deficiency in the highly inbred South Indian population of Karnataka revealed that of the 5140 neonates screened, 7.8% were G6PD deficient with no correlation between the reported level of inbreeding and enzyme deficiency. An interesting finding was the equal number of male (198) and female (207) individuals, with G6PD activity of less than 3 IU. The possible implications of this finding with regard to the expression of G6PD gene is discussed.

A quasi-steady performance prediction model for dynamic characteristics of a volute pump

A performance prediction model generally applicable for volute-type centrifugal pumps has been extended to predict the dynamic characteristics of a pump during its normal starting and stopping periods. Experiments have been conducted on a volute pump with different valve openings to study the dynamic behaviour of the pump during normal start-up and stopping, when a small length of discharge pipeline is connected to the discharge flange of the pump. Such experiments have also been conducted when the test pump was part of a hydraulic system, an experimental rig, where it is pumping against three similar pumps, known as supply pumps, connected in series, with the supply pumps kept idle or running. Instantaneous rotational speed, flowrate, and delivery and suction pressures of the pump were recorded and it was observed in all the tested cases that the change of pump behaviour during the transient period was quasi-steady, which validates the quasi-steady approach presented in this paper. The nature of variation of parameters during the transients has been discussed. The model-predicted dynamic head-capacity curves agree well with the experimental data for almost all the tested cases.

Characterization of a variant glucose-6-phosphate dehydrogenase from the south Indian population.

Glucose-6-phosphate dehydrogenase (G6PD) is coded by a gene on the X-chromosome. Earlier studies have shown that the South Indian population has a high incidence of this enzyme deficiency. The electrophoretic mobility, pH optimum and the K-m values for G6PD from normal and variant individuals were identical. However, the specific activity of the variant enzyme was 8 times less compared to the value of the normal enzyme. Western blot analysis of partially purified G6PD from normal and variant individuals performed using equal amounts of total protein showed that the variant protein was 3 times less in concentration. Similar analysis performed using protein corresponding to equal enzyme activity units in the normal and variant samples showed that the variant enzyme was 2.25 times less efficient compared to the normal enzyme. RNA dot blot analysis using full length G6PD cDNA probe (PGDT5B, a kind gift from Prof. L Luzzatto) revealed that lymphocytes from normal and variant individuals had equal amounts of G6PD specific mRNA.

Enhancement in Bath Mixing and Plume area in a New Degassing Process - A Computational Fluid Dynamic Study

Reaction between the various species in slag and metal phase is usually mass transfer controlled. There have been continuous efforts to increase the reaction efficiency in slag-metal system, especially during decarburization of steel to produce the ultra low carbon steel (ULCS) in secondary steelmaking. It has been found that the surface reaction is a dominant factor in the final stage of decarburization. In the initial stage, the inner site reaction is major factor in the refining process. The mixing of bath affects the later reaction. However, the former reaction (surface reaction) is affected by the plume size area at the top of the metal surface. Therefore, a computational study has been made to understand the fluid dynamics of a new secondary steelmaking process called Revolutionary Degasser Activator (REDA) to study the bath mixing and plume area. REDA process has been considered as it is claimed that this process can reduce the carbon content in steel below 10ppm in a less time than the other existing processes such as RH and Tank degasser. This study shows that both bath mixing and plume area are increased in REDA process facilitating it to give the desired carbon content in less time. Qualitative comments are made on slag-metal reaction system based on this finding.

Dynamic analysis of three point bend specimens under impact

A simple one dimensional inertial model is presented for transient response analysis of notched beams under impact, and extracting dynamic initiation toughness values. The model includes the effects of striker mass interactions, and contact deformations of the beam. Displacement time history of the striker mass is applied to the model as forcing function. The model is validated by comparison with the experimental investigation on ductile aluminium 6061 alloy and brittle polymer, PMMA.

Dynamic scheduling in manufacturing systems using brownian approximations

Recently, Brownian networks have emerged as an effective stochastic model to approximate multiclass queueing networks with dynamic scheduling capability, under conditions of balanced heavy loading. This paper is a tutorial introduction to dynamic scheduling in manufacturing systems using Brownian networks. The article starts with motivational examples. It then provides a review of relevant weak convergence concepts, followed by a description of the limiting behaviour of queueing systems under heavy traffic. The Brownian approximation procedure is discussed in detail and generic case studies are provided to illustrate the procedure and demonstrate its effectiveness. This paper places emphasis only on the results and aspires to provide the reader with an up-to-date understanding of dynamic scheduling based on Brownian approximations.

Dynamic structure factors of a dense mixture

We compute the dynamic structure factors of a dense binary liquid mixture. These describe dynamics on molecular length scales, where structural relaxation is important. We find that the presence of a few large particles in a dense fluid of small particles slows down the dynamics considerably. We also observe a deep narrowing of the spectrum for a disordered mixture composed of a nearly equal packing of the two species. In contrast, a few small particles diffuse easily in the background of a dense fluid of large particles. We expect our results to describe neutron scattering from a dense mixture.

Dynamic structure of charge carrier in polyaniline by near-infrared excited resonance Raman spectroscopy

New vibrational Raman features characteristic to the conductive form of polyaniline have been observed with the near-infrared excitation at 1047 nm. Based on an analogy with the resonance Raman spectrum of Michler's ketone in the lowest excited triplet (T-1) state, we consider these features as due to a dynamic structure of a diimino-1,4-phenylene unit in the polyaniline chain exchanging a positive charge very rapidly. This consideration directly leads to a conducting mechanism in which a positive charge migrates from one nitrogen to the other through the conjugated chain of polyaniline.