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.

Size dependence of the bulk modulus of semiconductor nanocrystals from first-principles calculations

The variation in the bulk modulus of semiconductor nanoparticles has been studied within first-principles electronic-structure calculations using the local density approximation (LDA) for the exchange correlation. Quantum Monte Carlo calculations carried out for a silicon nanocrystal Si87H76 provided reasonable agreement with the LDA results. An enhancement was observed in the bulk modulus as the size of the nanoparticle was decreased, with modest enhancements being predicted for the largest nanoparticles studied here, a size just accessible in experiments. To access larger sizes, we fit our calculated bulk moduli to the same empirical law for all materials, the asymptote of which is the bulk value of the modulus. This was found to be within 2-10% of the independently calculated value. The origin of the enhancement has been discussed in terms of Cohen's empirical law M.L. Cohen, Phys. Rev. B 32, 7988 (1985)] as well as other possible scenarios.

Paleoseismological evidence of surface faulting along the northeastern Himalayan front, India: Timing, size, and spatial extent of great earthquakes

The similar to 2500 km long Himalayan arc has experienced three large to great earthquakes of M-w 7.8 to 8.4 during the past century, but none produced surface rupture. Paleoseismic studies have been conducted during the last decade to begin understanding the timing, size, rupture extent, return period, and mechanics of the faulting associated with the occurrence of large surface rupturing earthquakes along the similar to 2500 km long Himalayan Frontal Thrust (HFT) system of India and Nepal. The previous studies have been limited to about nine sites along the western two-thirds of the HFT extending through northwest India and along the southern border of Nepal. We present here the results of paleoseismic investigations at three additional sites further to the northeast along the HFT within the Indian states of West Bengal and Assam. The three sites reside between the meizoseismal areas of the 1934 Bihar-Nepal and 1950 Assam earthquakes. The two westernmost of the sites, near the village of Chalsa and near the Nameri Tiger Preserve, show that offsets during the last surface rupture event were at minimum of about 14 m and 12 m, respectively. Limits on the ages of surface rupture at Chalsa (site A) and Nameri (site B), though broad, allow the possibility that the two sites record the same great historical rupture reported in Nepal around A.D. 1100. The correlation between the two sites is supported by the observation that the large displacements as recorded at Chalsa and Nameri would most likely be associated with rupture lengths of hundreds of kilometers or more and are on the same order as reported for a surface rupture earthquake reported in Nepal around A.D. 1100. Assuming the offsets observed at Chalsa and Nameri occurred synchronously with reported offsets in Nepal, the rupture length of the event would approach 700 to 800 km. The easternmost site is located within Harmutty Tea Estate (site C) at the edges of the 1950 Assam earthquake meizoseismal area. Here the most recent event offset is relatively much smaller (<2.5 m), and radiocarbon dating shows it to have occurred after A.D. 1100 (after about A.D. 1270). The location of the site near the edge of the meizoseismal region of the 1950 Assam earthquake and the relatively lesser offset allows speculation that the displacement records the 1950 M-w 8.4 Assam earthquake. Scatter in radiocarbon ages on detrital charcoal has not resulted in a firm bracket on the timing of events observed in the trenches. Nonetheless, the observations collected here, when taken together, suggest that the largest of thrust earthquakes along the Himalayan arc have rupture lengths and displacements of similar scale to the largest that have occurred historically along the world's subduction zones.

Grain size effect on the phase transformation temperature of nanostructured CuFe2O4

We report a large decrease in tetragonal to cubic phase transformation temperature when grain size of bulk CuFe2O4 is reduced by mechanical ball milling. The change in phase transformation temperature was inferred from in situ high temperature conductivity and x-ray diffraction measurements. The decrease in conductivity with grain size suggests that ball milling has not induced any oxygen vacancy while the role of cation distribution in the observed decrease in phase transformation temperature is ruled out from in-field Fe-57 Mossbauer and extended x-ray absorption fine structure measurements. The reduction in the phase transformation temperature is attributed to the stability of structures with higher crystal symmetry at lower grain sizes due to negative pressure effect. (C) 2011 American Institute of Physics. doi: 10.1063/1.3493244]

Grinding abrasive wear and associated particle size effect

The type of abrasion that the grinding medium experiences inside a ball mill is classified as high stress or grinding abrasion, because the stress levels at the surface of the medium exceed the yield stress of the metal when hard abrasives are crushed. During dry grinding of ores the medium undergoes not only abrasion but also erosion and impact. As all three mechanisms of wear occur simultaneously, it is difficult to follow the individual components of wear. However, it is possible to show that the overall kinetics of wear follows a simple power law of the type w = at(b), where w is the weight loss of the grinding medium for a specified grinding time t and a and b are constants. Experimental data, obtained from dry grinding of quartz for a wide range of times using AISI 52100 steel balls having various microstructures in a laboratory scale batch mill, are fitted to the proposed equation and the wear rate w is calculated from the first derivative of the equation. The mean particle sizes of the quartz charge DBAR corresponding to 50 and 80% retained size are determined by mechanical sieving of the ground product after a grinding time t and thus the relationship between wear rate and particle size of the abrasive is established. It is found that w increases rapidly with DBAR up to some critical size and then increases at a much lower rate.

Influence of grain size on high temperature fracture in a Mg AZ31 alloy

Tensile experiments at 673 K and grain sizes from similar to 8 to 17 mu m revealed large ductility at a low strain rate and a reduced ductility at a high strain rate, corresponding to a change from a high to a low value for the strain rate sensitivity. High strain rate deformation led to fracture by flow localization, whereas low strain rate deformation involved fracture by cavity nucleation and growth. Analysis revealed that grain boundary migration can assist significantly in reducing the stress concentrations caused by grain boundary sliding, thereby retarding cavity nucleation. Calculations demonstrate that the interlinkage of voids parallel and perpendicular to the tensile axis occurs significantly, so that it is not always possible to use the cavity shapes to distinguish between diffusion and plasticity controlled growth. Cavitation damage evolves slowly in materials with a coarser grain size because of reduced nucleation related to a reduction in the strain rate sensitivity and associated grain boundary sliding. (C) 2011 Elsevier B.V. All rights reserved.

An experimental study on acoustic emission energy as a quantitative measure of size independent specific fracture energy of concrete beams

Notched three point bend specimens (TPB) were tested under crack mouth opening displacement (CMOD) control at a rate of 0.0004 mm/s and during the fracture process acoustic emissions (AE) were simultaneously monitored. It was observed that AE energy could be related to fracture energy. An experimental study was done to understand the behavior of AE energy with parameters of concrete like its strength and size. In this study, AE energy was used as a quantitative measure of size independent specific fracture energy of concrete beams and the concepts of boundary effect and local fracture energy were used to obtain size independent AE energy from which size independent fracture energy was obtained. (C) 2010 Elsevier Ltd. All rights reserved.

Dependence of the strength of interaction of carbon monoxide with transition metal clusters on the cluster size

The interaction of CO with Cu, Pd, and Ni at different coverages of the metals on solid substrates has been investigated by He II and core-level spectroscopies, after the nature of variation of the metal core-level binding energies with the coverage or the cluster size is established. The separation between the (1 pi + 5 sigma) and 4 sigma levels of CO increases with a decrease in the size of the metal clusters, accompanied by an increase in the desorption temperature. In the case of Cu, the intramolecular shakeup satellite of CO disappears on small clusters. More importantly, CO dissociates on small Ni clusters, clearly confirming that metal-CO interaction strength increases with a decrease in the cluster size.

Diffusion of sorbates in zeolites Y and A novel dependence on sorbate size and strength of sor ba t e-Zeoli t e interaction

A systematic investigation of monatomic spherical sorbates in the supercages of zeolites Y and A by molecular dynamics technique is presented. Rates of intercage diffusion, rates of cage visits, and the diffusion coefficients have been calculated as a function of the sorbate-zeolite interaction strength. These properties exhibit markedly different dependences on interaction strength for the two zeolites. The observed behavior is shown to be a consequence of the two principal mechanisms of intercage diffusion and the energetic barrier associated with them. The diffusion coefficient and other properties associated with intercage diffusion are found to be directly proportional to the reciprocal of the square of the sorbate diameter when the sorbate diameter is significantly smaller than the window diameter. As the sorbate diameter increases, a peak is observed in all the transport properties investigated including the diffusion coefficient. We call this surprising effect as the ring or levitation effect and it explains several anomalous results reported in the literature and suggests a breakdown of the geometrical criterion for diffusion of sorbates. It shows that under certain conditions nongeometrical factors play a major role and geometrical factors become secondary in the determination of the molecular sieve property. A generalized parameter has been proposed which suggests conditions under which one can expect the ring or levitation effect in any porous medium. Inverse size selectivity becomes operative under these conditions.

Fe-Cr/Al2O3 metal-ceramic composites: Nature and size of the metal particles formed during hydrogen reduction

Fe-Cr/Al2O3 metal-ceramic composites prepared by hydrogen reduction at different temperatures and for different periods have been investigated by a combined use of Mossbauer spectroscopy, x-ray diffraction, transmission electron microscopy, and energy-dispersive x-ray spectroscopy in order to obtain information on the nature of the metallic species formed. Total reduction of Fe3+ does not occur by increasing the reduction time at 1320 K from 1 to 30 h, and the amount of superparamagnetic metallic species is essentially constant (about 10%). Temperatures higher than 1470 K are needed to achieve nearly total reduction of substitutional Fe3+. Interestingly, iron favors the reduction of chromium. The composition of the Fe-Cr particles is strongly dependent on their size, the Cr content being higher in particles smaller than 10 nm.

Fuel drop size measurement in a carburetted induction system with 2 throttling methods

A new throttling system far SI engines is examined. The SMD of the fuel droplets in the induction system is measured to evaluate the performance of the new device with respect to the conventional throttle plate arrangement. The measurements are conducted at steady now conditions. A forward angular scattering technique with a He-Ne laser beam is used for droplet size measurement. The experiments are carried out with different mixture strength, stream velocity and throttle positions. It is observed that A/F ratio has no effect on SMD. However, stream velocity and throttle position have a significant influence on SMD. The new throttling method is found to be more effective in reducing the SMD, particularly at low throttle opening and high stream velocity compared to the conventional throttle plate.

Molecular Dynamics Simulations of Orientational Relaxation in Dipolar Lattice: Lack of Diffusive Decay for Second and Higher Rank Correlation Functions

Extensive molecular dynamics simulations have been carried out to calculate the orientational correlation functions Cl(t), G(t) = [4n/(21 + l)]Ci=-l (Y*lm(sZ(0)) Ylm(Q(t))) (where Y,,(Q) are the spherical harmonics) of point dipoles in a cubic lattice. The decay of Cl(t) is found to be strikingly different from higher l-correlation functions-the latter do not exhibit diffusive dynamics even in the long time. Both the cumulant expansion expression of Lynden-Bell and the conventional memory function equation provide very good description of the Cl(t) in the short time but fail to reproduce the observed slow, long time decay of c1 (t) .

Rank dependence of orientational relaxation in dipolar systems

An important yet unsolved problem in the field of orientational relaxation in dipolar liquids is the dependence of the correlation functions C(l)(t), C(l)(t) = [4pi/(2l + 1)SIGMA(m = -l)l [Y(lm)(OMEGA(0)Y(lm)(OMEGA(t))] on the rank l (where Y(lm)(OMEGA) are the usual spherical harmonics). The existing theories on this effect differ in their predictions. To investigate this, we have carried out extensive computer simulations of a Brownian dipolar lattice. The dielectric friction was found to decrease rapidly with increasing l, in qualitative agreement with the predictions of Hubbard-Wolynes. However, the observed effect is much stronger than the predictions of the existing theories.

Fatigue crack propagation model and size effect in concrete using dimensional analysis

It is well known that fatigue in concrete causes excessive deformations and cracking leading to structural failures. Due to quasi-brittle nature of concrete and formation of a fracture process zone, the rate of fatigue crack growth depends on a number of parameters, such as, the tensile strength, fracture toughness, loading ratio and most importantly the structural size. In this work, an analytical model is proposed for estimating the fatigue crack growth in concrete by using the concepts of dimensional analysis and including the above parameters. Knowing the governed and the governing parameters of the physical problem and by using the concepts of self-similarity, a relationship is obtained between different parameters involved. It is shown that the proposed fatigue law is able to capture the size effect in plain concrete and agrees well with different experimental results. Through a sensitivity analysis, it is shown that the structural size plays a dominant role followed by loading ratio and the initial crack length in fatigue crack propagation. (C) 2010 Elsevier Ltd. 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.