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.

Dynamics of crystal size distributions with size-dependent rates

The growth and dissolution dynamics of nonequilibrium crystal size distributions (CSDs) can be determined by solving the governing population balance equations (PBEs) representing reversible addition or dissociation. New PBEs are considered that intrinsically incorporate growth dispersion and yield complete CSDs. We present two approaches to solving the PBEs, a moment method and a numerical scheme. The results of the numerical scheme agree with the moment technique, which can be solved exactly when powers on mass-dependent growth and dissolution rate coefficients are either zero or one. The numerical scheme is more general and can be applied when the powers of the rate coefficients are non-integers or greater than unity. The influence of the size dependent rates on the time variation of the CSDs indicates that as equilibrium is approached, the CSDs become narrow when the exponent on the growth rate is less than the exponent on the dissolution rate. If the exponent on the growth rate is greater than the exponent on the dissolution rate, then the polydispersity continues to broaden. The computation method applies for crystals large enough that interfacial stability issues, such as ripening, can be neglected. (C) 2002 Elsevier Science B.V. All rights reserved.

Size-dependent and strain rate effects in quantum dot nanostructures with molecular dynamic simulations

Size and strain rate effects are among several factors which play an important role in determining the response of nanostructures, such as their deformations, to the mechanical loadings. The mechanical deformations in nanostructure systems at finite temperatures are intrinsically dynamic processes. Most of the recent works in this context have been focused on nanowires [1, 2], but very little attention has been paid to such low dimensional nanostructures as quantum dots (QDs). In this contribution, molecular dynamics (MD) simulations with an embedded atom potential method(EAM) are carried out to analyse the size and strain rate effects in the silicon (Si) QDs, as an example. We consider various geometries of QDs such as spherical, cylindrical and cubic. We choose Si QDs as an example due to their major applications in solar cells and biosensing. The analysis has also been focused on the variation in the deformation mechanisms with the size and strain rate for Si QD embedded in a matrix of SiO2 [3] (other cases include SiN and SiC matrices).It is observed that the mechanical properties are the functions of the QD size, shape and strain rate as it is in the case for nanowires [2]. We also present the comparative study resulted from the application of different EAM potentials in particular, the Stillinger-Weber (SW) potential, the Tersoff potentials and the environment-dependent interatomic potential (EDIP) [1]. Finally, based on the stabilized structural properties we compute electronic bandstructures of our nanostructures using an envelope function approach and its finite element implementation.

Size-dependent elasticity of nanocrystalline titania

Synchrotron-based high-pressure x-ray diffraction measurements indicate that compressibility, a fundamental materials property, can have a size-specific minimum value. The bulk modulus of nanocrystalline titania has a maximum at particle size of 15 nm. This can be explained by dislocation behavior because very high dislocation contents can be achieved when shear stress induced within nanoparticles counters the repulsion between dislocations. As particle size decreases, compression increasingly generates dislocation networks hardened by overlap of strain fields that shield intervening regions from external pressure. However, when particles become too small to sustain high dislocation concentrations, elastic stiffening declines. The compressibility has a minimum at intermediate sizes.

Size-dependent melting of nanoparticles: Hundred years of thermodynamic model

Thermodynamic model first published in 1909, is being used extensively to understand the size-dependent melting of nanoparticles. Pawlow deduced an expression for the size-dependent melting temperature of small particles based on the thermodynamic model which was then modified and applied to different nanostructures such as nanowires, prism-shaped nanoparticles, etc. The model has also been modified to understand the melting of supported nanoparticles and superheating of embedded nanoparticles. In this article, we have reviewed the melting behaviour of nanostructures reported in the literature since 1909.

Size-dependent magnetic properties of iron carbide nanoparticles embedded in a carbon matrix

Here we report on the magnetic properties of iron carbide nanoparticles embedded in a carbon matrix. Granular distributions of nanoparticles in an inert matrix, of potential use in various applications, were prepared by pyrolysis of organic precursors using the thermally assisted chemical vapour deposition method. By varying the precursor concentration and preparation temperature, compositions with varying iron concentration and nanoparticle sizes were made. Powder x-ray diffraction, transmission electron microscopy and Mossbauer spectroscopy studies revealed the nanocrystalline iron carbide (Fe3C) presence in the partially graphitized matrix. The dependence of the magnetic properties on the particle size and temperature (10 K < T < 300 K) were studied using superconducting quantum interference device magnetometry. Based on the affect of surrounding carbon spins, the observed magnetic behaviour of the nanoparticle compositions, such as the temperature dependence of magnetization and coercivity, can be explained.

Size-Dependent Melting of Finite-Length Nanowires

We report on the size-dependent melting of nanowires with finite length based on the thermodynamic as well as liquid drop model. It has been inferred that the length dependency cannot be ignored, unlike the case of infinite length nanowires. To validate the length dependency, we have analyzed a few experimental results reported in the literature.

Size-Dependent Tuning of Mn2+ d Emission in Mn2+-Doped CdS Nanocrystals: Bulk vs Surface

We show that the characteristic Mn2+ d emission color from Mn2+-doped CdS nanocrystals can be tuned over as much as 40 nm, in contrast to what should be expected from such a nearly localized d-d transition. This is achieved surprisingly by a fine-tuning of the host particle diameter from 1.9 to 2.6 nm, thereby changing the overall emission color from red to yellow. Systematic experiments in conjunction with state-of-the-art ab initio calculations with full geometry optimization establish that Mn2+ ions residing at surface/subsurface regions have a distorted tetrahedral coordination resulting in a larger ligand field splitting. Consequently, these near-surface Mn2+ species exhibit a lower Mn2+ d emission energy, compared to those residing at the core of the nanocrystal with an undisturbed tetrahedral coordination. The origin of the tunability of the observed Mn2+ emission is the variation of emission contributions arising from Mn2+ doped at the core, subsurface, and surface of the host. Our findings provide a unique and easy method to identify the location of an emitting Mn2+ ion in the nanocrystal, which would be otherwise very difficult to decipher.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

Size-dependent cohesive energy and melting of non-spherical nanoparticles

All most all theoretical models assume spherical nanoparticles. However, thermodynamic properties of non-spherical nanoparticles are the subject of recent interests. In this article, we have discussed the size-dependent cohesive energy and melting of non-spherical nanoparticles based on liquid-drop model. The surface to volume ratio is different for different shapes of nanoparticles and as a consequence, the variation of cohesive energy and melting of non-spherical nanoparticles is different from that of spherical case. By analyzing the reported experimental results, it has been observed that liquid-drop model can be used to understand the size-dependent cohesive energy and melting of non-spherical nanoparticles.

Size dependent microstructure for Ag-Ni nanoparticles

The Ag-Ni system is characterized by large differences in atomic sizes (14%) and a positive heat of mixing (+23 kJ mol(-1)). The binary equilibrium diagram for this system therefore exhibits a large miscibility gap in both solid and liquid state. This paper explores the size-dependent changes in microstructure and the suppression of the miscibility gap which occurs when free alloy particles of nanometer size are synthesized by co-reduction of Ag and Ni metal precursors. The paper reports that complete mixing between Ag and Ni atoms could be achieved for smaller nanoparticles (<7 nm). These particles exhibit a single-phase solid solution with face-centered cubic (fcc) structure. With increase in size, the nanoparticles revealed two distinct regions. One of the regions is composed of pure Ag. This region partially surrounds a region of fcc solid solution at an early stage of decomposition. Experimental observations were compared with the results obtained from the thermodynamic calculations, which compared the free energies corresponding to a physical mixture of pure Ag and Ni phases and a fcc Ag-Ni solid solution for different particle sizes. Results from the theoretical calculations revealed that, for the Ag-Ni system, solid solution was energetically preferred over the physical mixture configuration for particle sizes of 7 nm and below. The experimentally observed two-phase microstructure for larger particles was thus primarily due to the growth of Ag-rich regions epitaxially on initially formed small fcc Ag-Ni nanoparticles. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Size dependent bandgap of molecular beam epitaxy grown InN quantum dots measured by scanning tunneling spectroscopy

InN quantum dots (QDs) were grown on Si (111) by epitaxial Stranski-Krastanow growth mode using plasma-assisted molecular beam epitaxy. Single-crystalline wurtzite structure of InN QDs was verified by the x-ray diffraction and transmission electron microscopy. Scanning tunneling microscopy has been used to probe the structural aspects of QDs. A surface bandgap of InN QDs was estimated from scanning tunneling spectroscopy (STS) I-V curves and found that it is strongly dependent on the size of QDs. The observed size-dependent STS bandgap energy shifts with diameter and height were theoretical explained based on an effective mass approximation with finite-depth square-well potential model.

Efficiency enhancement in DSSC using metal nanoparticles: A size dependent study

The photoelectrode of Eosin-Y sensitised DSSC was modified by incorporating Au-nanoparticles to enhance the power conversion efficiency via scattering from surface plasmon polaritons. Size dependence of Au nanoparticle on conversion efficiency was performed in DSSC for the first time by varying the particle size from 20 to 94 nm. It was found that, the conversion efficiency is highly dependent on the size of the Au nanoparticles. For larger particles (>50 nm), the efficiency was found to be increased due to constructive interference between the transmitted and scattered waves from the Au nanoparticle while for smaller particles, the efficiency decreases due to destructive interference. Also a reduction in the V-oc was observed in general, due to the negative shifting of the TiO2 Fermi level on the adsorption of Au nanoparticle. This shift was negligible for larger particles. When 94 nm size particles were employed the conversion efficiency was doubled from 0.74% to 1.52%. This study points towards the application of the scattering effect of metal nanoparticle to enhance the conversion efficiency in DSSCs. (C) 2011 Elsevier Ltd. All rights reserved.

Thermodynamic Models for the Size-dependent Melting of Nanoparticles: Different Hypotheses

A careful comparison of the experimental results reported in the literature reveals different variations of the melting temperature even for the same materials. Though there are different theoretical models, thermodynamic model has been extensively used to understand different variations of size-dependent melting of nanoparticles. There are different hypotheses such as homogeneous melting (HMH), liquid nucleation and growth (LNG) and liquid skin melting (LSM) to resolve different variations of melting temperature as reported in the literature. HMH and LNG account for the linear variation where as LSM is applied to understand the nonlinear behaviour in the plot of melting temperature against reciprocal of particle size. However, a bird's eye view reveals that either HMH or LSM has been extensively used by experimentalists. It has also been observed that not a single hypothesis can explain the size-dependent melting in the complete range. Therefore we describe an approach which can predict the plausible hypothesis for a given data set of the size-dependent melting temperature. A variety of data have been analyzed to ascertain the hypothesis and to test the approach.