A new set of relativistic screening constants for the screened hydrogenic model

AnewRelativisticScreenedHydrogenicModel has been developed to calculate atomic data needed to compute the optical and thermodynamic properties of high energy density plasmas. The model is based on anewset of universal screeningconstants, including nlj-splitting that has been obtained by fitting to a large database of ionization potentials and excitation energies. This database was built with energies compiled from the National Institute of Standards and Technology (NIST) database of experimental atomic energy levels, and energies calculated with the Flexible Atomic Code (FAC). The screeningconstants have been computed up to the 5p3/2 subshell using a Genetic Algorithm technique with an objective function designed to minimize both the relative error and the maximum error. To select the best set of screeningconstants some additional physical criteria has been applied, which are based on the reproduction of the filling order of the shells and on obtaining the best ground state configuration. A statistical error analysis has been performed to test the model, which indicated that approximately 88% of the data lie within a ±10% error interval. We validate the model by comparing the results with ionization energies, transition energies, and wave functions computed using sophisticated self-consistent codes and experimental data.

Frequency-dependent opacity calculations for radiation transport simulations

We will present recent developments in the calculation of opacity tables suitable for including in the radiation hydrodynamic code ARWEN [1] to study processes like ICF or X-ray secondary sources. For these calculations we use the code BiG BART in LTE conditions, with self-consistent data generated with the Flexible Atomic Code (FAC) [2]. Non-LTE effects are approximately taken into account by means of the improved RADIOM model [3], which makes use of existing LTE data tables.

Equation of State and Opacities for Warm Dense Matter.

We will present recent developments in the calculation of opacity and equation of state tables suitable for including in the radiation hydrodynamic code ARWEN [1] to study processes like ICF or X-ray secondary sources. For these calculations we use the code BiG BART to compute opacities in LTE conditions, with self-consistent data generated with the Flexible Atomic Code (FAC) [2]. Non-LTE effects are approximately taken into account by means of the improved RADIOM model [3], which makes use of existing LTE data tables. We use the screened-hydrogenic model [4] to derive the Equation of State using the population and energy of the levels avaliable from the atomic data

Ab-Initio calculations including Van der Waals interactions: the SnS2 layered material

Tin disulfide SnS2 was recently proposed as a high efficiency solar cell precursor [1]. The aim of this work is a deep study of the structural disposition of the most important polytipes of this layered material, not only describing the electronic correlation but also the interatomic Van der Waals interactions that is present between the layers. The two recent implementations to take Van der Waals interactions into account in the VASP code are the self-consistent Dion et al. [2] functional optimized for solids by Michaelides et al [3] and the Grimme [4] dispersion correction that is applied after each autoconsistent PBE electronic calculation. In this work these two methods are compared with DFT PBE functional. The results we will presented at this Conference, demonstrates the enhancement of the geometric parameters by the use of the Van der Waals interactions in agreement with the experimental values.

Analysis of the performance of tapered semiconductor optical amplifiers: role of the taper angle

The beam properties of tapered semiconductor optical amplifiers emitting at 1.57 μm are analyzed by means of simulations with a self-consistent steady state electro-optical and thermal simulator. The results indicate that the self-focusing caused by carrier lensing is delayed to higher currents for devices with taper angle slightly higher than the free diffraction angle.

Building intuition of iron evolution during solar cell processing through analysis of different process models

An important aspect of Process Simulators for photovoltaics is prediction of defect evolution during device fabrication. Over the last twenty years, these tools have accelerated process optimization, and several Process Simulators for iron, a ubiquitous and deleterious impurity in silicon, have been developed. The diversity of these tools can make it difficult to build intuition about the physics governing iron behavior during processing. Thus, in one unified software environment and using self-consistent terminology, we combine and describe three of these Simulators. We vary structural defect distribution and iron precipitation equations to create eight distinct Models, which we then use to simulate different stages of processing. We find that the structural defect distribution influences the final interstitial iron concentration ([Fe-i]) more strongly than the iron precipitation equations. We identify two regimes of iron behavior: (1) diffusivity-limited, in which iron evolution is kinetically limited and bulk [Fe-i] predictions can vary by an order of magnitude or more, and (2) solubility-limited, in which iron evolution is near thermodynamic equilibrium and the Models yield similar results. This rigorous analysis provides new intuition that can inform Process Simulation, material, and process development, and it enables scientists and engineers to choose an appropriate level of Model complexity based on wafer type and quality, processing conditions, and available computation time.

From point defects to plate tectonic faults

Understanding and explaining emergent constitutive laws in the multi-scale evolution from point defects, dislocations and two-dimensional defects to plate tectonic scales is an arduous challenge in condensed matter physics. The Earth appears to be the only planet known to have developed stable plate tectonics as a means to get rid of its heat. The emergence of plate tectonics out of mantle convection appears to rely intrinsically on the capacity to form extremely weak faults in the top 100 km of the planet. These faults have a memory of at least several hundred millions of years, yet they appear to rely on the effects of water on line defects. This important phenomenon was first discovered in laboratory and dubbed ``hydrolytic weakening''. At the large scale it explains cycles of co-located resurgence of plate generation and consumption (the Wilson cycle), but the exact physics underlying the process itself and the enormous spanning of scales still remains unclear. We present an attempt to use the multi-scale non-equilibrium thermodynamic energy evolution inside the deforming lithosphere to move phenomenological laws to laws derived from basic scaling quantities, develop self-consistent weakening laws at lithospheric scale and give a fully coupled deformation-weakening constitutive framework. At meso- to plate scale we encounter in a stepwise manner three basic domains governed by the diffusion/reaction time scales of grain growth, thermal diffusion and finally water mobility through point defects in the crystalline lattice. The latter process governs the planetary scale and controls the stability of its heat transfer mode.

Phase equilibrium studies at normal pressures

A total pressure apparatus has been developed to measure vapour-liquid equilibrium data on binary mixtures at atmospheric and sub-atmospheric pressures. The method gives isothermal data which can be obtained rapidly. Only measurements of total pressure are made as a direct function of composition of synthetic liquid phase composition, the vapour phase composition being deduced through the Gibbs-Duhem relationship. The need to analyse either of the phases is eliminated. As such the errors introduced by sampling and analysis are removed. The essential requirements are that the pure components be degassed completely since any deficiency in degassing would introduce errors into the measured pressures. A similarly essential requirement was that the central apparatus would have to be absolutely leak-tight as any leakage of air either in or out of the apparatus would introduce erroneous pressure readings. The apparatus was commissioned by measuring the saturated vapour pressures of both degassed water and ethanol as a function of temperature. The pressure-temperature data on degassed water measured were directly compared with data in the literature, with good agreement. Similarly the pressure-temperature data were measured for ethanol, methanol and cyclohexane and where possible a direct comparison made with the literature data. Good agreement between the pure component data of this work and those available in the literature demonstrates firstly that a satisfactory degassing procedure has been achieved and that secondly the measurements of pressure-temperature are consistent for any one component; since this is true for a number of components, the measurements of both temperature and pressure are both self-consistent and of sufficient accuracy, with an observed compatibility between the precision/accuracy of the separate means of measuring pressure and temperature. The liquid mixtures studied were of ethanol-water, methanol-water and ethanol-cyclohexane. The total pressure was measured as the composition inside the equilibrium cell was varied at a set temperature. This gave P-T-x data sets for each mixture at a range of temperatures. A standard fitting-package from the literature was used to reduce the raw data to yield y-values to complete the x-y-P-T data sets. A consistency test could not be applied to the P-T-x data set as no y-values were obtained during the experimental measurements. In general satisfactory agreement was found between the data of this work and those available in the literature. For some runs discrepancies were observed, and further work recommended to eliminate the problems identified.

A systematic approach to establish fundamental principles of computer applications packages design

This work attempts to create a systemic design framework for man-machine interfaces which is self consistent, compatible with other concepts, and applicable to real situations. This is tackled by examining the current architecture of computer applications packages. The treatment in the main is philosophical and theoretical and analyses the origins, assumptions and current practice of the design of applications packages. It proposes that the present form of packages is fundamentally contradictory to the notion of packaging itself. This is because as an indivisible ready-to-implement solution, current package architecture displays the following major disadvantages. First, it creates problems as a result of user-package interactions, in which the designer tries to mould all potential individual users, no matter how diverse they are, into one model. This is worsened by the minute provision, if any, of important properties such as flexibility, independence and impartiality. Second, it displays rigid structure that reduces the variety and/or multi-use of the component parts of such a package. Third, it dictates specific hardware and software configurations which probably results in reducing the number of degrees of freedom of its user. Fourth, it increases the dependence of its user upon its supplier through inadequate documentation and understanding of the package. Fifth, it tends to cause a degeneration of the expertise of design of the data processing practitioners. In view of this understanding an alternative methodological design framework which is both consistent with systems approach and the role of a package in its likely context is proposed. The proposition is based upon an extension of the identified concept of the hierarchy of holons* which facilitates the examination of the complex relationships of a package with its two principal environments. First, the user characteristics and his decision making practice and procedures; implying an examination of the user's M.I.S. network. Second, the software environment and its influence upon a package regarding support, control and operation of the package. The framework is built gradually as discussion advances around the central theme of a compatible M.I.S., software and model design. This leads to the formation of the alternative package architecture that is based upon the design of a number of independent, self-contained small parts. Such is believed to constitute the nucleus around which not only packages can be more effectively designed, but is also applicable to many man-machine systems design.

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

Structure of dysprosium and holmium phosphate glasses by the method of isomorphic substitution in neutron diffraction

The relative distribution of rare-earth ions R3+ (Dy3+ or Ho3+) in the phosphate glass RAl0.30P3.05O9.62 was measured by employing the method of isomorphic substitution in neutron diffraction and, by taking the role of Al into explicit account, a self-consistent model of the glass structure was developed. The glass network is found to be made from corner sharing PO4 tetrahedra in which there are, on average, 2.32(9) terminal oxygen atoms, OT, at 1.50(1) Å and 1.68(9) bridging oxygen atoms, OB, at 1.60(1) Å. The network modifying R3+ ions bind to an average of 6.7(1) OT and are distributed such that 7.9(7) R–R nearest neighbours reside at 5.62(6) Å. The Al3+ ion also has a network modifying role in which it helps to strengthen the glass through the formation of OT–Al–OT linkages. The connectivity of the R-centred coordination polyhedra in (M2O3)x(P2O5)1−x glasses, where M3+ denotes a network modifying cation (R3+ or Al3+), is quantified in terms of a parameter fs. Methods for reducing the clustering of rare-earth ions in these materials are then discussed, based on a reduction of fs via the replacement of R3+ by Al3+ at fixed total modifier content or via a change of x to increase the number of OT available per network modifying M3+ cation.

Structure of lanthanum and cerium phosphate glasses by the method of isomorphic substitution in neutron diffraction

Neutron diffraction was used to measure the total structure factors for several rare-earth ion R3+ (La3+ or Ce3+) phosphate glasses with composition close to RAl0.35P3.24O10.12. By assuming isomorphic structures, difference function methods were employed to separate, essentially, those correlations involving R3+ from the remainder. A self-consistent model of the glass structure was thereby developed in which the Al correlations were taken into explicit account. The glass network was found to be made from interlinked PO4 tetrahedra having 2.2(1) terminal oxygen atoms, OT, at 1.51(1) Angstrom, and 1.8(1) bridging oxygen atoms, OB, at 1.60(1) Angstrom. Rare-earth cations bonded to an average of 7.5(2) OT nearest neighbors in a broad and asymmetric distribution. The Al3+ ion acted as a network modifier and formed OT-A1-OT linkages that helped strengthen the glass. The connectivity of the R-centered coordination polyhedra was quantified in terms of a parameter f(s) and used to develop a model for the dependence on composition of the A1-OT coordination number in R-A1-P-O glasses. By using recent 17 A1 nuclear-magnetic-resonance data, it was shown that this connectivity decreases monotonically with increasing Al content. The chemical durability of the glasses appeared to be at a maximum when the connectivity of the R-centered coordination polyhedra was at a minimum. The relation of f(s) to the glass transition temperature, Tg, was discussed.

Identification of the relative distribution of rare-earth ions in phosphate glasses

The relative distribution of rare-earth ions R3+ (Dy3+ or Ho3+) in the phosphate glass RAl0.30P3.05O9.62 was measured by employing the method of isomorphic substitution in neutron diffraction. It is found that 7.9(7) R-R nearest neighbors reside at 5.62(6) Angstrom in a network made from interlinked PO4 tetrahedra. Provided that the role of Al is explicitly considered, a self-consistent account of the local matrix atom correlations can be developed in which there are 1.68(9) bridging and 2.32(9) terminal oxygen atoms per phosphorus.

Bridging large and small scales of water models using hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework

This thesis presents a two-dimensional water model investigation and development of a multiscale method for the modelling of large systems, such as virus in water or peptide immersed in the solvent. We have implemented a two-dimensional ‘Mercedes Benz’ (MB) or BN2D water model using Molecular Dynamics. We have studied its dynamical and structural properties dependence on the model’s parameters. For the first time we derived formulas to calculate thermodynamic properties of the MB model in the microcanonical (NVE) ensemble. We also derived equations of motion in the isothermal–isobaric (NPT) ensemble. We have analysed the rotational degree of freedom of the model in both ensembles. We have developed and implemented a self-consistent multiscale method, which is able to communicate micro- and macro- scales. This multiscale method assumes, that matter consists of the two phases. One phase is related to micro- and the other to macroscale. We simulate the macro scale using Landau Lifshitz-Fluctuating Hydrodynamics, while we describe the microscale using Molecular Dynamics. We have demonstrated that the communication between the disparate scales is possible without introduction of fictitious interface or approximations which reduce the accuracy of the information exchange between the scales. We have investigated control parameters, which were introduced to control the contribution of each phases to the matter behaviour. We have shown, that microscales inherit dynamical properties of the macroscales and vice versa, depending on the concentration of each phase. We have shown, that Radial Distribution Function is not altered and velocity autocorrelation functions are gradually transformed, from Molecular Dynamics to Fluctuating Hydrodynamics description, when phase balance is changed. In this work we test our multiscale method for the liquid argon, BN2D and SPC/E water models. For the SPC/E water model we investigate microscale fluctuations which are computed using advanced mapping technique of the small scales to the large scales, which was developed by Voulgarakisand et. al.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).