Relevant bibliographies by topics / Interaction energy calculation

Academic literature on the topic 'Interaction energy calculation'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Interaction energy calculation"

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WILLIAMSON, ANDREW J. "ENERGY STATES IN QUANTUM DOTS." International Journal of High Speed Electronics and Systems 12, no. 01 (March 2002): 15–43. http://dx.doi.org/10.1142/s0129156402001101.

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We describe a procedure for calculating the electronic structure of semiconductor quantum dots containing over one million atoms. The single particle electron levels are calculated by solving a Hamiltonian constructed from screened atomic pseudopotentials. Effects beyond the single particle level such as electron and hole exchange and correlation interactions are described using a configuration interaction (CI) approach. Application of these methods to the calculation of the optical absorption spectrum, Coulomb repulsions and multi-exciton binding energies of InGaAs self-assembled quantum dots are presented.
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Hasan, Ali K., and Amir A. Salih. "Energy Levels and B(E2) Calculation for 50Fe Isotope Using F754 and F7mbz Interactions." NeuroQuantology 20, no. 5 (April 30, 2022): 115–21. http://dx.doi.org/10.14704/nq.2022.20.5.nq22154.

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In this work was calculated energy levels and reduced electric quadrupole transition probability B(E2) for 50Fe isotope using OXBASH code within the 1f7/2 shell and using the F754 and F7mbz effective interaction. 50Fe isotope contain 6 proton and 4 neutron out side 40Ca core in shell. In general, an acceptable agreement was obtained for a number of energy levels, and the total angular momentum and ground state parity were matched for all these isotopes, also new energy levels were obtained that have no practical values so far.
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Khvesyuk, V. I., W. Qiao, and A. A. Barinov. "Kinetics of Phonon Interaction Taken into Account in Determining Thermal Conductivity of Silicon." Herald of the Bauman Moscow State Technical University. Series Natural Sciences, no. 3 (102) (June 2022): 57–68. http://dx.doi.org/10.18698/1812-3368-2022-3-57-68.

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The thorough study of the heat carriers --- quasiparticles --- phonons interaction resulted in a pioneering method for calculating the thermal conductivity of nonmetallic solids. As the interactions of phonons are much more complicated than those of usual atoms and molecules, it is necessary to take into account the presence of two types of phonons with different properties; the decay of one phonon into two or the fusion of two phonons into one as a result of interaction; the presence of two types of interaction of phonons, one of which is elastic, the other is inelastic (moreover, the type of interaction results from solving the energy and quasi-momentum conservation equations). The existing methods for determining thermal conductivity, which typically involve solving the Boltzmann transport equation, use the iteration method, whose parameter is the average time between successive phonon interactions, and the calculation results provide little information on all types of interactions. In this research, we developed a method of direct Monte Carlo simulation of phonon diffusion with strict account for their interaction owing to the energy and quasi-momentum conservation laws. Calculations of the thermal conductivity coefficient for pure silicon in the temperature range of 100---300 K showed good agreement with the experiment and calculations of other authors, and also made it possible to consider the phonon kinetics in detail
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Hong-Jun, BAI, and LAI Lu-Hua. "Protein-Protein Interactions: Interface Analysis, Binding Free Energy Calculation and Interaction Design." Acta Physico-Chimica Sinica 26, no. 07 (2010): 1988–97. http://dx.doi.org/10.3866/pku.whxb20100725.

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SA-YAKANIT, VIRULH, and WATTANA LIM. "GROUND STATE ENERGY OF BOSE-EINSTEIN CONDENSATION IN A DISORDERED SYSTEM." International Journal of Modern Physics B 22, no. 25n26 (October 20, 2008): 4398–406. http://dx.doi.org/10.1142/s0217979208050152.

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A modeled Bose system consisting of N particles with two-body interaction confined within volume V under inhomogeneity of the system is investigated using the Feynman path integral approach. The two-body interaction energy is assumed to be dependent on the two-parameter interacting strength a and the correlation length l. The inhomogeneity of the system or the porosity can be represented as density [Formula: see text] with interacting strength b and correlation length L. The mean field approximation on the two-body interaction in the Feynman path integrals representation is performed to obtain the one-body interaction. This approximation is equivalent to the Hartree approximation in the many-body electron gas problem. This approximation has shown that the calculation can be reduced to the effective one-body propagator. Performing the variational calculations, we obtain analytical results of the ground state energy which is in agreement with that from Bugoliubov's approach.
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LOPES, JULIANA FEDOCE, JÚLIO C. S. DA SILVA, WILLIAN R. ROCHA, WAGNER B. DE ALMEIDA, and HÉLIO F. DOS SANTOS. "QUANTUM CHEMICAL STUDY OF CISPLATIN-WATER COMPLEXES: AN INVESTIGATION OF ELECTRON CORRELATION EFFECTS." Journal of Theoretical and Computational Chemistry 10, no. 03 (June 2011): 371–91. http://dx.doi.org/10.1142/s0219633611006517.

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The interaction of cisplatin ([ Pt(NH3)2Cl2] ) with water was studied for distinct complexation modes aiming to investigate the level of calculation required to describe transition metal complexes of biological relevance, where large scale ab initio post-Hartree-Fock calculations are usually precluded. Coupled Cluster (CCSD(T)) single point calculations employing MP2 and MP4(SDQ) optimized geometries and good quality basis sets, using effective core potential for platinum atom, are reported as well as Density Functional Theory (DFT) results employing various exchange-correlation functional. The importance of electron correlation effects for the calculation of interaction energies is discussed. The extension of correlation energy recovered by DFT was assessed considering the CCSD(T) results as reference. The recently developed M06-2x functional showed the best overall agreement with CCSD(T) calculations. The relative importance of the electrostatic and dispersion contributions to the interaction energy was estimated with the aid of the atoms in molecules theory and also using an empirical approach based on the multipole expansion method. It was found a strong dependence of the energy contributions on the spatial orientation of water and cisplatin monomers, with the electrostatic contribution dominating the interaction energy for the lowest energy equilibrium structures.
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ZHANG, D. W., and J. Z. H. ZHANG. "FULL AB INITIO COMPUTATION OF PROTEIN-WATER INTERACTION ENERGIES." Journal of Theoretical and Computational Chemistry 03, no. 01 (March 2004): 43–49. http://dx.doi.org/10.1142/s0219633604000891.

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A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.
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Laurinc, Viliam, Vladimír Lukeś, and Stanislav Biskupič. "Perturbation calculation of the interaction energy using orthogonalized orbitals." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 99, no. 1 (February 20, 1998): 53–59. http://dx.doi.org/10.1007/s002140050302.

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Roshanbakht, Nafiseh, and Mohammadreza Shojaei. "Clustering energy calculation in light alpha-conjugated nuclei." Canadian Journal of Physics 98, no. 10 (October 2020): 976–79. http://dx.doi.org/10.1139/cjp-2019-0468.

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In this paper, clustering energy was investigated in light alpha-conjugate nuclei considering cluster–cluster interaction instead of nucleon–nucleon interaction and using the phenomenological non-microscopic method. The observed energy levels were calculated from the rotational band of 8Be, 12C, and 16O isotopes. The results showed that these isotopes, in their cluster state, have a non-spherical structure.
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Zhang, Zhijun, Liang Zhao, Yanan Li, and Mo Chu. "A Modified Method to Calculate Critical Coagulation Concentration Based on DLVO Theory." Mathematical Problems in Engineering 2015 (2015): 1–5. http://dx.doi.org/10.1155/2015/317483.

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The critical coagulation concentration (CCC) is defined as the minimum concentration of counterions to induce coagulation of colloidal particles. A modified calculation method was proposed to calculate CCC. Comparing the modified calculation method of CCC with the traditional calculation method, the critical condition of modified calculation method is stricter than traditional calculation method. The critical condition of modified calculation method is the maximum value of interaction force that is zero, and the critical condition of traditional calculation method is the maximum value of interaction energy that is zero. The calculation result of CCC based on interaction force is greater than the calculation value based on interaction energy. The CCC value of modified calculation method can ensure particles to coagulate definitely.
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Dissertations / Theses on the topic "Interaction energy calculation"

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Almlöf, Martin. "Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.

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The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.

For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.

A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.

A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.

The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

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Panel, Nicolas. "Étude computationnelle du domaine PDZ de Tiam1." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX062/document.

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Les interactions protéine-protéine sont souvent contrôlées par de petits domaines protéiques qui régulent les chemins de signalisation au sein des cellules eucaryotes. Les domaines PDZ sont parmi les domaines les plus répandus et les plus étudiés. Ils reconnaissent spécifiquement les 4 à 10 acides aminés C-terminaux de leurs partenaires. Tiam1 est un facteur d'échange de GTP de la protéine Rac1 qui contrôle la migration et la prolifération cellulaire et dont le domaine PDZ lie les protéines Syndecan-1 (Sdc1), Caspr4 et Neurexine. Des petits peptides ou des molécules peptidomimétiques peuvent potentiellement inhiber ou moduler son activité et être utilisés à des fins thérapeutiques. Nous avons appliqué des approches de dessin computationnel de protéine (CPD) et de calcul d'énergie libre par simulations dynamique moléculaire (DM) pour comprendre et modifier sa spécificité. Le CPD utilise un modèle structural et une fonction d'énergie pour explorer l'espace des séquences et des structures et identifier des variants protéiques ou peptidiques stables et fonctionnels. Nous avons utilisé le programme de CPD Proteus, développé au laboratoire, pour redessiner entièrement le domaine PDZ de Tiam1. Les séquences générées sont similaires à celles des domaines PDZ naturels, avec des scores de similarité et de reconnaissance de pli comparables au programme Rosetta, un outil de CPD très utilisé. Des séquences contenant environ 60 positions mutées sur 90, ont été testées par simulations de DM et des mesures biophysiques. Quatre des cinq séquences testées expérimentalement (par nos collaborateurs) montrent un dépliement réversible autour de 50°C. Proteus a également déterminer correctement la spécificité de la liaison de quelques variants protéiques et peptidiques. Pour étudier plus finement la spécificité, nous avons paramétré un modèle d'énergie libre semi-empirique de Poisson-Boltzmann ayant la forme d'une énergie linéaire d'interaction, ou PB/LIE, appliqué à des conformations issues de simulations de DM en solvant explicite de complexes PDZ:peptide. Avec trois paramètres ajustables, le modèle reproduit correctement les affinités expérimentales de 41 variants, avec une erreur moyenne absolue de 0,4~kcal/mol, et donne des prédictions pour 10 nouveaux variants. Le modèle PB/LIE a ensuite comparé à la méthode non-empirique de calcul d'énergie libre par simulations alchimiques, qui n'a pas de paramètre ajustable et qui prédit correctement l'affinité de 12 complexes Tiam1:peptide. Ces outils et les résultats obtenus devraient nous permettre d'identifier des peptides inhibiteurs et auront d'importantes retombées pour l'ingénierie des interactions PDZ:peptide
Small protein domains often direct protein-protein interactions and regulate eukaryotic signalling pathways. PDZ domains are among the most widespread and best-studied. They specifically recognize the 4-10 C-terminal amino acids of target proteins. Tiam1 is a Rac GTP exchange factor that helps control cellmigration and proliferation and whose PDZ domain binds the proteins syndecan-1 (Sdc1), Caspr4, and Neurexin. Short peptides and peptidomimetics can potentially inhibit or modulate its action and act as bioreagents or therapeutics. We used computational protein design (CPD) and molecular dynamics (MD) free energy simulations to understand and engineer its peptide specificity. CPD uses a structural model and an energy function to explore the space of sequences and structures and identify stable and functional protein or peptide variants. We used our in-house Proteus CPD package to completely redesign the Tiam1 PDZ domain. The designed sequences were similar to natural PDZ domains, with similarity and fold recognition scores comarable to the widely-used Rosetta CPD package. Selected sequences, containing around 60 mutated positions out of 90, were tested by microsecond MD simulations and biophysical experiments. Four of five sequences tested experimentally (by our collaborators) displayed reversible unfolding around 50°C. Proteus also accurately scored the binding specificity of several protein and peptide variants. As a more refined model for specificity, we parameterized a semi-empirical free energy model of the Poisson-Boltzmann Linear Interaction Energy or PB/LIE form, which scores conformations extracted from explicit solvent MD simulations of PDZ:peptide complexes. With three adjustable parameters, the model accurately reproduced the experimental binding affinities of 41 variants, with a mean unsigned error of just 0.4 kcal/mol, andgave predictions for 10 new variants. The PB/LIE model was tested further by comparing to non-empirical, alchemical, MD free energy simulations, which have no adjustable parameters and were found to give chemical accuracy for 12 Tiam1:peptide complexes. The tools and insights obtained should help discover new tight binding peptides or peptidomimetics and have broad implications for engineering PDZ:peptide interactions
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Ramadugu, Sai Kumar. "Carbohydrate-protein interactions: structure, dynamics and free energy calculations." Diss., University of Iowa, 2013. https://ir.uiowa.edu/etd/1731.

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The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulation, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecular dynamics as well as the thermodynamic integration formalism, we have been able to study the role of water on the surface of homopolysaccharides as well as complex oligosachharides, we have been able to produce a prediction of the bound structure of triantennary oligosaccride on the asialoglycoprotein receptor, we have been able to estimate the free energy of binding of ManΑ1→2Man to the HIV-1 inactivating protein, Cyanovirin-N as well as the relative binding free energies of mutants of Cyanovirin-N to the same ligand.
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Chang, Zhongwen, Pär Olsson, Nils Sandberg, and Dmitry Terentyev. "Interaction Energy Calculations of Edge Dislocation with Point Defects in FCC Cu." KTH, Reaktorfysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-122396.

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In order to improve the dislocation bias (DB) model of swelling under irradiation, a large scale of atomistic simulation of the interaction in face centered cubic (FCC) Cu model lattice between an edge dislocation (ED) and point defects such as a vacancy, a self-interstital atom (SIA) have been performed for various configurations. It is found dislocation core splits into partial cores after energy relaxation. Interactions with any SIA conficurations is one order of magnitute larger than with a vacancy. The reason that SIA creats a larger dilatation volumn than the vacancy is directly observed from calculation. Furthurmore, within the interaction range, an octahedron position rather than dumbbell in <100> direction is observed in the stable state after relaxation in interactions between a edge dislocation and a dumbbell SIA. Comparision of interaction energy in analytical and atomistic calculation shows that analytical one has a stronger interaction in vacancy-ED systems, suggesting that the bias factor (BF) from analytical calculation is larger than from atomistic calculation.

QC 20130530


Generation IV reactor research and development (GENIUS)
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Reid, K. S. C. "Application of interactive force and energy calculations to enzyme-substrate docking." Thesis, Imperial College London, 1987. http://hdl.handle.net/10044/1/47803.

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Hermansson, Anders. "Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-170722.

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Indications that existing parameter sets of extended Linear Interaction Energy (LIE) models are transferable between lipases from Rhizomucor Miehei and Thermomyces Lanigunosus in complex with a small set of vinyl esters are demonstrated. By calculat- ing energy terms that represents the cost of forming cavities filled by the ligand and the complex we can add them to a LIE model with en established parameter set. The levels of precision attained will be comparable to those of an optimal fit. It is also demonstrated that the Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods are in- applicable to the problem of calculating absolute binding energies, even when the largest source of variance has been reduced.
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Kumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.

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Nervall, Martin. "Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8338.

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Vazquez, Montelongo Erik Antonio. "Computational Study of Intermolecular Interactions in Complex Chemical Systems." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703283/.

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This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).
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Chaudhari, Mrunalkumar. "First Principles Calculations of the Site Substitution Behavior in Gamma Prime Phase in Nickel Based Superalloys." Thesis, University of North Texas, 2012. https://digital.library.unt.edu/ark:/67531/metadc149571/.

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Nickel based superalloys have superior high temperature mechanical strength, corrosion and creep resistance in harsh environments and found applications in the hot sections as turbine blades and turbine discs in jet engines and gas generator turbines in the aerospace and energy industries. The efficiency of these turbine engines depends on the turbine inlet temperature, which is determined by the high temperature strength and behavior of these superalloys. The microstructure of nickel based superalloys usually contains coherently precipitated gamma prime (?) Ni3Al phase within the random solid solution of the gamma () matrix, with the ? phase being the strengthening phase of the superalloys. How the alloying elements partition into the and ? phases and especially in the site occupancy behaviors in the strengthening ? phases play a critical role in their high temperature mechanical behaviors. The goal of this dissertation is to study the site substitution behavior of the major alloying elements including Cr, Co and Ti through first principles based calculations. Site substitution energies have been calculated using the anti-site formation, the standard defect formation formalism, and the vacancy formation based formalism. Elements such as Cr and Ti were found to show strong preference for Al sublattice, whereas Co was found to have a compositionally dependent site preference. In addition, the interaction energies between Cr-Cr, Co-Co, Ti-Ti and Cr-Co atoms have also been determined. Along with the charge transfer, chemical bonding and alloy chemistry associated with the substitutions has been investigated by examining the charge density distributions and electronic density of states to explain the chemical nature of the site substitution. Results show that Cr and Co atoms prefer to be close by on either Al sublattice or on a Ni-Al mixed lattice, suggesting a potential tendency of Cr and Co segregation in the ? phase.
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Books on the topic "Interaction energy calculation"

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Zuev, Sergey, Ruslan Maleev, and Aleksandr Chernov. Energy efficiency of electrical equipment systems of autonomous objects. ru: INFRA-M Academic Publishing LLC., 2021. http://dx.doi.org/10.12737/1740252.

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When considering the main trends in the development of modern autonomous objects (aircraft, combat vehicles, motor vehicles, floating vehicles, agricultural machines, etc.) in recent decades, two key areas can be identified. The first direction is associated with the improvement of traditional designs of autonomous objects (AO) with an internal combustion engine (ICE) or a gas turbine engine (GTD). The second direction is connected with the creation of new types of joint-stock companies, namely electric joint-stock companies( EAO), joint-stock companies with combined power plants (AOKEU). The energy efficiency is largely determined by the power of the generator set and the battery, which is given to the electrical network in various driving modes. Most of the existing methods for calculating power supply systems use the average values of disturbing factors (generator speed, current of electric energy consumers, voltage in the on-board network) when choosing the characteristics of the generator set and the battery. At the same time, it is obvious that when operating a motor vehicle, these parameters change depending on the driving mode. Modern methods of selecting the main parameters and characteristics of the power supply system do not provide for modeling its interaction with the power unit start-up system of a motor vehicle in operation due to the lack of a systematic approach. The choice of a generator set and a battery, as well as the concept of the synthesis of the power supply system is a problem studied in the monograph. For all those interested in electrical engineering and electronics.
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Eriksson, Olle, Anders Bergman, Lars Bergqvist, and Johan Hellsvik. Aspects of the Solid State. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198788669.003.0002.

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Symmetries play an important role in the theory of the solid state. As will be developed in this Chapter, DFT calculations for crystalline materials are commonly performed for the irreducible part of the first Brillouin zone, an approach which relies on the use of translational and point group symmetries. Two central properties that result from a calculation in reciprocal space are the wave vector resolved energy spectra, the so called band structure, and the energy resolved density of states. For magnetic materials, atomic magnetic moment moments can be defined and calculated, as well as effective inter-atomic exchange interactions.
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Tiwari, Sandip. Semiconductor Physics. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780198759867.001.0001.

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A graduate-level text, Semiconductor physics: Principles, theory and nanoscale covers the central topics of the field, together with advanced topics related to the nanoscale and to quantum confinement, and integrates the understanding of important attributes that go beyond the conventional solid-state and statistical expositions. Topics include the behavior of electrons, phonons and photons; the energy and entropic foundations; bandstructures and their calculation; the behavior at surfaces and interfaces, including those of heterostructures and their heterojunctions; deep and shallow point perturbations; scattering and transport, including mesoscale behavior, using the evolution and dynamics of classical and quantum ensembles from a probabilistic viewpoint; energy transformations; light-matter interactions; the role of causality; the connections between the quantum and the macroscale that lead to linear responses and Onsager relationships; fluctuations and their connections to dissipation, noise and other attributes; stress and strain effects in semiconductors; properties of high permittivity dielectrics; and remote interaction processes. The final chapter discusses the special consequences of the principles to the variety of properties (consequences of selection rules, for example) under quantum-confined conditions and in monolayer semiconductor systems. The text also bring together short appendices discussing transform theorems integral to this study, the nature of random processes, oscillator strength, A and B coefficients and other topics important for understanding semiconductor behavior. The text brings the study of semiconductor physics to the same level as that of the advanced texts of solid state by focusing exclusively on the equilibrium and off-equilibrium behaviors important in semiconductors.
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Peskin, Michael E. Concepts of Elementary Particle Physics. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198812180.001.0001.

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This is a textbook of elementary particle physics whose goal is to explain the Standard Model of particle interactions. Part I introduces the basic concepts governing high-energy particle physics: elements of relativity and quantum field theory, the quark model of hadrons, methods for detection and measurement of elementary particles, methods for calculating predictions for observable quantitites. Part II builds up our understanding of the strong interaction from the key experiments to the formulation of Quantum Chromodynamics and its application to the description of evetns at the CERN Large Hadron Collider. Part III build up our understanding of the weak interaction from the key experiments to the formulation of spontaneously broken gauge theories. It then describes the tests and extensions of this theory, including the precision study of the W and Z bosons, CP violation, neutrino mass, and the Higgs boson.
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Thygesen, K. S., and A. Rubio. Correlated electron transport in molecular junctions. Edited by A. V. Narlikar and Y. Y. Fu. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199533046.013.23.

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This article focuses on correlated electron transport in molecular junctions. More specifically, it considers how electronic correlation effects can be included in transport calculations using many-body perturbation theory within the Keldysh non-equilibrium Green’s function formalism. The article uses the GW self-energy method (G denotes the Green’s function and W is the screened interaction) which has been successfully applied to describe quasi-particle excitations in periodic solids. It begins by formulating the quantum-transport problem and introducing the non-equilibrium Green’s function formalism. It then derives an expression for the current within the NEGF formalism that holds for interactions in the central region. It also combines the GW scheme with a Wannier function basis set to study electron transport through two prototypical junctions: a benzene molecule coupled to featureless leads and a hydrogen molecule between two semi-infinite platinum chains. The results are analyzed using a generic two-level model of a molecular junction.
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Silverleaf, D. J., F. Abbey, and Thomas A. F. Calculational Methods for Interacting Arrays of Fissile Material: International Series of Monographs in Nuclear Energy. Elsevier Science & Technology Books, 2013.

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Kerr, Del Grande Nancy, Society of Photo-optical Instrumentation Engineers., and American Academy of Otolaryngology--Head and Neck Surgery., eds. X-ray and vacuum ultraviolet interaction data bases, calculations, and measurements, 14-15 January 1988, Los Angeles, California. Bellingham, Wash., USA: SPIE, 1988.

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Allen, Michael P., and Dominic J. Tildesley. Nonequilibrium molecular dynamics. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198803195.003.0011.

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This chapter explains some of the fundamental issues associated with applying perturbations to a molecular dynamics simulation, along with practical details of methods for studying systems out of equilibrium. The main emphasis is on fluid flow and viscosity measurements. Spatially homogeneous perturbations are described to study shear and extensional flow. Non-equilibrium methods are applied to the study of heat flow and the calculation of the thermal conductivity. Issues of thermostatting, and the modelling of surface-fluid interactions for inhomogeneous systems, are discussed. The measurement of free energy changes through non-equilibrium work expressions such as those of Jarzynski and Crooks is also explained.
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Zhang, H. Mesoscopic Structures and Their Effects on High-Tc Superconductivity. Edited by A. V. Narlikar. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780198738169.013.12.

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This article presents the results of model calculations carried out to determine the mesoscopic structural features of high-temperature superconducting (HTS) crystal structures, and especially their characteristic high critical temperature (Tc) and anisotropy. The crystal structure of high-temperature superconductors (HTSc) is unique in having some mesoscopic features. For example, the structures of a majority of cuprite superconductors are comprised of two structural blocks, perovskite and rock salt, stacked along the c-direction. This article calculates the interaction between the perovskite and rock salt blocks in the form of combinative energy in order to elucidate the effects of mesoscopic structures on high-Tc superconductivity. Both X-ray diffraction and Raman spectroscopy show that a ‘fixed triangle’ exists in the samples under investigation. The article also examines the importance of electron–phonon coupling in high-Tc superconductors.
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Milonni, Peter W. An Introduction to Quantum Optics and Quantum Fluctuations. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780199215614.001.0001.

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This book is an introduction to quantum optics for students who have studied electromagnetism and quantum mechanics at an advanced undergraduate or graduate level. It provides detailed expositions of theory with emphasis on general physical principles. Foundational topics in classical and quantum electrodynamics, including the semiclassical theory of atom-field interactions, the quantization of the electromagnetic field in dispersive and dissipative media, uncertainty relations, and spontaneous emission, are addressed in the first half of the book. The second half begins with a chapter on the Jaynes-Cummings model, dressed states, and some distinctly quantum-mechanical features of atom-field interactions, and includes discussion of entanglement, the no-cloning theorem, von Neumann’s proof concerning hidden variable theories, Bell’s theorem, and tests of Bell inequalities. The last two chapters focus on quantum fluctuations and fluctuation-dissipation relations, beginning with Brownian motion, the Fokker-Planck equation, and classical and quantum Langevin equations. Detailed calculations are presented for the laser linewidth, spontaneous emission noise, photon statistics of linear amplifiers and attenuators, and other phenomena. Van der Waals interactions, Casimir forces, the Lifshitz theory of molecular forces between macroscopic media, and the many-body theory of such forces based on dyadic Green functions are analyzed from the perspective of Langevin noise, vacuum field fluctuations, and zero-point energy. There are numerous historical sidelights throughout the book, and approximately seventy exercises.
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Book chapters on the topic "Interaction energy calculation"

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Kulik, Dmitri A. "Calculation of equilibria in aquatic systems involving surface complexation on dispersed solid phases by means of Gibbs free energy minimization." In Water-Rock Interaction, 737–40. London: Routledge, 2021. http://dx.doi.org/10.1201/9780203734049-183.

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Chen, Junkai, Wenxue Gao, Xiangjun Hao, Zheng Wei, Xiaojun Zhang, and Zhaochen Liu. "Multilateral Boundary Blasting Theory of High and Steep Slope in Open Pit Mine and Its Application." In Lecture Notes in Civil Engineering, 347–57. Singapore: Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-1260-3_32.

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AbstractAt present, the blasting theory of high and steep rock slope mainly focuses on flat terrain, ignoring the influence of micro-terrain boundary factors on blasting effect, which leads to excessive blasting energy and affects the stability of slope. Therefore, based on the theory of multilateral boundary rock blasting, this paper deduces the calculation formula of blasting charge for high and steep rock slope under multilateral boundary conditions, and verifies it with field test. The results show that: (1) The multilateral boundary charge calculation formula directly includes micro-topography boundary conditions and blasting effect, and the rock blasting theory is based on the interaction of blasting energy provided by explosives and potential energy in medium, which effectively improves the energy utilization rate of explosives. (2) The influence of surplus blasting energy on the surrounding environment under different boundary conditions is controlled, and the explosive explosion effect is effectively controlled, so that a stable high and steep slope of open pit mine is formed after blasting.
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Tyulkina, Ekaterina, Pavel Vassiliev, Timur Janovsky, and Maxim Shcherbakov. "Evaluation of Interaction Level between Potential Drug and Protein by Hydrogen Bond Energy Calculation." In Communications in Computer and Information Science, 542–55. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11854-3_47.

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Schiwietz, G. "Accurate Quantum Mechanical Calculation of Stopping Powers for Intermediate Energy Light Ions Penetrating Atomic H and He Targets." In Interaction of Charged Particles with Solids and Surfaces, 517–28. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4684-8026-9_24.

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Steinbrecher, Thomas. "Free Energy Calculations in Drug Lead Optimization." In Protein-Ligand Interactions, 207–36. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch11.

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Weiss, M. S. "Calculating the Interaction Between Atomic Nuclei." In Energy in Physics, War and Peace, 87–100. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-009-3031-5_6.

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Fukushima, Kimichika. "Comparison of Contributions to Interatomic Interactions Between Covalent and Ionic Bonds from Total Energy Calculations." In The DV-Xα Molecular-Orbital Calculation Method, 135–39. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11185-8_5.

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Elvati, Paolo, and Angela Violi. "Free Energy Calculation of Permeant–Membrane Interactions Using Molecular Dynamics Simulations." In Methods in Molecular Biology, 189–202. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-002-1_14.

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Gómez-Quintero, Teresa, Iris Serratos-Alvarez, Rafael Godínez, and Roberto Olayo. "Collagen/Plasma-Polymerized Pyrrole Interaction: Molecular Docking and Binding Energy Calculations." In IFMBE Proceedings, 153–61. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-18256-3_16.

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Negm, Hani, Mohamed Omer, Ryota Kinjo, Yong Woon Choi, Kyohei Yoshida, Torgasin Konstantin, Marie Shibata, et al. "Monte Carlo Calculations of γ-Rays Angular Distribution Scattering from 11B in (γ, γ) Interaction." In Zero-Carbon Energy Kyoto 2012, 197–203. Tokyo: Springer Japan, 2013. http://dx.doi.org/10.1007/978-4-431-54264-3_21.

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Conference papers on the topic "Interaction energy calculation"

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Baker, Jonathan, Robert N. Hill, and John D. Morgan. "High precision calculation of helium and atom energy levels." In Relativistic, quantum electrodynamics, and weak interaction effects in atoms. AIP, 1989. http://dx.doi.org/10.1063/1.38424.

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Kozmutza, Cornelia, Ede Kapuy, and Earl M. Evleth. "Localized supermolecular model for the calculation of intermolecular interaction energy." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47872.

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Zheng, Xingrong, and Xiaojun Liu. "Quantum Calculation of Four-body interaction of Solid Neon." In 2018 7th International Conference on Energy, Environment and Sustainable Development (ICEESD 2018). Paris, France: Atlantis Press, 2018. http://dx.doi.org/10.2991/iceesd-18.2018.295.

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"BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003167703180321.

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Brito, Sara S., Luiz Antônio R. Junior, and Pedro Henrique de Oliviera Netro. "Interaction energy calculation in Azaacenes type molecular crystals applied in organic electronics." In VII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Editora Letra1, 2018. http://dx.doi.org/10.21826/9788563800374004.

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Hirano, Toshiyuki, and Fumitoshi Sato. "Interaction energy analysis based on canonical Kohn-Sham molecular orbitals calculation of protein." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING ICCMSE 2020. AIP Publishing, 2021. http://dx.doi.org/10.1063/5.0047812.

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TANAKA, SATORU, and HISASHI TANIGAWA. "QUANTUM CHEMICAL CALCULATION ON THE INTERACTION OF HYDROGEN ISOTOPES WITH MATERIALS FOR ENERGY SYSTEM." In Proceedings of the Seventh China–Japan Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812705198_0008.

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Ouchi, Kei, Hiroshi Kaneko, and Yutaka Tamaura. "Heliostat Field Design Using Visualization Method for Optical Heliostat Interaction." In ASME 2011 5th International Conference on Energy Sustainability. ASMEDC, 2011. http://dx.doi.org/10.1115/es2011-54571.

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For the heliostat field design, the optical interaction of heliostat by shadowing and blocking should be considered besides cosine efficiency. In the present study, in order to visualize the optical interaction it is enabled to visualize the power loss image due to a poor heliostat layout. The optical interaction area among the two heliostats is calculated for several hundreds of pairs between the given heliostat and the surrounding heliostats which are virtually seated around the given heliostat. The resultant plot gives a power loss distribution around the given heliostat. An approximation method to calculate the heliostat distribution was applied for the visualization method for a remarkable time reduction for calculation. The magnitude of the interference can be seen easily from the area where the both borders of the optical interaction areas are overlapped. And the arrangement calculation method using the power loss distribution and the cosine efficiency distribution is proposed, which gives theoretically better heliostat field layouts.
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Li, Xunfeng, Lifang Zheng, Li Wang, and Quan Ji. "Numerical Study of Temperature Field in BEPCII Interaction Region." In ASME 2008 2nd International Conference on Energy Sustainability collocated with the Heat Transfer, Fluids Engineering, and 3rd Energy Nanotechnology Conferences. ASMEDC, 2008. http://dx.doi.org/10.1115/es2008-54146.

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The temperature field of the beam pipe was calculated at the maximum heat loads and designed flow rates of the cooling liquids. The maximum difference between the predicted and measured temperature on the outer surface of the beam pipe was found to be 0.6 K. In addition, the temperature field between the beam pipe and the inner barrel of the main drift chamber (MDC) was calculated assuming natural convection heat transfer of the air in the enclosed cavity under three different conditions. The results of the calculation showed that only the use of insulation covers on the transition sections of the beam pipe keeps the temperature of the inner barrel in the range of 293.0±1.0 K. The thermal conductivity of the heat insulators under the heat insulation covers must be less than 0.5 W/(m·K).
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Yu, Yiqi, Elia Merzari, and Jerome Solberg. "Coupled Calculation on Fluid Structure Interaction in Plate-Type Fuel Element." In 2018 26th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/icone26-82418.

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In nuclear reactors that use plate-type fuel, the fuel plates are thermally managed with coolant flowing through channels between the plates. Depending on the flow rates and sizes of the fluid channels, the hydraulic forces exerted on a plate can be quite large. Currently, there is a worldwide effort to convert research reactors that use highly enriched uranium (HEU) fuel, some of which are plate-type, to low-enriched uranium (LEU). Because of the proposed changes to the fuel structure and thickness, a need exists to characterize the potential for flow-induced deflection of the LEU fuel plates. In this study, as an initial step, calculations of Fluid-Structure Interaction (FSI) for a flat aluminum plate separating two parallel rectangular channels are performed using the commercial code STAR-CCM+ and the integrated multi-physics code SHARP, developed under the Nuclear Energy Advanced Modeling and Simulation program. SHARP contains the high-fidelity single physics packages Diablo and Nek5000, both highly scalable and extensively validated. In this work, verification studies are performed to assess the results from both STAR-CCM+ and SHARP. The predicted deflections of the plate agree well with each other as well as exhibiting good agreement with simulations performed by the University of Missouri utilizing STAR-CCM+ coupled with the commercial structural mechanics code ABAQUS. The study provides a solid basis for FSI modeling capability for plate-type fuel element with SHARP.
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Reports on the topic "Interaction energy calculation"

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Ків, Арнольд Юхимович, D. Fuks, Наталя Володимирівна Моісеєнко, and Володимир Миколайович Соловйов. Silicon-aluminum bonding in Al alloys. Transport and Telecommunication Institute, 2002. http://dx.doi.org/10.31812/0564/1033.

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Ab initio calculation was performed to investigate the nature of Si-Al bonding in Al based alloys. Total electronic energy Etot for different configurations of the model cluster Si2Al6 was calculated. When the model cluster consists of two perfect tetrahedrons there is a strong influence of the Si-Si distance on the Si-Al adiabatic potential. The equilibrium distance between Si and Al atoms increases with the length of Si-Si bond increasing. It was concluded that description of Si clusters in Al matrix demands an account of the angle depending part of Si-Al interaction.
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Dickens, J. K. Computed secondary-particle energy spectra following nonelastic neutron interactions with sup 12 C for E sub n between 15 and 60 MeV: Comparisons of results from two calculational methods. Office of Scientific and Technical Information (OSTI), April 1991. http://dx.doi.org/10.2172/6135206.

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