Relevant bibliographies by topics / In silico calculations

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'In silico calculations'

Author: Grafiati
Published: 10 March 2023

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Journal articles on the topic "In silico calculations"

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Triveni, S., C. Naresh Babu, E. Bhargav, and M. Vijaya Jyothi. "in silico Design, ADME Prediction, Molecular Docking, Synthesis of Novel Triazoles, Indazoles & Aminopyridines and in vitro Evaluation of Antitubercular Activity." Asian Journal of Chemistry 32, no. 11 (2020): 2713–21. http://dx.doi.org/10.14233/ajchem.2020.22790.

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To design and synthesize novel triazoles, indazoles and aminopyridines from various (thiophene-2-yl)prop-2-en-1-one derivatives as antitubercular leads by in silico and in vitro methods. in silco Drug design, ADME prediction and molecular docking studies were performed to assess drug likeliness and antitubercular potential of all 30 novel triazoles, indazoles and aminopyridines. in silico Drug design studies revealed that the synthetic routes applied were appropriate according to the calculations of Swiss-ADME that measure synthetic accessibility. Most of the synthesized compounds found to have considerable binding score with enoyl ACP reductase enzyme of Mycobacterium tuberculosis. All the synthesized compounds were evaluated for antitubercular potential against Drug Resistant Mycobacterium tuberculosis H37Rv strain by Luciferase reporter assay method. Most of the synthesized compounds exhibited remarkable antitubercular potential against resistant strain.
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Herrera-Calderon, Oscar, Andres F. Yepes-Pérez, Jorge Quintero-Saumeth, Juan Pedro Rojas-Armas, Miriam Palomino-Pacheco, José Manuel Ortiz-Sánchez, Edwin César Cieza-Macedo, et al. "Carvacrol: An In Silico Approach of a Candidate Drug on HER2, PI3Kα, mTOR, hER-α, PR, and EGFR Receptors in the Breast Cancer." Evidence-Based Complementary and Alternative Medicine 2020 (October 26, 2020): 1–12. http://dx.doi.org/10.1155/2020/8830665.

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Carvacrol is a phenol monoterpene found in aromatic plants specially in Lamiaceae family, which has been evaluated in an experimental model of breast cancer. However, any proposed mechanism based on its antitumor effect has not been reported. In our previous study, carvacrol showed a protective effect on 7,12-dimethylbenz[α]anthracene- (DMBA-) induced breast cancer in female rats. The main objective in this research was to evaluate by using in silico study the carvacrol on HER2, PI3Kα, mTOR, hER-α, PR, and EGFR receptors involved in breast cancer progression by docking analysis, molecular dynamic, and drug-likeness evaluation. A multilevel computational study to evaluate the antitumor potential of carvacrol focusing on the main targets involved in the breast cancer was carried out. The in silico study starts with protein-ligand docking of carvacrol followed by ligand pathway calculations, molecular dynamic simulations, and molecular mechanics energies combined with the Poisson–Boltzmann (MM/PBSA) calculation of the free energy of binding for carvacrol. As result, the in silico study led to the identification of carvacrol with strong binding affinity on mTOR receptor. Additionally, in silico drug-likeness index for carvacrol showed a good predicted therapeutic profile of druggability. Our findings suggest that mTOR signaling pathway could be responsible for its preventive effect in the breast cancer.
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Maillard, Julien F., Johann Le Maître, Christopher P. Rüger, Mark Ridgeway, Christopher J. Thompson, Benoit Paupy, Marie Hubert-Roux, Melvin Park, Carlos Afonso, and Pierre Giusti. "Structural analysis of petroporphyrins from asphaltene by trapped ion mobility coupled with Fourier transform ion cyclotron resonance mass spectrometry." Analyst 146, no. 13 (2021): 4161–71. http://dx.doi.org/10.1039/d1an00140j.

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Combination of experimentally determined collision-cross sections provided by trapped ion mobility high-resolution mass spectrometry with in-silico calculations for structural assessment of petroporphyrins within an ultra-complex crude oil matrix.
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Hajzer, Viktória, Roman Fišera, Attila Latika, Július Durmis, Jakub Kollár, Vladimír Frecer, Zuzana Tučeková, et al. "Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation." Organic & Biomolecular Chemistry 15, no. 8 (2017): 1828–41. http://dx.doi.org/10.1039/c6ob02673g.

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Chen, Zihao, and Kristen A. Fichthorn. "Adsorption of alkylamines on Cu surfaces: identifying ideal capping molecules using first-principles calculations." Nanoscale 13, no. 44 (2021): 18536–45. http://dx.doi.org/10.1039/d1nr05759f.

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We used dispersion-corrected density-functional theory to perform an in silico search over a series of primary alkylamines, including linear, branched, and cyclic molecules, to identify capping molecules for shape-selective Cu nanocrystal synthesis.
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Kawczak, Piotr, Leszek Bober, and Tomasz Bączek. "Application of QSAR Analysis and Different Quantum Chemical Calculation Methods in Activity Evaluation of Selected Fluoroquinolones." Combinatorial Chemistry & High Throughput Screening 21, no. 7 (November 15, 2018): 468–75. http://dx.doi.org/10.2174/1386207321666180827105856.

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Background: A set of antibiotic fluoroquinolones with confirmed antimicrobial activity were analyzed with the use of two types of quantum chemical calculation methods and quantitative structure-activity relationships (QSAR). Objective: The purpose of this study was to demonstrate the common and differentiating characteristics of the above-mentioned chemical compounds alike physicochemically as well as pharmacologically based on the quantum chemical calculations and microbiological activity data. Methods: During the study PCA and MLR analysis were performed, as the types of proposed chemometric approach. The semi-empirical level of in silico molecular modeling was performed for calculations of molecular descriptors. Results: QSAR models were proposed based on chosen descriptors. The relationship between the structure and microbiological activity and physicochemical parameters data was able to class and describe them with the use of statistically significant molecular descriptors. Conclusion: The applied chemometric approaches revealed the influential features of tested structures responsible for the antimicrobial activity of analyzed compounds.
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Aguilera-Porta, Neus, Giovanni Granucci, Jordi Muñoz-Muriedas, and Ines Corral. "Can in silico calculations assess phototoxicity of non-steroidal anti-inflammatory drugs?" Toxicology Letters 280 (October 2017): S282. http://dx.doi.org/10.1016/j.toxlet.2017.07.788.

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Pitera, Jed W., and Peter A. Kollman. "Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides." Proteins: Structure, Function, and Genetics 41, no. 3 (2000): 385–97. http://dx.doi.org/10.1002/1097-0134(20001115)41:3<385::aid-prot100>3.0.co;2-r.

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Manolov, Stanimir, Iliyan Ivanov, and Dimitar Bojilov. "Microwave-assisted synthesis of 1,2,3,4-tetrahydroisoquinoline sulfonamide derivatives and their biological evaluation." Journal of the Serbian Chemical Society, no. 00 (2020): 76. http://dx.doi.org/10.2298/jsc200802076m.

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Herein we report an alternative eco-friendly method for the synthesis of 1,2,3,4-tetrahydroisoquinoline sulfonamide derivatives. All obtained compounds were screened for their in vitro inhibition of albumin denaturation, antioxidant, antitryptic, and antibacterial activity and have shown significant results. The lipophilicity was established using both reversed-phase thin layer chromatography and in silico calculations.
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Faletrov, Y. V., V. O. Maliugin, N. S. Frolova, and V. M. Shkumatov. "<i>In silico</i> evaluation of new affine interactions of methylcoumarin with cytochromes P450." Proceedings of the National Academy of Sciences of Belarus, Chemical Series 58, no. 2 (June 8, 2022): 186–90. http://dx.doi.org/10.29235/1561-8331-2022-58-2-186-190.

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4-methyl-7-methoxycoumarin (CumOMe) has been synthesized and in silico calculations demonstrated localization of methoxy group within 0.4 nm from Fe ion of hem groups for some structures of human CYP19 & CYP46 as well as CYP152 S. paucimobilis, CYP158 St. coelicolor, HMUO C. diphtheriae, XPLA R. rhodochrous, CYP199A4 Rh. palustris, CYP101A1 Ps. putida and CYP51 M. tuberculosis.
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Dissertations / Theses on the topic "In silico calculations"

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Elisée, Eddy. "Towards in silico prediction of mutations related to antibiotic resistance." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS350.

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La résistance aux antibiotiques est une menace sérieuse pour la santé publique. En effet, si on ne change pas rapidement notre consommation excessive d'antibiotiques, la situation actuelle va se dégrader jusqu'à basculer dans une ère dite "post-antibiotique", dans laquelle plus aucun antibiotique ne sera efficace contre les infections microbiennes. Bien que ce phénomène de résistance apparaît naturellement, l'utilisation abusive d'antibiotiques accélère le processus. De plus, la présence de pathogènes multi-résistants neutralise l'effet des traitements existants et dans le cas de chirurgies courantes (césariennes, transplantations d'organe...), la situation peut rapidement s'aggraver voire devenir mortelle. C'est pourquoi des directives, émanant des autorités sanitaires, doivent être mises en place afin de contrôler l'utilisation des médicaments, et ce, à tous les niveaux de la société, des individus au secteur agricole en passant par les professionnels de santé et les industries pharmaceutiques. Le monde de la recherche scientifique, quant à elle, doit trouver des nouvelles stratégies pour enrayer la propagation de la résistance. Dans ce contexte, cette thèse a pour objectif le développement d'une méthode de prédiction, par calculs d'énergie libre, des mutations de β-lactamases favorables à l'hydrolyse des β-lactames. Ces travaux méthodologiques ont donc conduit au développement : (1) de nouveaux paramètres pour les enzymes à zinc, implémentés dans le champ de force OPLS-AA et validés par des simulations de dynamique moléculaire sur un panel de métalloenzymes représentatives, (2) d'un protocole de paramétrisation de ligands covalents pour étudier le comportement de certains β-lactames dans CMY-136, une nouvelle β-lactamase caractérisée au laboratoire, et (3) d'un protocole de calcul d'énergie libre évalué au moyen de compétitions internationales de prédiction. Ce dernier a ensuite été utilisé pour tenter d'expliquer pourquoi la carbamylation de la sérine catalytique n'a pas lieu dans certaines oxacillinases. Au travers de ces travaux, nous avons pu améliorer significativement notre approche computationnelle et désormais tout est en place pour une exploration exhaustive des mutations possibles dans les β-lactamases
Antibiotic resistance is a global concern threatening worldwide health. Indeed, if we don't change our overconsumption of antibiotics, the current situation could worsen until a "post-antibiotic" era in which existing treatment would be ineffective against microbial infections. Despite the natural occurrence of antibiotic resistance, the misuse of antibiotics is speeding up the process. Furthermore, presence of multi-resistant pathogens negates the effect of modern treatments and usual surgeries (caesarean sections, organ transplantations...) might be riskier in the future, or even lethal. That's why, common guidelines have to be edicted by health authorities in order to control antibiotic use at every level of society, from individuals to healthcare industry including health professionals and agriculture sector. As for scientific research, new strategies have to be considered in order to limit the spread of antibiotic resistance. In that context, the presented thesis aimed at developing a protocol to predict, by free energy calculations, β-lactamase mutations which could promote the hydolysis of β-lactams antibiotics. In order to achieve that, we developed several methodological approaches including: (1) new parameters for zinc enzymes implemented in OPLS-AA force field and thereafter validated using molecular dynamics simulations of representative zinc-containing metalloenzymes, (2) a protocol to parameterize covalent ligands in order to analyze the dynamical behavior of some β-lactams in CMY-136, a novel β-lactamase recently characterized in our laboratory, and (3) a pmx-based free energy protocol. The latter was also assessed through several international blinded prediction challenges, and finally used to find out why carbamylation of the catalytic serine is not observed in certain OXA enzymes. Throughout this work, we made significant improvements in our protocol, and now everything is in place for an exhaustive prediction of possible mutations in β-lactamases
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Ahmad, Shah Masood. "Filling the Structure-Reactivity Gap: in silico approaches to rationalize the design of molecular catalysts." Doctoral thesis, Università degli studi di Padova, 2019. http://hdl.handle.net/11577/3422346.

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The design of molecular catalysts is an ambitious task implying the fundamental issue of relating the molecular structure to the reactivity, i.e., to the catalytic activity. The rationalization of the experimental data is often not straightforward and mechanistic schemes are not transferrable when the conditions of the process are changed or the catalyst is modified even slightly. Computer-aided investigations proved to be a more and more valid support in the last decade, but in most of the cases the aim is limited to investigate in detail the catalytic mechanism of a specific reaction and no general conclusions are drawn that can be used as a guide for designing novel catalysts for the same or analogous processes. In this Project, a computational approach has been set up to investigate the family of organometallic complexes displaying catalytic activity toward [2+2+2] cycloadditions of unsaturated molecules. In a recent book (Transition-metal-mediated aromatic ring construction, John Wiley & Sons, 2013, Chapter 4), Ken Tanaka describes Rhodium mediated [2+2+2] cycloadditions and writes ‘…Although mechanistic aspects of these reactions attract interest, only a few studies have been reported in specific catalysts and substrates…’. Thus this project, abbreviated with the acronym of STREGA (Filling the Structure-Reactivity Gap: in silico approaches to rationalize the design of molecular catalysts), aims at filling the gap between the goldmine of experimental data on this class of very important reactions and their mechanistic rationalization with the purpose of outlining the essential electronic and structural features of the catalyst leading to optimal performance, selectivity, and product yield. In particular, the roles of different metal, different ancillary ligands, different aromatic ligands, and substrates have been accurately investigated; existing data from the literature were also employed for this analysis. Larger polycyclic ligands can in principle host more than a metal center; for example, Cr can be coordinated to the benzene moiety of a rhodium indenyl complex. This might lead to interesting inter metal cooperative effects which might enhance or inhibit the catalytic activity; thus bimetallic catalysts have been considered. The effect of different cooperative metal nuclei was explored changing from Cr to Mo and W, which all belong to Group 6. Finally, the role of the polycyclic aromatic ligand was investigated and found that indeed it is an important factor since it influences rhodium hapticity and consequently its reactivity. All these results allowed to establish a solid structure-activity relationship which is of general validity for rhodium half-sandwich catalysts towards alkyne [2+2+2] cycloadditions and likely is transferrable to analogous Co, Ru, and Ir based fragments.
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黃新祥 and Sun-cheung Wong. "Ab initio calculations of silicon clusters." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B3122197X.

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Wong, Sun-cheung. "Ab initio calculations of silicon clusters." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20192708.

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Wright, K. T. "Electrical transport calculations for off-axis silicon." Thesis, Cardiff University, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373877.

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Wu, Wei. "Exchange calculations between donors in silicon and metal-phthalocyanine dimer." Thesis, University College London (University of London), 2007. http://discovery.ucl.ac.uk/1445188/.

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This thesis describes the calculation of exchange interactions for systems of electrons, and their potential uses for quantum information processing. The first part treats exchange between donor impurities (including especially deep donors) in silicon, while the second describes exchange in copper and manganese phthalocyanines. Part I uses the quantum defect method and a model central-cell correction to evaluate the exchange interaction between two deep donors by a Heitler-London-type approach. This part also describes calculations of the exchange in a three-donor complex, where one donor plays the role of a 'control atom' whose optical excitation switches the coupling strengths, and the other two are qubits embodying the quantum information. Variational calculations are described which give the control electron freedom to reside on different parts of the complex it is found that the exchange between two qubits is increased when the control electron be comes delocalized, and that it is possible for the exchange to become ferromagnetic. These observations are rationalised in terms of multi-centre exchange processes using Green's function perturbation theory. In Part II, exchange interactions between copper(II) phthalocyanine (Cu(II)Pc) and manganese (II) phthalocyanine dimers (Mn(II)Pc) are described these systems have both long excited-state lifetimes and tunable magnetic properties. The theoretical studies described include both a model Green's function calculation, to understand the roles of the competing exchange processes, and ab initio density functional theory calculations. The model calculations of Cu(II)Pc show that the dominant contribution comes from so-called indirect exchange, and depends strongly on the stacking angle. The magnitude of the exchange interaction from the ab initio calculations of Cu(II)Pc roughly agrees with the experiment.
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Markevich, Alexander. "Ab-initio calculations of diffusion barriers of small vacancy clusters in silicon." Master's thesis, Universidade de Aveiro, 2009. http://hdl.handle.net/10773/2288.

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Mestrado em Ciência e Engenharia de Materiais
Esta tese apresenta os resultados de um programa de investigação sobre a difusão da lacuna, bi-lacuna e tri-lacuna em silício utilizando simulações numéricas pelo método da teoria do funcional da densidade. Este método está implementado na forma de um programa informático referido como AIMPRO (Ab Initio Modelling PROgram). Para o cálculo dos pontos cela dos mecanismos de difusão foi usado o método “Nudged Elastic Band”. As condições fronteira dos problemas foram impostas recorrendo à utilização de agregados esféricos de silício com 275 atomos, cuja superfície foi saturada por ligações Si-H. As lacunas foram então introduzidas no centro destes agregados. Os valores calculados das barreiras de difusão para a lacuna simples e para a bi-lacuna são respectivamente 0.68 e 1.75 eV. Estes valores apresentam um acordo razoável com os obtidos experimentalmente e obtidos em outros cálculos anteriores. A barreira de difusão da tri-lacuna foi, de acordo com a literatura disponível, calculada pela primeira vêz. O mecanismo de difusão mais favorável apresenta uma barreira de 2.2 eV. No seguimento dos resultados para a lacuna e bi-lacuna, pensamos que este resultado sobrestima a barreira em cerca de 0.25 eV, colocando a nossa melhor estimativa em 1.9- 2.0 eV. Varias fontes de erro nos resultados são comentadas, assim como são sugeridas várias formas de as evitar. ABSTRACT: This work presents the results of a computational investigation into the diffusion of the single vacancy (V) and small vacancy clusters, divacancy (V2) and trivacancy (V3), in silicon. The calculations were performed principally using local density functional theory as implemented by the AIMPRO (Ab Initio Modelling PROgram) code. The Nudged Elastic Band Method was used for elucidating diffusion paths and obtaining the energy barriers for diffusion of the defects considered. Based on ab-initio calculations with H-terminated Si clusters with 275 host atoms, diffusion paths for neutral Vn (n = 1 to 3) defects were found. Calculated values of the activation energy for the diffusion of the Si vacancy and divacancy are 0.68 and 1.75 eV, respectively. These values are in a reasonable agreement with those derived from experimental and previous ab-initio modelling studies. The diffusion of trivacancy in Si has been modelled for the first time. The diffusion barrier of V3 along the proposed diffusion path was found to be about 2.2 eV. This result comes overestimated as the experimental data indicates that the values of diffusion barriers for divacancy and trivacancy in Si should be similar. Probable sources of the calculation errors have been considered and possible ways to surmount these difficulties are proposed.
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Foster, A. S., M. A. Gosálvez, T. Hynninen, R. M. Nieminen, and K. Sato. "First-principles calculations of Cu adsorption on an H-terminated Si surface." American Physical Society, 2007. http://hdl.handle.net/2237/11269.

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Corsetti, Fabiano. "On the properties of point defects in silicon nanostructures from ab initio calculations." Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/9754.

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In this thesis we apply a variety of computational methods based on density-functional theory (DFT) to the study of defect centres in bulk silicon and silicon nanostructures. Firstly, we discuss the system-size convergence of point defect properties in the supercell method for deep-level defects in bulk silicon; we consider both the vacancy and gold impurity. For the vacancy, we investigate systematically the main contributions to the finite size error that lead to the well-known slow convergence with respect to system size of defect properties, and demonstrate that different properties of interest can benefit from the use of different k-point sampling schemes. We also present a simple and accurate method for calculating the potential alignment correction to the valence band maximum of charged defect supercells by using maximally-localised Wannier functions, and show that the localised view of the electronic structure provided by them gives a clear description of the nature of the electronic bonding at the defect centre. For the gold impurity, we show that the system becomes a non-spin-polarised negative-U centre due to the effect of Jahn-Teller distortion, thus providing a simple explanation for the absent electron paramagnetic resonance signal for gold in silicon. The calculated transition levels are found to be in excellent agreement with experimental measurements. We then investigate the segregation of arsenic impurities in silicon close to an interface with amorphous silica. We employ a multiscale approach, generating a realistic disordered interface structure from Monte Carlo simulation, with a continuous random network model of the system parametrised from DFT. We calculate the segregation energy using DFT for a large number of substitutional sites encompassing all the oxidation states of silicon, and show that the results can be understood with a minimal model based only on the local strain and volume of the defect site.
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Diebel, Milan. "Application of ab-initio calculations to modeling of nanoscale diffusion and activation in silicon /." Thesis, Connect to this title online; UW restricted, 2004. http://hdl.handle.net/1773/9727.

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Books on the topic "In silico calculations"

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Townsend, Lawrence W. Optical model calculations of 14.6A GeV silicon fragmentation cross sections. Hampton, Va: Langley Research Center, 1993.

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K, Tripathi Ram, Khan Ferdous, and United States. National Aeronautics and Space Administration. Scientific and Technical Information Program., eds. Optical model calculations of 14.6A GeV silicon fragmentation cross sections. [Washington, DC]: National Aeronautics and Space Administration, Office of Management, Scientific and Technical Information Program, 1993.

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Zhang, Rui-Qin. Growth Mechanisms and Novel Properties of Silicon Nanostructures from Quantum-Mechanical Calculations. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-40905-9.

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Albers, John. Results of the Monte Carlo calculation of one-and two-dimensional distributions of particles and damage: Ion implanteddopants in silicon. Washington, D.C: National Bureau of Standards, 1987.

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Albers, John. Results of the Monte Carlo calculation of one- and two-dimensional distributions of particles and damage: Ion implanted dopants in silicon. Gaithersburg, MD: U.S. Dept. of Commerce, National Bureau of Standards, 1987.

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Quantum Mechanical Calculations of Monoxides of Silicon Carbide Molecules. Storming Media, 2003.

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Zhang, Rui-Qin. Growth Mechanisms and Novel Properties of Silicon Nanostructures from Quantum-Mechanical Calculations. Springer London, Limited, 2013.

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Zhang, Rui-Qin. Growth Mechanisms and Novel Properties of Silicon Nanostructures from Quantum-Mechanical Calculations. Springer, 2013.

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Use of Quantum Mechanical Calculations to Investigate Small Silicon Carbide Clusters. Storming Media, 2001.

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Book chapters on the topic "In silico calculations"

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Ezebuo, Fortunatus Chidolue, Prem P. Kushwaha, Atul K. Singh, Shashank Kumar, and Pushpendra Singh. "In-silico Methods of Drug Design: Molecular Simulations and Free Energy Calculations." In Phytochemistry: An in-silico and in-vitro Update, 521–33. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-6920-9_28.

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Roma, Guido, Yves Limoge, and Layla Martin-Samos. "Oxygen and Silicon Self-Diffusion in Quartz and Silica: The Contribution of First Principles Calculations." In Defect and Diffusion Forum, 542–53. Stafa: Trans Tech Publications Ltd., 2006. http://dx.doi.org/10.4028/3-908451-36-1.542.

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Sverdlov, Viktor. "Perturbative Methods for Band Structure Calculations in Silicon." In Computational Microelectronics, 63–81. Vienna: Springer Vienna, 2010. http://dx.doi.org/10.1007/978-3-7091-0382-1_6.

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Strauch, Dieter, B. Dorner, A. A. Ivanov, M. Krisch, J. Serrano, A. Bosak, W. J. Choyke, B. Stojetz, and Michael Malorny. "Phonons in SiC from INS, IXS, and Ab-Initio Calculations." In Silicon Carbide and Related Materials 2005, 689–94. Stafa: Trans Tech Publications Ltd., 2006. http://dx.doi.org/10.4028/0-87849-425-1.689.

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Möller, H. J., and H. H. Singer. "Computer Calculations of Grain Boundary Energies in Germanium and Silicon." In Springer Series in Solid-State Sciences, 18–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 1985. http://dx.doi.org/10.1007/978-3-642-82441-8_2.

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Sax, Alexander F., and Thomas Krüger. "Methodological Problems in the Calculations on Amorphous Hydrogenated Silicon, a-Si:H." In Lecture Notes in Computer Science, 950–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-47789-6_100.

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Makhkamov, Sh, F. Umarova, A. Normurodov, N. Sulaymonov, O. Ismailova, A. E. Kiv, and M. Yu Tashmetov. "Quantum-Chemical Calculations of Pure and Phosphorous Doped Ultra-small Silicon Nanocrystals." In Advanced Nanomaterials for Detection of CBRN, 111–21. Dordrecht: Springer Netherlands, 2020. http://dx.doi.org/10.1007/978-94-024-2030-2_7.

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Diebel, Milan, Srini Chakravarthi, Scott T. Dunham, and Charles F. Machala. "Ab-initio Calculations to Predict Stress Effects on Boron Solubility in Silicon." In Simulation of Semiconductor Processes and Devices 2004, 37–40. Vienna: Springer Vienna, 2004. http://dx.doi.org/10.1007/978-3-7091-0624-2_9.

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Windl, Wolfgang. "Energetics and Kinetics of Defects and Impurities in Silicon from Atomistic Calculations." In Solid State Phenomena, 125–32. Stafa: Trans Tech Publications Ltd., 2005. http://dx.doi.org/10.4028/3-908451-13-2.125.

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Cheikh, M., M. Deyehe, A. Hairie, F. Hairie, G. Nouet, and E. Paumier. "Energy Calculation of the ∑9{511} Twist Grain Boundary in Silicon." In Springer Proceedings in Physics, 200–204. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76385-4_27.

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Conference papers on the topic "In silico calculations"

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Miranda, Vanessa Regina, and Nelson Henrique Morgon. "Estudo Teórico in silico da Interação entre Geraniol e o Sítio Ativo da Opsina Bovina." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol202053.

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The bovine opsin protein, 6PGS, is present in the eye of the Bos taurus species, and has activity throughout the period of development of the retina, remaining until its adult stage. The interaction of the geraniol ligand, which has anti-inflammatory, antimicrobial and antioxidant activities, with the active site of the protein was studied through theoretical calculations using Density Functional Theory. The molecular structure results show that in the interaction process of geraniol with the active site of 6PGS there is a distortion in the geometry of the ligand. Through the UV-Vis spectra, a shift of the wavelength maximum value in relation to the free geraniol is observed, of the order of 50 nm.
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Orlenson, Vulf, Alim Mazinov, and Alexey Shevchenko. "MODEL FOR CALCULATION OF THE OPTICAL ABSORPTION SPECTRA OF SEMICONDUCTOR MATERIALS." In International Forum “Microelectronics – 2020”. Joung Scientists Scholarship “Microelectronics – 2020”. XIII International conference «Silicon – 2020». XII young scientists scholarship for silicon nanostructures and devices physics, material science, process and analysis. LLC MAKS Press, 2020. http://dx.doi.org/10.29003/m1607.silicon-2020/224-226.

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Sakiyama, Yukinori, Shu Takagi, and Yoichiro Matsumoto. "Multiscale Analysis of Silicon LPCVD Reactor." In ASME 2005 Summer Heat Transfer Conference collocated with the ASME 2005 Pacific Rim Technical Conference and Exhibition on Integration and Packaging of MEMS, NEMS, and Electronic Systems. ASMEDC, 2005. http://dx.doi.org/10.1115/ht2005-72051.

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We demonstrate the multiscale analysis of the transport phenomena in a low pressure reactor. In this method, the macroscopic phenomena such as the temperature and the density distribution are related to the microscopic electronic structure of atom/molecule. By connecting the different scales with physical models, the macroscopic properties are obtained starting from the first principle calculation without any empirical parameters. Here, we take the silicon epitaxial growth from a gas mixture of silane and hydrogen as an example. As the first step of this method, we calculated the intermolecular potential energy of SiH4/H2 using the ab initio molecular orbital calculations. Then, an analytical pair potential model was constructed to reproduce the potential energy surface obtained from the ab initio calculation. We have confirmed the validation of the potential model by comparing the experimental data of the transport properties with the molecular dynamics simulation using the potential model. Subsequently, the binary molecular collision models were constructed by the classical trajectory calculation using the potential model as the second step of the multiscale analysis. The trajectory calculations were conducted for the various combinations of the initial translational and the rotational energy. Through the statistical analysis of the trajectory calculations, the elastic/inelastic collision cross section and the scattering angle model were constructed. Finally, the direct simulation Monte Carlo simulation of flow field in a low parssure reactor was executed. The thin film thickness distribution was also investigated and discussed. This method was extended to analyze the surface reaction, which is an ongoing research work and only the current progress is reported here.
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Miller, David A. B. "Designing Arbitrary Linear Optical Components Without Calculations." In Integrated Photonics Research, Silicon and Nanophotonics. Washington, D.C.: OSA, 2014. http://dx.doi.org/10.1364/iprsn.2014.jm4b.1.

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Douhan, R. M. H., A. P. Kokhanenko, and K. A. Lozovoy. "Dark current behaviour analysis for avalanche photodiodes." In 8th International Congress on Energy Fluxes and Radiation Effects. Crossref, 2022. http://dx.doi.org/10.56761/efre2022.n4-p-052901.

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This paper deals with the results of serial of analytical calculations which have been done on an avalanche photodiode made of germanium with silicon quantum dots (QD) which has multilayers of QDs to determine its characteristics. In these calculations we focus on the main parameters that determine the performance of avalanche photodiode such as tunneling current, photosensitivity, multiplication factor, noise spectral density and avalanche noise factor. The study also compares the results of germanium silicon avalanche photodiode with other avalanche photodiodes made with different materials. The model which has been used for calculation is considered with a separated absorption and multiplication regions operation under several conditions varied between classical and Geiger mode.
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He, Yuhui, Chun Fan, Yu Ning Zhao, Jinfeng Kang, Xiao Yan Liu, and Ruqi Han. "Band structure calculations of Ge-Si core-shell nanowires." In 2008 IEEE Silicon Nanoelectronics Workshop (SNW). IEEE, 2008. http://dx.doi.org/10.1109/snw.2008.5418413.

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Itoh, Kohei M. "Single atom calculation in silicon." In 2011 International Meeting for Future of Electron Devices, Kansai (IMFEDK). IEEE, 2011. http://dx.doi.org/10.1109/imfedk.2011.5944823.

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Park, Yongjin, Ki-jeong Kong, Hyunju Chang, and Mincheol Shin. "Device characteristics of double-gate MOSFETs with Si-dielectric interface model from first principle calculations." In 2010 Silicon Nanoelectronics Workshop (SNW). IEEE, 2010. http://dx.doi.org/10.1109/snw.2010.5562571.

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Hirasawa, Shigeki, and Satoru Isomura. "Fast Computation of Microscale Temperature Distribution in LSI Chips." In ASME 2003 Heat Transfer Summer Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/ht2003-47014.

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A network method for quickly calculating the temperature distributions in an LSI chip with silicon-on-insulator (SOI) transistors and multi-layered lines has been developed. Its calculation time is less than 1/1000 of that of the finite element method, and its error is within 15%. The developed fast calculation method can be used in the case of more than 300 heating devices and more than 1000 lines in an LSI chip. It is thus a practical tool for designing the optimum layout of devices to prevent local temperature increases in an LSI chip.
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Balan, Nikita, Vladimir Ivanov, Alexander Pankratov, and Ekaterina Kharchenko. "METHOD FOR CALCULATION OF MASK SPECIFICATION CONTRIBUTION TO LITHOGRAPHIC BUDGETS." In International Forum “Microelectronics – 2020”. Joung Scientists Scholarship “Microelectronics – 2020”. XIII International conference «Silicon – 2020». XII young scientists scholarship for silicon nanostructures and devices physics, material science, process and analysis. LLC MAKS Press, 2020. http://dx.doi.org/10.29003/m1653.silicon-2020/372-374.

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In this work we consider the contribution of tolerances on the mask pattern quality to the error budgets of lithographic operations. A method for developing a photomask specification based on the lithography modeling is proposed.
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Reports on the topic "In silico calculations"

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Rucinski, Russ. D0 Silicon Upgrade: Control Dewar Valve Calculations. Office of Scientific and Technical Information (OSTI), October 1995. http://dx.doi.org/10.2172/1033294.

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Cease, Herman. D0 Silicon Upgrade: Engineering Calculation for the Silicon Cooling System. Office of Scientific and Technical Information (OSTI), February 2001. http://dx.doi.org/10.2172/1481391.

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Xie, J., and S. P. Chen. Ab initio calculations of As-vacancy interactions in silicon. Office of Scientific and Technical Information (OSTI), April 1999. http://dx.doi.org/10.2172/334208.

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Zhu, Richard, Ernian Pan, Peter W. Chung, Xinli Cai, Kim M. Liew, and Alper Buldum. Atomistic Calculation of Elastic Moduli in Strained Silicon. Fort Belvoir, VA: Defense Technical Information Center, April 2007. http://dx.doi.org/10.21236/ada466493.

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Rucinski, Russ. D0 Silicon Upgrade: West End Assembly Hall Platform Design Calculations. Office of Scientific and Technical Information (OSTI), January 1996. http://dx.doi.org/10.2172/1033290.

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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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Anderson, Brent. D0 Silicon Upgrade: A Layer Drawbridge Access: Platforms Calculations and Analysis. Office of Scientific and Technical Information (OSTI), May 2000. http://dx.doi.org/10.2172/1481382.

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Kuwazaki, Andrew, and Todd Leicht. D0 Silicon Upgrade: ASME Code and Pressure Calculations for Liquid Nitrogen Subcooler. Office of Scientific and Technical Information (OSTI), October 1995. http://dx.doi.org/10.2172/1033296.

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Ratzmann, Paul M. D0 Silicon Upgrade: Heat Transfer and Thermal Bowing Calculations of the D0 F-Diskl. Office of Scientific and Technical Information (OSTI), August 1996. http://dx.doi.org/10.2172/1033275.

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Zaczek, Mauiusz. D0 Silicon Upgrade: Calculating Mass Flow Rates at Sub-Sonic Conditions Trhough Venturis (FT-4052-H & FT-4053-H) and an Orifice Plate (F)-2019-H). Office of Scientific and Technical Information (OSTI), August 1996. http://dx.doi.org/10.2172/1033281.

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