Relevant bibliographies by topics / Atomic and molecular modeling

Contents

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

Academic literature on the topic 'Atomic and molecular modeling'

Author: Grafiati
Published: 9 November 2024
Last updated: 25 July 2025

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Journal articles on the topic "Atomic and molecular modeling"

1

Dubernet, M. L., C. M. Zwölf, N. Moreau, and Y. A. Ba. "Atomic and Molecular Databases, VAMDC." Proceedings of the International Astronomical Union 11, A29A (2015): 347–48. http://dx.doi.org/10.1017/s1743921316003252.

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AbstractThe VAMDC Consortium is a worldwide consortium which federates Atomic and Molecular databases through an e-science infrastructure and a political organisation. About 90% of the inter-connected databases handle data that are used for the interpretation of spectra and for the modeling of media of many fields of astrophysics. This paper presents how the VAMDC Consortium is organised in order to publish atomic and molecular data for astrophysics.
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van Dishoeck, Ewine F. "Atomic and Molecular Data for Diffuse Cloud Chemistry." Highlights of Astronomy 8 (1989): 323–30. http://dx.doi.org/10.1017/s1539299600007942.

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Goldenstein, Christopher S., Victor A. Miller, R. Mitchell Spearrin, and Christopher L. Strand. "SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases." Journal of Quantitative Spectroscopy and Radiative Transfer 200 (October 2017): 249–57. http://dx.doi.org/10.1016/j.jqsrt.2017.06.007.

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Zavodinskii, V. G., and E. A. Mikhailenko. "Modeling of carbon combustion in molecular and atomic oxygen." Combustion, Explosion, and Shock Waves 42, no. 3 (2006): 247–53. http://dx.doi.org/10.1007/s10573-006-0047-1.

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Murakami, Izumi, and Takako Kato. "NIFS Atomic Numerical Databases." Highlights of Astronomy 13 (2005): 672–73. http://dx.doi.org/10.1017/s1539299600016804.

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AbstractWe have compiled the atomic and molecular numerical databases which are available through internet. The databases provide basic atomic data, such as collisional ionization and excitation cross sections, which are important for modeling and diagnosing astrophysical plasmas.
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Stevens, Kyle, Thien Tran-Duc, Ngamta Thamwattana, and James M. Hill. "Modeling Interactions between Graphene and Heterogeneous Molecules." Computation 8, no. 4 (2020): 107. http://dx.doi.org/10.3390/computation8040107.

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The Lennard–Jones potential and a continuum approach can be used to successfully model interactions between various regular shaped molecules and nanostructures. For single atomic species molecules, the interaction can be approximated by assuming a uniform distribution of atoms over surfaces or volumes, which gives rise to a constant atomic density either over or throughout the molecule. However, for heterogeneous molecules, which comprise more than one type of atoms, the situation is more complicated. Thus far, two extended modeling approaches have been considered for heterogeneous molecules,
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Lei, Xue, and Anatoly F. Zatsepin. "First principles modeling of molecular adsorption on InSe-monolayer." Emerging Materials Research 12, no. 4 (2023): 1–7. http://dx.doi.org/10.1680/jemmr.22.00216.

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In this paper, it demonstrates that the calculated physical adsorption energies, substrate-adsorbent distances, and substrate distortions strongly depend on the size of employed supercell and especially on the type of optimization in the case of very flexible 2D monolayers, such as InSe. It has been established that calculations with optimization of only atomic positions and calculations with optimization of atomic positions and lattice parameters can give energies of different signs and values. In-plane (stretching and compression) and out-of-plane (ripple formation) distortions also lead to
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Balaban, Alexandru T. "Local versus Global (i.e. Atomic versus Molecular) Numerical Modeling of Molecular Graphs." Journal of Chemical Information and Modeling 34, no. 2 (1994): 398–402. http://dx.doi.org/10.1021/ci00018a028.

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Catlow, C. R. A. "Computer modeling in materials chemistry." Pure and Applied Chemistry 77, no. 8 (2005): 1345–48. http://dx.doi.org/10.1351/pac200577081345.

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This short article concerns the application of computer modeling techniques to the growing field of materials chemistry, where modeling techniques are widely used in an increasingly predictive manner. The article focuses on modeling at the atomic and molecular level.
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Wang, Shao Qing. "Atomic Modeling and Simulation of AlCoCrCuFeNi Multi-Principal-Element Alloy." Materials Science Forum 749 (March 2013): 479–83. http://dx.doi.org/10.4028/www.scientific.net/msf.749.479.

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Atomic structure model of bulk AlCoCrCuFeNi multi-principal-element alloy was build by following the principle of maximum entropy. Morse pair-potentials to describe the inter-atomic interaction among neighboring atoms in the alloy were generated directly from first-principles calculations within density-functional theory. Molecular statics simulation was carried out to achieve the optimized atomic configuration of AlCoCrCuFeNi alloy. The results show that the crystallographic behavior in lattice structure observed experimentally is just caused by the average of the disordered atomic position a
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Dissertations / Theses on the topic "Atomic and molecular modeling"

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Tuesday, Andrew J. "Modeling Atomic Defects in a Two-Dimensional Lennard-Jones Lattice Using Molecular Dynamics Simulations." University of Akron / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=akron1334579948.

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Ruscio, Jory Zmuda. "Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution." Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/27219.

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While experiments provide valuable information about biological molecules, current technology cannot yet monitor atomic fluctuations at relevant time scales. Theoretical computational simulations are able to model the appropriate interactions at atomic resolution. Computational techniques have become widely used for identifying interactions in biological systems. Such methods have proven quite accurate in their ability to reproduce experimental data and also in screening and predicting pertinent activities. Molecular modeling employs theoretical and computational techniques to elucidate biolog
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Hooshmand, Mohammad Shahriar. "Atomic-scale modeling of twinning in titanium and other HCP alloys." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1566143337320934.

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Shuaib, Mohammed Firas Elkheir. "Atomic Scale Modeling via Molecular Dynamics and Machine Learning of Na2O-V2O5-TeO2 Glass-Based Cathodes." Electronic Thesis or Diss., Limoges, 2025. http://www.theses.fr/2025LIMO0005.

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L’industrie mondiale de l’électricité évolue pour atteindre les objectifs de l’Accord de Paris d’ici 2050, en s’appuyant sur les énergies renouvelables et les technologies avancées de stockage. Les batteries à ions sodium (NIBs) apparaissent comme une alternative durable aux batteries à ions lithium (LIBs), limitées par les ressources en lithium. Cette thèse explore les moyens d’optimiser les NIBs en utilisant des techniques computationnelles pour relever leurs défis actuels.Bien que les LIBs aient transformé les appareils portables et les véhicules électriques, leur dépendance au lithium just
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Tang, Ming. "Atomic-scale biophysics modelling of type I collagen in the extracellular matrix." Thesis, Queensland University of Technology, 2019. https://eprints.qut.edu.au/124650/1/Ming_Tang_Thesis.pdf.

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This thesis explores the biophysics of collagen in the extracellular matrix under external stimuli, by performing cutting edge MD simulations. The obtained results provide significant insights into the design and manufacturing of artificial biomaterials for surgical tissue treatments, of collagen for regenerative medicine applications, and of gold nanoparticles for biomedical applications. The probed biophysical properties consist of the structural properties and the mechanical properties, where the mechanical properties of collagen are regulated by its structure at different levels of hierarc
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Marsh, R. J. "Kinematic modelling of non reactive and reactive collisions." Thesis, University of Sussex, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270740.

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Gao, D. "Modeling of adsorption and atomic force microscopy imaging of molecules on insulating surfaces." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1468925/.

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The study of atoms and molecules on bulk insulating surfaces is of critical importance to many fields of surface science including lubrication, and molecular electronics. I studied these systems by using a variety of theoretical methods to predict adsorption geometry, diffusion pathways, and film structure, and to interpret noncontact atomic force microscopy (NCAFM) data. I began by using molecular dynamics (MD) simulations to predict that Pd atoms deposited onto MgO(100) exhibit some transient mobility. They were initially able to move across the surface, but were eventually captured at an ad
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Mead, Robert Nielle. "Molecular dynamics modelling of the amorphous calcium silicate and titania silicate atomic-scale structure." Thesis, University of Kent, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443767.

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Lerebourg, Christophe Jean-Yves Joel. "Development and modelling of a point source integrating cavity absorption meter (PSICAM)." Thesis, University of Plymouth, 2003. http://hdl.handle.net/10026.1/1712.

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The absorption coefficient is a fundamental parameter in understanding the underwater light field, for solving the Radiative Tranfer Equation and understanding/interpreting remotely sensed data from the ocean. Measuring the absorption coefficient is particularly complicated in coastal areas where the optical properties of the water body are the result of a complex mixture of dissolved and particulate components, but mainly because of the interfering effect that scattering has upon the measurements. A great variety of in situ instruments and laboratory techniques have been developed to measure
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Mallett, Michael John Disney. "An analytical and computer modelling study of atomic motion in fluids constrained by barriers." Thesis, University of Kent, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358039.

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Books on the topic "Atomic and molecular modeling"

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Tan, Cher Ming. Electromigration Modeling at Circuit Layout Level. Springer Singapore, 2013.

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Comba, Peter, and Trevor W. Hambley, eds. Molecular Modeling. Wiley-VCH Verlag GmbH, 1995. http://dx.doi.org/10.1002/9783527615292.

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Kumosinski, Thomas F., and Michael N. Liebman, eds. Molecular Modeling. American Chemical Society, 1994. http://dx.doi.org/10.1021/bk-1994-0576.

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Comba, Peter. Molecular modeling. VCH, 1995.

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Svanberg, Sune. Atomic and molecular spectroscopy. Springer-Verlag, 1990.

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Wilson, Stephen, ed. Atomic and Molecular Properties. Springer US, 1992. http://dx.doi.org/10.1007/978-1-4899-1639-6.

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Svanberg, Sune. Atomic and Molecular Spectroscopy. Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-97258-4.

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Joachim, Christian, and Siegmar Roth, eds. Atomic and Molecular Wires. Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5882-4.

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Campargue, Roger, ed. Atomic and Molecular Beams. Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56800-8.

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Svanberg, Sune. Atomic and Molecular Spectroscopy. Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-98107-4.

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Book chapters on the topic "Atomic and molecular modeling"

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Roth, Michael. "Atomic and molecular modeling." In Modeling and Simulation of Everyday Things, 2nd ed. CRC Press, 2025. https://doi.org/10.1201/9781003604518-8.

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Solov’yov, Ilia A., Andrey V. Korol, and Andrey V. Solov’yov. "Atomic Clusters and Nanoparticles." In Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-56087-8_4.

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Dasgupta, Arati, Robert W. Clark, John L. Giuliani, et al. "High Accuracy Non-LTE Modeling of X-Ray Radiation in Dense Matter." In New Trends in Atomic and Molecular Physics. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-38167-6_5.

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Fallani, Alessio, José Arjona-Medina, Konstantin Chernichenko, Ramil Nugmanov, Jörg Kurt Wegner, and Alexandre Tkatchenko. "Atom-Level Quantum Pretraining Enhances the Spectral Perception of Molecular Graphs in Graphormer." In Lecture Notes in Computer Science. Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-72381-0_7.

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AbstractThis study explores the impact of pretraining Graph Transformers using atom-level quantum-mechanical features for molecular property modeling. We utilize the ADMET Therapeutic Data Commons datasets to evaluate the benefits of this approach. Our results show that pretraining on quantum atomic properties improves the performance of the Graphormer model. We conduct comparisons with two other pretraining strategies: one based on molecular quantum properties (specifically the HOMO-LUMO gap) and another using a self-supervised atom masking technique. Additionally, we employ a spectral analys
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Reiter, D. "Modeling of Fusion Edge Plasmas: Atomic and Molecular Data Issues." In Springer Series in Chemical Physics. Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-27362-x_2.

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Bourgogne, C., I. Bury, L. Gehringer, et al. "Molecular Dynamics Simulations of Liquid-Crystalline Dendritic Architectures." In Advances in the Atomic-Scale Modeling of Nanosystems and Nanostructured Materials. Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04650-6_4.

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Allen, Gregory S., and David L. Stokes. "Modeling, Docking, and Fitting of Atomic Structures to 3D Maps from Cryo-Electron Microscopy." In Methods in Molecular Biology. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-176-9_13.

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Shimokawa, Tomotsugu. "Roles of Grain Boundaries in the Strength of Metals by Using Atomic Simulations." In Molecular Modeling and Multiscaling Issues for Electronic Material Applications. Springer US, 2012. http://dx.doi.org/10.1007/978-1-4614-1728-6_4.

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Novoseletsky, Valery, Olfat A. Malak, Gildas Loussouarn, and Olga S. Sokolova. "Building Atomic Models of the Ion Channels Based on Low Resolution Electron Microscopy Maps and Homology Modeling." In Methods in Molecular Biology. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7362-0_23.

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Le Bourlot, J., G. Pincau des Forêts, and E. Roueff. "Modelling the SMC: atomic to molecular transition and emissivities." In New Aspects of Magellanic Cloud Research. Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/3-540-56432-2_191.

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Conference papers on the topic "Atomic and molecular modeling"

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Sikes, C. S., and Andrzej Wierzbicki. "Atomic Force Microscopy and Molecular Modeling of Branched and Unbranched Polyaspartate Bound to Calcite and Mica." In CORROSION 1997. NACE International, 1997. https://doi.org/10.5006/c1997-97166.

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Abstract Polyaspartate molecules made by dry, thermal polycondensation of aspartic acid are thought to be moderately branched. Polyaspartates made by thermal polycondensation in the presence of phosphoric acid as a solvent/catalyst are thought to be linear, unbranched molecules. Examples of these two forms of poly aspartate were synthesized. When viewed by atomic force microscopy (AFM) on mica, the poly aspartates did appear to be different, but there was no evidence for or against the presence of branching as such. When viewed by AFM on calcite, the phosphoric-catalyzed, thermal polyaspmtates
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Aroutiounian, Vladimir M., and Mher Z. Ghoolinian. "Fractal modeling of porous semiconductors." In New Trends in Atomic and Molecular Spectroscopy, edited by Gagik G. Gurzadyan and Artashes V. Karmenyan. SPIE, 1999. http://dx.doi.org/10.1117/12.375283.

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Brunger, M. J., and L. Campbell. "Data Needs and Modeling of the Upper Atmosphere." In ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS: 5th International Conference on Atomic and Molecular Data and Their Applications (ICAMDATA). AIP, 2007. http://dx.doi.org/10.1063/1.2727350.

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Stancil, P. C. "Charge Transfer Data Needs for Cometary X-ray Emission Modeling." In ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS: 3rd International Conference on Atomic and Molecular Data and Their Applications ICAMDATA. AIP, 2002. http://dx.doi.org/10.1063/1.1516331.

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Srećković, V. A., N. Pop, V. Vujčić, M. S. Dimitrijević, M. D. Christova, and Z. Mijić. "New molecular dataset for planet formation chemistry and modeling." In International Meeting on Data for Atomic and Molecular Processes in Plasmas: Advances in Standards and Modelling. Institute of Physics Belgrade, 2024. https://doi.org/10.69646/aob241115.

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Detailed astrochemical models are essential for interpreting observations of interstellar and circumstellar molecules because they allow important physical features of the gas and its evolutionary history to be derived (Williams and Cieza 2011). Advances in astrochemical models are linked to changes in astrochemical databases, as well as experimental and theoretical estimations of rate coefficients (see e.g. Öberg et al. 2021). The science community now need access to such molecular data, including preferred ones, for further modeling, and it is critical to our knowledge of the chemistry of pl
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Bashkirov, Eugene K. "Influence of atomic coherence on entanglement between dipole-coupled Jaynes-Cummings and isolated atom." In Saratov Fall Meeting 2018: Laser Physics, Photonic Technologies, and Molecular Modeling, edited by Vladimir L. Derbov. SPIE, 2019. http://dx.doi.org/10.1117/12.2522425.

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Hassouni, K. "Modeling of Moderate Pressure Microwave Plasmas Used for Diamond Deposition: Collisional Data Required for Process Simulation." In ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS: 3rd International Conference on Atomic and Molecular Data and Their Applications ICAMDATA. AIP, 2002. http://dx.doi.org/10.1063/1.1516324.

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Kumar, Navin, and Kishore Pochiraju. "Molecular Dynamics Modeling of Thermal Transport in Damaged Continua." In 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. ASMEDC, 2008. http://dx.doi.org/10.1115/micronano2008-70070.

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The interaction between the damage state and the thermal conductivity is studied in this paper. The damage propagation and the effective thermal conductivity of the damaged continuum is studied using equilibrium molecular dynamics (EMD) method based on the Green-Kubo relation. A solid gold lattice is considered and the damage is initiated and propagated by stretching two opposite ends while system is maintained at constant volume, constant temperature (NVT) condition. Both Lennard-Jones (LJ) 6–12 and embedded-atom method (EAM) potentials are used to model the inter-atomic interactions. Results
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Yakubovich, Alexander V., Eugene Surdutovich, and Andrey V. Solov’yov. "Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach." In 7TH INTERNATIONAL CONFERENCE ON ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS - ICAMDATA-2010. AIP, 2011. http://dx.doi.org/10.1063/1.3585822.

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Margot, J., L. Stafford, J. S. Poirier, et al. "Modeling Etching Plasmas: Needs and Challenges in Atomic and Molecular Data." In ICAMDATA-2008: 6th International Conference on Molecular Data and Their Applications. AIP, 2009. http://dx.doi.org/10.1063/1.3141690.

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Reports on the topic "Atomic and molecular modeling"

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Hill, Christian. Consultancy Meeting on Evaluation of Fundamental Data on Beryllium-containing Species for Edge Plasma Modelling. IAEA Nuclear Data Section, 2020. http://dx.doi.org/10.61092/iaea.t5at-c64q.

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Beryllium is a major plasma-facing material in the ITER fusion energy research reactor, where 440 beryllium-coated panels form the first wall (FW) of the vacuum reactor vessel. It is expected that plasma–wall interactions will result in the creation of a complex mixture of atomic, ionic and molecular species containing He, Be and isotopes of H. The aim of this meeting was to advise the IAEA Atomic and Molecular Data Unit on the data required for modelling edge plasma processes in fusion devices and to recommend state-resolved data sets for electron-collision excitation, de-excitation and disso
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Hill, Christian. Technical Meeting on the Development of Software Programs and Database Tools for Modelling Edge Plasma Processes in Fusion Devices. IAEA Nuclear Data Section, 2019. http://dx.doi.org/10.61092/iaea.0nm2-cc83.

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A Technical Meeting formulating new and reviewing existing standards and software tools for representing, storing and classifying atomic and molecular species, states and plasma-relevant processes was held at IAEA Headquarters in Vienna from 27 – 29 November 2019. 12 IAEA staff and participants from 6 Member States attended the meeting. This report summarises their discussions and the meeting conclusions and includes drafts of the updated standards documents, which are freely-available on the website of the Atomic and Molecular Data Unit in their final form.
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Hill, C. Summary Report of the First Research Coordination Meeting on the Formation and Properties of Molecules in Edge Plasmas. IAEA Nuclear Data Section, 2023. http://dx.doi.org/10.61092/iaea.4w1d-eec2.

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11 experts in the field of atomic collisional physics and edge plasma modelling for magnetic confinement fusion devices, together with IAEA Staff met from 6 – 8 December 2023 for the First Research Coordination Meeting of the IAEA Coordinated Research Project (CRP) F43027: The Formation and Properties of Molecules in Edge Plasmas. This report summarizes the CRP participants’ workplans for the duration of the project and for its first cycle (12 – 18 months). Collaborative sub-projects were initiated in the specific areas of data needed for molecular hydrogen, boron-containing species, water-der
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McGee, Steven, Randi McGee-Tekula, and Jennifer Duck. Does a Focus on Modeling and Explanation of Molecular Interactions Impact Student Learning and Identity? The Learning Partnership, 2017. http://dx.doi.org/10.51420/conf.2017.1.

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The Interactions curriculum and professional development program is designed to support high school teachers in their transition to the physical science Next Generation Science Standards. Through curriculum materials, an online portal for delivering the digital materials, interactive models of molecular phenomena, and educative teacher guide, teachers are able to support students in bridging the gap between macroscopic and sub-microscopic ideas in physical science by focusing on a modeling and explanation-oriented exploration of attractions and energy changes at the atomic level. During the fa
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Wolf, R. J., and K. A. Mansour. Molecular modeling of metal hydrides: 2. Calculation of lattice defect structures and energies utilizing the Embedded Atom Method. Office of Scientific and Technical Information (OSTI), 1990. http://dx.doi.org/10.2172/6335193.

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Braams, B. J., D. Reiter, X. Urbain, V. Kokoouline, D. Wuenderlich, and H. K. Chung. Atomic and Molecular Data for State-Resolved Modelling of Hydrogen and Helium and Their Isotopes in Fusion Plasma (Summary Report of the Third Research Coordination Meeting). IAEA Nuclear Data Section, 2017. http://dx.doi.org/10.61092/iaea.j9ht-ffsf.

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Lane, N. F. Atomic and molecular sciences. Office of Scientific and Technical Information (OSTI), 1989. http://dx.doi.org/10.2172/5026215.

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Eberly, J. H. Theoretical atomic and molecular photophysics. Office of Scientific and Technical Information (OSTI), 1987. http://dx.doi.org/10.2172/6267158.

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Hill, Christian. International Atomic and Molecular Code Centres Network: Virtual Atomic and Molecular Data Centres Consortium Annual Meeting. International Atomic Energy Agency, 2023. http://dx.doi.org/10.61092/iaea.s57n-ra6p.

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The International Code Centres Network (CCN) is a group of experts developing codes and models for atomic, molecular and plasma-surface interaction data relevant to fusion applications. Variable subsets of the group are brought together by the IAEA Atomic and Molecular Data (AMD) Unit in order to discuss computational and scientific issues associated with code developments. At the 8th Technical Meeting described in this report, which was held virtually from 15 – 17 November 2023, 31 experts in the field of atomic and molecular physics met, representing 23 databases within the Virtual Atomic an
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Lancaster, James. Committee on Atomic, Molecular and Optical Sciences. Office of Scientific and Technical Information (OSTI), 2015. http://dx.doi.org/10.2172/1233308.

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