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Journal articles on the topic 'Atomic and molecular modeling'

Author: Grafiati

Published: 9 November 2024

Last updated: 25 July 2025

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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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2

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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3

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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4

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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9

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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10

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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11

Chen, Jingrun, and Pingbing Ming. "An Efficient Multigrid Method for Molecular Mechanics Modeling in Atomic Solids." Communications in Computational Physics 10, no. 1 (2011): 70–89. http://dx.doi.org/10.4208/cicp.270910.131110a.

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AbstractWe propose a multigrid method to solve the molecular mechanics model (molecular dynamics at zero temperature). The Cauchy-Born elasticity model is employed as the coarse grid operator and the elastically deformed state as the initial guess of the molecular mechanics model. The efficiency of the algorithm is demonstrated by three examples with homogeneous deformation, namely, one dimensional chain under tensile deformation and aluminum under tension and shear deformations. The method exhibits linear-scaling computational complexity, and is insensitive to parameters arising from iterativ

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12

Havrysh, Oleh H., Vladyslav Kholodovych, and Evgen A. Andreev. "Modeling of atomic-molecular structures by contiguous filling of space with Frank-Kasper atomic domains." Journal of Molecular Graphics and Modelling 90 (July 2019): 9–17. http://dx.doi.org/10.1016/j.jmgm.2019.03.004.

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13

Shtablavyi, I., N. Popilovskyi, Yu Nykyruy, and S. Mudry. "Selective laser sintering of amorphous nanoparticles: Molecular dynamics simulations." Physics and Chemistry of Solid State 25, no. 1 (2024): 5–13. http://dx.doi.org/10.15330/pcss.25.1.5-13.

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The paper investigates the process of liquid-phase sintering of amorphous iron-based nanoparticles by the method of molecular dynamics simulations. The classical molecular dynamics package LAMMPS was used for modeling. Visual analysis of the atomic configurations of nanoparticles during their rapid cooling revealed the self-purification effect of the particles. Partial pair correlation functions and coordination number distribution functions were used to analyze the atomic structure of nanoparticles after sintering. As a result of the analysis of the main structural parameters, which were obta

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14

Yazawa, Hiroyuki, Akira Tonegawa, Masataka Ono, Takehisa Shibuya, and Kazutaka Kawamura. "Observation and Modeling of Molecular and Atomic Ions in Hydrogen Plasma." Japanese Journal of Applied Physics 45, no. 10B (2006): 8208–11. http://dx.doi.org/10.1143/jjap.45.8208.

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15

Belikov, Sergey, and Sergei Magonov. "True Molecular-Scale Imaging in Atomic Force Microscopy: Experiment and Modeling." Japanese Journal of Applied Physics 45, no. 3B (2006): 2158–65. http://dx.doi.org/10.1143/jjap.45.2158.

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16

Dednam, W., C. Sabater, M. A. Fernandez, C. Untiedt, J. J. Palacios, and M. J. Caturla. "Modeling contact formation between atomic-sized gold tips via molecular dynamics." Journal of Physics: Conference Series 574 (January 21, 2015): 012045. http://dx.doi.org/10.1088/1742-6596/574/1/012045.

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17

Chaney, Michael O., W. Blaine Stine, Tyler A. Kokjohn, et al. "RAGE and amyloid beta interactions: Atomic force microscopy and molecular modeling." Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1741, no. 1-2 (2005): 199–205. http://dx.doi.org/10.1016/j.bbadis.2005.03.014.

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18

Behdinan, Kamran, Yigui Xu, and Zouheir Fawaz. "MOLECULAR ELEMENT METHOD (MEM) FOR MULTI-SCALE MODELING AND SIMULATIONS OF NANO/MICRO-SYSTEMS." Transactions of the Canadian Society for Mechanical Engineering 29, no. 3 (2005): 403–21. http://dx.doi.org/10.1139/tcsme-2005-0025.

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A new technique called Molecular Element Method is proposed for multi-scale modeling and simulations of nano/micro-systems. In this technique, the system is divided into molecular elements whose properties are represented by sets of equivalent physical parameters obtained from atomic information. The discrete system is solved based on continuum mechanics theories. The resultant element information from system solving is then used as an external constraint for the elements, to investigate the atomic information within, using molecular dynamics calculations. Both system properties and atomic inf

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19

Pietikäinen, Otso, Perttu Hämäläinen, Jaakko Lehtinen, and Antti J. Karttunen. "VRChem: A Virtual Reality Molecular Builder." Applied Sciences 11, no. 22 (2021): 10767. http://dx.doi.org/10.3390/app112210767.

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Virtual reality provides a powerful way to visualize the three-dimensional, atomic-level structures of molecules and materials. We present new virtual reality software for molecular modeling and for testing the use of virtual reality in organic chemistry education. The open-source software, named VRChem, was developed primarily for building, visualizing and manipulating organic molecules using a head-mounted virtual reality system. The design goal of the VRChem software was to create an easy-to-use and entertaining user experience for molecular modeling in virtual reality. We discuss the desig

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20

Srećković, Vladimir A., Darko Jevremović, Veljko Vujčić, et al. "Mol-D a Database and a Web Service within the Serbian Virtual Observatory and the Virtual Atomic and Molecular Data Centre." Proceedings of the International Astronomical Union 12, S325 (2016): 393–96. http://dx.doi.org/10.1017/s1743921316012643.

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AbstractIn this contribution we report the current stage of the MOLecular Dissociation (MOL-D) database which is a web service within the Serbian virtual observatory (SerVO) and node within Virtual Atomic and Molecular Data Center (VAMDC). MOL-D is an atomic and molecular (A&M) database devoted to the modelling of stellar atmospheres, laboratory plasmas, industrial plasmas etc. The initial stage of development was done at the end of 2014, when the service for data connected with hydrogen and helium molecular ions was done. In the next stage of the development of MOL-D, we include new cross

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21

Namba, Yoshiharu, Jin Yu, Jean M. Bennett, and Koujun Yamashita. "Modeling and measurements of atomic surface roughness." Applied Optics 39, no. 16 (2000): 2705. http://dx.doi.org/10.1364/ao.39.002705.

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22

Mishin, Yuri M. "Atomistic Computer Modeling of Intermetallic Alloys." Materials Science Forum 502 (December 2005): 21–26. http://dx.doi.org/10.4028/www.scientific.net/msf.502.21.

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The paper gives a brief overview of our recent work on atomistic computer modeling of ordered intermetallic compounds of the Ni-Al and Ti-Al systems. Atomic interactions in these systems are modeled by semi-empirical potentials fit to experimental and first-principles data. The methodology includes a large variety of techniques ranging from harmonic lattice dynamics to molecular dynamics and Monte Carlo simulations. The properties studied include lattice characteristics (elastic constants, phonons, thermal expansion), point-defect properties, atomic diffusion, generalized stacking faults, disl

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23

Amyot, Romain, Arin Marchesi, Clemens M. Franz, Ignacio Casuso, and Holger Flechsig. "Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images." PLOS Computational Biology 18, no. 3 (2022): e1009970. http://dx.doi.org/10.1371/journal.pcbi.1009970.

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Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale

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24

Paes, Lilian W., Roberto B. Faria, Juan O. Machuca-Herrera, Ademir Neves, and Sérgio P. Machado. "Molecular modeling utilizing purple acid phosphatase biomimetic models." Canadian Journal of Chemistry 82, no. 11 (2004): 1619–24. http://dx.doi.org/10.1139/v04-134.

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Purple acid phosphatases (PAPs) constitute a new class of metalloenzymes that catalyze the hydrolysis of certain phosphate esters, including nucleoside di- and triphosphates and aryl phosphates, under acidic conditions. To provide some insight into these metalloenzymes we have performed quantum chemical and molecular mechanics calculations based on the mixed-valence [FeIIFeIII(BPBPMP)(OAc)2]+ model complex (1) (H2BPBPMP = 2-bis[{(2-pyridylmethyl)-aminomethyl}-6-{(2-hydroxybenzyl)-(2-pyridylmethyl)}-aminomethyl]-4-methylphenol). The geometric and the vibrational parameters calculated by molecul

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25

Ayoola, Oluwasegun M., Alper Buldum, Siamak Farhad, and Sammy A. Ojo. "A Review on the Molecular Modeling of Argyrodite Electrolytes for All-Solid-State Lithium Batteries." Energies 15, no. 19 (2022): 7288. http://dx.doi.org/10.3390/en15197288.

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Solid-state argyrodite electrolytes are promising candidate materials to produce safe all-solid-state lithium batteries (ASSLBs) due to their high ionic conductivity. These batteries can be used to power electric vehicles and portable consumer electronics which need high power density. Atomic-scale modeling with ab initio calculations became an invaluable tool to better understand the intrinsic properties and stability of these materials. It is also used to create new structures to tailor their properties. This review article presents some of the recent theoretical investigations based on atom

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26

Diemer, Benedikt, Adam R. H. Stevens, John C. Forbes, et al. "Modeling the Atomic-to-molecular Transition in Cosmological Simulations of Galaxy Formation." Astrophysical Journal Supplement Series 238, no. 2 (2018): 33. http://dx.doi.org/10.3847/1538-4365/aae387.

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27

Romine, Devon, and Ridwan Sakidja. "Modeling atomic layer deposition of alumina using reactive force field molecular dynamics." MRS Advances 7, no. 9 (2022): 185–89. http://dx.doi.org/10.1557/s43580-022-00271-w.

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28

Loukhovitski, B. I., and A. M. Starik. "Modeling of vibration–electronic–chemistry coupling in the atomic–molecular oxygen system." Chemical Physics 360, no. 1-3 (2009): 18–26. http://dx.doi.org/10.1016/j.chemphys.2009.04.003.

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29

Goh, Boon Chong, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven, and Klaus Schulten. "Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis." Structure 23, no. 8 (2015): 1414–25. http://dx.doi.org/10.1016/j.str.2015.05.017.

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30

Mendoza, Claudio, Manuel A. Bautista, Jérôme Deprince, et al. "The XSTAR Atomic Database." Atoms 9, no. 1 (2021): 12. http://dx.doi.org/10.3390/atoms9010012.

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We describe the atomic database of the xstar spectral modeling code, summarizing the systematic upgrades carried out in the past twenty years to enable the modeling of K-lines from chemical elements with atomic number Z≤30 and recent extensions to handle high-density plasmas. Such plasma environments are found, for instance, in the inner region of accretion disks round compact objects (neutron stars and black holes), which emit rich information about the system’s physical properties. Our intention is to offer a reliable modeling tool to take advantage of the outstanding spectral capabilities o

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31

Laas, Jacob C., and Paola Caselli. "Modeling sulfur depletion in interstellar clouds." Astronomy & Astrophysics 624 (April 2019): A108. http://dx.doi.org/10.1051/0004-6361/201834446.

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Context. The elemental depletion of interstellar sulfur from the gas phase has been a recurring challenge for astrochemical models. Observations show that sulfur remains relatively non-depleted with respect to its cosmic value throughout the diffuse and translucent stages of an interstellar molecular cloud, but its atomic and molecular gas-phase constituents cannot account for this cosmic value toward lines of sight containing higher-density environments. Aims. We have attempted to address this issue by modeling the evolution of an interstellar cloud from its pristine state as a diffuse atomic

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32

Seidler, Tomasz, Marlena Gryl, Benoît Champagne, and Katarzyna Stadnicka. "Modeling of the optical properties of molecular crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C384. http://dx.doi.org/10.1107/s2053273314096156.

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In this contribution we present our current findings in the calculations of the linear and second-order nonlinear electric susceptibility tensor components of organic crystals. The methodology used for this purpose is based on a combination of the electrostatic interaction scheme developed by Hurst and Munn (Hurst & Munn, 1986) with electronic structure calculations for the isolated molecules. Our modification of the method consists in i) running periodic boundary condition (PBC) calculations for an adequate chromophore geometry (either experimental or optimized) to obtain atomic charges a

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33

Kunene, Thokozane Justin, Lagouge Kwanda Tartibu, Sina Karimzadeh, Peter Ozaveshe Oviroh, Kingsley Ukoba, and Tien-Chien Jen. "Molecular Dynamics of Atomic Layer Deposition: Sticking Coefficient Investigation." Applied Sciences 12, no. 4 (2022): 2188. http://dx.doi.org/10.3390/app12042188.

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This study focused on the atomic scale growth dynamics of amorphous Al2O3 films microscale structural relaxation. Classical Molecular Dynamics (MD) can not entirely model the challenging ALD dynamics due to the large timescales. The all-atom approach has rules based on deposition actions modelled MD relaxations that form as input to attain a single ALD cycle. MD relaxations are used to create a realistic equilibrium surface. This approach is fitting to this study as the investigation of the sticking coefficient is only at the first monolayer that includes the layering of a hydroxyl surface of

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34

Bacchini, Cecilia, Matilde Mingozzi, Bianca M. Poggianti, et al. "3D Modeling of the Molecular Gas Kinematics in Optically Selected Jellyfish Galaxies." Astrophysical Journal 950, no. 1 (2023): 24. http://dx.doi.org/10.3847/1538-4357/acc9b9.

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Abstract Cluster galaxies are subject to the ram pressure exerted by the intracluster medium, which can perturb or even strip away their gas while leaving the stars undisturbed. We model the distribution and kinematics of the stars and the molecular gas in four late-type cluster galaxies (JO201, JO204, JO206, and JW100), which show tails of atomic and ionized gas indicative of ongoing ram pressure stripping. We analyze MUSE@VLT data and CO data from the Atacama Large Millimeter Array searching for signatures of radial gas flows, ram pressure stripping, and other perturbations. We find that all

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35

Hryc, Corey F., and Matthew L. Baker. "Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps." Biomolecules 12, no. 6 (2022): 773. http://dx.doi.org/10.3390/biom12060773.

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Single-particle electron cryomicroscopy (cryoEM) has become an indispensable tool for studying structure and function in macromolecular assemblies. As an integral part of the cryoEM structure determination process, computational tools have been developed to build atomic models directly from a density map without structural templates. Nearly a decade ago, we created Pathwalking, a tool for de novo modeling of protein structure in near-atomic resolution cryoEM density maps. Here, we present the latest developments in Pathwalking, including the addition of probabilistic models, as well as a compa

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36

Oleynichenko, Alexander V., Andréi Zaitsevskii, Leonid V. Skripnikov, and Ephraim Eliav. "Relativistic Fock Space Coupled Cluster Method for Many-Electron Systems: Non-Perturbative Account for Connected Triple Excitations." Symmetry 12, no. 7 (2020): 1101. http://dx.doi.org/10.3390/sym12071101.

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The Fock space relativistic coupled cluster method (FS-RCC) is one of the most promising tools of electronic structure modeling for atomic and molecular systems containing heavy nuclei. Until recently, capabilities of the FS-RCC method were severely restricted by the fact that only single and double excitations in the exponential parametrization of the wave operator were considered. We report the design and the first computer implementation of FS-RCC schemes with full and simplified non-perturbative account for triple excitations in the cluster operator. Numerical stability of the new computat

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37

Sare, Hadarou, and Dongmei Dong. "Novel High-Strength and High-Temperature Resistant Composite Material for In-Space Optical Mining Applications: Modeling, Design, and Simulation at the Polymer and Atomic/Molecular Levels." Materials 17, no. 19 (2024): 4723. http://dx.doi.org/10.3390/ma17194723.

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This study explores the modeling, design, simulation, and testing of a new composite material designed for high-strength and high-temperature resistance in in-space optical mining, examining its properties at both the polymer and atomic/molecular levels. At the polymer level, the investigation includes mechanical and thermal performance analyses using COMSOL Multiphysics 6.1, employing layerwise theory, equivalent single layer (ESL) theory, and a multiple-model approach for mechanical modeling, alongside virtual thermal experiments simulating laser heating. Experimentally, porous Polyaniline (

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38

Piron, Robin. "Atomic Models of Dense Plasmas, Applications, and Current Challenges." Atoms 12, no. 4 (2024): 26. http://dx.doi.org/10.3390/atoms12040026.

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Modeling plasmas in terms of atoms or ions is theoretically appealing for several reasons. When it is relevant, the notion of atom or ion in a plasma provides us with an interpretation scheme of the plasma’s internal functioning. From the standpoint of quantitative estimation of plasma properties, atomic models of plasma allow one to extend many theoretical tools of atomic physics to plasmas. This notably includes the statistical approaches to the detailed accounting for excited states, or the collisional-radiative modeling of non-equilibrium plasmas, which is based on the notion of atomic pro

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39

Stacey, Weston M., and Edward W. Thomas. "Sensitivity of Predicted Tokamak Physics Parameters to Divertor Atomic/Molecular Data and Modeling." Fusion Technology 39, no. 1 (2001): 18–26. http://dx.doi.org/10.13182/fst01-a147.

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Wierzbicki, A., C. S. Sikes, J. D. Madura, and B. Drake. "Atomic force microscopy and molecular modeling of protein and peptide binding to calcite." Calcified Tissue International 54, no. 2 (1994): 133–41. http://dx.doi.org/10.1007/bf00296064.

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Smith, Nicholas, Brandon Campbell, Lin Li, Chuan Li, and Emil Alexov. "Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling." BMC Structural Biology 12, no. 1 (2012): 31. http://dx.doi.org/10.1186/1472-6807-12-31.

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42

Wang, Jennifer J., Tonglei Li, Simon D. Bateman, Robert Erck, and Kenneth R. Morris. "Modeling of Adhesion in Tablet Compression—I. Atomic Force Microscopy and Molecular Simulation." Journal of Pharmaceutical Sciences 92, no. 4 (2003): 798–814. http://dx.doi.org/10.1002/jps.10339.

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43

Yan, Liuming, and Jorge M. Seminario. "Moletronics modeling toward molecular potentials." International Journal of Quantum Chemistry 106, no. 8 (2006): 1964–69. http://dx.doi.org/10.1002/qua.20949.

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Ershova, Maria O., Amir Taldaev, Petr V. Konarev, et al. "Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins." Biomolecules 13, no. 12 (2023): 1776. http://dx.doi.org/10.3390/biom13121776.

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Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors―highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microsco

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Yang, Xiao Jing, and Xiao Jiang Yang. "Molecular Dynamics Simulation of Nanoscale Contact Process of Plane on Plane." Advanced Materials Research 662 (February 2013): 122–26. http://dx.doi.org/10.4028/www.scientific.net/amr.662.122.

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Considering the process of the plane of rectangular indenter contacting on the plane of rectangular basal body in nanoscale as research object, molecular dynamics method is used for modeling, solving and simulation analysis. The change of atomic state and acting force in the contact process of nanoscale plane and plane is analysis from atomic aspect. The result showed that: when the plane of the rectangular indenter is from the surface of the base body a certain distance, due to attractive force, produced by inter-atomic force, the surface of the substrate produces atoms projection phenomenon;

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46

Miner, Jacob C., Anna Lappala, Paul W. Fenimore, et al. "Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail." Biomolecules 11, no. 1 (2021): 124. http://dx.doi.org/10.3390/biom11010124.

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Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for

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47

Böke, Aysun. "Molecular scattering function data of brain tissue." Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 27, no. 1 (2025): 253–58. https://doi.org/10.25092/baunfbed.1436370.

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The interaction of photons with matter is of great importance for the study of energy transfer to the medium. The most sensitive studies on energy transfer are Monte Carlo simulation applications. In Monte Carlo modeling, the calculation of incoherent scattering is important. The incoherent scattering of a photon in a medium is decisive in terms of scattering angle and energy transfer to the medium. By incorporating the incoherent scattering coefficients into the Monte Carlo modeling program, it will be possible to determine the attenuation properties of photons of different energies interacti

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48

Vargas, Ernesto, Vladimir Yarov-Yarovoy, Fatemeh Khalili-Araghi, et al. "An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations." Journal of General Physiology 140, no. 6 (2012): 587–94. http://dx.doi.org/10.1085/jgp.201210873.

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Developing an understanding of the mechanism of voltage-gated ion channels in molecular terms requires knowledge of the structure of the active and resting conformations. Although the active-state conformation is known from x-ray structures, an atomic resolution structure of a voltage-dependent ion channel in the resting state is not currently available. This has motivated various efforts at using computational modeling methods and molecular dynamics (MD) simulations to provide the missing information. A comparison of recent computational results reveals an emerging consensus on voltage-depend

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Khaliullin, I. G., D. K. Nilov, I. V. Shapovalova, and V. K. Švedas. "Construction of a Full-Atomic Mechanistic Model of Human Apurinic/Apyrimidinic Endonuclease APE1 for Virtual Screening of Novel Inhibitors." Acta Naturae 4, no. 2 (2012): 80–86. http://dx.doi.org/10.32607/20758251-2012-4-2-80-86.

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Abstract:

A full-atomic molecular model of human apurinic/apyrimidinic endonuclease APE1, an important enzyme in the DNA repair system, has been constructed. The research consisted of hybrid quantum mechanics/ molecular mechanics modeling of the enzyme-substrate interactions, as well as calculations of the ionization states of the amino acid residues of the active site of the enzyme. The choice of the APE1 mechanism with an Asp210 residue as a proton acceptor was validated by means of a generalization of modeling and experimental data. Interactions were revealed in the active site that are of greatest s

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50

Khaliullin, I. G., D. K. Nilov, I. V. Shapovalova, and V. K. Švedas. "Construction of a Full-Atomic Mechanistic Model of Human Apurinic/Apyrimidinic Endonuclease APE1 for Virtual Screening of Novel Inhibitors." Acta Naturae 4, no. 2 (2012): 80–86. http://dx.doi.org/10.32607/actanaturae.10648.

Full text

Abstract:

A full-atomic molecular model of human apurinic/apyrimidinic endonuclease APE1, an important enzyme in the DNA repair system, has been constructed. The research consisted of hybrid quantum mechanics/ molecular mechanics modeling of the enzyme-substrate interactions, as well as calculations of the ionization states of the amino acid residues of the active site of the enzyme. The choice of the APE1 mechanism with an Asp210 residue as a proton acceptor was validated by means of a generalization of modeling and experimental data. Interactions were revealed in the active site that are of greatest s

APA, Harvard, Vancouver, ISO, and other styles

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