Journal articles: 'Atomic and molecular modeling'

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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 (August 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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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 (May 2006): 247–53. http://dx.doi.org/10.1007/s10573-006-0047-1.

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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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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 (March 1, 1994): 398–402. http://dx.doi.org/10.1021/ci00018a028.

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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 (December 1, 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 significant changes in the calculated adsorption energies. Influence of the substrate flexibility and adsorption on electronic structure and optical properties are also discussed.

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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 (December 21, 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, namely a multi-surface semi-continuous model and a fully continuous model with average smearing of atomic contribution. In this paper, we propose yet another modeling approach using a single continuous surface, but replacing the atomic density and attractive and repulsive constants in the Lennard–Jones potential with functions, which depend on the heterogeneity across the molecules, and the new model is applied to study the adsorption of coronene onto a graphene sheet. Comparison of results is made between the new model and two other existing approaches as well as molecular dynamics simulations performed using the LAMMPS molecular dynamics simulator. We find that the new approach is superior to the other continuum models and provides excellent agreement with molecular dynamics simulations.

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Catlow, C. R. A. "Computer modeling in materials chemistry." Pure and Applied Chemistry 77, no. 8 (January 1, 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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Chen, Jingrun, and Pingbing Ming. "An Efficient Multigrid Method for Molecular Mechanics Modeling in Atomic Solids." Communications in Computational Physics 10, no. 1 (July 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 iterative solvers. In addition, we study two examples with inhomogeneous deformation: vacancy and nanoindentation of aluminum. The results are still satisfactory while the linear-scaling property is lost for the latter example.

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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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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 and composition in wide range since there is neither short-range nor long-range order in the local atomic arrangement of this kind of materials.

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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 (October 24, 2006): 8208–11. http://dx.doi.org/10.1143/jjap.45.8208.

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Belikov, Sergey, and Sergei Magonov. "True Molecular-Scale Imaging in Atomic Force Microscopy: Experiment and Modeling." Japanese Journal of Applied Physics 45, no. 3B (March 27, 2006): 2158–65. http://dx.doi.org/10.1143/jjap.45.2158.

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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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Chaney, Michael O., W. Blaine Stine, Tyler A. Kokjohn, Yu-Min Kuo, Chera Esh, Afroza Rahman, Dean C. Luehrs, 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 (June 2005): 199–205. http://dx.doi.org/10.1016/j.bbadis.2005.03.014.

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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 (February 4, 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 obtained using the specified functions, differences in the atomic composition and structure of the volume and surface of nanoparticles were established.

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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 (September 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 information at local zones can be obtained accurately and efficiently in this way, A crystal of Cu having 285,883 atoms with a through the thickness hole inside is investigated using this technique. Tension stresses of the crystal and the slip of atoms around the hole’s edge are revealed corresponding to five strain loads. Compared with the results obtained from the classical molecular dynamics method, the maximum stress error is 2.7%, while the computational time is only 7.2-11.8% of that taken by the classical method.

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Namba, Yoshiharu, Jin Yu, Jean M. Bennett, and Koujun Yamashita. "Modeling and measurements of atomic surface roughness." Applied Optics 39, no. 16 (June 1, 2000): 2705. http://dx.doi.org/10.1364/ao.39.002705.

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Pietikäinen, Otso, Perttu Hämäläinen, Jaakko Lehtinen, and Antti J. Karttunen. "VRChem: A Virtual Reality Molecular Builder." Applied Sciences 11, no. 22 (November 15, 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 design and implementation of VRChem, together with real-life user experiences collected from students and academic research staff.

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Srećković, Vladimir A., Darko Jevremović, Veljko Vujčić, Ljubinko M. Ignjatović, Nenad Milovanović, Sanja Erkapić, and Milan S. Dimitrijević. "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 (October 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-sections and rate coefficients for processes which involve species such as XH+, where X is atom of some metal. Data are important for the exploring of the interstellar medium as well as for the early Universe chemistry and for the modeling of stellar and solar atmospheres. In this poster, we present our ongoing work and plans for the future.

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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, dislocations, surfaces, grain boundaries, interphase boundaries, and phase diagrams. We especially emphasize the recent progress in the understanding of diffusion mechanisms in NiAl and TiAl, calculation of stacking fault energies in Ni3Al in relation to dislocation behavior, and calculations of / 0 interface boundaries in Ni-Al alloys.

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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 (March 16, 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 assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com, presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images.

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Diemer, Benedikt, Adam R. H. Stevens, John C. Forbes, Federico Marinacci, Lars Hernquist, Claudia del P. Lagos, Amiel Sternberg, et al. "Modeling the Atomic-to-molecular Transition in Cosmological Simulations of Galaxy Formation." Astrophysical Journal Supplement Series 238, no. 2 (October 23, 2018): 33. http://dx.doi.org/10.3847/1538-4365/aae387.

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

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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 (June 2009): 18–26. http://dx.doi.org/10.1016/j.chemphys.2009.04.003.

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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 (August 2015): 1414–25. http://dx.doi.org/10.1016/j.str.2015.05.017.

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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 (November 1, 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 molecular mechanics show that the force fields established in this work reproduce the binuclear iron core with µ-phenoxo or µ-alkoxo and di-µ-acetate bridges presented in the PAPs model complexes. The atomic orbital analysis of the SOMO contributions indicated that the FeIII atom and the terminal phenolate are involved in the phenolate to FeIII charge transfer electronic transition in 1 as argued from electronic spectroscopic data in the PAPs. Key words: mixed-valence FeIIFeIII complex, purple acid phosphatases, molecular modeling.

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Mendoza, Claudio, Manuel A. Bautista, Jérôme Deprince, Javier A. García, Efraín Gatuzz, Thomas W. Gorczyca, Timothy R. Kallman, Patrick Palmeri, Pascal Quinet, and Michael C. Witthoeft. "The XSTAR Atomic Database." Atoms 9, no. 1 (February 5, 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 of the new generation of X-ray space telescopes (e.g., xrism and athena) to be launched in the coming years. Data curatorial aspects are discussed and an updated list of reference sources is compiled to improve the database provenance metadata. Two xstar spin-offs—the ISMabs absorption model and the uaDB database—are also described.

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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 (October 4, 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 atomic-scale modeling to study argyrodite electrolytes for ASSLBs. A comparison of the effectiveness of argyrodite materials used for ASSLBs and the underlying advantages and disadvantages of the argyrodite materials are also presented in this article.

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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 (August 5, 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 and in ii) performing the calculations of the molecular properties within a non-uniform embedding field generated by point charges located spherically around the reference molecule. Using this approach good accuracy is achieved on the electric susceptibility tensor components in comparison with the uniform dipole electric field (Seidler et al., 2013). We extend here the application of this method to other molecular crystals as well as we present the first attempt to predict the chi(1) and chi(2) components of two-component organic crystals (Gryl et al., 2014).

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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 (February 19, 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 alumina. The study provides insight between atomic-level numerical information and experimental measurements of the sticking coefficient related to the atomic layer deposition. The MD modeling was for the deposition of Al2O3, using trimethylaluminum (TMA) and water as precursors. The film thickness of 1.7 Å yields an initial sticking coefficient of TMA to be 4.257 × 10−3 determined from the slope of the leading front of the thickness profile at a substrate temperature of 573 K. This work adds to the knowledge of the kinetic nature of ALD at the atomic level. It provides quantitative information on the sticking coefficient during ALD.

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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 cloud to a molecular environment of much higher density, using a gas-grain astrochemical code and an enhanced sulfur reaction network. Methods. A common gas-grain astrochemical reaction network has been systematically updated and greatly extended based on previous literature and previous sulfur models, with a focus on the grain chemistry and processes. A simple astrochemical model was used to benchmark the resulting network updates, and the results of the model were compared to typical astronomical observations sourced from the literature. Results. Our new gas-grain astrochemical model is able to reproduce the elemental depletion of sulfur, whereby sulfur can be depleted from the gas-phase by two orders of magnitude, and that this process may occur under dark cloud conditions if the cloud has a chemical age of at least 106 years. The resulting mix of sulfur-bearing species on the grain ranges across all the most common chemical elements (H/C/N/O), not dissimilar to the molecules observed in cometary environments. Notably, this mixture is not dominated simply by H2S, unlike all other current astrochemical models. Conclusions. Despite our relatively simple physical model, most of the known gas-phase S-bearing molecular abundances are accurately reproduced under dense conditions, however they are not expected to be the primary molecular sinks of sulfur. Our model predicts that most of the “missing” sulfur is in the form of organo-sulfur species that are trapped on grains.

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Bacchini, Cecilia, Matilde Mingozzi, Bianca M. Poggianti, Alessia Moretti, Marco Gullieuszik, Antonino Marasco, Bernardo Cervantes Sodi, et al. "3D Modeling of the Molecular Gas Kinematics in Optically Selected Jellyfish Galaxies." Astrophysical Journal 950, no. 1 (June 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 galaxies, with the possible exception of JW100, host stellar bars. Signatures of ram pressure are found in JO201 and JO206, which also shows clear indications of ongoing stripping in the molecular disk outskirts. The stripping affects the whole molecular gas disk of JW100. The molecular gas kinematics in JO204 is instead dominated by rotation rather than ram pressure. We also find indications of enhanced turbulence of the molecular gas compared to field galaxies. Large-scale radial flows of molecular gas are present in JO204 and JW100, but more uncertain in JO201 and JO206. We show that our sample follows the molecular gas mass–size relation, confirming that it is essentially independent of environment even for the most extreme cases of stripping. Our findings are consistent with the molecular gas being affected by the ram pressure on different timescales and less severely than the atomic and ionized gas phases, likely because the molecular gas is denser and more gravitationally bound to the galaxy.

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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 (June 2, 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 companion tool for modeling waters and ligands. This software was evaluated on the 2021 CryoEM Ligand Challenge density maps, in addition to identifying ligands in three IP3R1 density maps at ~3 Å to 4.1 Å resolution. The results clearly demonstrate that the Pathwalking de novo modeling pipeline can construct accurate protein structures and reliably localize and identify ligand density directly from a near-atomic resolution map.

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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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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 (January 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 (February 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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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 (April 2003): 798–814. http://dx.doi.org/10.1002/jps.10339.

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Piron, Robin. "Atomic Models of Dense Plasmas, Applications, and Current Challenges." Atoms 12, no. 4 (April 17, 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 processes. This paper is focused on the theoretical challenges raised by the atomic modeling of dense, non-ideal plasmas. It is intended to give a synthetic and pedagogical view on the evolution of ideas in the field, with an accent on the theoretical consistency issues, rather than an exhaustive review of models and experimental benchmarks. First we make a brief, non-exhaustive review of atomic models of plasmas, from ideal plasmas to strongly-coupled and pressure-ionized plasmas. We discuss the limitations of these models and pinpoint some open problems in the field of atomic modeling of plasmas. We then address the peculiarities of atomic processes in dense plasmas and point out some specific issues relative to the calculation of their cross-sections. In particular, we discuss the modeling of fluctuations, the accounting for channel mixing and collective phenomena in the photoabsorption, or the impact of pressure ionization on collisional processes.

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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 (September 26, 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 (PANI) films are fabricated via electrochemical polymerization, with variations in voltage and deposition time, to study their morphology, optical performance, and electrochemical behavior. At the atomic and molecular levels, this study involves modeling the composite material, composed of Nomex, Kevlar, and Spirooxazine-Doped PANI, and simulating its behavior. The significance of this work lies in developing a novel composite material for in-space optical mining, integrating it into optical mining systems, and introducing innovative thermal management solutions, which contribute to future space exploration by improving resource efficiency and sustainability, while also enhancing the understanding of PANI film properties for in-space applications.

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Miner, Jacob C., Anna Lappala, Paul W. Fenimore, William M. Fischer, Benjamin H. McMahon, Nicolas W. Hengartner, Karissa Y. Sanbonmatsu, and Chang-Shung Tung. "Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail." Biomolecules 11, no. 1 (January 19, 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 viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

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Ershova, Maria O., Amir Taldaev, Petr V. Konarev, Georgy S. Peters, Anastasia A. Valueva, Irina A. Ivanova, Sergey V. Kraevsky, et al. "Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins." Biomolecules 13, no. 12 (December 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 microscope―the cantilever―the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe–target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes.

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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 (July 2, 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 computational scheme and thus its applicability to a wide variety of molecular electronic states is ensured using the dynamic shift technique combined with the extrapolation to zero-shift limit. Pilot applications to atomic (Tl, Pb) and molecular (TlH) systems reported in the paper indicate that the breakthrough in accuracy and predictive power of the electronic structure calculations for heavy-element compounds can be achieved. Moreover, the described approach can provide a firm basis for high-precision modeling of heavy molecular systems with several open shells, including actinide compounds.

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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 (June 15, 2012): 80–86. http://dx.doi.org/10.32607/20758251-2012-4-2-80-86.

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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 significance for binding the substrate and potential APE1 inhibitors (potential co-drugs of interest in the chemo- and radiotherapy of oncological diseases).

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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 (June 15, 2012): 80–86. http://dx.doi.org/10.32607/actanaturae.10648.

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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 significance for binding the substrate and potential APE1 inhibitors (potential co-drugs of interest in the chemo- and radiotherapy of oncological diseases).

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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; As the indenter continue to move down,the inter-atomic force becomes repulsive force, generates the contact pressure which gradually increases as the contact depth increases; The lattice under the indenter is deformed with pressure action. When indenter is in disengagement stage, the contact pressure decreases rapidly, and appears to reverse tensile stress. With action of the reverse tensile stress, dislocation configuration gradually change and restructuring. At same time, due to the surface effect, a number of substrate atoms are adsorbed in the surface of indenter, which caused by adhesion,and pulled out of the base body with the indenter.

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Vargas, Ernesto, Vladimir Yarov-Yarovoy, Fatemeh Khalili-Araghi, William A. Catterall, Michael L. Klein, Mounir Tarek, Erik Lindahl, et al. "An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations." Journal of General Physiology 140, no. 6 (November 26, 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-dependent gating from computational modeling and MD simulations. This progress is highlighted in the broad context of preexisting work about voltage-gated channels.

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Ng, Mei Ling, Zaidah binti Rahmat, and Mohd Shahir Shamsir bin Omar. "Molecular Modeling and Simulation of Transketolase from Orthosiphon stamineus." Current Computer-Aided Drug Design 15, no. 4 (July 1, 2019): 308–17. http://dx.doi.org/10.2174/1573409914666181022141753.

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Background: Orthosiphon stamineus is a traditional medicinal plant in Southeast Asia countries with various well-known pharmacological activities such as antidiabetic, diuretics and antitumor activities. Transketolase is one of the proteins identified in the leaves of the plant and transketolase is believed able to lower blood sugar level in human through non-pancreatic mechanism. In order to understand the protein behavioral properties, 3D model of transketolase and analysis of protein structure are of obvious interest. Methods: In the present study, 3D model of transketolase was constructed and its atomic characteristics revealed. Besides, molecular dynamic simulation of the protein at 310 K and 368 K deciphered transketolase may be a thermophilic protein as the structure does not distort even at elevated temperature. This study also used the protein at 310 K and 368 K resimulated back at 310 K environment. Results: The results revealed that the protein is stable at all condition which suggest that it has high capacity to adapt at different environment not only at high temperature but also from high temperature condition to low temperature where the structure remains unchanged while retaining protein function. Conclusion: The thermostability properties of transketolase is beneficial for pharmaceutical industries as most of the drug making processes are at high temperature condition.

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Journal articles on the topic 'Atomic and molecular modeling'

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