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Journal articles on the topic 'Ab-initio simulations'

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Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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1

Ogitsu, Tadashi, Joel Varley, Alexander D. DeAngelis, Kimberly Horsley, and Nicolas Gaillard. "(Invited) Integrating Ab-Initio Simulations and Experimental Characterization Methods: Towards Accelerated Chalcopyrite Materials Development for Hydrogen Production." ECS Meeting Abstracts MA2018-01, no. 31 (April 13, 2018): 1855. http://dx.doi.org/10.1149/ma2018-01/31/1855.

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Recent development of ab-initio simulation and experimental characterization techniques enabled us to obtain information that is crucial for accelerated materials development for sustainable energy solutions. In this presentation, we will particularly focus on some of the most complex problems currently facing hydrogen production technology and how these ab-initio simulations can be used to gain insights about them. Taking what we know from ab-initio simulations we can then validate multiple and independent experimental results to provide a theoretically grounded interpretation. This cross-validation between theory and experiment is one of the capabilities that the new HydroGEN consortium (h2awsm.org), established under DOE EERE, provides to scientific community. As the use examples, we will discuss about an effective use of ab-initio simulations for development of high performance materials for a photoelectrochemical hydrogen production device. We emphasize an importance on the comprehensive use of ab-initio simulations on multiple aspects of materials developments, such as usable synthesis conditions, detrimental defect formation for a given synthesis condition, and the consequential saturation of open circuit voltage. We emphasize that systematic comparisons between the multiple aspects of theory and experiment are important for rapid materials development procedure via effective identification of the roadblocks. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and funded by the U. S. Department of Energy, Office of Energy Efficiency & Renewable Energy (EERE).

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2

Gu, Hong-Yang, Weiguo Gao, and Xin-Gao Gong. "Hyperdynamics simulations with ab initio forces." Journal of Chemical Physics 154, no. 21 (June 7, 2021): 214112. http://dx.doi.org/10.1063/5.0047669.

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3

Osborn, Tim H., Amir A. Farajian, Olga V. Pupysheva, Rachel S. Aga, and L. C. Lew Yan Voon. "Ab initio simulations of silicene hydrogenation." Chemical Physics Letters 511, no. 1-3 (July 2011): 101–5. http://dx.doi.org/10.1016/j.cplett.2011.06.009.

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4

Knoop, Florian, Thomas Purcell, Matthias Scheffler, and Christian Carbogno. "FHI-vibes: Ab Initio Vibrational Simulations." Journal of Open Source Software 5, no. 56 (December 2, 2020): 2671. http://dx.doi.org/10.21105/joss.02671.

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5

Baty, Samuel R., Leonid Burakovsky, and Daniel Errandonea. "Ab Initio Phase Diagram of Copper." Crystals 11, no. 5 (May 12, 2021): 537. http://dx.doi.org/10.3390/cryst11050537.

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Copper has been considered as a common pressure calibrant and equation of state (EOS) and shock wave (SW) standard, because of the abundance of its highly accurate EOS and SW data, and the assumption that Cu is a simple one-phase material that does not exhibit high pressure (P) or high temperature (T) polymorphism. However, in 2014, Bolesta and Fomin detected another solid phase in molecular dynamics simulations of the shock compression of Cu, and in 2017 published the phase diagram of Cu having two solid phases, the ambient face-centered cubic (fcc) and the high-PT body-centered cubic (bcc) ones. Very recently, bcc-Cu has been detected in SW experiments, and a more sophisticated phase diagram of Cu with the two solid phases was published by Smirnov. In this work, using a suite of ab initio quantum molecular dynamics (QMD) simulations based on the Z methodology, which combines both direct Z method for the simulation of melting curves and inverse Z method for the calculation of solid–solid phase boundaries, we refine the phase diagram of Smirnov. We calculate the melting curves of both fcc-Cu and bcc-Cu and obtain an equation for the fcc-bcc solid–solid phase transition boundary. We also obtain the thermal EOS of Cu, which is in agreement with experimental data and QMD simulations. We argue that, despite being a polymorphic rather than a simple one-phase material, copper remains a reliable pressure calibrant and EOS and SW standard.

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6

Tat, Pham Van, and Ulrich K. Deiters. "Thermodynamic Properties of Vapor-Liquid Equilibria from Monte-Carlo Simulation using ab initio Intermolecular Potentials of Systems H2-H2 and F2-F2." Zeitschrift für Physikalische Chemie 233, no. 4 (April 24, 2019): 493–525. http://dx.doi.org/10.1515/zpch-2018-1260.

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Abstract In this work, we have been carried out GEMC-NVT simulations in the temperature range 18 K–32 K for fluid hydrogen and in range 60 K–140 K for fluid fluorine using four our developed ab initio 5-site intermolecular potentials for dimers H2-H2 and F2-F2, respectively. The thermodynamic properties of vapor-liquid equilibria and the critical points of fluids hydrogen and fluorine were calculated with the obtained densities of coexisting phases and vapor pressures. The simulation results drived from ab initio pair potentials were compared with those from ab initio potential plus three-body Axilrod-Teller potential and experimental data as well as those from Monte Carlo simulation using Lennard-Jones potentials, Deiters equation of state (D1-EOS) and Benedict-Webb-Rubin equation of state (EOS) reported in the literature.

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7

Durandurdu, Murat. "Amorphous zirconia: ab initio molecular dynamics simulations." Philosophical Magazine 97, no. 16 (February 23, 2017): 1334–45. http://dx.doi.org/10.1080/14786435.2017.1296201.

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8

Hug, Susanna, Graeme K. Hunter, Harvey Goldberg, and Mikko Karttunen. "Ab initio simulations of peptide-mineral interactions." Physics Procedia 4 (2010): 51–60. http://dx.doi.org/10.1016/j.phpro.2010.08.008.

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9

Ponga, Mauricio, Kaushik Bhattacharya, and Michael Ortiz. "Large scale ab-initio simulations of dislocations." Journal of Computational Physics 407 (April 2020): 109249. http://dx.doi.org/10.1016/j.jcp.2020.109249.

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10

Hammerich, A. D., V. Buch, and F. Mohamed. "Ab initio simulations of sulfuric acid solutions." Chemical Physics Letters 460, no. 4-6 (July 2008): 423–31. http://dx.doi.org/10.1016/j.cplett.2008.06.053.

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11

Yıldız, Tevhide Ayça, and Murat Durandurdu. "Amorphous boron carbide from ab initio simulations." Computational Materials Science 173 (February 2020): 109397. http://dx.doi.org/10.1016/j.commatsci.2019.109397.

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12

JUN, S., S. PENDURTI, I. H. LEE, S. Y. KIM, H. S. PARK, and Y. H. KIM. "ACTION-DERIVED AB INITIO MOLECULAR DYNAMICS." International Journal of Applied Mechanics 01, no. 03 (September 2009): 469–82. http://dx.doi.org/10.1142/s1758825109000277.

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Action-derived molecular dynamics (ADMD) is a numerical method to search for minimum-energy dynamic pathways on the potential-energy surface of an atomic system. The method is based on Hamilton's least-action principle and has been developed for problems of activated processes, rare events, and long-time simulations. In this paper, ADMD is further extended to incorporate ab initio total-energy calculations, which enables the detailed electronic analysis of transition states as well as the exploration of energy landscapes. Three numerical examples are solved to demonstrate the capability of this action-derived ab initio molecular dynamics (MD). The proposed approach is expected to circumvent the severe time-scale limitation of conventional ab intio MD simulations.

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13

Previti, Emanuele, Claudia Foti, Ottavia Giuffrè, Franz Saija, Jiri Sponer, and Giuseppe Cassone. "Ab initio molecular dynamics simulations and experimental speciation study of levofloxacin under different pH conditions." Physical Chemistry Chemical Physics 23, no. 42 (2021): 24403–12. http://dx.doi.org/10.1039/d1cp03942c.

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By means of ab initio molecular dynamics simulations we characterize the behaviour of the water solvation shells as well as the (de)protonation mechanisms, here we present the unprecedented quantum-based simulation of levofloxacin in aqueous environments.

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14

Ko, Eunjung, M. M. G. Alemany, Jeffrey J. Derby, and James R. Chelikowsky. "Ab Initio simulations of nonstoichiometric CdxTe1−x liquids." Journal of Chemical Physics 123, no. 8 (August 22, 2005): 084508. http://dx.doi.org/10.1063/1.2008247.

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15

Sepliarsky, M., R. L. Migoni, and M. G. Stachiotti. "Ab initio supported model simulations of ferroelectric perovskites." Computational Materials Science 10, no. 1-4 (February 1998): 51–56. http://dx.doi.org/10.1016/s0927-0256(97)00175-4.

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16

Yonezawa, Fumiko, Shoichi Sakamoto, and Motoo Hori. "Ab-initio molecular dynamics simulations of amorphous silicon." Journal of Non-Crystalline Solids 137-138 (1991): 135–40. http://dx.doi.org/10.1016/s0022-3093(05)80075-4.

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17

Godlevsky, V., and James R. Chelikowsky. "Ab initio molecular dynamics simulations of liquid GaAs." Journal of Chemical Physics 109, no. 17 (November 1998): 7312–18. http://dx.doi.org/10.1063/1.477408.

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18

Tuckerman, M. E., K. Laasonen, M. Sprik, and M. Parrinello. "Ab initio simulations of water and water ions." Journal of Physics: Condensed Matter 6, no. 23A (June 6, 1994): A93—A100. http://dx.doi.org/10.1088/0953-8984/6/23a/010.

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19

Shao, Xuecheng, Qiang Xu, Sheng Wang, Jian Lv, Yanchao Wang, and Yanming Ma. "Large-scale ab initio simulations for periodic system." Computer Physics Communications 233 (December 2018): 78–83. http://dx.doi.org/10.1016/j.cpc.2018.07.009.

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20

De Angelis, Filippo, Simona Fantacci, and Antonio Sgamellotti. "Ab initio molecular dynamics simulations of organometallic reactivity." Coordination Chemistry Reviews 250, no. 11-12 (June 2006): 1497–513. http://dx.doi.org/10.1016/j.ccr.2006.02.008.

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21

Ruiz-Barragan, Sergi, Kazuya Ishimura, and Motoyuki Shiga. "On the hierarchical parallelization of ab initio simulations." Chemical Physics Letters 646 (February 2016): 130–35. http://dx.doi.org/10.1016/j.cplett.2016.01.017.

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22

Iswanto, Ponco, Ria Armunanto, and Harno D. Pranowo. "STRUCTURE OF IRIDIUM(III) HYDRATION BASED ON AB INITIO QUANTUM MECHANICAL CHARGE FIELD MOLECULAR DYNAMICS SIMULATIONS." Indonesian Journal of Chemistry 10, no. 3 (December 14, 2010): 352–56. http://dx.doi.org/10.22146/ijc.21442.

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Structural properties of Iridium(III) hydration have been studied based on an ab initio Quantum Mechanical Charge Field (QMCF) Molecular Dynamics (MD) Simulations. The most chemical-relevant region was treated by ab initio calculation at Hartree-Fock level. For the remaining region was calculated by Molecular Mechanics method. LANL2DZ ECP and DZP Dunning basis sets were applied to Ir3+ ion and water, respectively. The average distance of Ir-O in the first hydration shell is 2.03 Å. The QMCF MD Simulation can detect only one complex structure with coordination number of 6 in the first hydration shell. Bond angle analysis shows that Ir3+ ion hydration in the first hydration shell has octahedral structure.

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23

Santra, Biswajit, Hsin-Yu Ko, Yao-Wen Yeh, Fausto Martelli, Igor Kaganovich, Yevgeny Raitses, and Roberto Car. "Root-growth of boron nitride nanotubes: experiments and ab initio simulations." Nanoscale 10, no. 47 (2018): 22223–30. http://dx.doi.org/10.1039/c8nr06217j.

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24

Tsuchida, Eiji, Yoong-Kee Choe, and Takahiro Ohkubo. "An adaptive finite-element method for large-scale ab initio molecular dynamics simulations." Physical Chemistry Chemical Physics 17, no. 47 (2015): 31444–52. http://dx.doi.org/10.1039/c5cp00320b.

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25

Bellshaw, Darren, Russell S. Minns, and Adam Kirrander. "Correspondence between electronic structure calculations and simulations: nonadiabatic dynamics in CS2." Physical Chemistry Chemical Physics 21, no. 26 (2019): 14226–37. http://dx.doi.org/10.1039/c8cp05693e.

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26

Chaban, Vitaly V. "Force field development and simulations of senior dialkyl sulfoxides." Physical Chemistry Chemical Physics 18, no. 15 (2016): 10507–15. http://dx.doi.org/10.1039/c5cp08006a.

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Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

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27

Thomas, Martin, Martin Brehm, and Barbara Kirchner. "Voronoi dipole moments for the simulation of bulk phase vibrational spectra." Physical Chemistry Chemical Physics 17, no. 5 (2015): 3207–13. http://dx.doi.org/10.1039/c4cp05272b.

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28

Chalabala, Jan, and Petr Slavíček. "Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer." Physical Chemistry Chemical Physics 18, no. 30 (2016): 20422–32. http://dx.doi.org/10.1039/c6cp02714h.

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29

Li, Xuejiao, Liuming Yan, and Baohua Yue. "Maleimide: a potential building block for the design of proton exchange membranes studied by ab initio molecular dynamics simulations." RSC Advances 5, no. 98 (2015): 80220–27. http://dx.doi.org/10.1039/c5ra14272e.

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30

Imoto, Sho, Harald Forbert, and Dominik Marx. "Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water." Physical Chemistry Chemical Physics 20, no. 9 (2018): 6146–58. http://dx.doi.org/10.1039/c7cp07003a.

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31

Borowska-Centkowska, Anna, Xi Liu, Marcin Krynski, Marzena Leszczynska, Wojciech Wrobel, Marcin Malys, Stephen Hull, Stefan T. Norberg, Franciszek Krok, and Isaac Abrahams. "Defect structure in δ-Bi5PbY2O11.5." RSC Advances 9, no. 17 (2019): 9640–53. http://dx.doi.org/10.1039/c9ra01233h.

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32

Ásgeirsson, Vilhjálmur, Christoph A. Bauer, and Stefan Grimme. "Unimolecular decomposition pathways of negatively charged nitriles by ab initio molecular dynamics." Physical Chemistry Chemical Physics 18, no. 45 (2016): 31017–26. http://dx.doi.org/10.1039/c6cp06180j.

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33

Wolf, T. J. A., T. S. Kuhlman, O. Schalk, T. J. Martínez, K. B. Møller, A. Stolow, and A. N. Unterreiner. "Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations." Phys. Chem. Chem. Phys. 16, no. 23 (2014): 11770–79. http://dx.doi.org/10.1039/c4cp00977k.

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34

Bandura, Andrei V., Robert A. Evarestov, and Yuri F. Zhukovskii. "Energetic stability and photocatalytic activity of SrTiO3 nanowires: ab initio simulations." RSC Advances 5, no. 31 (2015): 24115–25. http://dx.doi.org/10.1039/c5ra00306g.

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35

Peng, Wei-Tao, B. Scott Fales, Yinan Shu, and Benjamin G. Levine. "Dynamics of recombination via conical intersection in a semiconductor nanocrystal." Chemical Science 9, no. 3 (2018): 681–87. http://dx.doi.org/10.1039/c7sc04221c.

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36

Stirling, András, Nisanth N. Nair, Agustí Lledós, and Gregori Ujaque. "Challenges in modelling homogeneous catalysis: new answers from ab initio molecular dynamics to the controversy over the Wacker process." Chem. Soc. Rev. 43, no. 14 (2014): 4940–52. http://dx.doi.org/10.1039/c3cs60469a.

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37

Sisto, Aaron, Clem Stross, Marc W. van der Kamp, Michael O’Connor, Simon McIntosh-Smith, Graham T. Johnson, Edward G. Hohenstein, Fred R. Manby, David R. Glowacki, and Todd J. Martinez. "Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model." Physical Chemistry Chemical Physics 19, no. 23 (2017): 14924–36. http://dx.doi.org/10.1039/c7cp00492c.

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38

Hühn, Carolin, Lothar Wondraczek, and Marek Sierka. "Dynamics of ultrathin gold layers on vitreous silica probed by density functional theory." Physical Chemistry Chemical Physics 17, no. 41 (2015): 27488–95. http://dx.doi.org/10.1039/c5cp04803f.

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39

Mones, Letif, Gábor Pohl, and László Turi. "Ab initio molecular dynamics study of solvated electrons in methanol clusters." Physical Chemistry Chemical Physics 20, no. 45 (2018): 28741–50. http://dx.doi.org/10.1039/c8cp05052j.

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40

Arunachalam, Vaishali, Anil Kumar Tummanapelli, and Sukumaran Vasudevan. "The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations." Physical Chemistry Chemical Physics 21, no. 18 (2019): 9212–17. http://dx.doi.org/10.1039/c9cp00761j.

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41

Qu, Bingyan, Dongdong Li, Lei Wang, Jili Wu, Rulong Zhou, Bo Zhang, and Xiao Cheng Zeng. "Mechanistic study of pressure and temperature dependent structural changes in reactive formation of silicon carbonate." RSC Advances 6, no. 32 (2016): 26650–57. http://dx.doi.org/10.1039/c5ra21981g.

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42

Molpeceres, Germán, and Johannes Kästner. "Adsorption of H2 on amorphous solid water studied with molecular dynamics simulations." Physical Chemistry Chemical Physics 22, no. 14 (2020): 7552–63. http://dx.doi.org/10.1039/d0cp00250j.

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43

Dorfman, Simon, Ronan R. Braga, Kleber C. Mundim, and David Fuks. "Modeling of Boron Adsorption on the (110) Tungsten Surface." Surface Review and Letters 10, no. 02n03 (April 2003): 213–19. http://dx.doi.org/10.1142/s0218625x03004846.

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We have performed the atomistic simulations of the adhesion process of a boron atom on the tungsten (110) surface on the basis of the generalized simulation annealing formalism. The interatomic potentials used in these simulations were obtained from ab initio total energy calculations on the basis of the recursion procedure. The nonempirical calculations have been carried out in the framework of density functional theory in the coherent potential approximation.

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44

Iglesias-Fernández, Javier, Lluís Raich, Albert Ardèvol, and Carme Rovira. "The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases." Chemical Science 6, no. 2 (2015): 1167–77. http://dx.doi.org/10.1039/c4sc02240h.

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45

Brandt, Erik G., Lorenzo Agosta, and Alexander P. Lyubartsev. "Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations." Nanoscale 8, no. 27 (2016): 13385–98. http://dx.doi.org/10.1039/c6nr02791a.

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46

Yue, Ling, Le Yu, Chao Xu, Chaoyuan Zhu, and Yajun Liu. "Quantum yields of singlet and triplet chemiexcitation of dimethyl 1,2-dioxetane: ab initio nonadiabatic molecular dynamic simulations." Physical Chemistry Chemical Physics 22, no. 20 (2020): 11440–51. http://dx.doi.org/10.1039/d0cp00811g.

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47

Hiyama, Miyabi, Motoyuki Shiga, Nobuaki Koga, Osamu Sugino, Hidefumi Akiyama, and Yoshifumi Noguchi. "The effect of dynamical fluctuations of hydration structures on the absorption spectra of oxyluciferin anions in an aqueous solution." Physical Chemistry Chemical Physics 19, no. 15 (2017): 10028–35. http://dx.doi.org/10.1039/c7cp01067b.

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48

El Koura, Zakaria, Giacomo Rossi, Marco Calizzi, Lucia Amidani, Luca Pasquini, Antonio Miotello, and Federico Boscherini. "XANES study of vanadium and nitrogen dopants in photocatalytic TiO2 thin films." Physical Chemistry Chemical Physics 20, no. 1 (2018): 221–31. http://dx.doi.org/10.1039/c7cp06742a.

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49

Liu, Y. L., S. Q. Wang, and H. Q. Ye. "Shear deformation in TiAl: Atomic dynamic and static simulations." Journal of Materials Research 22, no. 6 (June 2007): 1685–93. http://dx.doi.org/10.1557/jmr.2007.0218.

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The dynamic shear deformation process and the related stacking fault transitions in TiAl have been systematically investigated using both the molecular dynamics and ab initio methods. The details of the dislocation initiation and microstructural evolution are presented, and the concomitant potential energy variation and the radial distribution functions have been analyzed. The results show, interestingly, that some deformation-induced hexagonal close-packed (hcp) structures are metastable, and that a higher velocity field promotes more hcp segments. The phenomena are interpreted based on ab initio calculations of the detailed energy variation at the different fault transition stages, i.e., superlattice intrinsic stacking fault (SISF) → TWIN, SISF → hcp, and hcp → TWIN. The intrinsic factor that governs the deformation process is discussed. The results promote new understanding of the stress-induced interfaces and dislocation behaviors in experimental observations.

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50

Mendes de Oliveira, Denilson, Samual R. Zukowski, Vladimir Palivec, Jérôme Hénin, Hector Martinez-Seara, Dor Ben-Amotz, Pavel Jungwirth, and Elise Duboué-Dijon. "Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy." Physical Chemistry Chemical Physics 22, no. 41 (2020): 24014–27. http://dx.doi.org/10.1039/d0cp02987d.

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