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Journal articles on the topic 'Ab-initio molecular dynamics simulation'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Yamamoto, Jun-ichi. "Ab initio molecular dynamics simulation on reaction." Journal of Molecular Structure: THEOCHEM 957, no. 1-3 (2010): 55–60. http://dx.doi.org/10.1016/j.theochem.2010.07.008.

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2

Peng, Jie, and Liping Wang. "The study of the convergence conditions of the deep-learning method in the Li₁₀GeP₂S₁₂ solid state electrolyte system." Journal of Physics: Conference Series 2713, no. 1 (2024): 012071. http://dx.doi.org/10.1088/1742-6596/2713/1/012071.

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Abstract The ionic conductivity of solid-state electrolytes at room temperature is crucial for commercializing lithium-ion batteries with solid-state electrolytes. Ab initio methods encounter a challenge due to their substantial computational resource demands. Classical molecular dynamics methods, on the other hand, are suitable for large-scale systems with simulation times reaching the nanosecond scale. However, they rely on empirical parameters in force fields, limiting their use to systems with well-established and extensively validated parameters, which is a constraint in studying new mate

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3

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 (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 thi

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4

Kolev, S., I. Balchev, K. Cvetkov, S. Tinchev, and T. Milenov. "Ab-Initio Molecular Dynamics Simulation of Graphene Sheet." Journal of Physics: Conference Series 780 (January 2017): 012014. http://dx.doi.org/10.1088/1742-6596/780/1/012014.

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5

Zhu, X. F., and L. F. Chen. "Ab initio molecular-dynamics simulation of liquid alloys." Physica B: Condensed Matter 403, no. 18 (2008): 3302–6. http://dx.doi.org/10.1016/j.physb.2008.04.025.

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6

Krynski, M., W. Wrobel, J. R. Dygas та ін. "Ab-initio molecular dynamics simulation of δ-Bi3YO6". Solid State Ionics 245-246 (вересень 2013): 43–48. http://dx.doi.org/10.1016/j.ssi.2013.05.015.

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7

Galli, G., and M. Parrinello. "Ab initio molecular dynamics simulation of molten KSi." Journal of Physics: Condensed Matter 2, S (1990): SA227—SA231. http://dx.doi.org/10.1088/0953-8984/2/s/033.

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8

Ghatee, Mohammad Hadi, and Younes Ansari. "Ab initio molecular dynamics simulation of ionic liquids." Journal of Chemical Physics 126, no. 15 (2007): 154502. http://dx.doi.org/10.1063/1.2718531.

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9

Paquet, Eric, and Herna L. Viktor. "Computational Methods for Ab Initio Molecular Dynamics." Advances in Chemistry 2018 (April 29, 2018): 1–14. http://dx.doi.org/10.1155/2018/9839641.

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Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as t

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10

Büchel, Ralf, Luis Álvarez, Jan Grage, Dominykas Maniscalco, and Irmgard Frank. "On the Simulation of Photoreactions Using Restricted Open-Shell Kohn–Sham Theory." Molecules 29, no. 18 (2024): 4509. http://dx.doi.org/10.3390/molecules29184509.

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It is a well-established standard to describe ground-state chemical reactions at an ab initio level of multi-electron theory. Fast reactions can be directly simulated. The most widely used approach is density functional theory for the electronic structure in combination with molecular dynamics for the nuclear motion. This approach is known as ab initio molecular dynamics. In contrast, the simulation of excited-state reactions at this level of theory is significantly more difficult. It turns out that the self-consistent solution of the Kohn–Sham equations is not easily reached in excited-state

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11

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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12

Cao, Liqun, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, and John Z. H. Zhang. "Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion." Molecules 26, no. 11 (2021): 3120. http://dx.doi.org/10.3390/molecules26113120.

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We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculation

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13

Jono, R., T. Terada, R. Ishitani, S. Nakamura, and K. Shimizu. "2P009 ab initio Molecular Dynamics simulation : Optimization of biomolecule." Seibutsu Butsuri 45, supplement (2005): S122. http://dx.doi.org/10.2142/biophys.45.s122_1.

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14

Röthlisberger, Ursula, and Michele Parrinello. "Ab initio molecular dynamics simulation of liquid hydrogen fluoride." Journal of Chemical Physics 106, no. 11 (1997): 4658–64. http://dx.doi.org/10.1063/1.473988.

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15

Shimojo, Fuyuki, Kozo Hoshino, and Y. Zempo. "Ab initio molecular-dynamics simulation method for complex liquids." Computer Physics Communications 142, no. 1-3 (2001): 364–67. http://dx.doi.org/10.1016/s0010-4655(01)00377-0.

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16

Wang, Songyou, C. Z. Wang, Feng-Chuan Chuang, James R. Morris, and K. M. Ho. "Ab initio molecular dynamics simulation of liquid Al88Si12 alloys." Journal of Chemical Physics 122, no. 3 (2005): 034508. http://dx.doi.org/10.1063/1.1833355.

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17

Seifert, G., G. Pastore, and R. Car. "Ab initio molecular dynamics simulation of liquid NaSn alloy." Journal of Physics: Condensed Matter 4, no. 11 (1992): L179—L183. http://dx.doi.org/10.1088/0953-8984/4/11/002.

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18

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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19

Kim, Cheolhee, Min Sun Yeom, and Eunae Kim. "Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation." Korean Journal of Chemical Engineering 33, no. 1 (2015): 255–59. http://dx.doi.org/10.1007/s11814-015-0125-8.

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20

Payal, Rajdeep Singh, and Sundaram Balasubramanian. "Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study." Phys. Chem. Chem. Phys. 16, no. 33 (2014): 17458–65. http://dx.doi.org/10.1039/c4cp02219j.

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21

Kurt, Barış, and Hamdi Temel. "Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation." Molecules 25, no. 9 (2020): 2196. http://dx.doi.org/10.3390/molecules25092196.

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Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program cont

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22

Xu, Chao, Feng Long Gu, and Chaoyuan Zhu. "Ultrafast intersystem crossing for nitrophenols: ab initio nonadiabatic molecular dynamics simulation." Physical Chemistry Chemical Physics 20, no. 8 (2018): 5606–16. http://dx.doi.org/10.1039/c7cp08601f.

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Ultrafast intersystem crossing mechanisms for two p- and m-nitrophenol groups (PNP and MNP) have been investigated using ab initio nonadiabatic molecular dynamics simulations at the 6SA-CASSCF level of theory.

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23

Piechota, Jacek, Stanislaw Krukowski, Bohdan Sadovyi, Petro Sadovyi, Sylwester Porowski, and Izabella Grzegory. "Ab Initio Molecular Dynamics Insight to Structural Phase Transition and Thermal Decomposition of InN." International Journal of Molecular Sciences 25, no. 15 (2024): 8281. http://dx.doi.org/10.3390/ijms25158281.

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Extensive ab initio density functional theory molecular dynamics calculations were used to evaluate stability conditions for relevant phases of InN. In particular, the p-T conditions of the thermal decomposition of InN and pressure-induced wurtzite–rocksalt solid–solid phase transition were established. The comparison of the simulation results with the available experimental data allowed for a critical evaluation of the capabilities and limitations of the proposed simulation method. It is shown that ab initio molecular dynamics can be used as an efficient tool for simulations of phase transfor

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24

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 (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

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25

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

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26

Lei, Xueling, Youngseok Jee, and Kevin Huang. "Amorphous Na2Si2O5 as a fast Na+ conductor: an ab initio molecular dynamics simulation." Journal of Materials Chemistry A 3, no. 39 (2015): 19920–27. http://dx.doi.org/10.1039/c5ta04474j.

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27

Gao, Liang, and Yuxiang Bu. "Protonation-modulated localization of excess electrons in histidine aqueous solutions revealed by ab initio molecular dynamics simulations: anion-centered versus cation-centered localization." Physical Chemistry Chemical Physics 19, no. 21 (2017): 13807–18. http://dx.doi.org/10.1039/c7cp01847a.

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28

Acher, Eléonor, Michel Masella, Valérie Vallet, and Florent Réal. "Properties of the tetravalent actinide series in aqueous phase from a microscopic simulation self-consistent engine." Physical Chemistry Chemical Physics 22, no. 4 (2020): 2343–50. http://dx.doi.org/10.1039/c9cp04912f.

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29

Frank, Irmgard, and Ebrahim Nadimi. "Ab-Initio Molecular Dynamics Simulation of the Electrolysis of Nucleobases." Energies 14, no. 16 (2021): 5021. http://dx.doi.org/10.3390/en14165021.

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Electrolysis is potentially a valuable tool for cleansing waste water. One might even hope that it is possible to synthesize valuable products in this way. The question is how the reaction conditions can be chosen to obtain desired compounds. In the present study we use Car–Parrinello molecular dynamics to simulate the reaction of nucleobases under electrolytic conditions. We use our own scheme (F. Hofbauer, I. Frank, Chem. Eur. J., 18, 277, 2012) for simulating the conditions after the electron transfer in a self-consistent field calculation. This scheme was employed previously to the electro

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30

Silvestrelli, Pier Luigi, and Michele Parrinello. "Ab initio molecular dynamics simulation of laser melting of graphite." Journal of Applied Physics 83, no. 5 (1998): 2478–83. http://dx.doi.org/10.1063/1.366989.

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31

KINOSHITA, Yusuke, Yoshitaka UMENO, and Takayuki KITAMURA. "Ab initio molecular dynamics simulation on properties of compound semiconductor." Proceedings of the JSME annual meeting 2004.6 (2004): 219–20. http://dx.doi.org/10.1299/jsmemecjo.2004.6.0_219.

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32

Haase, Frank, Joachim Sauer, and Jürg Hutter. "Ab initio molecular dynamics simulation of methanol adsorbed in chabazite." Chemical Physics Letters 266, no. 3-4 (1997): 397–402. http://dx.doi.org/10.1016/s0009-2614(97)00006-7.

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33

Blumberger, Jochen, Yoshitaka Tateyama, and Michiel Sprik. "Ab initio molecular dynamics simulation of redox reactions in solution." Computer Physics Communications 169, no. 1-3 (2005): 256–61. http://dx.doi.org/10.1016/j.cpc.2005.03.059.

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34

Kerisit, Sebastien N., and Micah P. Prange. "Ab initio molecular dynamics simulation of Nd3+ incorporation in calcite." Chemical Geology 534 (February 2020): 119460. http://dx.doi.org/10.1016/j.chemgeo.2019.119460.

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35

Ramaniah, Lavanya M., Marco Bernasconi, and Michele Parrinello. "Ab initio molecular-dynamics simulation of K+ solvation in water." Journal of Chemical Physics 111, no. 4 (1999): 1587–91. http://dx.doi.org/10.1063/1.479418.

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36

Lyubartsev, A. P., K. Laasonen, and A. Laaksonen. "Hydration of Li+ ion. An ab initio molecular dynamics simulation." Journal of Chemical Physics 114, no. 7 (2001): 3120–26. http://dx.doi.org/10.1063/1.1342815.

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37

Yu, Hua-Gen. "Ab initio molecular dynamics simulation of photodetachment reaction of cyclopentoxide." Chemical Physics Letters 441, no. 1-3 (2007): 20–24. http://dx.doi.org/10.1016/j.cplett.2007.04.079.

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38

TACHIKAWA, MASANORI, and MOTOYUKI SHIGA. "AB INITIO PATH INTEGRAL STUDY ON ISOTOPE EFFECT OF AMMONIA MOLECULE." Journal of Theoretical and Computational Chemistry 04, no. 01 (2005): 175–81. http://dx.doi.org/10.1142/s0219633605001337.

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We have applied ab initio path integral molecular dynamics simulation to study the quantum feature and proton/deuteron isotope effect of ammonia molecule. This method treats all the rotational and vibrational degrees of freedom fully quantum mechanically, while the potential energies of the respective molecular configurations are calculated "on the fly" using ab initio quantum chemical approach. The differences on the geometry and the electronic structure between NH 3 and ND 3 molecules are investigated in detail.

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39

Baty, Samuel R., Leonid Burakovsky, and Daniel Errandonea. "Ab Initio Phase Diagram of Copper." Crystals 11, no. 5 (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) o

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40

Bauchy, M. "Structure and dynamics of liquid AsSe4 from ab initio molecular dynamics simulation." Journal of Non-Crystalline Solids 377 (October 2013): 39–42. http://dx.doi.org/10.1016/j.jnoncrysol.2012.12.018.

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41

Perichta, P., Marek Liška, Jan Macháček, and Ondrej Gedeon. "The Yttria-Alumina Glasses - MD and TD Models." Advanced Materials Research 39-40 (April 2008): 93–96. http://dx.doi.org/10.4028/www.scientific.net/amr.39-40.93.

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The ab-initio molecular dynamics (MD) calculations of the yttrium - aluminate binary system 23Y2O3·77Al2O3 were performed with help of the Vienna ab-initio simulation package VASP. The thermodynamic model (TD) of glasses of the studied binary system was constructed. Both the Y/O and Al/O coordination numbers calculated from the partial pair radial distribution function (PP RDF) obtained for MD simulated melt at the temperature of 2500 K were significantly lower than the corresponding coordination numbers obtained from the TD model. The published neutron diffraction and X-ray diffraction studie

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42

Moin, Syed Tarique, and Thomas S. Hofer. "Hydration of iron–porphyrins: ab initio quantum mechanical charge field molecular dynamics simulation study." Physical Chemistry Chemical Physics 19, no. 45 (2017): 30822–33. http://dx.doi.org/10.1039/c7cp04436d.

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The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe<sup>2+</sup>–P and Fe<sup>3+</sup>–P in water to evaluate their structural, dynamical and energetic properties.

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43

Raulot, Jean Marc, S. Chentouf, T. Grosdidier, and Hafid Aourag. "Ti and Zr Transition Metals Effect in the D03 Fe3Al by Ab Initio Study Approach." Materials Science Forum 783-786 (May 2014): 1640–45. http://dx.doi.org/10.4028/www.scientific.net/msf.783-786.1640.

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The effect of the Ti and Zr transition metals on the D03-Fe3Al intermetallic compounds has been investigated by means of ab initio Pseudo Potentials numerical simulations based on Density Functional Theory. Two main issues will be addressed the understanding of the role of these two transition metals in terms of stability of the bulk at the light of their site preference in the D03-Fe3Al structure the behaviour of Ti and Zr transition metals in the sigma 5 (310) [001] grain boundary and their effect on the structural stability of this interface. An important issue when studying these aspects i

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44

Yu, Shi, Ruizhi Chu, Xiao Li, Guoguang Wu, and Xianliang Meng. "Combined ReaxFF and Ab Initio MD Simulations of Brown Coal Oxidation and Coal–Water Interactions." Entropy 24, no. 1 (2021): 71. http://dx.doi.org/10.3390/e24010071.

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In this manuscript, we use a combination of Car–Parrinello molecular dynamics (CPMD) and ReaxFF reactive molecular dynamics (ReaxFF-MD) simulations to study the brown coal–water interactions and coal oxidation. Our Car–Parrinello molecular dynamics simulation results reveal that hydrogen bonds dominate the water adsorption process, and oxygen-containing functional groups such as carboxyl play an important role in the interaction between brown coal and water. The discrepancy in hydrogen bonds formation between our simulation results by ab initio molecular dynamics (CPMD) and that by ReaxFF-MD i

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45

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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46

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

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47

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

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48

Zhao, N., Y. Q. He, and C. C. Yang. "A new approach to construct bulk and size-dependent continuous binary solution phase diagrams of alloys." RSC Advances 5, no. 117 (2015): 96323–27. http://dx.doi.org/10.1039/c5ra18541f.

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In this work, we report a new approach to construct both bulk and size-dependent continuous binary solution phase diagrams (e.g. the Au–Ag system) by combining ab initio molecular dynamics simulation and nanothermodynamics modeling.

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49

Amokrane, S., A. Ayadim, L. Levrel, and N. Jakse. "Pair structure, diffusion and pressure in liquid CuZr alloys from ab initio simulations: assessing the sensitivity to the energy cutoff." Modelling and Simulation in Materials Science and Engineering 30, no. 3 (2022): 035010. http://dx.doi.org/10.1088/1361-651x/ac5232.

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Abstract An accurate determination of the liquid structure, dynamics and thermodynamics on the same footing from ab initio molecular dynamics requires particular attention in setting up the electronic structure calculation. Using two well established simulation codes implementing the density functional theory with modern projector augmented wave sets, extensive ab initio molecular dynamics runs have been performed on the CuZr liquid alloy, a prototype of glass-forming alloys. Simulation cells involving about 3000 electrons and energy cutoffs from 285 up to 640 eV, well above the values usually

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50

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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