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Journal articles on the topic 'MM simulations'

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Author: Grafiati

Published: 14 March 2023

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1

de la Lande, Aurélien, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, et al. "Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review." Molecules 24, no. 9 (April 26, 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.

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deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

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2

Field, Martin J. "An Algorithm for Adaptive QC/MM Simulations." Journal of Chemical Theory and Computation 13, no. 5 (April 6, 2017): 2342–51. http://dx.doi.org/10.1021/acs.jctc.7b00099.

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3

Alameldeen, A. R., and D. A. Wood. "Addressing workload variability in architectural simulations." IEEE Micro 23, no. 6 (November 2003): 94–98. http://dx.doi.org/10.1109/mm.2003.1261392.

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4

Wymore, Troy, David W. Deerfield, Martin J. Field, John Hempel, and Hugh B. Nicholas. "Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations." Chemico-Biological Interactions 143-144 (February 2003): 75–84. http://dx.doi.org/10.1016/s0009-2797(02)00175-8.

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5

Zurek, Jolanta, Anna L. Bowman, W. Andrzej Sokalski, and Adrian J. Mulholland. "MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations." Structural Chemistry 15, no. 5 (October 2004): 405–14. http://dx.doi.org/10.1023/b:stuc.0000037896.80027.2c.

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6

Suh, Donghyuk, Kwangho Nam, and Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.

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7

Anam, Muhammad Syaekhul, and S. Suwardi. "Hydration Structures and Dynamics of Ga3+ Ion Based on Molecular Mechanics Molecular Dynamics Simulation (Classical DM)." Indonesian Journal of Chemistry and Environment 4, no. 2 (March 10, 2022): 49–56. http://dx.doi.org/10.21831/ijoce.v4i2.48401.

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The structure and hydration dynamics of Ga3+ ion have been studied using classical Molecular Dynamics (MD) simulations. The data collection procedure includes determining the best base set, constructing 2-body and 3-body potential equations, classical molecular dynamics simulations based on 2-body potentials, classical molecular dynamics simulations based on 2-body + 3 potential-body. The trajectory file data analysis was done to obtain structural properties parameters such as RDF, CND, ADF, and dynamic properties, namely the movement of H2O ligands between hydrations shells. The results of the research indicated that the hydration complex structure of Ga(H2O)83+ and Ga(H2O)63+ was observed in molecular dynamics simulations (MM-2 body) and (MM-2 body + 3-body), respectively. The movement of H2O ligands occurs between the first and second shell or vice versa in the MD simulation of MM-2 bodies but does not occur in MD simulations of (MM-2 bodies + MM-3 bodies). Therefore, the water ligands in the first hydrated shell are stable.

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8

Shimada, J., T. Sakuma, K. Nakata, T. Wasiho, and T. Takada. "3K1015 BioMolecular Simulations : MD and QM/MM calculations." Seibutsu Butsuri 42, supplement2 (2002): S180. http://dx.doi.org/10.2142/biophys.42.s180_2.

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9

Solt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, and Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations." Journal of Physical Chemistry B 113, no. 17 (April 30, 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.

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10

Morzan, Uriel N., Diego J. Alonso de Armiño, Nicolás O. Foglia, Francisco Ramírez, Mariano C. González Lebrero, Damián A. Scherlis, and Darío A. Estrin. "Spectroscopy in Complex Environments from QM–MM Simulations." Chemical Reviews 118, no. 7 (March 21, 2018): 4071–113. http://dx.doi.org/10.1021/acs.chemrev.8b00026.

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11

Martins Costa, M. T. C. "QM/MM simulations of polyols in aqueous solution." Journal of Molecular Structure: THEOCHEM 729, no. 1-2 (September 2005): 47–52. http://dx.doi.org/10.1016/j.theochem.2005.03.016.

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12

Jász, Ádám, Ádám Rák, István Ladjánszki, Gábor János Tornai, and György Cserey. "Towards chemically accurate QM/MM simulations on GPUs." Journal of Molecular Graphics and Modelling 96 (May 2020): 107536. http://dx.doi.org/10.1016/j.jmgm.2020.107536.

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13

Riahi, Saleh, and Christopher N. Rowley. "QM/MM Simulations of Mg and Zn Solvation." Biophysical Journal 106, no. 2 (January 2014): 405a. http://dx.doi.org/10.1016/j.bpj.2013.11.2281.

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14

Dohm, Sebastian, Eckhard Spohr, and Martin Korth. "Developing adaptive QM/MM computer simulations for electrochemistry." Journal of Computational Chemistry 38, no. 1 (October 28, 2016): 51–58. http://dx.doi.org/10.1002/jcc.24513.

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15

Watanabe, Hiroshi C., and Qiang Cui. "Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 15, no. 7 (May 16, 2019): 3917–28. http://dx.doi.org/10.1021/acs.jctc.9b00180.

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16

Thelen, Bryce C., and Elisa Toulson. "A computational study on the effect of the orifice size on the performance of a turbulent jet ignition system." Proceedings of the Institution of Mechanical Engineers, Part D: Journal of Automobile Engineering 231, no. 4 (August 20, 2016): 536–54. http://dx.doi.org/10.1177/0954407016659199.

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Fully three-dimensional computational fluid dynamic simulations with detailed combustion chemistry of a turbulent jet ignition system installed in a rapid compression machine are presented. The turbulent jet ignition system is a prechamber-initiated combustion system intended to allow lean-burn combustion in spark ignition internal-combustion engines. In the presented configuration, the turbulent jet ignition prechamber has a volume that is 2% of the volume of the main combustion chamber in the rapid compression machine and is separated from the main chamber by a nozzle containing a single orifice. Four simulations with orifice diameters of 1.0 mm, 1.5 mm, 2.0 mm, and 3.0 mm respectively are presented in order to demonstrate the effect of the orifice diameter on the combustion behavior of the turbulent jet ignition process. Data generated by the simulations is shown including combustion chamber pressures, temperature fields, jet velocities and mass fraction burn durations. From the combustion pressure trace, the jet velocity, and other field data, five distinct phases of the turbulent jet ignition process are identified. These phases are called the compression phase, the prechamber combustion initiation phase, the cold jet phase, the hot jet phase, and the flow reversal phase. The four simulations show that the orifice diameter of 1.5 mm provides the fastest ignition and the fastest overall combustion as reflected in the 0–10% and 10–90% mass fraction burn duration data generated. Meanwhile, the simulation for the orifice diameter of 1.0 mm produces the highest jet velocity and has the shortest delay between the spark and the exit of a jet of hot gases into the main chamber but produces a slower burn duration than the simulation for the larger orifice diameter of 1.5 mm. The simulations for orifice diameters of 2.0 mm and 3.0 mm demonstrate that the combustion speed is reduced as the orifice diameter increases above 1.5 mm. Finally, a discussion is given which examines the implications that the results generated have in regard to implementation of the turbulent jet ignition system in an internal-combustion engine.

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17

Karstensen, Anders, Wei Fan, Fengchun Zhang, Jesper Ø. Nielsen, and Gert F. Pedersen. "Analysis of Simulated and Measured Indoor Channels for mm-Wave Beamforming Applications." International Journal of Antennas and Propagation 2018 (2018): 1–17. http://dx.doi.org/10.1155/2018/2642904.

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Ray tracing- (RT-) assisted beamforming, where beams are directly steered to dominant paths tracked by ray tracing simulations, is a promising beamforming strategy, since it avoids the time-consuming exhaustive beam searching adopted in conventional beam steering strategies. The performance of RT-assisted beamforming depends directly on how accurate the spatial profiles of the radio environment can be predicted by the RT simulation. In this paper, we investigate how ray tracing-assisted beamforming performs in both poorly furnished and richly furnished indoor environments. Single-user beamforming performance was investigated using both single beam and multiple beams, with two different power allocation schemes applied to multibeamforming. Channel measurements were performed at 28–30 GHz using a vector network analyzer equipped with a biconical antenna as the transmit antenna and a rotated horn antenna as the receive antenna. 3D ray tracing simulations were carried out in the same replicated propagation environments. Based on measurement and ray tracing simulation data, it is shown that RT-assisted beamforming performs well both for single and multibeamforming in these two representative indoor propagation environments.

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18

Peguiron, Anke, Lucio Colombi Ciacchi, Alessandro De Vita, James R. Kermode, and Gianpietro Moras. "Accuracy of buffered-force QM/MM simulations of silica." Journal of Chemical Physics 142, no. 6 (February 14, 2015): 064116. http://dx.doi.org/10.1063/1.4907786.

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19

Messner, Christoph B., Günther K. Bonn, and Thomas S. Hofer. "QM/MM MD simulations of La(iii)–phosphopeptide complexes." Molecular BioSystems 11, no. 1 (2015): 232–38. http://dx.doi.org/10.1039/c4mb00424h.

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20

Wang, Meiting, Ye Mei, and Ulf Ryde. "Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations." Journal of Chemical Theory and Computation 14, no. 12 (October 26, 2018): 6613–22. http://dx.doi.org/10.1021/acs.jctc.8b00685.

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21

Bulo, Rosa E., Bernd Ensing, Jetze Sikkema, and Lucas Visscher. "Toward a Practical Method for Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 5, no. 9 (July 30, 2009): 2212–21. http://dx.doi.org/10.1021/ct900148e.

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22

Fogolari, Federico, Alessandro Brigo, and Henriette Molinari. "Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins." Biophysical Journal 85, no. 1 (July 2003): 159–66. http://dx.doi.org/10.1016/s0006-3495(03)74462-2.

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23

Lu, Xiya, Dong Fang, Shingo Ito, Yuko Okamoto, Victor Ovchinnikov, and Qiang Cui. "QM/MM free energy simulations: recent progress and challenges." Molecular Simulation 42, no. 13 (July 5, 2016): 1056–78. http://dx.doi.org/10.1080/08927022.2015.1132317.

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24

Cooper, April M., and Johannes Kästner. "Averaging Techniques for Reaction Barriers in QM/MM Simulations." ChemPhysChem 15, no. 15 (September 5, 2014): 3264–69. http://dx.doi.org/10.1002/cphc.201402382.

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25

Kim, Wan-Il, Se-Hoon Kim, and Kwang-Cheol Ko. "Investigation of the Optimum Diameter of the Ring Reflector for an Axial Virtual Cathode Oscillator." Electronics 11, no. 13 (June 26, 2022): 2002. http://dx.doi.org/10.3390/electronics11132002.

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The optimum hole diameter of a ring reflector was experimentally investigated using an axial virtual cathode oscillator (vircator) to enhance its microwave power. The ring reflector enhances the microwave power from the axial vircator by forming a cavity. The ring reflector was installed 9 mm behind the anode. The optimum hole diameter of the ring reflector was analyzed through simulations and experiments by changing the diameter from 60 mm to 160. PIC simulations show that the maximum peak microwave power was generated when the hole diameter was 116 mm and enhanced by 210%. The experiments show similar results to the simulations. The largest peak maximum power was 23.67 MW when the hole diameter was 120 mm. The simulations show that the dominant microwave frequency was formed between 5.33 GHz and 6.7 GHz. The experiments show that the dominant microwave frequency was formed between 5.3 GHz and 5.8 GHz. The frequency trend was approximately similar to that of the simulation results. However, the trend depending on the hole diameter was not as obvious as in the simulations. Although the frequency change was not as clear as in the simulations, experiments show that the hole diameter of the ring reflector affects the vircator operation.

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26

Yang, Wei, Ryan Bitetti-Putzer, and Martin Karplus. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials." Journal of Chemical Physics 120, no. 20 (May 22, 2004): 9450–53. http://dx.doi.org/10.1063/1.1738106.

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27

Xia, Shu-Hua, Ganglong Cui, Wei-Hai Fang, and Walter Thiel. "How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations." Angewandte Chemie 128, no. 6 (January 6, 2016): 2107–12. http://dx.doi.org/10.1002/ange.201509622.

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28

Xia, Shu-Hua, Ganglong Cui, Wei-Hai Fang, and Walter Thiel. "How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations." Angewandte Chemie International Edition 55, no. 6 (January 6, 2016): 2067–72. http://dx.doi.org/10.1002/anie.201509622.

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29

Miranda, Sebastião, Jonas Feldt, Frederico Pratas, Ricardo A. Mata, Nuno Roma, and Pedro Tomás. "Efficient parallelization of perturbative Monte Carlo QM/MM simulations in heterogeneous platforms." International Journal of High Performance Computing Applications 31, no. 6 (July 27, 2016): 499–516. http://dx.doi.org/10.1177/1094342016649420.

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A novel perturbative Monte Carlo mixed quantum mechanics (QM)/molecular mechanics (MM) approach has been recently developed to simulate molecular systems in complex environments. However, the required accuracy to efficiently simulate such complex molecular systems is usually granted at the cost of long executing times. To alleviate this problem, a new parallelization strategy of multi-level Monte Carlo molecular simulations is herein proposed for heterogeneous systems. It simultaneously exploits fine-grained (at the data level), coarse-grained (at the Markov chain level) and task-grained (pure QM, pure MM and QM/MM procedures) parallelism to ensure an efficient execution in heterogeneous systems composed of central processing units and multiple and possibly different graphical processing units. This is achieved by making use of the OpenCL library, together with appropriate dynamic load balancing schemes. From the conducted evaluation with real benchmarking data, a speed-up of 56x in the computational bottleneck part was observed, which results in a global speed-up of 38x for the whole simulation, reducing the time of a typical simulation from 80 hours to only 2 hours.

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30

Susanto, Tri Nugroho Hadi. "COMPUTATIONAL FLUID DYNAMICS SIMULATION OF KARTINI REACTOR FUELED PLATE." Indonesian Journal of Physics and Nuclear Applications 4, no. 2 (June 30, 2019): 33–38. http://dx.doi.org/10.24246/ijpna.v4i2.33-38.

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The purpose of this study is to determine the characteristics of the cooling system on the new design of the Kartini Reactor plate fuel based on numerical calculations (Computational Fluid Dynamics). The fuel plate model was simplified and made in 3D. The model dimensions are 17.3 mm x 68 mm x 900 mm. The space between the two plates called the narrow rectangular channels has a gap of 2 mm. On these simulations a heat flux of 10612,7 watt/m2 was used which was obtained from the MCNP calculation program. Simulations were conducted in a steady state condition and single-phase model laminar flow of an incompressible fluid through the gap between the two fuel plates. This simulation uses UDF (User Define Function) to approach heat flux behaviour that follows the neutron distribution in the reactor core. The simulation results show that the maximum temperature that occur at a flow rate of 0.01 m/s was 43.5 °C.

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31

Schwenk, C. F., and B. M. Rode. "Ab initio QM/MM MD simulations of the hydrated Ca2+ ion." Pure and Applied Chemistry 76, no. 1 (January 1, 2004): 37–47. http://dx.doi.org/10.1351/pac200476010037.

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The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (<100 ps) have been strongly overestimated by conclusions from experimental data.

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32

Chalmet, S., D. Rinaldi, and M. F. Ruiz-López. "A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations." International Journal of Quantum Chemistry 84, no. 5 (2001): 559–64. http://dx.doi.org/10.1002/qua.1410.

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33

Williams, Christopher R. "How Much Attenuation Extinguishes mm-Wave Vertically Pointing Radar Return Signals?" Remote Sensing 14, no. 6 (March 8, 2022): 1305. http://dx.doi.org/10.3390/rs14061305.

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Vertically pointing radars (VPRs) operating at millimeter wavelengths measure the power return from raindrops enabling precipitation retrievals as a function of height. However, as the rain rate increases, there are combinations of rain rate and rain path length that produce sufficient attenuation to prevent the radar from detecting raindrops all the way through rain shafts. This study explores the question: Which rain rate and path length combinations completely extinguish radar return signals for VPRs operating between 3 and 200 GHz? An important step in these simulations is converting attenuated radar reflectivity factor into radar received signal-to-noise ratio (SNR) in order to determine the range where the SNR drops below the receiver detection threshold. Configuring the simulations to mimic a U.S. Department of Energy Atmospheric Radiation Mission (ARM) W-band (95 GHz) radar deployed in Brazil, the simulation results indicate that a W-band radar could observe raindrops above 3.5 km only when the rain rate was less than approximately 4 mm h−1. The deployed W-band radar measurements confirm the simulation results with maximum observed heights ranging between 3 and 4.5 km when a surface disdrometer measured 4 mm h−1 rain rate (based on 25-to-75 percentiles from over 25,000 W-band radar profiles). In summary, this study contributes to our understanding of how rain and atmospheric gas attenuation impacts the performance of millimeter-wave VPRs and will help with the design and configuration of multi-frequency VPRs deployed in future field campaigns.

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34

Kulkarni, Prajakta U., Harshil Shah, and Vivek K. Vyas. "Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery." Mini-Reviews in Medicinal Chemistry 22, no. 8 (May 2022): 1096–107. http://dx.doi.org/10.2174/1389557521666211007115250.

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Abstract: Quantum Mechanics (QM) is the physics-based theory that explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, when combined, hybrid quantum mechanics and molecular mechanics (QM/MM) can act as computer-based methods that can be used to calculate the structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical processes in solutions, as well as in the proteins, and has a great scope in structure-based drug design (SBDD) and discovery. Hybrid QM/MM can also be applied to HTS to derive QSAR models. Due to the availability of many protein crystal structures, it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however, the rest is defined through the molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

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35

Doll, K., and T. Jacob. "QM/MM description of periodic systems." Journal of Theoretical and Computational Chemistry 14, no. 07 (November 2015): 1550054. http://dx.doi.org/10.1142/s0219633615500546.

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A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.

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36

Liang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers, and Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations." Physical Chemistry Chemical Physics 20, no. 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.

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37

Saito, Toru, and Yu Takano. "QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease." Journal of Physical Chemistry B 126, no. 10 (March 3, 2022): 2087–97. http://dx.doi.org/10.1021/acs.jpcb.1c10200.

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38

Curchod, Basile F. E., Pabloc Campomanes, Andrey Laktionov, Marilisa Neri, Thomas J. Penfold, Stefano Vanni, Ivano Tavernelli, and Ursula Rothlisberger. "Mechanical (QM/MM) Simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena." CHIMIA International Journal for Chemistry 65, no. 5 (May 26, 2011): 330–33. http://dx.doi.org/10.2533/chimia.2011.330.

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39

Acevedo, Orlando, and William L. Jorgensen. "Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations." Journal of the American Chemical Society 128, no. 18 (May 2006): 6141–46. http://dx.doi.org/10.1021/ja057523x.

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40

Riccardi, Demian, Guohui Li, and Qiang Cui. "Importance of van der Waals Interactions in QM/MM Simulations." Journal of Physical Chemistry B 108, no. 20 (May 2004): 6467–78. http://dx.doi.org/10.1021/jp037992q.

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41

Hudson, Phillip S., H. Lee Woodcock, and Stefan Boresch. "Use of Interaction Energies in QM/MM Free Energy Simulations." Journal of Chemical Theory and Computation 15, no. 8 (May 29, 2019): 4632–45. http://dx.doi.org/10.1021/acs.jctc.9b00084.

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42

Sieffert, Nicolas, Michael Bühl, Marie-Pierre Gaigeot, and Carole A. Morrison. "Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations." Journal of Chemical Theory and Computation 9, no. 1 (October 30, 2012): 106–18. http://dx.doi.org/10.1021/ct300784x.

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43

Govender, Krishna K., and Kevin J. Naidoo. "Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations." Journal of Chemical Theory and Computation 10, no. 10 (September 18, 2014): 4708–17. http://dx.doi.org/10.1021/ct500373p.

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44

Lambros, Eleftherios, Filippo Lipparini, Gerardo Andrés Cisneros, and Francesco Paesani. "A Many-Body, Fully Polarizable Approach to QM/MM Simulations." Journal of Chemical Theory and Computation 16, no. 12 (November 19, 2020): 7462–72. http://dx.doi.org/10.1021/acs.jctc.0c00932.

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45

Difley, Seth, Lee-Ping Wang, Sina Yeganeh, Shane R. Yost, and Troy Van Voorhis. "Electronic Properties of Disordered Organic Semiconductors via QM/MM Simulations." Accounts of Chemical Research 43, no. 7 (July 20, 2010): 995–1004. http://dx.doi.org/10.1021/ar900246s.

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46

Jo, Ye-Joon, Jun-Seok Choi, Jin Kim, Hyo-Joon Kim, and Seong-Yong Moon. "Virtual Reality (VR) Simulation and Augmented Reality (AR) Navigation in Orthognathic Surgery: A Case Report." Applied Sciences 11, no. 12 (June 18, 2021): 5673. http://dx.doi.org/10.3390/app11125673.

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VR and AR technology have gradually developed to the extent that they could help operators in the surgical field. In this study, we present a case of VR simulation for preoperative planning and AR navigation applied to orthognathic surgery. The average difference between the preplanned data and the post-operative results was 3.00 mm, on average, and the standard deviation was 1.44 mm. VR simulation could provide great advantages for 3D medical simulations, with accurate manipulation and immersiveness. AR navigation has great potential in medical application; its advantages include displaying real time augmented 3D models of patients. Moreover, it is easily applied in the surgical field, without complicated 3D simulations or 3D-printed surgical guides.

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Qian, Ping, Li-Nan Lu, and Zhong-Zhi Yang. "Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model." Canadian Journal of Chemistry 87, no. 12 (December 2009): 1738–46. http://dx.doi.org/10.1139/v09-134.

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The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

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Kim, Se-Hoon, Chang-Jin Lee, Wan-Il Kim, and Kwang-Cheol Ko. "Experimental Investigation into the Optimum Position of a Ring Reflector for an Axial Virtual Cathode Oscillator." Electronics 10, no. 16 (August 5, 2021): 1878. http://dx.doi.org/10.3390/electronics10161878.

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A ring reflector was experimentally investigated using an axial virtual cathode oscillator (vircator). The ring reflector was installed behind the mesh anode of the axial vircator to enhance the microwave power output by forming a resonant cavity and increasing the electron beam to microwave energy conversion efficiency. The optimum position of the ring reflector is analyzed through simulations and experiments by varying the anode to reflector distance from 6 mm to 24 mm in 3 mm steps. PIC simulations show that the ring reflector enhances the microwave power of the axial vircator up to 220%. Experiments show that the microwave power from the axial vircator without the ring reflector is 11.22 MW. The maximum average peak microwave power of the axial vircator with the ring reflector is 25.82 MW when the anode to ring reflector distance is 18 mm. From the simulations and experiments, it can be seen that the ring reflector yields decaying enhancement that is inversely proportional to the anode to ring reflector distance and there is no noticeable microwave enhancement after 24 mm. The frequency range attained from the simulations and experiments is 5.8 to 6.7 GHz and 5.16 to 5.8 GHz, respectively. The difference between the simulation and experimental results is due to the error in the anode to cathode gap distance. Although the frequency is slightly changed, the ring reflector seems to have no influence on the frequency of the generated microwave.

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Davis, C. P., K. F. Evans, S. A. Buehler, D. L. Wu, and H. C. Pumphrey. "3-D polarised simulations of space-borne passive mm/sub-mm midlatitude cirrus observations: a case study." Atmospheric Chemistry and Physics Discussions 6, no. 6 (December 6, 2006): 12701–28. http://dx.doi.org/10.5194/acpd-6-12701-2006.

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Abstract. Global observations of ice clouds are needed to improve our understanding of their impact on earth's radiation balance and the water-cycle. Passive mm/sub-mm has some advantages compared to other space-borne cloud-ice remote sensing techniques. This paper presents detailed simulated observations for three such instruments, AMSU-B, CIWSIR, and EOS-MLS. The Monte-Carlo radiative transfer code, ARTS-MC, makes proper account of polarisation and uses 3-D spherical geometry. The actual field of view characteristics for each instrument are also accounted for. A 3-D midlatitude cirrus scenario is used, which is derived from Chilbolton cloud radar data and a stochastic method for generating 3-D ice water content fields. Although the main purpose of the work was to demonstrate the capability of accurately simulating observations of this type, the results suggest that cloud inhomogeneity will affect CIWSIR, and EOSMLS low tangent height observations via the beamfilling effect. Also, the results confirm that preferentially oriented ice crystals will produce significant polarisation effects.

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Davis, C. P., K. F. Evans, S. A. Buehler, D. L. Wu, and H. C. Pumphrey. "3-D polarised simulations of space-borne passive mm/sub-mm midlatitude cirrus observations: a case study." Atmospheric Chemistry and Physics 7, no. 15 (August 7, 2007): 4149–58. http://dx.doi.org/10.5194/acp-7-4149-2007.

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Abstract. Global observations of ice clouds are needed to improve our understanding of their impact on earth's radiation balance and the water-cycle. Passive mm/sub-mm has some advantages compared to other space-borne cloud-ice remote sensing techniques. The physics of scattering makes forward radiative transfer modelling for such instruments challenging. This paper demonstrates the ability of a recently developed RT code, ARTS-MC, to accurately simulate observations of this type for a variety of viewing geometries corresponding to operational (AMSU-B, EOS-MLS) and proposed (CIWSIR) instruments. ARTS-MC employs an adjoint Monte-Carlo method, makes proper account of polarisation, and uses 3-D spherical geometry. The actual field of view characteristics for each instrument are also accounted for. A 3-D midlatitude cirrus scenario is used, which is derived from Chilbolton cloud radar data and a stochastic method for generating 3-D ice water content fields. These demonstration simulations clearly demonstrate the beamfilling effect, significant polarisation effects for non-spherical particles, and also a beamfilling effect with regard to polarisation.

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