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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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Nowak C, Misra M, Escobedo FA. Framework for Inverse Mapping Chemistry-Agnostic Coarse-Grained Simulation Models into Chemistry-Specific Models. J Chem Inf Model 2019; 59:5045-5056. [DOI: 10.1021/acs.jcim.9b00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Christian Nowak
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Mayank Misra
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Fernando A. Escobedo
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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Bejagam KK, Singh S, An Y, Berry C, Deshmukh SA. PSO-Assisted Development of New Transferable Coarse-Grained Water Models. J Phys Chem B 2018; 122:1958-1971. [DOI: 10.1021/acs.jpcb.7b10542] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karteek K. Bejagam
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Samrendra Singh
- CNH Industrial, Burr Ridge, Chicago, Illinois 60527, United States
| | - Yaxin An
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Carter Berry
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A. Deshmukh
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Chen B, Zheng H, Riehn M, Bok S, Gangopadhyay K, Maschmann MR, Gangopadhyay S. In Situ Characterization of Photothermal Nanoenergetic Combustion on a Plasmonic Microchip. ACS APPLIED MATERIALS & INTERFACES 2018; 10:427-436. [PMID: 29210564 DOI: 10.1021/acsami.7b13226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plasmonic gratings facilitate a robust in situ diagnostic platform for photothermal combustion of nanoenergetic composite thin films using an optical microscope and a high-speed camera. Aluminum nanoparticles (Al NPs) embedded in a fluoropolymer oxidizer are cast onto a plasmonic grating microchip and ignited using a low-power laser. The plasmonic grating enhances both spatial resolution and sufficient photothermal coupling to combust small Al NP clusters, initiating localized flames as small as 600 nm in size. Two-color pyrometry obtained from a high-speed color camera indicates an average flame temperature of 3900 K. Scattering measurements using polarized light microscopy enabled precise identification of individual Al NPs over a large field of view, leading to 3D reconstruction of combustion events.
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Affiliation(s)
| | | | | | - Sangho Bok
- Department of Engineering and Technology, Southern Utah University , Cedar City, Utah 84720, United States
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Davari SA, Mukherjee D. Kinetic Monte Carlo simulation for homogeneous nucleation of metal nanoparticles during vapor phase synthesis. AIChE J 2017. [DOI: 10.1002/aic.15887] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Seyyed Ali Davari
- Dept. of Mechanical, Aerospace and Biomedical Engineering, Nano-BioMaterials Laboratory for Energy, Energetics & Environment (nbml-E ); University of Tennessee; Knoxville TN 37996
| | - Dibyendu Mukherjee
- Dept. of Mechanical, Aerospace and Biomedical Engineering, Nano-BioMaterials Laboratory for Energy, Energetics & Environment (nbml-E ); University of Tennessee; Knoxville TN 37996
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Sushko GB, Verkhovtsev AV, Kexel C, Korol AV, Schramm S, Solov'yov AV. Reconciling simulated melting and ground-state properties of metals with a modified embedded-atom method potential. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:145201. [PMID: 26977922 DOI: 10.1088/0953-8984/28/14/145201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum as case studies, we demonstrate that simulations performed with the modified force field yield quantitatively correctly both the melting temperature of the metals and their ground-state properties. It is shown that the accounting for the long-range interatomic interactions noticeably affects the melting point assessment. The introduced modification weakens the interaction at interatomic distances exceeding the equilibrium one by a characteristic vibration amplitude defined by the Lindemann criterion, thus allowing for the correct simulation of melting, while keeping its behavior in the vicinity of the ground state minimum. The modification of the many-body potential has a general nature and can be applicable to metals with different characteristics of the electron structure as well as for many different molecular and solid state systems experiencing phase transitions.
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Duan CL, Liu X, Shan B, Chen R. Fluidized bed coupled rotary reactor for nanoparticles coating via atomic layer deposition. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:075101. [PMID: 26233411 DOI: 10.1063/1.4926349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A fluidized bed coupled rotary reactor has been designed for coating on nanoparticles (NPs) via atomic layer deposition. It consists of five major parts: reaction chamber, dosing and fluidizing section, pumping section, rotary manipulator components, as well as a double-layer cartridge for the storage of particles. In the deposition procedure, continuous fluidization of particles enlarges and homogenizes the void fraction in the particle bed, while rotation enhances the gas-solid interactions to stabilize fluidization. The particle cartridge presented here enables both the fluidization and rotation acting on the particle bed, demonstrated by the analysis of pressure drop. Moreover, enlarged interstitials and intense gas-solid contact under sufficient fluidizing velocity and proper rotation speed facilitate the precursor delivery throughout the particle bed and consequently provide a fast coating process. The cartridge can ensure precursors flowing through the particle bed exclusively to achieve high utilization without static exposure operation. By optimizing superficial gas velocities and rotation speeds, minimum pulse time for complete coating has been shortened in experiment, and in situ mass spectrometry showed the precursor usage can reach 90%. Inductively coupled plasma-optical emission spectroscopy results suggested a saturated growth of nanoscale Al2O3 films on spherical SiO2 NPs. Finally, the uniformity and composition of the shells were characterized by high angle annular dark field-transmission electron microscopy and energy dispersive X-ray spectroscopy.
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Affiliation(s)
- Chen-Long Duan
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei 430074, People's Republic of China
| | - Xiao Liu
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei 430074, People's Republic of China
| | - Bin Shan
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei 430074, People's Republic of China
| | - Rong Chen
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei 430074, People's Republic of China
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10
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Mukherjee D, Wang M, Khomami B. Impact of particle morphology on surface oxidation of nanoparticles: A kinetic Monte Carlo based study. AIChE J 2012. [DOI: 10.1002/aic.13740] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Bowler DR, Miyazaki T. O(N) methods in electronic structure calculations. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:036503. [PMID: 22790422 DOI: 10.1088/0034-4885/75/3/036503] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Linear-scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed.
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Affiliation(s)
- D R Bowler
- London Centre for Nanotechnology, UCL, 17-19 Gordon St, London WC1H 0AH, UK.
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12
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Spagnoli D, Gale JD. Atomistic theory and simulation of the morphology and structure of ionic nanoparticles. NANOSCALE 2012; 4:1051-1067. [PMID: 22139365 DOI: 10.1039/c1nr11106j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Computational techniques are widely used to explore the structure and properties of nanomaterials. This review surveys the application of both quantum mechanical and force field based atomistic simulation methods to nanoparticles, with a particular focus on the methodologies available and the ways in which they can be utilised to study structure, phase stability and morphology. The main focus of this article is on partially ionic materials, from binary semiconductors through to mineral nanoparticles, with more detailed considered of three examples, namely titania, zinc sulphide and calcium carbonate.
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Affiliation(s)
- Dino Spagnoli
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, PO Box U1987, Perth, WA 6845, Australia
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13
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Divide-and-Conquer Approaches to Quantum Chemistry: Theory and Implementation. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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14
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Conner RW, Dlott DD. Ultrafast Condensed-Phase Emission from Energetic Composites of Teflon and Nanoaluminum. J Phys Chem A 2010; 114:6731-41. [DOI: 10.1021/jp101539u] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rusty W. Conner
- School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801
| | - Dana D. Dlott
- School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801
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Rahaman O, van Duin ACT, Bryantsev VS, Mueller JE, Solares SD, Goddard WA, Doren DJ. Development of a ReaxFF Reactive Force Field for Aqueous Chloride and Copper Chloride. J Phys Chem A 2010; 114:3556-68. [DOI: 10.1021/jp9090415] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Obaidur Rahaman
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Adri C. T. van Duin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Vyacheslav S. Bryantsev
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Jonathan E. Mueller
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Santiago D. Solares
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - William A. Goddard
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Douglas J. Doren
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
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Hamad IA, Novotny MA, Wipf DO, Rikvold PA. A new battery-charging method suggested by molecular dynamics simulations. Phys Chem Chem Phys 2010; 12:2740-3. [DOI: 10.1039/b920970k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Chenoweth K, van Duin A, Goddard W. The ReaxFF Monte Carlo Reactive Dynamics Method for Predicting Atomistic Structures of Disordered Ceramics: Application to the Mo3VOxCatalyst. Angew Chem Int Ed Engl 2009; 48:7630-4. [DOI: 10.1002/anie.200902574] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Chenoweth K, van Duin A, Goddard W. The ReaxFF Monte Carlo Reactive Dynamics Method for Predicting Atomistic Structures of Disordered Ceramics: Application to the Mo3VOxCatalyst. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Affiliation(s)
- Simon R. Phillpot
- Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Susan B. Sinnott
- Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611, USA
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Zhao M, Iron MA, Staszewski P, Schultz NE, Valero R, Truhlar DG. Valence–Bond Order (VBO): A New Approach to Modeling Reactive Potential Energy Surfaces for Complex Systems, Materials, and Nanoparticles. J Chem Theory Comput 2009; 5:594-604. [DOI: 10.1021/ct8004535] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Meiyu Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Theoretical Foundations of Biomedical Sciences and Medical Informatics, Collegium Medicum, Nicolaus Copernicus University, ul. Jagiellońska 13, 85-067 Bydgoszcz, Poland
| | - Mark A. Iron
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Theoretical Foundations of Biomedical Sciences and Medical Informatics, Collegium Medicum, Nicolaus Copernicus University, ul. Jagiellońska 13, 85-067 Bydgoszcz, Poland
| | - Przemysław Staszewski
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Theoretical Foundations of Biomedical Sciences and Medical Informatics, Collegium Medicum, Nicolaus Copernicus University, ul. Jagiellońska 13, 85-067 Bydgoszcz, Poland
| | - Nathan E. Schultz
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Theoretical Foundations of Biomedical Sciences and Medical Informatics, Collegium Medicum, Nicolaus Copernicus University, ul. Jagiellońska 13, 85-067 Bydgoszcz, Poland
| | - Rosendo Valero
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Theoretical Foundations of Biomedical Sciences and Medical Informatics, Collegium Medicum, Nicolaus Copernicus University, ul. Jagiellońska 13, 85-067 Bydgoszcz, Poland
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Theoretical Foundations of Biomedical Sciences and Medical Informatics, Collegium Medicum, Nicolaus Copernicus University, ul. Jagiellońska 13, 85-067 Bydgoszcz, Poland
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Jacob CR, Neugebauer J, Visscher L. A flexible implementation of frozen-density embedding for use in multilevel simulations. J Comput Chem 2008; 29:1011-8. [DOI: 10.1002/jcc.20861] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Karttunen M, Rottler J, Vattulainen I, Sagui C. Chapter 2 Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading? CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00002-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Heyden A, Lin H, Truhlar DG. Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations. J Phys Chem B 2007; 111:2231-41. [PMID: 17288477 DOI: 10.1021/jp0673617] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many applications of multilevel/multiscale methods, an active zone must be modeled by a high-level electronic structure method, while a larger environmental zone can be safely modeled by a lower-level electronic structure method, molecular mechanics, or an analytic potential energy function. In some cases though, the active zone must be redefined as a function of simulation time. Examples include a reactive moiety diffusing through a liquid or solid, a dislocation propagating through a material, or solvent molecules in a second coordination sphere (which is environmental) exchanging with solvent molecules in an active first coordination shell. In this article, we present a procedure for combining the levels smoothly and efficiently in such systems in which atoms or groups of atoms move between high-level and low-level zones. The method dynamically partitions the system into the high-level and low-level zones and, unlike previous algorithms, removes all discontinuities in the potential energy and force whenever atoms or groups of atoms cross boundaries and change zones. The new adaptive partitioning (AP) method is compared to Rode's "hot spot" method and Morokuma's "ONIOM-XS" method that were designed for multilevel molecular dynamics (MD) simulations. MD simulations in the microcanonical ensemble show that the AP method conserves both total energy and momentum, while the ONIOM-XS method fails to conserve total energy and the hot spot method fails to conserve both total energy and momentum. Two versions of the AP method are presented, one scaling as O(2N) and one with linear scaling in N, where N is the number of groups in a buffer zone separating the active high-level zone from the environmental low-level zone. The AP method is also extended to systems with multiple high-level zones to allow, for example, the study of ions and counterions in solution using the multilevel approach.
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Affiliation(s)
- Andreas Heyden
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
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Dahlke EE, Truhlar DG. Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters. J Chem Theory Comput 2006; 3:46-53. [DOI: 10.1021/ct600253j] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erin E. Dahlke
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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