Journal articles: 'Atomic scale description'

1

Cruz, Eduardo, and Klaus Schulten. "Atomic Scale Description of Ionic Behavior in Polymer Nanopores." Biophysical Journal 96, no. 3 (February 2009): 644a—645a. http://dx.doi.org/10.1016/j.bpj.2008.12.3835.

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Pignatelli, Isabella, Enrico Mugnaioli, Re´gine Mosser-Ruck, Odile Barres, Ute Kolb, and Nicolas Michau. "A multi-technique, micrometer- to atomic-scale description of a synthetic analogue of chukanovite, Fe2(CO3)(OH)2." European Journal of Mineralogy 26, no. 2 (April 11, 2014): 221–29. http://dx.doi.org/10.1127/0935-1221/2014/0026-2370.

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Fossati, Paul C. M., Michael J. D. Rushton, and William E. Lee. "Atomic-scale description of interfaces in rutile/sodium silicate glass–crystal composites." Physical Chemistry Chemical Physics 20, no. 26 (2018): 17624–36. http://dx.doi.org/10.1039/c8cp00675j.

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Zapolsky, H., G. Demange, and Rafal Abdank-Kozubski. "From the Atomistic to the Mesoscopic Scale Modeling of Phase Transition in Solids." Diffusion Foundations 12 (September 2017): 111–26. http://dx.doi.org/10.4028/www.scientific.net/df.12.111.

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The phase-field method is a very powerful tool to model the phase transformation and microstructural evolution of solids at mesoscopic scale. However, several important phenomena, like defect formation, grain boundary motion, or reconstructive phase transitions require an atomic scale study. Recently an approach called the quasi-particle approach, based on the Atomic Density Function theory was developed to incorporate the atomic-level crystalline structures into standard continuum theory for pure and multicomponent systems. This review focuses on the description of different computational methods used to model microstructural evolution and self-assembly phenomena at mesoscopic and atomistic scales. Various application examples of these methods are also presented.

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Zhao, Zheng, Haoxiang Xu, Yi Gao, and Daojian Cheng. "Universal description of heating-induced reshaping preference of core–shell bimetallic nanoparticles." Nanoscale 11, no. 3 (2019): 1386–95. http://dx.doi.org/10.1039/c8nr08889f.

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To achieve universal description of the reshaping process of core–shell bimetallic nanoparticles, we combined the tight-binding Ising Hamiltonian model with molecular dynamic simulations to propose a general theoretical model at the atomic scale while considering the temperature, bond energy, atomic size, and surface energy effects.

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Lynch, Diane, Dow Hurst, Patti Reggio, Alan Grossfield, and Mike Pitman. "Atomic Level Description of GPCR Activation Revealed by Microsecond Time Scale Molecular Dynamics." Biophysical Journal 96, no. 3 (February 2009): 365a. http://dx.doi.org/10.1016/j.bpj.2008.12.1965.

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Ruano Merchan, C., T. T. Dorini, F. Brix, L. Pasquier, M. Jullien, D. Pierre, S. Andrieu, et al. "Two-dimensional square and hexagonal oxide quasicrystal approximants in SrTiO₃ films grown on Pt(111)/Al₂O₃(0001)." Physical Chemistry Chemical Physics 24, no. 12 (2022): 7253–63. http://dx.doi.org/10.1039/d1cp05296a.

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An all-thin-film approach allows the synthesis of novel two-dimensional quasicrystalline approximants and an atomic scale description is provided based on combined experimental and theoretical investigations.

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Turlo, V., O. Politano, and F. Baras. "Microstructure evolution and self-propagating reactions in Ni-Al nanofoils: An atomic-scale description." Journal of Alloys and Compounds 708 (June 2017): 989–98. http://dx.doi.org/10.1016/j.jallcom.2017.03.051.

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Randrianandraina, Joharimanitra, Michael Badawi, Bruno Cardey, Manuel Grivet, Jean-Emmanuel Groetz, Christophe Ramseyer, Freddy Torrealba Anzola, Caroline Chambelland, and Didier Ducret. "Adsorption of water in Na-LTA zeolites: an ab initio molecular dynamics investigation." Physical Chemistry Chemical Physics 23, no. 34 (2021): 19032–42. http://dx.doi.org/10.1039/d1cp02624k.

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The very wide range of applications of LTA zeolites, including the storage of tritiated water, implies that a detailed and accurate atomic-scale description of the adsorption processes taking place in their structure is crucial.

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Caballero, Francisca G., Jonathan D. Poplawsky, Hung Wei Yen, Rosalia Rementeria, Lucia Morales-Rivas, Jer Ren Yang, and Carlos García-Mateo. "Complex Nano-Scale Structures for Unprecedented Properties in Steels." Materials Science Forum 879 (November 2016): 2401–6. http://dx.doi.org/10.4028/www.scientific.net/msf.879.2401.

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Processing bulk nanoscrystalline materials for structural applications still poses a significant challenge, particularly in achieving an industrially viable process. In this context, recent work has proved that complex nanoscale steel structures can be formed by solid reaction at low temperatures. These nanocrystalline bainitic steels present the highest strength ever recorded, unprecedented ductility, fatigue on par with commercial bearing steels and exceptional rolling-sliding wear performances. A description of the characteristics and significance of these remarkable structures in the context of the atomic mechanism of transformation is provided.

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Otranto, Sebastian. "Collisional Classical Dynamics at the Quantum Scale." Atoms 11, no. 11 (November 9, 2023): 144. http://dx.doi.org/10.3390/atoms11110144.

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During the past five decades, classical dynamics have been systematically used to gain insight on collision processes between charged particles and photons with atomic and molecular targets. These methods have proved to be efficient for systems in which numerical intensive quantum mechanical methods are not yet tractable. During the years, reaction cross sections for charge exchange and ionization have been scrutinized at the total and differential levels, leading to a clear understanding of the benefits and limitations inherent in a classical description. In this work, we present a review of the classical trajectory Monte Carlo method, its current status and the perspectives that can be envisaged for the near future.

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Hölscher, Hendrik, André Schirmeisen, and Udo D. Schwarz. "Principles of atomic friction: from sticking atoms to superlubric sliding." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366, no. 1869 (December 20, 2007): 1383–404. http://dx.doi.org/10.1098/rsta.2007.2164.

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Tribology—the science of friction, wear and lubrication—is of great importance for all technical applications where moving bodies are in contact. Nonetheless, little progress has been made in finding an exact atomistic description of friction since Amontons proposed his empirical macroscopic laws over three centuries ago. The advent of new experimental tools such as the friction force microscope, however, enabled the investigation of frictional forces occurring at well-defined contacts down to the atomic scale. This research field has been established as nanotribology. In the present article, we review our current understanding of the principles of atomic-scale friction based on recent experiments using friction force microscopy.

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Su, Yang, and Mi Lu. "Rate Allocation Algorithm with Successive Refinement in Peer-to-Peer Networks." Applied Mechanics and Materials 496-500 (January 2014): 2200–2203. http://dx.doi.org/10.4028/www.scientific.net/amm.496-500.2200.

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We introduce a new across-peer rate allocation algorithm with successive refinement to improve the video transmission performance in P2P networks, based on the combination of multiple description coding and network coding. Successive refinement is implemented through layered multiple description codes. The algorithm is developed to maximize the expected video quality at the receivers by partitioning video bitstream into different descriptions depending on different bandwidth conditions of each peer. Adaptive rate partition adjustment is applied to ensure the real reflection of the packet drop rate in the network. Also the granularity is changed to the scale of atomic blocks instead of stream rates in prior works. Through simulation results we show that the algorithm outperforms prior algorithms in terms of video playback quality at the peer ends, and helps the system more adjustable to the peer dynamics.

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Hong, Liang, Nitin Jain, Xiaolin Cheng, Ana Bernal, Madhusudan Tyagi, and Jeremy C. Smith. "Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering." Science Advances 2, no. 10 (October 2016): e1600886. http://dx.doi.org/10.1126/sciadv.1600886.

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Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

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Kawabata, S., Y. Tanaka, A. A. Golubov, A. S. Vasenko, S. Kashiwaya, and Y. Asano. "Tunneling Hamiltonian description of the atomic-scale 0–π transition in superconductor/ferromagnetic-insulator junctions." Physica C: Superconductivity and its Applications 471, no. 21-22 (November 2011): 1199–201. http://dx.doi.org/10.1016/j.physc.2011.05.158.

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Štich, I. "Computer simuations for the nano-scale." Acta Physica Slovaca. Reviews and Tutorials 57, no. 1 (February 1, 2007): 1–176. http://dx.doi.org/10.2478/v10155-010-0083-y.

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Computer simuations for the nano-scaleA review of methods for computations for the nano-scale is presented. The paper should provide a convenient starting point into computations for the nano-scale as well as a more in depth presentation for those already working in the field of atomic/molecular-scale modeling. The argument is divided in chapters covering the methods for description of the (i) electrons, (ii) ions, and (iii) techniques for efficient solving of the underlying equations. A fairly broad view is taken covering the Hartree-Fock approximation, density functional techniques and quantum Monte-Carlo techniques for electrons. The customary quantum chemistry methods, such as post Hartree-Fock techniques, are only briefly mentioned. Description of both classical and quantum ions is presented. The techniques cover Ehrenfest, Born-Oppenheimer, and Car-Parrinello dynamics. The strong and weak points of both principal and technical nature are analyzed. In the second part we introduce a number of applications to demonstrate the different approximations and techniques introduced in the first part. They cover a wide range of applications such as non-simple liquids, surfaces, molecule-surface interactions, applications in nanotechnology, etc. These more in depth presentations, while certainly not exhaustive, should provide information on technical aspects of the simulations, typical parameters used, and ways of analysis of the huge amounts of data generated in these large-scale supercomputer simulations.

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Rouquette, J., M. Hinterstein, J. Haines, Ph Papet, M. Knapp, J. Glaum, and H. Fuess. "Atomic scale description of the macroscopic piezo-ferroelectric properties of high-performance lead zirconate titanate (PZT)." Acta Crystallographica Section A Foundations of Crystallography 67, a1 (August 22, 2011): C705. http://dx.doi.org/10.1107/s0108767311082146.

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18

Sun, Xiao-Yu, Patrick Cordier, Vincent Taupin, Claude Fressengeas, and Sandro Jahn. "Continuous description of a grain boundary in forsterite from atomic scale simulations: the role of disclinations." Philosophical Magazine 96, no. 17 (May 5, 2016): 1757–72. http://dx.doi.org/10.1080/14786435.2016.1177232.

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19

Cheng, Tao, Andres Jaramillo-Botero, Qi An, Daniil V. Ilyin, Saber Naserifar, and William A. Goddard. "First principles-based multiscale atomistic methods for input into first principles nonequilibrium transport across interfaces." Proceedings of the National Academy of Sciences 116, no. 37 (August 3, 2018): 18193–201. http://dx.doi.org/10.1073/pnas.1800035115.

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This issue of PNAS features “nonequilibrium transport and mixing across interfaces,” with several papers describing the nonequilibrium coupling of transport at interfaces, including mesoscopic and macroscopic dynamics in fluids, plasma, and other materials over scales from microscale to celestial. Most such descriptions describe the materials in terms of the density and equations of state rather than specific atomic structures and chemical processes. It is at interfacial boundaries where such atomistic information is most relevant. However, there is not yet a practical way to couple these phenomena with the atomistic description of chemistry. The starting point for including such information is the quantum mechanics (QM). However, practical QM calculations are limited to a hundred atoms for dozens of picoseconds, far from the scales required to inform the continuum level with the proper atomistic description. To bridge this enormous gap, we need to develop practical methods to extend the scale of the atomistic simulation by several orders of magnitude while retaining the level of QM accuracy in describing the chemical process. These developments would enable continuum modeling of turbulent transport at interfaces to incorporate the relevant chemistry. In this perspective, we will focus on recent progress in accomplishing these extensions in first principles-based atomistic simulations and the strategies being pursued to increase the accuracy of very large scales while dramatically decreasing the computational effort.

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Sirindil, Abdullah, Raphael Kobold, Frédéric Mompiou, Sylvie Lartigue-Korinek, Loic Perriere, Gilles Patriarche, Marianne Quiquandon, and Denis Gratias. "Atomic scale analyses of {\bb Z}-module defects in an NiZr alloy." Acta Crystallographica Section A Foundations and Advances 74, no. 6 (October 4, 2018): 647–58. http://dx.doi.org/10.1107/s2053273318011439.

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Some specific structures of intermetallic alloys, like approximants of quasicrystals, have their unit cells and most of their atoms located on a periodic fraction of the nodes of a unique {\bb Z}-module [a set of the irrational projections of the nodes of a (N > 3-dimensional) lattice]. Those hidden internal symmetries generate possible new kinds of defects like coherent twins, translation defects and so-called module dislocations that have already been discussed elsewhere [Quiquandon et al. (2016). Acta Cryst. A72, 55–61; Sirindil et al. (2017). Acta Cryst. A73, 427–437]. Presented here are electron microscopy observations of the orthorhombic phase NiZr – and its low-temperature monoclinic variant – which reveal the existence of such defects based on the underlying {\bb Z}-module generated by the five vertices of the regular pentagon. New high-resolution electron microscopy (HREM) and scanning transmission electron microscopy high-angle annular dark-field (STEM-HAADF) observations demonstrate the agreement between the geometrical description of the structure in five dimensions and the experimental observations of fivefold twins and translation defects.

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Ko, Won-Seok, Jung Soo Lee, and Dong-Hyun Kim. "Atomistic simulations of Ag–Cu–Sn alloys based on a new modified embedded-atom method interatomic potential." Journal of Materials Research 37, no. 1 (October 18, 2021): 145–61. http://dx.doi.org/10.1557/s43578-021-00395-z.

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AbstractAn interatomic potential for the ternary Ag–Cu–Sn system, an important material system related to the applications of lead-free solders, is developed on the basis of the second nearest-neighbor modified embedded-atom-method formalism. Potential parameters for the ternary and related binary systems are determined based on the recently improved unary description of pure Sn and the present improvements to the unary descriptions of pure Ag and Cu. To ensure the sufficient performance of atomistic simulations in various applications, the optimization of potential parameters is conducted based on the force-matching method that utilizes density functional theory predictions of energies and forces on various atomic configurations. We validate that the developed interatomic potential exhibits sufficient accuracy and transferability to various physical properties of pure metals, intermetallic compounds, solid solutions, and liquid solutions. The proposed interatomic potential can be straightforwardly used in future studies to investigate atomic-scale phenomena in soldering applications. Graphical abstract

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Sasahara, Akira, and Hiroshi Onishi. "Surface Science Approach to Photochemistry of TiO₂." Solid State Phenomena 162 (June 2010): 115–33. http://dx.doi.org/10.4028/www.scientific.net/ssp.162.115.

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Surface science studies of photochemistry on titanium dioxide (TiO2) were reviewed. In the studies, photochemical processes were investigated in relation to atomic-scale surface structures by applying surface-sensitive analytical methods to single crystal TiO2 surfaces with well-defined structures. It is demonstrated that a surface science approach is promising for full description of the photochemical processes on TiO2.

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Imyanitov, Naum S. "Periodic law: new formulation and equation description." Pure and Applied Chemistry 91, no. 12 (December 18, 2019): 2007–21. http://dx.doi.org/10.1515/pac-2019-0802.

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Abstract The atomic weight, nuclear charge, electron configuration of an atom and the total number of i-electrons in an atom belonging to i-block (i = s, or p, or d, or f) are considered as the fundamental characteristics of an element (atom). Only in the latter case, the true periodicity is achieved: the repetitions occur at regular intervals. The total number of i-electrons in an atom belonging to i-block is used as the new basis for the description of the periodicity. This made possible to propose a new formulation of the Periodic law and to describe the Periodic law by an equation. The equation provides opportunities for large-scale prediction of the properties of elements and their compounds; it does not require special knowledge to work with it. Theoretical and applied aspects of the application of the new formulation and equation are outlined. Predictions are made for proton affinity and gas phase basicity of 20 elements, constants of inductive effects of 185 atoms and groups, electronic parameters of 222 neutral ligands. The suitability of the equation is exemplified by the description of the properties of atoms and elements, such as ionization energy, electron affinity, proton affinity, electronegativity, covalent atomic radii and the enthalpy of element formations in the gas phase. The equation makes possible to describe also the properties of compounds and their fragments: the acidic properties of the hydrogen compounds of the elements, the acidic properties of protonated atoms and molecules, gas phase basicity and proton affinity of compounds, inductive effects of ligands in coordination chemistry and substituents in organic chemistry, electronic parameters of neutral ligands, the electron effect constants of coordinating metals.

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Launey, K. D., J. P. Draayer, T. Dytrych, G. H. Sun, and S. H. Dong. "Approximate symmetries in atomic nuclei from a large-scale shell-model perspective." International Journal of Modern Physics E 24, no. 05 (May 2015): 1530005. http://dx.doi.org/10.1142/s0218301315300052.

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In this paper, we review recent developments that aim to achieve further understanding of the structure of atomic nuclei, by capitalizing on exact symmetries as well as approximate symmetries found to dominate low-lying nuclear states. The findings confirm the essential role played by the Sp(3, ℝ) symplectic symmetry to inform the interaction and the relevant model spaces in nuclear modeling. The significance of the Sp(3, ℝ) symmetry for a description of a quantum system of strongly interacting particles naturally emerges from the physical relevance of its generators, which directly relate to particle momentum and position coordinates, and represent important observables, such as, the many-particle kinetic energy, the monopole operator, the quadrupole moment and the angular momentum. We show that it is imperative that shell-model spaces be expanded well beyond the current limits to accommodate particle excitations that appear critical to enhanced collectivity in heavier systems and to highly-deformed spatial structures, exemplified by the second 0+ state in 12 C (the challenging Hoyle state) and 8 Be . While such states are presently inaccessible by large-scale no-core shell models, symmetry-based considerations are found to be essential.

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Sciammarella, Cesar A., Federico M. Sciammarella, and Luciano Lamberti. "Determination of Displacement Fields at the Sub-Nanometric Scale." Materials 12, no. 11 (June 3, 2019): 1804. http://dx.doi.org/10.3390/ma12111804.

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Macroscopic behavior of materials depends on interactions of atoms and molecules at nanometer/sub-nanometer scale. Experimental mechanics (EM) can be used for assessing relationships between the macro world and the atomic realm. Theoretical models developed at nanometric and sub-nanometric scales may be verified using EM techniques with the final goal of deriving comprehensive but manageable models. Recently, the authors have carried out studies on EM determination of displacements and their derivatives at the macro and microscopic scales. Here, these techniques were applied to the analysis of high-resolution transmission electron microscopy patterns of a crystalline array containing dislocations. Utilizing atomic positions as carriers of information and comparing undeformed and deformed configurations of observed area, displacements and their derivatives, as well as stresses, have been obtained in the Eulerian description of deformed crystal. Two approaches are introduced. The first establishes an analogy between the basic crystalline structure and a 120° strain gage rosette. The other relies on the fact that, if displacement information along three directions is available, it is possible to reconstruct the displacement field; all necessary equations are provided in the paper. Remarkably, the validity of the Cauchy-Born conjecture is proven to be correct within the range of observed deformations.

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Nahar, Sultana N. "Atomic Processes in Planetary Nebulae." Symposium - International Astronomical Union 209 (2003): 325–34. http://dx.doi.org/10.1017/s0074180900208942.

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A hot central star illuminating the surrounding ionized H II region usually produces very rich atomic spectra resulting from basic atomic processes: photoionization, electron-ion recombination, bound-bound radiative transitions, and collisional excitation of ions. Precise diagnostics of nebular spectra depend on accurate atomic parameters for these processes. Latest developments in theoretical computations are described, especially under two international collaborations known as the Opacity Project (OP) and the Iron Project (IP), that have yielded accurate and large-scale data for photoionization cross sections, transition probabilities, and collision strengths for electron impact excitation of most astrophysically abundant ions. As an extension of the two projects, a self-consistent and unified theoretical treatment of photoionization and electron-ion recombination has been developed where both the radiative and the dielectronic recombination processes are considered in an unified manner. Results from the Ohio State atomic-astrophysics group, and from the OP and IP collaborations, are presented. A description of the electronic web-interactive database, TIPTOPBASE, with the OP and the IP data, and a compilation of recommended data for effective collision strengths, is given.

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Szefer, G., and D. Jasińska. "Modeling of strains and stresses of material nanostructures." Bulletin of the Polish Academy of Sciences: Technical Sciences 57, no. 1 (March 1, 2009): 41–46. http://dx.doi.org/10.2478/v10175-010-0103-6.

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Modeling of strains and stresses of material nanostructuresStress and deformation analysis of materials and devices at the nanoscale level are topics of intense research in materials science and mechanics. In these investigations two approaches are observed. First, natural for the atomistic scale description is based on quantum and molecular mechanics. Second, characteristic for the macroscale continuum model description, is modified by constitutive laws taking atomic interactions into account. In the present paper both approaches are presented. For a discrete system of material points (atoms, molecules, clusters), measures of strain and stress, important from the mechanical viewpoint, are given. Numerical examples of crack propagation and deformation of graphite sheets (graphens) illustrate the behavior of the discrete systems.

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Schmidt, Alexander A., Yuri V. Trushin, K. L. Safonov, V. S. Kharlamov, Dmitri V. Kulikov, Oliver Ambacher, and Jörg Pezoldt. "Multi-Scale Simulation of MBE-Grown SiC/Si Nanostructures." Materials Science Forum 527-529 (October 2006): 315–18. http://dx.doi.org/10.4028/www.scientific.net/msf.527-529.315.

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The main obstacle for the implementation of numerical simulation for the prediction of the epitaxial growth is the variety of physical processes with considerable differences in time and spatial scales taking place during epitaxy: deposition of atoms, surface and bulk diffusion, nucleation of two-dimensional and three-dimensional clusters, etc. Thus, it is not possible to describe all of them in the framework of a single physical model. In this work there was developed a multi-scale simulation method for molecular beam epitaxy (MBE) of silicon carbide nanostructures on silicon. Three numerical methods were used in a complex: Molecular Dynamics (MD), kinetic Monte Carlo (KMC), and the Rate Equations (RE). MD was used for the estimation of kinetic parameters of atoms at the surface, which are input parameters for other simulation methods. The KMC allowed the atomic-scale simulation of the cluster formation, which is the initial stage of the SiC growth, while the RE method gave the ability to study the growth process on a longer time scale. As a result, a full-scale description of the surface evolution during SiC formation on Si substrates was developed.

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Pletikapić, Galja, and Nadica Ivošević DeNardis. "Application of surface analytical methods for hazardous situation in the Adriatic Sea: monitoring of organic matter dynamics and oil pollution." Natural Hazards and Earth System Sciences 17, no. 1 (January 6, 2017): 31–44. http://dx.doi.org/10.5194/nhess-17-31-2017.

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Abstract. Surface analytical methods are applied to examine the environmental status of seawaters. The present overview emphasizes advantages of combining surface analytical methods, applied to a hazardous situation in the Adriatic Sea, such as monitoring of the first aggregation phases of dissolved organic matter in order to potentially predict the massive mucilage formation and testing of oil spill cleanup. Such an approach, based on fast and direct characterization of organic matter and its high-resolution visualization, sets a continuous-scale description of organic matter from micro- to nanometre scales. Electrochemical method of chronoamperometry at the dropping mercury electrode meets the requirements for monitoring purposes due to the simple and fast analysis of a large number of natural seawater samples enabling simultaneous differentiation of organic constituents. In contrast, atomic force microscopy allows direct visualization of biotic and abiotic particles and provides an insight into structural organization of marine organic matter at micro- and nanometre scales. In the future, merging data at different spatial scales, taking into account experimental input on micrometre scale, observations on metre scale and modelling on kilometre scale, will be important for developing sophisticated technological platforms for knowledge transfer, reports and maps applicable for the marine environmental protection and management of the coastal area, especially for tourism, fishery and cruiser trafficking.

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Kalinin, Sergei V., Ondrej Dyck, Stephen Jesse, and Maxim Ziatdinov. "Exploring order parameters and dynamic processes in disordered systems via variational autoencoders." Science Advances 7, no. 17 (April 2021): eabd5084. http://dx.doi.org/10.1126/sciadv.abd5084.

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We suggest and implement an approach for the bottom-up description of systems undergoing large-scale structural changes and chemical transformations from dynamic atomically resolved imaging data, where only partial or uncertain data on atomic positions are available. This approach is predicated on the synergy of two concepts, the parsimony of physical descriptors and general rotational invariance of noncrystalline solids, and is implemented using a rotationally invariant extension of the variational autoencoder applied to semantically segmented atom-resolved data seeking the most effective reduced representation for the system that still contains the maximum amount of original information. This approach allowed us to explore the dynamic evolution of electron beam–induced processes in a silicon-doped graphene system, but it can be also applied for a much broader range of atomic scale and mesoscopic phenomena to introduce the bottom-up order parameters and explore their dynamics with time and in response to external stimuli.

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Hsu, Hsiang Chen, and Li Ming Chu. "Nanotribology Properties and Microscopic Interfacial Frictional Behavior Studied by Atomic Force Microscopy." Advanced Materials Research 230-232 (May 2011): 639–43. http://dx.doi.org/10.4028/www.scientific.net/amr.230-232.639.

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This paper deals with the description of a method for the measurement of the nanotribology properties and microscopic interfacial frictional behavior with Atomic Force Microscopy (AFM). AFM force-displacement curve is utilized to determine the nanotribology properties. The interfacial coefficient of frictional force can be derived from a serial of calculations. A well-defined contact area is measured to study the frictional force and friction stress. The roughness of contact surface influences the contact between friction and surface forces. The study of roughness parameters corresponds to evaluate the friction and the interfacial strengths. Local variation in micro/nano tribology is also measured. The measured surface topography (3D profiles) are then applied to determinate the potential energy in molecular dynamic (MD) method to study the atomic scale frictional interactions.

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Bulou, Hervé, Christine Goyhenex, and Carlo Massobrio. "Diffusion in Materials by Atomic-Scale Modeling: Exploiting the Predictive Power of Classical and First-Principles Molecular Dynamics." Defect and Diffusion Forum 297-301 (April 2010): 244–53. http://dx.doi.org/10.4028/www.scientific.net/ddf.297-301.244.

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This paper highlights the role played by diffusion processes to achieve a better characterization of structure and dynamics in atomic-scale studies of materials. Two classes of examples are presented. In the first, we take advantage of diffusion coefficients to assess the performances of different exchange-correlation functionals employed within the framework of density functional theory. By calculating the diffusion coefficients one is able to make a choice on the functional best suited to describe a prototypical disordered system, liquid GeSe2. In the second class of examples, we rely on classical molecular dynamics to describe diffusion mechanism on nanostructured substrates. The migration of a Co adatom on a stepped Pt(111) surface is analyzed in detail and correlated to the value of the different diffusion barriers. The diffusion behavior of Au adatoms on the reconstructed Au(111) substrate is described in terms of diffusion isotropy and anisotropy, by comparison with the case of Co/Au(111). Taken altogether, these studies exemplify the close link between diffusion properties, a realistic description of materials and the current level of performances of atomic-scale simulations methods.

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Woznica, Natalia, Lukasz Hawelek, Henry E. Fischer, Ivan Bobrinetskiy, and Andrzej Burian. "The atomic scale structure of graphene powder studied by neutron and X-ray diffraction." Journal of Applied Crystallography 48, no. 5 (August 18, 2015): 1429–36. http://dx.doi.org/10.1107/s1600576715014053.

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The structure of graphene obtained by chemical exfoliation of graphiteviathe oxidation/reduction procedure has been determined using wide-angle scattering of neutrons and X-rays combined with computer simulations based on classical molecular dynamics (MD). A comparison of results obtained from wide-angle neutron scattering (WANS) with the D4 neutron diffractometer dedicated for liquids and amorphous materials (Institute Laue–Langevin in Grenoble) and from wide-angle X-ray scattering (WAXS) with the laboratory Rigaku-Denki D/MAX RAPID II diffractometer has shown that both techniques provide data of a good quality that can be used to derive precise and valuable structural information about graphene. To obtain detailed structural information, the paracrystal formalism has been used along with MD simulations. The MD simulations were performed at 300 K with second-generation reactive empirical bond order potential for atoms lying in the same layer and the Lennard–Jones potential for interlayer interactions. The proposed models consist of three-layered systems, 36 Å in diameter, in which mono-vacancy, di-vacancy and Stone–Thrower–Wales types of defects are introduced. The reported results show that the WANS and WAXS methods together with the MD simulations contribute to a detailed description of the graphene materials, including the presence of topological defects, which is important as their structure at the atomic scale dramatically affects their electrical and mechanical properties.

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Evans, Paul G., and Simon J. L. Billinge. "Advances in Scattering Probes for Materials." MRS Bulletin 35, no. 7 (July 2010): 495–503. http://dx.doi.org/10.1557/mrs2010.598.

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AbstractRecent advances in x-ray and neutron sources, optics, and scattering methods are heralding a new age in the study of the structure and properties of complex materials. By providing unprecedented resolution in real space, reciprocal space, and time, new techniques address materials characterization challenges beyond anything possible before, at length scales ranging from the atomic scale to the mesoscale, and at times as short as femtoseconds. The high degree of coherence of third-generation synchrotron sources permits a new level of precision in the quantitative description and analysis of diffraction and scattering and allows beams with sizes probing individual nanostructures to be produced. As a result, in situx-ray and neutron analysis techniques now provide insight into the structure of nanomaterials and yield a more precise set of metrics describing the nanometer-scale structure of materials. Time resolution and in situ studies allow application of these techniques to materials driven far from equilibrium and to the challenging environment associated with materials processing.

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Scherer, Michael M., Stefan Floerchinger, and Holger Gies. "Functional renormalization for the Bardeen–Cooper–Schrieffer to Bose–Einstein condensation crossover." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 369, no. 1946 (July 13, 2011): 2779–99. http://dx.doi.org/10.1098/rsta.2011.0072.

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We review the functional renormalization group (RG) approach to the Bardeen–Cooper–Schrieffer to Bose–Einstein condensation (BCS–BEC) crossover for an ultracold gas of fermionic atoms. Formulated in terms of a scale-dependent effective action, the functional RG interpolates continuously between the atomic or molecular microphysics and the macroscopic physics on large length scales. We concentrate on the discussion of the phase diagram as a function of the scattering length and the temperature, which is a paradigm example for the non-perturbative power of the functional RG. A systematic derivative expansion provides for both a description of the many-body physics and its expected universal features as well as an accurate account of the few-body physics and the associated BEC and BCS limits.

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Haase, Kristina, and Andrew E. Pelling. "Investigating cell mechanics with atomic force microscopy." Journal of The Royal Society Interface 12, no. 104 (March 2015): 20140970. http://dx.doi.org/10.1098/rsif.2014.0970.

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Transmission of mechanical force is crucial for normal cell development and functioning. However, the process of mechanotransduction cannot be studied in isolation from cell mechanics. Thus, in order to understand how cells ‘feel’, we must first understand how they deform and recover from physical perturbations. Owing to its versatility, atomic force microscopy (AFM) has become a popular tool to study intrinsic cellular mechanical properties. Used to directly manipulate and examine whole and subcellular reactions, AFM allows for top-down and reconstitutive approaches to mechanical characterization. These studies show that the responses of cells and their components are complex, and largely depend on the magnitude and time scale of loading. In this review, we generally describe the mechanotransductive process through discussion of well-known mechanosensors. We then focus on discussion of recent examples where AFM is used to specifically probe the elastic and inelastic responses of single cells undergoing deformation. We present a brief overview of classical and current models often used to characterize observed cellular phenomena in response to force. Both simple mechanistic models and complex nonlinear models have been used to describe the observed cellular behaviours, however a unifying description of cell mechanics has not yet been resolved.

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López-Cepero, José M., Sheldon M. Wiederhorn, António Ramirez de Arellano-López, and Julian Martínez-Fernández. "AFM Study of Typical Fracture Surfaces in Room-Temperature Fracture of Sapphire." Key Engineering Materials 409 (March 2009): 113–22. http://dx.doi.org/10.4028/www.scientific.net/kem.409.113.

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Rhombohedral r-plane fracture surfaces in sapphire are analyzed by optical microscopy and by atomic force microscopy. Features of special interest include steps, lines and angles on the surface that appear to have crystallographic origins. A classification and description of these features is given over a scale ranging from hundreds of micrometers to tens of nanometers. Preferential directions in the surface are identified and related to the crystalline orientation of the sample; an attempt is made to identify the underlying phenomenology behind the appearance of each kind of feature.

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Abe, Hiroshi, Ryoji Fukushima, Michio Onji, Kentraro Hirayama, Hiroaki Kishimura, Yukihiro Yoshimura, and Shinichiro Ozawa. "Two-length scale description of hydrophobic room-temperature ionic liquid–alcohol systems." Journal of Molecular Liquids 215 (March 2016): 417–22. http://dx.doi.org/10.1016/j.molliq.2015.12.011.

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39

Pennycook, S. J., G. Duscher, R. Buczko, and S. T. Pantelides. "The Si/SiO2 Interface: Atomic Structures, Composition, Strain and Energetics." Microscopy and Microanalysis 7, S2 (August 2001): 768–69. http://dx.doi.org/10.1017/s1431927600029913.

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A number of recent studies of grain boundaries and heterophase interfaces have demonstrated the power of combining Z-contrast STEM imaging, EELS and first-principles theoretical modeling to give an essentially complete atomic scale description of structure, bonding and energetics. Impurity sites and valence can be determined experimentally and configurations determined through calculations.Here we present an investigation of the Si/SiO2 interface. The Z-contrast image in Fig. la, taken with the VG Microscopes HB603U STEM, shows that the atomic structure of Si is maintained up to the last layers visible. The decrease in intensity near the interface could originate from interfacial roughness of around one unit cell (∼0.5 nm), or may represent dechanneling in the slightly buckled columns induced by the oxide. Fig. lb, taken from a sample with ∼1 nm interface roughness, shows a band of bright contrast near the interface. This is not due to impurities or thickness variation since it disappears on increasing the detector angle from 25 mrad to 45 mrad (Fig. lc), and is therefore due to induced strain.

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Pennycook, S. J., G. Duscher, R. Buczko, and S. T. Pantelides. "The Si/SiO2 Interface: Atomic Structures, Composition, Strain And Energetics." Microscopy and Microanalysis 5, S2 (August 1999): 122–23. http://dx.doi.org/10.1017/s1431927600013933.

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A number of recent studies of grain boundaries and heterophase interfaces have demonstrated the power of combining Z-contrast STEM imaging, EELS and first-principles theoretical modeling to give an essentially complete atomic scale description of structure, bonding and energetics. Impurity sites and valence can be determined experimentally and configurations determined through calculations.Here we present an investigation of the Si/SiO2 interface. The Z-contrast image in Fig. la, taken with the VG Microscopes HB603U STEM, shows that the atomic structure of Si is maintained up to the last layers visible. The decrease in intensity near the interface could originate from interfacial roughness of around one unit cell (∼0.5 nm), or may represent dechanneling in the slightly buckled columns induced by the oxide. Fig. lb, taken from a sample with ∼1 nm interface roughness, shows a band of bright contrast near the interface. This is not due to impurities or thickness variation since it disappears on increasing the detector angle from 25 mrad to 45 mrad (Fig. lc), and is therefore due to induced strain.

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Szeląg, Agata, Katarzyna Baruch-Mazur, Krzysztof Brawata, Bartosz Przysucha, and Dominik Mleczko. "Validation of a 1:8 Scale Measurement Stand for Testing Airborne Sound Insulation." Sensors 21, no. 19 (October 7, 2021): 6663. http://dx.doi.org/10.3390/s21196663.

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This paper contains a detailed description of the design and validation of a measurement stand for testing the airborne sound insulation of specimens made at a small scale. The stand is comprised of two coupled reverberation rooms in which the geometry represents the full-size reverberation rooms used at the AGH University of Science and Technology at a 1:8 scale. The paper proves that both the scaled measurement stand and the testing methodology conform to the ISO 10140 standards, and that the obtained measurement uncertainty does not exceed the maximum values specified in ISO 12999-1. Moreover, the calculated uncertainty of measurements obtained for the 1:8 scale stand is comparable with the typical uncertainty given in ISO 12999-1 and the uncertainty obtained on the full-scale measurement stand. In connection with the above, the authors have proved that by using the scaled-down measurement stands, one can obtain reliable and repeatable results of measurements of airborne sound insulation.

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Carlini, Roger D., Willem T. H. van Oers, Mark L. Pitt, and Gregory R. Smith. "Determination of the Proton's Weak Charge and Its Constraints on the Standard Model." Annual Review of Nuclear and Particle Science 69, no. 1 (October 19, 2019): 191–217. http://dx.doi.org/10.1146/annurev-nucl-101918-023633.

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This article discusses some of the history of parity-violation experiments that culminated in the Qweak experiment, which provided the first determination of the proton's weak charge [Formula: see text]. The guiding principles necessary to the success of that experiment are outlined, followed by a brief description of the Qweak experiment. Several consistent methods used to determine [Formula: see text] from the asymmetry measured in the Qweak experiment are explained in detail. The weak mixing angle sin2θw determined from [Formula: see text] is compared with results from other experiments. A description of the procedure for using the [Formula: see text] result on the proton to set TeV-scale limits for new parity-violating semileptonic physics beyond the Standard Model (BSM) is presented. By also considering atomic parity-violation results on cesium, the article shows how this result can be generalized to set limits on BSM physics, which couples to any combination of valence quark flavors. Finally, the discovery space available to future weak-charge measurements is explored.

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van Spengen, W. Merlijn, Viviane Turq, and Joost W. M. Frenken. "The description of friction of silicon MEMS with surface roughness: virtues and limitations of a stochastic Prandtl–Tomlinson model and the simulation of vibration-induced friction reduction." Beilstein Journal of Nanotechnology 1 (December 22, 2010): 163–71. http://dx.doi.org/10.3762/bjnano.1.20.

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We have replaced the periodic Prandtl–Tomlinson model with an atomic-scale friction model with a random roughness term describing the surface roughness of micro-electromechanical systems (MEMS) devices with sliding surfaces. This new model is shown to exhibit the same features as previously reported experimental MEMS friction loop data. The correlation function of the surface roughness is shown to play a critical role in the modelling. It is experimentally obtained by probing the sidewall surfaces of a MEMS device flipped upright in on-chip hinges with an AFM (atomic force microscope). The addition of a modulation term to the model allows us to also simulate the effect of vibration-induced friction reduction (normal-force modulation), as a function of both vibration amplitude and frequency. The results obtained agree very well with measurement data reported previously.

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Dal Sasso, Gregorio, Maria Chiara Dalconi, Giorgio Ferrari, Jan Skov Pedersen, Sergio Tamburini, Federica Bertolotti, Antonietta Guagliardi, Marco Bruno, Luca Valentini, and Gilberto Artioli. "An Atomistic Model Describing the Structure and Morphology of Cu-Doped C-S-H Hardening Accelerator Nanoparticles." Nanomaterials 12, no. 3 (January 21, 2022): 342. http://dx.doi.org/10.3390/nano12030342.

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Calcium silicate hydrate (C-S-H) is the main binding phase in Portland cement. The addition of C-S-H nanoparticles as nucleation seeds has successfully been used to accelerate the hydration process and the precipitation of binding phases either in conventional Portland cement or in alternative binders. Indeed, the modulation of the hydration kinetics during the early-stage dissolution-precipitation reactions, by acting on the nucleation and growth of binding phases, improves the early strength development. The fine-tuning of concrete properties in terms of compressive strength and durability by designed structural modifications can be achieved through the detailed description of the reaction products at the atomic scale. The nano-sized, chemically complex and structurally disordered nature of these phases hamper their thorough structural characterization. To this aim, we implement a novel multi-scale approach by combining forefront small-angle X-ray scattering (SAXS) and synchrotron wide-angle X-ray total scattering (WAXTS) analyses for the characterization of Cu-doped C-S-H nanoparticles dispersed in a colloidal suspension, used as hardening accelerator. SAXS and WAXTS data were analyzed under a unified modeling approach by developing suitable atomistic models for C-S-H nanoparticles to be used to simulate the experimental X-ray scattering pattern through the Debye scattering equation. The optimization of atomistic models against the experimental pattern, together with complementary information on the structural local order from 29Si solid-state nuclear magnetic resonance and X-ray absorption spectroscopy, provided a comprehensive description of the structure, size and morphology of C-S-H nanoparticles from the atomic to the nanometer scale. C-S-H nanoparticles were modeled as an assembly of layers composed of 7-fold coordinated Ca atoms and decorated by silicate dimers and chains. The structural layers are a few tens of nanometers in length and width, with a crystal structure resembling that of a defective tobermorite, but lacking any ordering between stacking layers.

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Kajánek, Pavol, Alojz Kopáčik, Peter Kyrinovič, Ján Erdélyi, Marián Marčiš, and Marek Fraštia. "Metrology of Short-Length Measurers—Development of a Comparator for the Calibration of Measurers Based on Image Processing and Interferometric Measurements." Sensors 24, no. 5 (February 29, 2024): 1573. http://dx.doi.org/10.3390/s24051573.

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For the calibration of linear scales, comparators are generally used. Comparators are devices that enable the movement of an evaluation apparatus over a calibrated scale along a linear base with high precision. The construction of a comparator includes a movable carriage that carries the device for the evaluation of the position of the given edge of the line scale relative to the beginning of the scale. In principle, it involves a camera capturing the scale of the measurer, where the position of the camera’s projection center is measured using an interferometer. This article addresses the development of a comparator assembled from low-cost components, as well as the description of systematic influences related to the movement of individual parts of the system, such as the inclination and rotation of the camera and directional and height deviations during the carriage’s movement. This article also includes an evaluation of the edge of the given scale with subpixel accuracy, addressing distortion elimination and excluding the influences of impurities or imperfections on the scale. The proposed solution was applied to linear-scale measurers, such as leveling rods with coded and conventional scales and measuring tapes. The entire process of measurement and evaluation was automated.

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Frandsen, Benjamin A., and Simon J. L. Billinge. "Magnetic structure determination from the magnetic pair distribution function (mPDF): ground state of MnO." Acta Crystallographica Section A Foundations and Advances 71, no. 3 (April 25, 2015): 325–34. http://dx.doi.org/10.1107/s205327331500306x.

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An experimental determination of the magnetic pair distribution function (mPDF) defined in an earlier paper [Frandsenet al.(2014).Acta Cryst.A70, 3–11] is presented for the first time. The mPDF was determined from neutron powder diffraction data from a reactor and a neutron time-of-flight total scattering source on a powder sample of the antiferromagnetic oxide MnO. A description of the data treatment that allowed the measured mPDF to be extracted and then modelled is provided and utilized to investigate the low-temperature structure of MnO. Atomic and magnetic co-refinements support the scenario of a locally monoclinic ground-state atomic structure, despite the average structure being rhombohedral, with the mPDF analysis successfully recovering the known antiferromagnetic spin configuration. The total scattering data suggest a preference for the spin axis to lie along the pseudocubic [10{\overline 1}] direction. Finally,r-dependent PDF refinements indicate that the local monoclinic structure tends toward the average rhombohedralR{\overline 3}msymmetry over a length scale of approximately 100 Å.

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Lü, Jing-Tao, Tue Gunst, Per Hedegård, and Mads Brandbyge. "Current-induced dynamics in carbon atomic contacts." Beilstein Journal of Nanotechnology 2 (December 16, 2011): 814–23. http://dx.doi.org/10.3762/bjnano.2.90.

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Background: The effect of electric current on the motion of atoms still poses many questions, and several mechanisms are at play. Recently there has been focus on the importance of the current-induced nonconservative forces (NC) and Berry-phase derived forces (BP) with respect to the stability of molecular-scale contacts. Systems based on molecules bridging electrically gated graphene electrodes may offer an interesting test-bed for these effects. Results: We employ a semi-classical Langevin approach in combination with DFT calculations to study the current-induced vibrational dynamics of an atomic carbon chain connecting electrically gated graphene electrodes. This illustrates how the device stability can be predicted solely from the modes obtained from the Langevin equation, including the current-induced forces. We point out that the gate offers control of the current, independent of the bias voltage, which can be used to explore current-induced vibrational instabilities due the NC/BP forces. Furthermore, using tight-binding and the Brenner potential we illustrate how Langevin-type molecular-dynamics calculations including the Joule heating effect for the carbon-chain systems can be performed. Molecular dynamics including current-induced forces enables an energy redistribution mechanism among the modes, mediated by anharmonic interactions, which is found to be vital in the description of the electrical heating. Conclusion: We have developed a semiclassical Langevin equation approach that can be used to explore current-induced dynamics and instabilities. We find instabilities at experimentally relevant bias and gate voltages for the carbon-chain system.

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Bakhracheva, Yulia. "The Use of Fractal Formalism for the Description of Microstructures Engineering Materials." Solid State Phenomena 316 (April 2021): 923–27. http://dx.doi.org/10.4028/www.scientific.net/ssp.316.923.

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In this paper, the structures of spatial self-organization of steels after thermos-cyclic exposure were studied, using the fractal formalism method. It is shown that the structures, observed after cyclic heat exposure, can be characterized by the presence of the invariance property of their structure at different scale levels.

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Truesdale, Victor W., and Jim Greenwood. "Latent disciplinal clashes concerning the batch dissolution of minerals, and their wider implications." Environmental Chemistry 15, no. 2 (2018): 113. http://dx.doi.org/10.1071/en17199.

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Environmental contextMineral dissolution kinetics are important to understand natural processes including those increasingly used to store waste carbon dioxide and highly radio-active nuclides, and those involved in the amelioration of climate change and sea-level rise. We highlight a mistake made in the fundamental science that has retarded progress in the field for over 40 years. Its removal suggests improved ways to approach dissolution studies. AbstractMineral dissolution kinetics are fundamental to biogeochemistry, and to the application of science to reduce the deleterious effects of humanity’s waste products, e.g. CO2 and radio-nuclides. However, a mistake made in the selection of the rate equation appropriate for use at the macro-scale of the aquatic environment has stymied growth in major aspects of the subject for some 40 years. This paper identifies the mistake, shows how it represents a latent disciplinal clash between two rate equations, and explores the misunderstandings that resulted from it. The paper also briefly explores other disciplinal clashes. Using the example of calcite dissolution, the paper also shows how the phenomenon of ‘non-ideal’ dissolution, which is prevalent in alumino-silicate mineral dissolution, as well as with calcite, has obscured the clash. The paper provides new information on plausible mechanisms, the absence of which has contributed to the problem. Finally, it argues that disciplinal clashes need to be minimised so that a rigorous description of dissolution at the large scale can be matched to findings at the atomic, or near-atomic, scale.

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Viger‐Gravel, Jasmine, Federico M. Paruzzo, Corine Cazaux, Ribal Jabbour, Amandine Leleu, Françoise Canini, Pierre Florian, Frédéric Ronzon, David Gajan, and Anne Lesage. "Atomic‐Scale Description of Interfaces between Antigen and Aluminum‐Based Adjuvants Used in Vaccines by Dynamic Nuclear Polarization (DNP) Enhanced NMR Spectroscopy." Chemistry – A European Journal 26, no. 41 (July 8, 2020): 8976–82. http://dx.doi.org/10.1002/chem.202001141.

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Journal articles on the topic 'Atomic scale description'

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