Nanoparticles dynamics on a surface: fractal pattern formation and fragmentation

Dick, Veronika V.; Solov’yov, Ilia A.; Solov’yov, Andrey V.

doi:10.1088/1742-6596/248/1/012025

Cited by 12 publications

(16 citation statements)

References 29 publications

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“…For instance, different morphologies of C 60 films (including dendritic ones) were obtained with different thicknesses of the pristine fullerene films and the concentrations of Ag impurities (). Theoretically, the evolution of nanofractals’ morphologies has also been recently analyzed . The analysis based on the diffusion approach discretized on a lattice demonstrated that the suggested model reproduces well enough the experimentally observed scenario of the nanofractal evolution and fragmentation.…”

Section: Introductionmentioning

confidence: 78%

Thermally induced morphological transition of silver fractals

Solov’yov

Kébaı̈li

et al. 2013

Physica Status Solidi (b)

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We present both experimental and theoretical study of thermally induced morphological transition of silver nanofractals. Experimentally, those nanofractals formed from deposition and diffusion of preformed silver clusters on cleaved graphite surfaces exhibit dendritic morphologies that are highly sensitive to any perturbation, particularly caused by temperature. We analyze and characterize the morphological transition both in time and temperature using the recently developed Monte Carlo simulation approach for the description of nanofractal dynamics and compare the obtained results with the corresponding experimental data. The reported results reveal essential and general features of dynamical systems having dendritic shape.

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Section: Introductionmentioning

confidence: 78%

Thermally induced morphological transition of silver fractals

Solov’yov

Kébaı̈li

et al. 2013

Physica Status Solidi (b)

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“…The new module has been developed to permit simulations of multiscale physical, chemical, and biological processes in the 3D space. The KMC method described in the article extends the 2D–KMC methods introduced earlier in MBN Explorer , and generalizes several alternative KMC approaches . The unique feature of the present, 3D–KMC method, is to enable simulations of multiparticle systems, consisting of, for example, atoms, molecules, or nanoparticles, of different sizes, interacting through different potentials in the 3D space.…”

Section: Discussionmentioning

confidence: 99%

“…Although recent developments of MD‐based accelerated dynamics have successfully extended the simulation time scales to microseconds, it still remains computationally inefficient to employ atomistic MD for a large class of important problems such as, for example, diffusion, nucleation, growth, crystallization, defect evolution, and chemical reactions. Kinetic Monte Carlo (KMC) method is often the tool of choice for studying dynamic of processes occurring on long‐time scales, for example, milliseconds to hours . Instead of propagating individual atoms in time, as done in MD, the KMC method models the evolution of a molecular coarse‐grained system in a probabilistic way.…”

Section: Introductionmentioning

confidence: 99%

Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

Panshenskov

Solov’yov

2014

J Comput Chem

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Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system.

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“…Single CPU calculations are typically limited with up to ∼ 100,000 atoms, a constrain imposed by available processor speed and computer memory: it is difficult to study large molecular assemblies on a single CPU because the simulation time is expected to be significantly larger than in the case of parallel calculations. However, many scientific problems often do not require huge molecular systems, for example, studying mechanisms of atomic cluster formation,[18, 20, 21] stability of patterns on surface,[28–30] self‐assembly of composite nanocrystals and nanowires,[24–27] phase transition in polypeptide chains,[57–60] and many others. In these cases, one can do computations on a single processor in a reasonable time.…”

Section: Mbn Explorer Designmentioning

confidence: 99%

“…In particular, MBN Explorer is suited to compute the system's energy, to optimize molecular structures, as well as to explore the molecular and random walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters,[18–21] fullerenes, nanotubes,[22] polypeptides, proteins,[23] composite systems,[24–27] nanofractals,[28–30] and so forth.…”

Section: Introductionmentioning

confidence: 99%

MesoBioNano explorer—A universal program for multiscale computer simulations of complex molecular structure and dynamics

Solov’yov¹,

Yakubovich

Nikolaev³

et al. 2012

J Comput Chem

136

236

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We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, and so on. A distinct feature of the program, which makes it significantly different from the existing codes, is its universality and applicability to the description of a broad range of problems involving different molecular systems. Most of the existing codes are developed for particular classes of molecular systems and do not permit multiscale approach while MBN Explorer goes beyond these drawbacks. On demand, MBN Explorer allows to group particles in the system into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom. Despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes.

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Nanoparticles dynamics on a surface: fractal pattern formation and fragmentation

Cited by 12 publications

References 29 publications

Thermally induced morphological transition of silver fractals

Thermally induced morphological transition of silver fractals

Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

MesoBioNano explorer—A universal program for multiscale computer simulations of complex molecular structure and dynamics

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