scholarly journals REGULARITIES OF STRUCTURE FORMATION IN BIMETALLIC NANOPARTICLES WITH DIFFERENT CRYSTALLIZATION TEMPERATURES

2021 ◽  
pp. 568-579
Author(s):  
Владимир Сергеевич Мясниченко ◽  
Павел Михайлович Ершов ◽  
Ксения Геннадьевна Савина ◽  
Алексей Дмитриевич Веселов ◽  
Сергей Сергеевич Богданов ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structure Formation ◽  
Crystallization Temperature ◽  
Bimetallic Nanoparticles ◽  
Structural Transformations ◽  
Atomic Size ◽  
Mixing Energy ◽  
Low Concentrations ◽  
Concentration Dependences ◽  
The Given

В данной работе исследуются закономерности структурообразования на примере биметаллических наночастиц Au - Ag, Ti - Al, Ti - V. Данные биметаллические наночастицы обладают различным размерным несоответствием и различной температурой кристаллизации. Проведены серии молекулярно-динамических экспериментов, по результатам которых проанализированы конечные конфигурации с наименьшей энергией и получены концентрационные зависимости энергии смешения. Анализ концентрационных зависимостей энергии смешения позволяет прогнозировать составы и размеры биметаллических наночастиц, которые могут проявлять нестабильность, как например для биметаллических наночастиц Ti - V. Асимметричность отдельных концентрационных зависимостей энергии смешения свидетельствуют о специфических структурных превращениях, характерных именно для данного состава и размера. Установлено, что для биметаллических наночастиц Au - Ag, Ti - Al характерна структурная сегрегация, и она активно проявляется при малых концентрациях более легкоплавкого компонента. Конкурирующими фазами в данном случае выступают ГЦК и ГПУ фазы. Кроме того, для средних из рассматриваемых в статье размеров исследована зависимость температуры кристаллизации от состава биметаллических наночастиц. In this work, of the structure formation was investigated using Au - Ag, Ti - Al, Ti - V bimetallic nanoparticles as the patterns. These bimetallic nanoparticles have different atomic size mismatches and different crystallization temperatures. A series of molecular dynamics experiments was carried out. Based on their results, the final configurations with the lowest energy were analyzed and the concentration dependences of the mixing energy were obtained. An analysis of the concentration dependences of the mixing energy makes it possible to predict the compositions and sizes of bimetallic nanoparticles, which can exhibit instability, such as for Ti - V bimetallic nanoparticles. The asymmetry of individual concentration dependences of the mixing energy is evidence of specific structural transformations characteristic for the given composition and size. It has been established that structural segregation is characteristic for Au - Ag,Ti - Al bimetallic nanoparticles and it is actively manifested at low concentrations of a more low-melting component. The competing phases in this case are fcc and hcp phases. In addition, for the average sizes considered in the article, the dependence of the crystallization temperature on the composition of bimetallic nanoparticles was investigated.

scholarly journals INFLUENCE OF THE SIZE EFFECT ON THE REGULARITIES OF THE STRUCTURE FORMATION IN BIMETALLIC Au-Co NANOPARTICLES

2021 ◽  
pp. 612-623
Author(s):  
Николай Юрьевич Сдобняков ◽  
Сергей Сергеевич Богданов ◽  
Алексей Дмитриевич Веселов ◽  
Ксения Геннадьевна Савина ◽  
Никита Игоревич Непша ◽  
...  
Keyword(s):  
Structure Formation ◽  
Tight Binding ◽  
Internal Symmetry ◽  
Binding Potential ◽  
Icosahedral Symmetry ◽  
Mixing Energy ◽  
Concentration Dependences ◽  
Potential Part ◽  
Characteristic Features ◽  
Co Nanoparticles

В данной работе методом молекулярной динамики с использованием потенциала сильной связи исследовались биметаллические наночастицы Au - Co трёх стехиометрических составов различного размера. Установлены закономерности структурообразования, описаны их характерные особенности. В частности, в составах с 50ат.% и 75ат.% содержанием Au образуются множественные малые ядра локальной икосаэдрической симметрии. Только в составе Co -25ат.% Au с увеличением размера частиц преобладают кристаллические фазы. Выявлены составы, в которых внутренняя симметрия наночастицы определена наличием одного икосаэдра, либо сверхструктуры из нескольких икосаэдров. Рассчитаны концентрационные зависимости энергии смешения биметаллической наночастицы Au - Co. Показано, что в определённом диапазоне размеров существуют концентрационные составы, при которых биметаллический наносплав может проявлять нестабильность. С использованием калорических кривых потенциальной части внутренней энергии определены температуры кристаллизации. Установлено, что температура кристаллизации демонстрирует умеренный, либо существенный, в зависимости от состава, рост с увеличением размера биметаллических наночастиц Au - Co. This work studied bimetallic Au - Co nanoparticles of three stoichiometric compositions of various sizes by the molecular dynamics method using the tight-binding potential. The regularities of structure formation are established, their characteristic features are described. In particular, in compositions with 50at% and 75at% Au content, multiple small nuclei of local icosahedral symmetry are formed. Crystalline phases prevail only in the Co - 25 at% Au composition with an increase in the particle size. Compositions are revealed in which the internal symmetry of a nanoparticle is determined by the presence of one icosahedron or a superstructure of several icosahedrons. The concentration dependences of the mixing energy of a bimetallic Au - Co nanoparticle are calculated. It is shown that there are concentrations of compositions at which bimetallic nanoalloys can exhibit instability in a certain size range. Crystallization temperatures were determined using the caloric curves of the potential part of the internal energy. It was found that the crystallization temperature demonstrates a moderate or significant, depending on the composition as well as growth with an increase in the size of bimetallic Au - Co nanoparticles.

scholarly journals CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo

2020 ◽  
Author(s):  
Adrián López Martín ◽  
Mohamed Mounir ◽  
Irmtraud M Meyer
Keyword(s):  
Structure Formation ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Computational Method ◽  
Data Visualisation ◽  
Multiple Sequence ◽  
Functional Roles ◽  
Functional Classes ◽  
The Given

Abstract RNA structure formation in vivo happens co-transcriptionally while the transcript is being made. The corresponding co-transcriptional folding pathway typically involves transient RNA structure features that are not part of the final, functional RNA structure. These transient features can play important functional roles of their own and also influence the formation of the final RNA structure in vivo. We here present CoBold, a computational method for identifying different functional classes of transient RNA structure features that can either aid or hinder the formation of a known reference RNA structure. Our method takes as input either a single RNA or a corresponding multiple-sequence alignment as well as a known reference RNA secondary structure and identifies different classes of transient RNA structure features that could aid or prevent the formation of the given RNA structure. We make CoBold available via a web-server which includes dedicated data visualisation.

How Crystals Form from a Cloud of Atoms

2011 ◽  
Vol 675-677 ◽  
pp. 3-7
Author(s):  
Peter Häussler ◽  
Martin Stiehler
Keyword(s):  
Structure Formation ◽  
Fundamental Equation ◽  
Structural Features ◽  
Local Order ◽  
Total System ◽  
Angular Momenta ◽  
General Dynamics ◽  
Bloch’S Theorem ◽  
The Given ◽  
First Time

Structure formation, the condensation of a cloud of atoms to a crystal is still not well understood. Disordered sytems (amorphous/liquid) should be in the center of this research, they are the precursors of any crystal. We consider elementary systems, as well as binary, or ternary amorphous alloys, irrespective whether they are metallically, covalently or ionically bonded and describe the process of structure formation in the formal language of thermodynamics but, as far as we know for the first time, by an extended version (general dynamics), based on the complete Gibbs fundamental equation, applied to internal subsystems. Major structural features evolve from global resonances between formerly independent internal subsystems by exchanging momenta and angular momenta, both accompanied by energy. By this they adjust mutually their internal features and create spherical-periodic structural order at medium-range distances. Under the given external constraints the resonances get optimized by selforganization. Global resonances of the type considered have clearly to be distinguished from local resonances between individual ions (described by quantum chemistry) forming local order. The global resonances cause anti-bonding (non-equilibrium) as well as bonding (equilibrium) states of the coupled total system, occupying the latter to form new structurally extended order. The transition to equilibrium creates entropy which itself leaves the system together with energy. At resonance the energetical splitting between the bonding and anti-bonding state is largest, the creation of entropy and the decrease of the total energy therefore, too. The crystal, finally, evolves by additionally optimizing a resonance based on angular momentum, and the additional adjustments of the local resonances to the global ones, theoretically done by applying Bloch’s theorem.

scholarly journals Exploring Ruthenium-based organometallic inhibitors against Plasmodium Calcium Dependent Kinase 2 (PfCDPK2): a combined ensemble docking, QM paramterization and molecular dynamics study

2020 ◽  
Author(s):  
Dhaval Patel ◽  
Mohd Athar ◽  
Prakash C. Jha
Keyword(s):  
Molecular Dynamics ◽  
Metal Organic Framework ◽  
Calcium Dependent ◽  
Ensemble Docking ◽  
Metal Organic ◽  
Dependent Protein ◽  
Calcium Dependent Protein Kinases ◽  
Dynamics Simulations ◽  
The Given ◽  
Computational Drug Discovery

ABSTRACTRecent advances in the metal-organic framework (MOF) have accelerated the discovery of novel metal-based anticancer, antibacterial and antimalarial compounds. This is substantiated by many serendipitously discovered metals (Ru, Rh, and Ir) based inhibitors that established the importance of metal inserted into the known organic scaffold. Conversely, it is possible to design novel bioactive compounds by mimicking hypervalent carbon atoms by transition metals. This process can be facilitated by computational drug discovery by treating metal center using optimized parameters that can be used for molecular docking and molecular dynamics simulations. Further, the method can be plugged with high computational power and refined algorithms to interpret chemical phenomena with atomic-level insights. In the present work, we have demonstrated an approach for parameterizing three organometallic ligands (FLL, E52, and staurosporine) using MCPB.py. In particular, we report that E52 and FLL have a better shape complimentary and affinity compared to staurosporine identified inhibitor (staurosporine) against Calcium-dependent protein kinases 2 (CDPK2). This study also revealed that a flexible approach (ensemble) outperforms for the given target with dynamic movements. The calculated MMPBSA energies for staurosporine, FLL and E52 were −66.461 ± 2.192, −67.182 ± 1.971 and −91.339 ± 2.745 kcal/mol respectively.

Conceptual Approach to Development, Structure Formation and Hardening Micro-Alloyed by Steels for the Metallurgical Tool

2020 ◽  
Vol 299 ◽  
pp. 658-663
Author(s):  
S.E. Krylova ◽  
Sergey V. Gladkovskii ◽  
E.V. Romashkov
Keyword(s):  
Experimental Data ◽  
Mechanical Properties ◽  
Chemical Composition ◽  
Structure Formation ◽  
Structural Parameters ◽  
Structural Transformations ◽  
Conceptual Approach ◽  
Phase And Structural Transformations ◽  
Technological Cycle ◽  
Development Structure

The scientific bases for the development of rational compositions and methods for hardening a large-sized metallurgical tool from micro-alloyed steels are stated. Based on the generalization of the experimental data, the regularities of phase and structural transformations at various stages of the technological cycle are revealed; the relationships between structural parameters, chemical composition and mechanical properties have been studied and described.

Crystallization in Nano-Confinement Seeded by a Nanocrystal: A Molecular Dynamics Study

2014 ◽  
Author(s):  
Heng Pan ◽  
Costas Grigoropoulos
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Molecular Dynamics Simulations ◽  
Crystallization Temperature ◽  
Crystal Orientation ◽  
Thomson Effect ◽  
Sphere Model ◽  
Dynamics Simulations ◽  
Gold Nanocrystal ◽  
Seeded Crystallization

Seeded crystallization and solidification in nanoscale confinement volumes has become an important and complex topic in nanomanufacturing. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation and seed size as explained by classical two-sphere model and Gibbs-Thomson effect.

Molecular Dynamics Simulations of Breathing MOFs: Structural Transformations of MIL-53(Cr) upon Thermal Activation and CO2Adsorption

2008 ◽  
Vol 120 (44) ◽  
pp. 8615-8619 ◽  
Author(s):  
Fabrice Salles ◽  
Aziz Ghoufi ◽  
Guillaume Maurin ◽  
Robert G. Bell ◽  
Caroline Mellot-Draznieks ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermal Activation ◽  
Structural Transformations ◽  
Dynamics Simulations

scholarly journals Hydrogenation Dynamics of Biphenylene Carbon (Graphenylene) Membranes

MRS Advances ◽  
2017 ◽  
Vol 2 (29) ◽  
pp. 1571-1576
Author(s):  
Vinicius Splugues ◽  
Pedro Alves da Silva Autreto ◽  
Douglas S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Md Simulations ◽  
Structural Transformations ◽  
Extensive Study ◽  
Massively Parallel ◽  
Porous Membranes ◽  
Two Dimensional ◽  
Reactive Force

ABSTRACTThe advent of graphene created a revolution in materials science. Because of this there is a renewed interest in other carbon-based structures. Graphene is the ultimate (just one atom thick) membrane. It has been proposed that graphene can work as impermeable membrane to standard gases, such argon and helium. Graphene-like porous membranes, but presenting larger porosity and potential selectivity would have many technological applications. Biphenylene carbon (BPC), sometimes called graphenylene, is one of these structures. BPC is a porous two-dimensional (planar) allotrope carbon, with its pores resembling typical sieve cavities and/or some kind of zeolites. In this work, we have investigated the hydrogenation dynamics of BPC membranes under different conditions (hydrogenation plasma density, temperature, etc.). We have carried out an extensive study through fully atomistic molecular dynamics (MD) simulations using the reactive force field ReaxFF, as implemented in the well-known Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. Our results show that the BPC hydrogenation processes exhibit very complex patterns and the formation of correlated domains (hydrogenated islands) observed in the case of graphene hydrogenation was also observed here. MD results also show that under hydrogenation BPC structure undergoes a change in its topology, the pores undergoing structural transformations and extensive hydrogenation can produce significant structural damages, with the formation of large defective areas and large structural holes, leading to structural collapse.

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