scholarly journals CHANGE IN THE STRUCTURE OF TITANIUM NANOCLUSTERS UNDER THERMAL EXPOSURE: MOLECULAR DYNAMIC SIMULATION

2021 ◽  
pp. 580-592
Author(s):  
Николай Александрович Панькин
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Cooling Rate ◽  
Crystallization Temperature ◽  
Materials Science ◽  
Interatomic Interaction ◽  
Thermal Exposure ◽  
Cooling Rates ◽  
Macroscopic System ◽  
Body Potential

Исследование структуры нанокластеров при различных температурах является актуальной задачей современного материаловедения. Данный факт обусловлен перспективой их применения при создании материалов с уникальными физическими, механическими, химическими и эксплуатационными свойствами. Компьютерное моделирование проводилось методом классической молекулярной динамики в программном комплексе LAMMPS. Для описания межатомного взаимодействия в кластере использовалась модификация многочастичного потенциала Финниса-Синклера. Проведено изучение структуры нанокластеров титана различного размера. Они получены при различных скоростях охлаждения из жидкого состояния. Увеличение скорости охлаждения приводит к формированию субблочной структуры и росту числа атомов с неупорядоченным окружением. Они обусловлены тем, что большие скорости охлаждения препятствуют равновесному протеканию процессов перестройки атомной структуры с формированием дальнего порядка. Областей с икосаэдрической структурой не обнаружено. Показано, что температура кристаллизации и энергия связи уменьшаются при убывании размера нанокластера. Рост скорости охлаждения увеличивает разницу температур точек начала и конца кристаллизации, соответственно. Результаты моделирования свидетельствуют о менее выраженной размерной зависимости температуры кристаллизации - её оценочное значение для макроскопической системы (810 К) гораздо ниже значения для массивного титана (1940 К). Investigation of the structure of nanoclusters at different temperatures is an urgent task of modern materials science. This fact is due to the prospect of their application in the creation of materials with unique physical, mechanical, chemical and operational properties. Computer simulation was carried out by the method of classical molecular dynamics in the LAMMPS software package. To describe the interatomic interaction in the cluster, a modification of the Finnis-Sinclair many-body potential was used. The structure of titanium nanoclusters of various sizes has been studied. They are obtained at various cooling rates from the liquid state. An increase in the cooling rate leads to the formation of a subblock structure and an increase in the number of atoms with a disordered environment. They are due to the fact that high cooling rates impede the equilibrium process of rearrangement of the atomic structure with the formation of long-range order. No regions with an icosahedral structure were found. It is shown that the crystallization temperature and binding energy decrease with decreasing nanocluster size. An increase in the cooling rate increases the temperature difference between the start and end points of crystallization, respectively. The simulation results indicate a less pronounced dimensional dependence of the crystallization temperature - its estimated value for a macroscopic system (810 K) is much lower than the value for bulk titanium (1940 K). Keywords: nanocluster, binding energy, crystallization temperature, cooling rate, structure, molecular dynamics method.

The effect of cooling rate on crystallization behavior and tensile properties of CF/PEEK composites

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Guangming Dai ◽  
Lihua Zhan ◽  
Chenglong Guan ◽  
Minghui Huang
Keyword(s):  
Cooling Rate ◽  
Crystallization Temperature ◽  
Crystallization Behavior ◽  
Crystalline Polymer ◽  
Scanning Calorimetry ◽  
Nonisothermal Crystallization ◽  
Cooling Rates ◽  
Control Range ◽  
Temperature Range ◽  
Transverse Tensile

Abstract In this study, the differential scanning calorimetry (DSC) tests were performed to measure the nonisothermal crystallization behavior of carbon fiber reinforced polyether ether ketone (CF/PEEK) composites under different cooling rates. The characteristic parameters of crystallization were obtained, and the nonisothermal crystallization model was established. The crystallization temperature range of the material at different cooling rates was predicted by the model. The unidirectional laminates were fabricated at different cooling rates in the crystallization temperature range. The results showed that the crystallization temperature range shifted to a lower temperature with the increase of cooling rate, the established nonisothermal crystallization model was consistent with the DSC test results. It is feasible to shorten the cooling control range from the whole process to the crystallization range. The crystallinity and transverse tensile strength declined significantly with the increase of the cooling rate in the crystallization temperature range. The research results provided theoretical support for the selection of cooling conditions and temperature control range, which could be applied to the thermoforming process of semi-crystalline polymer matrixed composites to improve the manufacturing efficiency.

scholarly journals Effect of cooling rate on structural transformations in Ti-Al-V nanoalloy: molecular dynamics study

2021 ◽  
Vol 2052 (1) ◽  
pp. 012038
Author(s):  
N Yu Sdobnyakov ◽  
V M Samsonov ◽  
V S Myasnichenko ◽  
P M Ershov ◽  
A N Bazulev ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Size Effect ◽  
Cooling Rate ◽  
Tight Binding ◽  
Structural Transformations ◽  
Rate Effect ◽  
Binding Potential ◽  
Cooling Rates ◽  
Thermally Induced ◽  
Local Structures

Abstract Using the isothermal molecular dynamics and the tight-binding potential, crystallization of Ti6Al4V nanodroplets was simulated. The objects of the research consisted of 2869 atoms, including 172 Al atoms and 115 V ones. The OVITO program was employed to recognize local structures and nanophases arisen in the course of cooling nanoalloy with the cooling rates of 0.1 and 0.4 K/ps. We have found that the cooling rate effect on the structure of the Ti6Al4V nanoalloy and the thermally induced structural transformations is much more pronounced than the size effect.

A molecular dynamics study: Structures and thermal stability of PdmPt(13−m)Ag42 ternary nanoalloys

2018 ◽  
Vol 29 (09) ◽  
pp. 1850084 ◽  
Author(s):  
Ali Kemal Garip
Keyword(s):  
Molecular Dynamics ◽  
Cohesive Energy ◽  
Canonical Ensemble ◽  
Interatomic Interaction ◽  
Md Simulations ◽  
Many Body ◽  
Melting Temperatures ◽  
Body Potential ◽  
Basin Hopping ◽  
Thermal Stability Of

Structural optimization of ternary PdmPt[Formula: see text]Ag[Formula: see text] nanoalloys was performed using the basin-hopping algorithm, and the Gupta many-body potential was adopted to model interatomic interaction. The optimization results show that all compositions have a structure based on icosahedron with a core–shell segregation. While the Ag atoms prefer to segregate to the surface, Pd and Pt atoms were located at the core of the cluster due to the higher surface and cohesive energy. The single platinum atom with the highest cohesive energy in Pd[Formula: see text]Pt1Ag[Formula: see text] nanoalloy was located at the center of the cluster. Also in all other compositions except Pd[Formula: see text]Ag[Formula: see text], Pd atoms occupy the second shell position of the icosahedron structure. We used classical molecular dynamics (MD) simulations in canonical ensemble conditions (NVT) to investigate the melting temperatures of ternary PdmPt[Formula: see text]Ag[Formula: see text] nanoalloys with the interatomic interactions modeled by the same potential with optimizations. The icosahedral structures were taken as the initial configurations for MD simulations. We obtained caloric curves and Lindemann indexes to investigate the melting transitions. The simulation results showed that varying the composition gives rise to a fluctuation in melting temperatures. The highest melting temperature belongs to the Pd9Pt4Ag[Formula: see text] nanoalloy cluster within the other compositions. However, the relative stability investigation indicates the Pd8Pt5Ag[Formula: see text] nanoalloy cluster as the most stable composition. The Lindemann indexes obtained for the second and third shell of icosahedral structures show that the melting takes place as a whole without any surface premelting.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

scholarly journals Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1051
Author(s):  
Edgardo Becerra ◽  
Giovanny Aguilera-Durán ◽  
Laura Berumen ◽  
Antonio Romo-Mancillas ◽  
Guadalupe García-Alcocer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Binding Energy ◽  
Binding Site ◽  
Binding Sites ◽  
Adenosine Monophosphate ◽  
Competitive Inhibitor ◽  
Umbrella Sampling ◽  
Coarse Grained ◽  
Nucleotide Polymorphisms

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

Effects of RE on Critical Cooling Rate of Bearing-B Steel

2012 ◽  
Vol 535-537 ◽  
pp. 761-763 ◽  
Author(s):  
Yi Sheng Zhao ◽  
Xin Ming Zhang ◽  
Zhi Guo Gao
Keyword(s):  
Phase Change ◽  
Cooling Rate ◽  
Experimental Results ◽  
Cooling Rates ◽  
Critical Cooling Rate ◽  
The Law

The law of phase change of bearing-B steel during continual cooling was studied by adopting dilatometer. The CCT curves of bearing-B steel were drawn, and the effects of RE on critical cooling rates were studied. The experimental results show that the start temperatures of martensite TM was decreased from 438 to 404°C. The critical cooling rate was simultaneously decreased from 33 to 15°C/s.

Effects of the Cooling Rate on the Acoustic Properties of Pb-10Sn Solder

2012 ◽  
Vol 729 ◽  
pp. 356-360
Author(s):  
Endre Harkai ◽  
Tamás Hurtony ◽  
Péter Gordon
Keyword(s):  
Sound Velocity ◽  
Cooling Rate ◽  
Acoustic Microscopy ◽  
Acoustic Properties ◽  
Scanning Acoustic Microscopy ◽  
Cooling Rates ◽  
Reliability Parameters ◽  
Microscopy Characterization ◽  
The Given

Microhardness and sound velocity were measured in case of differently prepared solder samples. The used Pb-10Sn solder samples were melted then cooled down applying different cooling rates. These procedures caused variant microstructure thus different microhardness and sound velocity values. The sound velocity was measured by means of scanning acoustic microscopy. Characterization of solder materials by acoustic microscopy gives the possibility to non-destructively estimate mechanical and reliability parameters of the given material.

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