Molecular dynamics

This study focuses on investigating the effect of negative pressure on the structure and diffusion processes of Silicon dioxide at liquid nitrogen temperature. The insights gained from this study will serve as a foundation for future experimental research aimed at the development and manufacturing of advanced materials.

11p viengfa 28-10-2024 1 1   Download

In this research, Molecular Dynamics (MD) simulations were conducted to explore the temperature effect on the microstructure and phase transition of the Ag0.25Au0.75 alloy. The findings reveal that as the temperature rises, the material's phase transition switches from crystalline to liquid and vice versa.

9p viengfa 28-10-2024 2 1   Download

In this thesis atomistic level modelling is conducted to investigate the design of an environmentally adaptable self-cleaning polymer paint coating that incorporates biomimetics to remain clean in various environmental setting. This work will be used to aid in the development of stay-clean polymer paint coating.

116p runthenight07 01-03-2023 6 3   Download

In this Masters thesis computational modelling techniques were employed to investigate iron-free apo-Lactoferrin (apo-Lf) structural conformation changes in the presence of variant temperature and pH. These conditions represent the environment most milk protein goes through in food processing and the production of food products.

162p runthenight04 02-02-2023 7 2   Download

The thesis is organised as follows: Chapter 1 comprises the literature review of protein structure, amyloid fibrils and of the effect of nanomaterials on protein aggregation. Chapter 2 reviews the computational methods used to perform simulations and analysis. Chapter 3 comprises my published article on benchmarking forcefields and sampling methods for disordered proteins using amylin as a case study. Chapter 4 comprises my published article on the effect of oxidation on the properties of graphene oxide flakes in solution.

56p runthenight04 02-02-2023 12 3   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 11 3   Download

In particular, the system undergoes three stages. At first stage the relaxation proceeds slowly so that the energy of system slightly decreases and the samples structure remains amorphous. Within second stage a structural transformation occurs which significantly changes PRDF and DCN for the relatively short time. The energy of the system is dropped considerably and the amorphous structure transforms into the crystalline. Finally, the crystalline sample undergoes the slow relaxation which reduces the energy of system and eliminates structural defects in crystal lattices.

17p runordie3 27-06-2022 18 3   Download

The simulation finds a large number of vacancy-simplexes, which plays a role of diffusion vehicle for cobalt atom and varies with relaxation degree. A new diffusion mechanism for tracer diffusivity in cobalt amorphous solid is supposed as follows: The elemental atomic movement includes a jump of neighbouring atoms into the vacancy-simplexes and then collective displacement of a large number of atoms.

9p larachdumlanat127 20-12-2020 18 3   Download

This paper looks at the influence of SiO2-doped concentration, temperature and pressure on the microstructure of the Al2O3(SiO2)x (ASx) bulk model using the Molecular Dynamics (MD) method with a Born-Mayer pair interaction potential and periodic boundary conditions.

7p tamynhan5 10-12-2020 12 3   Download

At a temperature of 300 K, both Ni and Cu atoms are crystallized into the face-centered cubic (FCC) and the hexagonal close-packed (HCP) phases, respectively. The mechanical characteristics of the sample at 300 K were also analyzed in detail through the determination of elastic modulus, number of atoms, and void distribution during the tensile process.

8p tamynhan5 10-12-2020 15 3   Download

This paper studies the influence of temperature 500 K, 1500 K, 2500 K, 3500 K and 4000 K on the microstructure and phase transition of a CaSiO3 bulk model using the Molecular Dynamics method with the Born-Mayer pair interaction potential and periodic boundary conditions.

10p tamynhan9 02-12-2020 14 2   Download

This work presents a molecular dynamics simulation (MDS) of CaSiO3 glass using Born–Mayer–Huggins potentials. The structural organization and structural phase transition under compression as well as network structure of CaSiO3 are clarified through analysis and visualization of molecular dynamics simulation data.

11p tamynhan9 02-12-2020 15 4   Download

In our study, we used molecular dynamics simulation (MD) to study diffusion mechanism in liquid MgO at a temperature of 3800K at a pressure ranging from 0 to 25 GPa. The calculated results and analysis of dynamical properties, spatially heterogeneous dynamics and diffusion mechanisms in MgO liquids will be reported in detail in this work.

10p tamynhan8 04-11-2020 14 3   Download

This paper presents the influence of temperature on microstructure and phase transition when heating 3000 nano-iron and bulk-iron particles at a temperature of 300 K, 500 K, 700 K, 900 K, 1100 K, 1300 K, 1500 K, 1700 K, 1900 K and 2100 K using the molecular dynamics (MD) simulation method.

7p tamynhan8 04-11-2020 19 2   Download

This paper studies the structure of the Mullite system (3Al2O3.2SiO2) by Molecular Dynamics simulation (MDs) using the Born–Mayer–Huggins pair interaction and periodic boundary conditions. The simulation was performed with model of 5250 atoms at different pressure and at 3500 K temperature.

7p tamynhan6 14-09-2020 17 2   Download

The additional network-modifying cation oxide breaking up this network by the generation of nonbridging O atoms and it has a slight effect on the topology of SiOx and OSiy units. Moreover, the diffusion of network- former atom in sodium-silicate melt is anomaly and diffusion coefficient for sodium atom is much larger than for oxygen or silicon atom. The simulation proves two diffusion mechanisms of the network-former atoms and modifier atoms.

10p tamynhan6 14-09-2020 16 4   Download

In this work, we use molecular dynamic (MD) simulation to study the structure transition and crystallization of amorphous silica (SiO2) under compression. The structural evolution of amorphous SiO2 is explained through radial distribution function, coordination number distribution, bond angle distribution and visualization.

10p tamynhan6 14-09-2020 13 2   Download

We present machine learning models for fast estimating atomic forces and energies. In our method, the total energy of a system is approximated as the summation of atomic energy which is the interaction energy with its surrounding chemical environment within a certain cutoff radius.

7p tamynhan6 14-09-2020 16 1   Download

In this paper a molecular dynamics simulation of nano-metric cutting of copper with a diamond tool is presented. MD simulations require the determination of the interaction of the involved atoms through a function of potential for the materials involved in the analysis and the accurate topography of the studied area, leading to high demand of computational time.

12p tohitohi 19-05-2020 27 1   Download

The dynamic properties of iron liquid (Fe) are studied by molecular dynamics (MD) simulation. We trace the evolution of local density fluctuations (LDFs) in Fe liquid over the simulation time and in the 300-2300 K temperature range. The result simulation reveals that atomic diffusion is realized through the LDFs and the high localization LDFs at low temperature in the iron liquid is the cause of the anomalous dynamics slowdown. We find that the diffusion depends on both rate of LDFs and the averaged square displacement of particles Fe as one LDF occurs.

6p blackwidow123 15-06-2018 28 3   Download