Papers by Keyword: Molecular Dynamic Simulation

Abstract: GPU computing is the use of a graphics processing unit together with a CPU to accelerate large scale scientific and engineering applications, such as molecule simulation. The paper use NVIDIA Tesla C2050NVIDIA GTX580 and NAMD 2.9 simulates three differences molecule systems: Beta2,SET9 and Ubiquitin. We compared and analyzed the results of the simulations experiment, and come to conclusion that the difference molecule systems will get the difference speed accelerated. The computing times of four GPU is nearly half of the time used by one GPU; and this is especially in the case of macromolecules system. Furthermore, from the GPUs memory utilization rate, the larger the protein system is, the higher the memory use of the GPU is. The performance of NVIDIA GTX580 is only half of the NVIDIAC2050. NVIDIA Tesla C2050 is can satisfy an even larger system simulation.

Abstract: Shape memory polymers (SMPs) possess the capability of shape frozen and recovery via thermomechanical processing. Over the last decades, great work has focused on their macro-properties. In order to have a better understanding of the micro-deformation mechanisms of this class of functional materials, the thermomechanical behaviors of three types of epoxy SMPs with varied curing agent contents were simulated by the molecular dynamics (MD) method. Special attention was paid on the different responses of the materials in the rubbery and glassy states. Moreover, structure-property analyses were presented.

Abstract: The multi-pass nanometric machining of copper with diamond tool was carried out using the Molecular Dynamics (MD) simulation. The copper-copper interactions were modelled by the EAM potential and the copper-diamond interactions were modelled by the Morse potential. The diamond tool was modelled as a deformable body and the Tersoff potential was applied for the carbon-carbon interactions. It was observed that the average tangential and the normal components of the cutting forces reduced in the consecutive cutting passes. Also, the lateral force components are affected by atomic vibrations and the cross sectional area during the cutting process.

Abstract: Wear of diamond tool has always been a limiting factor in ductile regime machining of large size silicon components. In order to understand the tool wear phenomena, it is non-trivial to know the process outputs especially cutting forces, stresses and temperature during nanometric turning. In this paper, a realistic potential energy function has been deployed through molecular dynamic (MD) simulation, to simulate the process outputs of single diamond turning operation against single crystal silicon. The simulation result suggests that wear mechanism of diamond tool is fundamentally governed by these process parameters and thus critical.

Abstract: Silicon carbide can meet the additional requirements of operation in hostile environments where conventional silicon-based electronics (limited to 623K) cannot function. However, being recent in nature, significant study is required to understand the various machining properties of silicon carbide as a work material. In this paper, a molecular dynamic (MD) simulation has been adopted, to simulate single crystal β-silicon carbide (cubic) in an ultra precision machining process known as single point diamond turning (SPDT). β-silicon carbide (cubic), similar to other materials, can also be machined in ductile regime. It was found that a high magnitude of compression in the cutting zone causes a sp3- sp2 order-disorder transition which appears to be fundamental cause of wear of diamond tool during the SPDT process.

Abstract: This work was try to study the relationship between the damping properties and the hydrogen bonds, fractional free volumes of nitrile-butadiene rubber (NBR)/hindered phenol (AO-80) composites from the microstructural point of view by combining the experimental and molecular simulation studies. The results indicated that the hydrogen bonds (HBs) were formed between AO-80 small molecules and NBR polymer chains. According to simulation results, because of the formed strongest HBs, highest binding energy and the smallest fractional free volume in the NBR/AO-80 composites with the blending ratio of 100/68, it contributed the maximum loss factor and highest modulus. It concluded that there was a suitable proportion of rubber blended with small hindered phenol molecules in the design of damping materials.

Abstract: Conformational changes of wild-type (WT) hIAPP and the S20P mutant in explicit water are investigated using molecular dynamics. In the whole simulation, WT shows compacter structure and has more hydrogen-bond networks than S20P. The residues 14-18 in WT is always maintained as a helical structure which is stabilized by the hydrogen bond between Ser20 and NH group of His18, and the other regions in WT partially loosen from α-helix structures into the coil structures. The S20P mutant in a shortage of hydrogen-bond interaction unfolds faster than WT. This work provides insight into the specific conformation of IAPP which is associated with the generation of amyloid fibrils.

Abstract: Three dimensional molecular dynamics simulation on the nanocutting of monocrystalline silicon is carried out to investigate the material deformation behaviors and atomic motion characteristics of the machined workpiece. A deformation criterion is developed to determine the material deformation and phase transformation behavior in the subsurface layer based on the single-atom potential energy variations. The results show that the machined chips suffer a complex phase transformation and eventually present an amorphous structure caused by the plastic deformation behavior. A polycrystalline structure is obtained on the machined surface. Both plastic and elastic deformation simultaneously takes place on the machined surface, and elastic deformation takes place under the machined surface. In order to further unveil the mechanism of nanocutting process, the displacements of all atoms are also simulated. The simulation results shows that different atomic motions occur in different regions in the workpiece, and the chips formations occur via extrusion.

Abstract: Carbon nanotube has attracted tremendous scientific and industrial interests due to its exceptional mechanical, electrical and thermal properties. In this paper, classic molecular dynamic simulations are carried out to investigate the buckling behaviors and mechanical properties of single-walled carbon nanotubes under axial compression, both for perfect and imperfect ones introducing atomic vacancies. The effect of chirality, diameter, quantity and position of vacancy are systematically studied. The simulation results reveal that their mechanical properties such as Young’s modulus, critical strain and stress suffering a significant decline as the increasing numbers of vacancies. It is also found that the critical stress and strain are sensitive to position of atomic vacancy. Carbon nanotubes with vacancies located at the center have lower critical strain and are easier to reach the failure stage than those with vacancies at both sides.

Abstract: Experimental observations have shown that cardio toxins (cobra cytotoxins), small proteins of three-fingered cytotoxin group, damage nanobiomembranes in different cells and vesicles. However, the molecular mechanism of this damage is not yet completely cleared. Molecular dynamics simulations have been used here to study the interaction of cardiotoxins A3 and A4 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid bilayer in two separate systems. Each of studied systems included one cytotoxin molecule, 128 lipid molecules (64 molecules in each monolayer) and 11817 water molecules. It has been found that the toxin interacts with zwitterionic bilayer formed by POPC. At the beginning of simulation the cytotoxins have been oriented toward nanobiomembrane surface by their loops’ tips. This orientation has changed during first 50 ns of classical molecular dynamics simulation for both of studied cytotoxins. The A3 toxin finally meets POPC nanobiomembrane with sides of loops near tips including cytotoxin region THR148 and VAL155. The A4 cytotoxin molecule has been finally oriented toward surface of nanobiomembrane with base and one of loop's tip including THR184, ARG186 and LEU158 amino acids, after 50 ns molecular dynamics simulation. Then 25 ns steered molecular dynamics simulation has been done for both of systems. The obtained data suggest that cytotoxin A3 meets the nanobiomembrane with sides of loops near tips and A4 meets POPC nanobiomembrane with base and one of loop's tips. The difference between final orientations of these two cytotoxins comes from the difference in the structure of them.