Molecular Dynamics Investigation on Shearing between Osteopontin and Hydroxyapatite in Biological Materials

2014 ◽  
Vol 891-892 ◽  
pp. 3-8
Author(s):  
Zheng Bo Lai ◽  
Cheng Yan ◽  
Adekunle Oloyede
Keyword(s):  
Molecular Dynamics ◽  
Mechanical Response ◽  
Building Blocks ◽  
Biological Materials ◽  
High Energy ◽  
Shear Loading ◽  
Mineral Surfaces ◽  
Protein Matrix ◽  
Unique Material ◽  
High Energy Dissipation

Bone, a hard biological material, possesses a combination of high stiffness and toughness, even though the main basic building blocks of bone are simply mineral platelets and protein molecules. Bone has a very complex microstructure with at least seven hierachical levels. This unique material characteristic attracts great attention, but the deformation mechanisms in bone have not been well understood. Simulation at nanolength scale such as molecular dynamics (MD) is proven to be a powerful tool to investigate bone nanomechanics for developing new artificial biological materials. This study focuses on the ultra large and thin layer of extrafibrillar protein matrix (thickness = ~ 1 nm) located between mineralized collagen fibrils (MCF). Non-collagenous proteins such as osteopontin (OPN) can be found in this protein matrix, while MCF consists mainly of hydroxyapatite (HA) nanoplatelets (thickness = 1.5 4.5 nm). By using molecular dynamics method, an OPN peptide was pulled between two HA mineral platelets with water in presence. Periodic boundary condition (PBC) was applied. The results indicate that the mechanical response of OPN peptide greatly depends on the attractive electrostatics interaction between the acidic residues in OPN peptide and HA mineral surfaces. These bonds restrict the movement of OPN peptide, leading to a high energy dissipation under shear loading.

Multifunctional Non-Woven Carbon Nanopaper: Fabrication, Properties, and Applications

2013 ◽  
Vol 423-426 ◽  
pp. 97-105 ◽  
Author(s):  
Ji Hua Gou ◽  
Fei Liang ◽  
Yun Jun Xu ◽  
Bob Mabbott
Keyword(s):  
Carbon Nanofibers ◽  
Shape Memory Polymer ◽  
High Energy ◽  
Lightning Strike ◽  
Fundamental Study ◽  
Infiltration Process ◽  
Pressure Infiltration ◽  
Infiltration Pressure ◽  
Unique Material ◽  
High Energy Dissipation

This paper presents a fundamental study of processing, morphologies, properties, and applications of a novel non-woven nanopaper based on carbon nanofibers (CNFs). Unique material formulations were developed to tailor the non-woven nanopaper to specific engineering applications. The non-woven nanopaper was made from a variety of nanomaterials (e.g. carbon nanotubes, carbon nanofibers, graphene, nanoclay, nickel nanostrands, POSS, etc.) with tailored nanostructures by precisely controlling composition, dispersion, functionalization, orientation, porosity, and thickness during the vacuum infiltration, pressure infiltration, or spray/infiltration process. The polymer matrix was impregnated into the stacked nanopapers to form multi-layered laminated composites. Such non-woven nanopaper based composites were designed and fabricated to achieve high energy dissipation capability for vibrational damping, high thermal conductivity and thermal stability for fire retardancy, ultra-high electrical conductivity and current-carrying capacity for lightning strike protection, and electro-actuation of shape memory polymer composites.

Application of Aluminium Alloys in a Structural Joint With Great Shear Deformation Capacity

2006 ◽  
Author(s):  
S. V. Khonsari ◽  
G. L. England ◽  
M. Ghahramaninezhad-Gharehlar
Keyword(s):  
Shear Deformation ◽  
Aluminium Alloys ◽  
High Energy ◽  
Shear Loading ◽  
Deformation Capacity ◽  
High Shear ◽  
Energy Dissipation Capacity ◽  
Structural Connection ◽  
High Energy Dissipation ◽  
Very High

A new structural connection, already discussed in previous papers, with very special and, in some respects, unique, features, such as having very high rotational capacity in bending, and high shear deformation capacity under shear, hence high energy-dissipation capacity under either type of loading, was developed. Specimens of either variant of this joint, fabricated with steel components, were already tested under bending and shear in a mainly separate manner. However, due to the particular shape of the connection, and its ability to be extruded in aluminium, in the most recent work the behaviour of its aluminium specimens under shear loading was studied. A series of specimens fabricated from various classes of aluminium alloys were tested whose results are reported here. All of the specimens except one were tested under ‘monotonic’ loading, and one specimen was tested ‘cyclically.’ Despite the deficiencies in the specimens caused by poor welding of their components, the results show the high shear deformation capacity of the aluminium specimens which was accompanied by appreciable strength.

Molecular dynamics study on the mechanical response and failure behaviour of graphene: performance enhancement via 5–7–7–5 defects

RSC Advances ◽  
2016 ◽  
Vol 6 (31) ◽  
pp. 26361-26373 ◽  
Author(s):  
G. Rajasekaran ◽  
Avinash Parashar
Keyword(s):  
Molecular Dynamics ◽  
Tensile Strength ◽  
Structural Properties ◽  
Elastic Moduli ◽  
Mechanical Response ◽  
Performance Enhancement ◽  
Structural Defects ◽  
Thick Sheet ◽  
Failure Behaviour ◽  
Production Techniques

A one atom-thick sheet of carbon exhibits outstanding elastic moduli and tensile strength in its pristine form but structural defects which are inevitable in graphene due to its production techniques can alter its structural properties.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

scholarly journals Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1259
Author(s):  
Maksymilian Dziura ◽  
Basel Mansour ◽  
Mitchell DiPasquale ◽  
P. Charukeshi Chandrasekera ◽  
James W. Gauld ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pulmonary Surfactant ◽  
Lung Surfactant ◽  
Protein Composition ◽  
Md Simulations ◽  
Building Blocks ◽  
Future Research ◽  
Total Composition ◽  
Protein Components ◽  
Dynamics Simulations

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

Molecular Dynamics Modeling the Nano-Identation of Titanium

2021 ◽  
Author(s):  
Peiqiang Yang ◽  
Xueping Zhang ◽  
Zhenqiang Yao ◽  
Rajiv Shivpuri
Keyword(s):  
Molecular Dynamics ◽  
Plastic Deformation ◽  
Titanium Alloys ◽  
Large Scale ◽  
Mechanical Response ◽  
Pure Titanium ◽  
Dynamics Modeling ◽  
Dynamics Model ◽  
Nano Indentation ◽  
Molecular Dynamics Modeling

Abstract Titanium alloys’ excellent mechanical and physical properties make it the most popular material widely used in aerospace, medical, nuclear and other significant industries. The study of titanium alloys mainly focused on the macroscopic mechanical mechanism. However, very few researches addressed the nanostructure of titanium alloys and its mechanical response in Nano-machining due to the difficulty to perform and characterize nano-machining experiment. Compared with nano-machining, nano-indentation is easier to characterize the microscopic plasticity of titanium alloys. This research presents a nano-indentation molecular dynamics model in titanium to address its microstructure alteration, plastic deformation and other mechanical response at the atomistic scale. Based on the molecular dynamics model, a complete nano-indentation cycle, including the loading and unloading stages, is performed by applying Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The plastic deformation mechanism of nano-indentation of titanium with a rigid diamond ball tip was studied under different indentation velocities. At the same time, the influence of different environment temperatures on the nano-plastic deformation of titanium is analyzed under the condition of constant indentation velocity. The simulation results show that the Young’s modulus of pure titanium calculated based on nano-indentation is about 110GPa, which is very close to the experimental results. The results also show that the mechanical behavior of titanium can be divided into three stages: elastic stage, yield stage and plastic stage during the nano-indentation process. In addition, indentation speed has influence on phase transitions and nucleation of dislocations in the range of 0.1–1.0 Å/ps.

scholarly journals Shape-Dependent Aggregation of Silver Particles by Molecular Dynamics Simulation

Crystals ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 405 ◽  
Author(s):  
Xue Wang ◽  
Chaofeng Hou ◽  
Chengxiang Li ◽  
Yongsheng Han
Keyword(s):  
Building Blocks ◽  
High Viscosity ◽  
High Energy ◽  
Dynamics Simulation ◽  
Structure Evolution ◽  
Shape Effect ◽  
Silver Particles ◽  
Large Area ◽  
Research Problems ◽  
High Possibility

In crystallization, nanoparticle aggregation often leads to the formation of orderly structures, even single crystals. Why can nanoparticles form orderly structures and what is the mechanism dominating their orderly aggregation? These questions raise interesting research problems, but the occurrences that could answer them often fail to be directly observed, since the interaction among particles is invisible. Here, we report an attempt to discover the interaction and aggregation of building blocks through a computer simulation, focusing on the shape effect of building blocks on the aggregation. Four types of silver building blocks were selected, each consisting of (100) and (111) facets, but the ratio of these two facets was different. It was found that the area of facets played an important role in selecting the aggregation mode. The facets with a large area and high energy had a high possibility of aggregation. In addition, the effects of solvent viscosity and temperature were also investigated. High viscosity and low temperature enhanced the orderliness of aggregation. This paper reports a detailed view of the aggregation process of silver nanoparticles, which is expected to be helpful in understanding the structure evolution of materials in nonclassical crystallization.

scholarly journals Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

2018 ◽  
Vol 115 (45) ◽  
pp. 11519-11524 ◽  
Author(s):  
Caitlin M. Quinn ◽  
Mingzhang Wang ◽  
Matthew P. Fritz ◽  
Brent Runge ◽  
Jinwoo Ahn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Building Blocks ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Capsid Assembly ◽  
Dynamic Regulation ◽  
Angle Spinning ◽  
Dynamics Simulations ◽  
Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

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