Molecular Dynamics Study of Collagen Fibrils: Relation between Mechanical Properties and Molecular Chirality

Collagen is a basic biopolymer usually found in animal bodies, but its mechanical property and behavior are not sufficiently understood so as to apply to effective regenerative medicine and so on. Since the collagen material is composed of many hierarchical structures from atomistic level to tissue or organ level, we need to well understand fundamental and atomistic mechanism of the collagen in mechanical response. First, we approach at exactly atomistic level by using all-atom modeling of tropocollagen (TC) molecule, which is a basic structural unit of the collagen. We perform molecular dynamics (MD) simulations concerning tensile loading of a single TC model. The main nature of elastic (often superelastic) behavior and the dependency on temperature and size are discussed. Then, to aim at coarse-graining of atomic configuration into some bundle structure of TC molecules (TC fibril), as a model of higher collagen structure, we construct a kind of mesoscopic model by adopting a simulation framework of beads-spring model which is ordinarily used in polymer simulation. Tensile or compression simulation to the fibril model reveals that the dependency of yield or buckling limit on the number of TCs in the model. Also, we compare the models with various molecular orientations in winding process of initial spiral of TC. The results are analyzed geometrically and it shows that characteristic orientational change of molecules increases or decreases depending on the direction and magnitude of longitudinal strain.

Particle Modeling Based on Interatomic Potential and Crystal Structure: A Multi-Scale Simulation of Elastic-Plastic Deformation of Metallic Material

We formulate a macroscopic particle modeling analysis of metallic materials (aluminum and copper, etc.) based on theoretical energy and atomic geometries derivable from their interatomic potential. In fact, particles in this framework are presenting a large mass composed of huge collection of atoms and are interacting with each other. We can start from cohesive energy of metallic atoms and basic crystalline unit (e.g. face-centered cubic). Then, we can reach to interparticle (macroscopic) potential function which is presented by the analytical equation with terms of exponent of inter-particle distance, like a Lennard-Jones potential usually used in molecular dynamics simulation. Equation of motion for these macroscopic particles has dissipative term and fluctuation term, as well as the conservative term above, in order to express finite temperature condition. First, we determine the parameters needed in macroscopic potential function and check the reproduction of mechanical behavior in elastic regime. By using the present framework, we are able to carry out uniaxial loading simulation of aluminum rod. The method can also reproduce Young’s modulus and Poisson’s ratio as elastic behavior, though the result shows the dependency on division number of particles. Then, we proceed to try to include plasticity in this multi-scale framework. As a result, a realistic curve of stress-strain relation can be obtained for tensile and compressive loading and this new and simple framework of materials modeling has been confirmed to have certain effectiveness to be used in materials simulations. We also assess the effect of the order of loadings in opposite directions including yield and plastic states and find that an irreversible behavior depends on different response of the particle system between tensile and compressive loadings.

Structure and Mechanical Behavior of Cellulose Nanofiber and Micro-Fibrils by Molecular Dynamics Simulation

Cellulose nanofiber (CNF) and CNF micro-fibrils (CNF-MFs) are computationally modeled by molecular dynamics with united atom (UA) methodology of polymers. Structural stability and mechanical properties of these materials are focused on. Diffusion coefficient decreases with increase of the number of shells in CNF-MF. The structure of CNF-MFs with crystalline alignment is totally stabilized with twist which is an accumulation of torsion angles at Glycosidic bonds between monomers inside CNFs. Unique fiber drawing simulation, where a single CNF fiber is taken out of CNF-MF structure, is first conducted. The CNF fiber which is drawn out stretches up to relatively large strain, with linear increase of tensile stress. The computation results show that, the larger the number of shell structure of CNF-MF is, the larger the stretch and the stress of drawn fibers are.

Molecular Dynamics Study on Transmission Mechanism of Torsional Deformation in Cellulose Nanofibers with Hierarchical Structure

Cellulose nanofiber (CNF) is a fibrous and nano-sized substance produced by decomposition of bulk-type cellulose which is a main component of plants. It has high strength comparable to steel, and it shows low environmental load during a cycle of production and disposal. Besides it has many excellent properties and functions such as high rigidity, light-weight, flexibility and shape memory effect, so it is expected as a next-generation new material. Usually it is composed of many cellulose micro fibrils (CMFs) in which molecular chains of cellulose are aggregated in a crystal structure, the knowledge of mechanical properties for each CMF unit is important. Since actual fibrils are complicatedly intertwined, it is also crucial to elucidate the transmission mechanism of force and deformation not only in one fibril but also in between fibrils. How the dynamic and hierarchical structure composed of CMFs responds to bending or torsion is an interesting issue. However, little is known on torsional characteristics (shear modulus, torsional rigidity, etc.) concerning CMF. In general, in a wire-like structure, it is difficult to enhance torsional rigidity and strength, compared with tensile ones. Therefore, in this study, we try to build a hierarchical model of CNF by multiplying CMF fibers and to conduct molecular dynamics simulation for torsional deformation, by using hybrid model between all-atom and united-atoms model. First, shear modulus was estimated for one CMF fibril and it showed a value close to the experimental values. Also, we assume a state in which two CMFs are ideally arranged in parallel, and create a hierarchical structure. We evaluate the dependence on the temperature for the bond strength and toughness in the hierarchical structures. Furthermore, we mentioned the transmission mechanism between components of a hierarchical structure.

Nano-Scale Modelling and Simulation of Metal Wiredrawing by Using Molecular Dynamics Method

In this paper, molecular dynamics (MD) simulations of nano-sized wiredrawing are performed. The wiredrawing is a traditional plastic working method, but there has not been any insight to develop it in a nano-sized scale. Therefore, to materialize the concept of the nano-sized wiredrawing, a numerical modelling is pursued at first in this paper, and the interatomic potential, a crystalline orientation, the drawing condition realized by a die geometry are thoroughly investigated. In particular, to reduce the friction between a wire and a die, a simple friction model for the MD analysis is newly proposed, where the interatomic interaction is adequately modified by a single factor ω. Then, the fruitful results are obtained by using ω = 0.1. We checked the availability of such nano-sized MD simulation by constructing a two-dimensional wiredrawing model, at first. The analysis of atomic stress during drawing is also assessed. It is useful to use invariant of the atomic stress tensor, such as hydrostatic stress (average stress, σm) or von Mises equivalent stress (σeq). The former is related to the phase transformation from the body-centered-cubic (bcc) structure to the face-centered-cubic (fcc) one, which is found in the present MD simulation. It is observed that an initial α-iron crystal with bcc structure changes partially into the fcc phase. It is recognized that the phase transformation is caused by the positive hydrostatic stress values, which is occurring especially inside the die region. We observed that a lot of dislocation core structures occur in wiredrawing process and their existence and evolution are well related to the equivalent stress values.

Molecular Dynamics Study on Mechanical Properties in the Structure of Self-Assembled Quantum Dot

Stress and strain in the structure of self-assembled quantum dots constructed in the Ge/Si(001) system is calculated by using molecular dynamics simulation. Pyramidal hut cluster composed of Ge crystal with {105} facets surfaces observed in the early growth stage are computationally modeled. We calculate atomic stress and strain in relaxed pyramidal structure. Atomic stress for triplet of atoms is approximately defined as an average value of pairwise (virial) quantity inside triplet, which is the product of vectors between each two atoms. Atomic strain by means of atomic strain measure (ASM) which is formulated on the Green’s definition of continuum strain. We find the stress (strain) relaxation in pyramidal structure and stress (strain) concentration in the edge of pyramidal structure. We discuss size dependency of stress and strain distribution in pyramidal structure. The relationship between hydrostatic stress and atomic volumetric strain is basically linear for all models, but for the surface of pyramidal structure and Ge-Si interface. This means that there is a reasonable correlation between atomic stress proposed in the present study and atomic strain measure, ASM.