scholarly journals Symmetry Based Material Optimization

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 315
Author(s):  
Zeyun Shi ◽  
Jinkeng Lin ◽  
Jiong Chen ◽  
Yao Jin ◽  
Jin Huang

Many man-made or natural objects are composed of symmetric parts and possess symmetric physical behavior. Although its shape can exactly follow a symmetry in the designing or modeling stage, its discretized mesh in the analysis stage may be asymmetric because generating a mesh exactly following the symmetry is usually costly. As a consequence, the expected symmetric physical behavior may not be faithfully reproduced due to the asymmetry of the mesh. To solve this problem, we propose to optimize the material parameters of the mesh for static and kinematic symmetry behavior. Specifically, under the situation of static equilibrium, Young’s modulus is properly scaled so that a symmetric force field leads to symmetric displacement. For kinematics, the mass is optimized to reproduce symmetric acceleration under a symmetric force field. To efficiently measure the deviation from symmetry, we formulate a linear operator whose kernel contains all the symmetric vector fields, which helps to characterize the asymmetry error via a simple ℓ2 norm. To make the resulting material suitable for the general situation, the symmetric training force fields are derived from modal analysis in the above kernel space. Results show that our optimized material significantly reduces the asymmetric error on an asymmetric mesh in both static and dynamic simulations.

Materials ◽  
2019 ◽  
Vol 12 (12) ◽  
pp. 1982 ◽  
Author(s):  
Adam Ciszkiewicz ◽  
Grzegorz Milewski

Typical artificial joints for humanoid robots use actual human body joints only as an inspiration. The load responses of these structures rarely match those of the corresponding joints, which is important when applying the robots in environments tailored to humans. In this study, we proposed a novel, automated method for designing substitutes for a human intervertebral joint. The substitutes were considered as two platforms, connected by a set of flexible links. Their structural and material parameters were obtained through optimization with a structured Genetic Algorithm, based on the reference angular stiffnesses. The proposed approach was tested in three numerical scenarios. In the first test, a mechanism with angular stiffnesses corresponded to the actual L4–L5 intervertebral joint. Scenarios 2 and 3 featured mechanisms with geometry and structure comparable to the joint, but with custom stiffness profiles. The obtained results proved the effectiveness of the proposed method. It could be employed in the design of artificial joints for humanoid robots and orthotic structures for the human spine. As the approach is general, it could also be extended to different body joints.


Glycobiology ◽  
2020 ◽  
Vol 30 (10) ◽  
pp. 830-843
Author(s):  
Ming Tang ◽  
Xiaocong Wang ◽  
Neha S Gandhi ◽  
Bethany Lachele Foley ◽  
Kevin Burrage ◽  
...  

Abstract Collagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.


RSC Advances ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 6795-6799 ◽  
Author(s):  
Shuling Xiong ◽  
Shusen Chen ◽  
Shaohua Jin ◽  
Zhe Zhang ◽  
Yan Zhang ◽  
...  

TKX-50/HMX cocrystal model was established and calculated using PCFF force field by molecular dynamics simulations.


Author(s):  
Mauricio P. Sica ◽  
Cristian R. Smulski

The Tumor Necrosis Factor (TNF) and the TNF receptor (TNFR) superfamilies are composed of 19 ligands and 30 receptors, respectively. The oligomeric properties of ligands, both membrane bound and soluble, has been studied most. However, less is known about the oligomeric properties of TNFRs. Earlier reports identified the extracellular, membrane-distal, cysteine-rich domain as a pre-ligand assembly domain which stabilizes receptor dimers and/or trimers in the absence of ligand. Nevertheless, recent reports based on structural nuclear magnetic resonance (NMR) highlight the intrinsic role of the transmembrane domains to form dimers (p75NTR), trimers (Fas), or dimers of trimers (DR5). Thus, understanding the structural basis of transmembrane oligomerization may shed light on the mechanism for signal transduction and the impact of disease-associated mutations in this region. To this end, here we used an in silico coarse grained molecular dynamics approach with Martini force field to study TNFR transmembrane homotypic interactions. We have first validated this approach studying the three TNFR described by NMR (p75NTR, Fas, and DR5). We have simulated membrane patches composed of 36 helices of the same receptor equidistantly distributed in order to get unbiassed information on spontaneous proteins assemblies. Good agreement was found in the specific residues involved in homotypic interactions and we were able to observe dimers, trimers, and higher-order oligomers corresponding to those reported in NMR experiments. We have, applied this approach to study the assembly of disease-related mutations being able to assess their impact on oligomerization stability. In conclusion, our results showed the usefulness of coarse grained simulations with Martini force field to study in an unbiased manner higher order transmembrane oligomerization.


2021 ◽  
Author(s):  
Mohamed Arar

The goal of this thesis is to shed light on the elastic properties, especially the Young modulus, of clinker phases and hydration products of cement paste through molecular dynamic simulation by COMPASS force field. The parameters that can affect the elastic properties of cement phases were also targeted, with special attention paid to analog C-S-H minerals, in which the Tobermorite family and Jennite were simulated to render their structures representative of C-S-H structure. The molecular dynamic simulations of this study show that CO force field can be applicable for most clinker phases and hydration products. Jennite, with its porosity and finite silicate chain accounted for, can be considered the closer and representative structure of C-S-H. In addition, this study confirms the important effect of C/S ratio, packing factor and chain length on elastic properties of C-S-H.


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