Mechanical behavior of actin and spectrin subjected to high strain rate: A molecular dynamics simulation study.
Ontology highlight
ABSTRACT:
SUBMITTER: Khan MI
PROVIDER: S-EPMC8050423 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In this research, a molecular dynamics (MD) model was adopted to investigate the essence of the effect of strain rate on the mechanical behavior of the Fe14.6Ni (at%) elastocaloric refrigeration alloy. The study showed that the mechanical behavior of the Fe14.6Ni (at%) alloy was dependent on the strain rate. Besides, the investigation of temperature demonstrated that the strain rate influenced mechanical behavior by changing the transient temperatures. Furthermore, it was found that the adiabatic temperature change (ΔTadi) was high and up to 51 K, which was a 1.57 times improvement. Finally, the conclusion was drawn that the strain rate influenced the mechanical behavior by changing the transient total kinetic energy and the phase content evolution processes, which was the essence of the effect of strain rate on the mechanical behavior. This work has clarified the essence and enriched the theory of the effect of strain rate on the mechanical behavior of elastocaloric refrigeration alloys.
| S-EPMC10825924 | biostudies-literature
Project description:Carbon products such as anodes and ramming paste must have well-defined physical, mechanical, chemical, and electrical properties to perform their functions effectively in the aluminum electrolysis cell. The physical and mechanical properties of these products are assigned during the shaping procedure in which compaction stresses are applied to the green carbon paste. The optimization of the shaping process is crucial to improving the properties of the carbon products and consequently to increasing the energy efficiency and decreasing the greenhouse gas emissions of the Hall-Héroult process. The objective of this study is to experimentally investigate the effect(s) of the strain rate, of the stress maximum amplitude, and of the unloading level on the behavior of a green carbon paste subjected to cyclic loading. To this end, experiments consisting of (1) cyclic compaction tests at different maximum stress amplitudes and strain rates, and (2) cyclic compaction tests with different unloading levels were carried out. The study obtained the following findings about the behavior of carbon paste subjected to cyclic loads. The strain rate in the studied range had no effect either on the evolution of the permanent strain as a function of the cycle number, nor on the shape of the stress-strain hysteresis during the cyclic loading. Moreover, samples of the same density that had been subjected to different maximum stress amplitudes in their loading history did not have the same shape of the stress-strain curve. On the other hand, despite having different densities, samples subjected to the same number of cycles produce the same stress-strain curve during loading even though they were subjected to different maximum stress amplitudes in their loading histories. Finally, the level of unloading during each cycle of a cyclic test proved significant; when the sample was unloaded to a lower level of stress during each cycle, the permanent strain as a function of the cycle number was higher.
| S-EPMC8839192 | biostudies-literature
Project description:Although the properties of carbon nanotubes (CNTs) are very well-known and are still extensively studied, a thorough understanding of other carbon-based nanomaterials such as C3N nanotubes (C3NNTs) is still missing. In this article, we used molecular dynamics simulation to investigate the effects of parameters such as chirality, diameter, number of walls, and temperature on the mechanical properties of C3N nanotubes, C3N nanobuds, and C3NNTs with various kinds of defects. We also modeled and tested the corresponding CNTs to validate the results and understand how replacing one C atom of CNT by one N atom affects the properties. Our results demonstrate that the Young's modulus of single-walled C3NNTs (SWC3NNTs) increased with diameter, irrespective of the chirality, and was higher in armchair SWC3NNTs than in zigzag ones, unlike double-walled C3NNTs. Besides, adding a second and then a third wall to SWC3NNTs significantly improved their properties. In contrast, the properties of C3N nanobuds produced by attaching an increasing number of C60 fullerenes gradually decreased. Moreover, considering C3NNTs with different types of defects revealed that two-atom vacancies resulted in the greatest reduction of all the properties studied, while Stone-Wales defects had the lowest effect on them.
| S-EPMC7279212 | biostudies-literature
Project description:Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and calculations of the structure and properties of HAP showed that various structural defects have a significant effect on the properties of the material. By varying these structural heterogeneities, it is possible to increase the biocompatibility of HAP. An important role here is played by OH group vacancies, which are easily formed when these hydroxyl groups leave OH channels of HAP. In this case, the temperature dependence of the concentration of OH ions, which also determines the thermal behavior of HAP, is important. To study the evaporation of OH ions from HAP structures with increasing temperatures, molecular dynamics simulation (MDS) methods were used in this work. As a program for MDS modeling, we used the PUMA-CUDA software package. The initial structure of HAP, consisting of 4 × 4 × 2 = 32 unit cells of the hexagonal HAP phase, surrounded by a 15-Å layer of water was used in the modelling. Multiple and statistically processed MDS, running calculations in the range of 700-1400 K, showed that active evaporation of OH ions begins at the temperature of 1150 K. The analysis of the obtained results in comparison with those available in the literature data shows that these values are very close to the experiments. Thus, this MDS approach demonstrates its effective applicability and shows good results in the study of the thermal behavior of HAP.
| S-EPMC9740815 | biostudies-literature
Project description:Spectrin, a large cytoskeletal protein, consists of a heterodimeric structure comprising α and β subunits. Here, we have studied the mechanics of spectrin filament as a major constituent of dendrites and dendritic spines. Given the intricate biological details and compact biological construction of spectrin, we've developed a constitutive model of spectrin that describes its continuous deformation over three distinct stages and it's progressive failure mechanisms. Our model closely predicts both the force at which uncoiling begins and the ultimate force at which spectrin fails, measuring approximately 93 ~ 100 pN. Remarkably, our predicted failure force closely matches the findings from AFM experiments focused on the uncoiling of spectrin repeats, which reported a force of 90 pN. Our theoretical model proposes a plausible pathway for the potential failure of dendrites and the intricate connection between strain and strain rate. These findings deepen our understanding of how spectrin can contribute to traumatic brain injury risk analysis.
| S-EPMC11258356 | biostudies-literature
Project description:Microtubule-associated protein (MAP) tau is a cross-linking molecule that provides structural stability to axonal microtubules (MT). It is considered a potential biomarker for Alzheimer's disease (AD), dementia, and other neurological disorders. It is also a signature protein for Traumatic Brain Injury (TBI) assessment. In the case of TBI, extreme dynamic mechanical energies can be felt by the axonal cytoskeletal members. As such, fundamental understandings of the responses of single tau protein, polymerized tau protein, and tau-microtubule interfaces under high-rate mechanical forces are important. This study attempts to determine the high-strain rate mechanical behavior of single tau, dimerized tau, and tau-MT interface using molecular dynamics (MD) simulation. The results show that a single tau protein is a highly stretchable soft polymer. During deformation, first, it significantly unfolds against van der Waals and electrostatic bonds. Then it stretches against strong covalent bonds. We found that tau acts as a viscoelastic material, and its stiffness increases with the strain rate. The unfolding stiffness can be ~50-500 MPa, while pure stretching stiffness can be >2 GPa. The dimerized tau model exhibits similar behavior under similar strain rates, and tau sliding from another tau is not observed until it is stretched to >7 times of original length, depending on the strain rate. The tau-MT interface simulations show that very high strain and strain rates are required to separate tau from MT suggesting Tau-MT bonding is stronger than MT subunit bonding between themselves. The dimerized tau-MT interface simulations suggest that tau-tau bonding is stronger than tau-MT bonding. In summary, this study focuses on the structural response of individual cytoskeletal components, namely microtubule (MT) and tau protein. Furthermore, we consider not only the individual response of a component, but also their interaction with each other (such as tau with tau or tau with MT). This study will eventually pave the way to build a bottom-up multiscale brain model and analyze TBI more comprehensively.
| S-EPMC8472149 | biostudies-literature
Project description:Microtubules (MTs) are the largest type of cellular filament, essential in processes ranging from mitosis and meiosis to flagellar motility. Many of the processes depend critically on the mechanical properties of the MT, but the elastic moduli, notably the Young's modulus, are not directly revealed in experiment, which instead measures either flexural rigidity or response to radial deformation. Molecular dynamics (MD) is a method that allows the mechanical properties of single biomolecules to be investigated through computation. Typically, MD requires an atomic resolution structure of the molecule, which is unavailable for many systems, including MTs. By combining structural information from cryo-electron microscopy and electron crystallography, we have constructed an all-atom model of a complete MT and used MD to determine its mechanical properties. The simulations revealed nonlinear axial stress-strain behavior featuring a pronounced softening under extension, a possible plastic deformation transition under radial compression, and a distinct asymmetry in response to the two senses of twist. This work demonstrates the possibility of combining different levels of structural information to produce all-atom models suitable for quantitative MD simulations, which extends the range of systems amenable to the MD method and should enable exciting advances in our microscopic knowledge of biology.
| S-EPMC2905083 | biostudies-literature
Project description:Mechanical metamaterials are usually designed to exhibit novel properties and functionalities that are rare or even unprecedented. What is common among most previous designs is the quasi-static nature of their mechanical behavior. Here, we introduce a previously unidentified class of strain rate-dependent mechanical metamaterials. The principal idea is to laterally attach two beams with very different levels of strain rate-dependencies to make them act as a single bi-beam. We use an analytical model and multiple computational models to explore the instability modes of such a bi-beam construct, demonstrating how different combinations of hyperelastic and viscoelastic properties of both beams, as well as purposefully introduced geometric imperfections, could be used to create robust and highly predictable strain rate-dependent behaviors of bi-beams. We then use the bi-beams to design and experimentally realize lattice structures with unique strain rate-dependent properties including switching between auxetic and conventional behaviors and negative viscoelasticity.
| S-EPMC7299623 | biostudies-literature
Project description:The behavior at an interface between carbon nanotubes (CNTs) and silver nanowire (AgNW) could hardly be observed experimentally on an atomic scale, and the interaction is difficult to accurately calculate due to nanometer size effects. In this work, the contact behavior is studied with the molecular dynamics (MD) simulation, which indicates that the CNTs and AgNW can move towards each other to form aligned structures with their interfaces in full contact. In these different composite systems, nanotubes may either keep their form of an inherent cylindrical structure or completely collapse into the nanoribbons that can tightly scroll on the AgNW periphery while wrapping it in a core-shell structure. Thus, the atomic configuration evolution that is affected by the van der Waals (vdW) interaction is closely analyzed to assist the understanding of interfacial contact behavior.
| S-EPMC7142578 | biostudies-literature
Project description:Heavy oil and bitumen play a vital role in the global energy supply, and to unlock such resources, thermal methods, e.g., steam injection, are applied. To improve the performance of these methods, different additives, such as air, solvents, and chemicals, can be used. As a subset of chemicals, surfactants are one of the potential additives for steam-based bitumen recovery methods. Molecular interactions between surfactant/steam/bitumen have not been addressed in the literature. This paper investigates molecular interactions between anionic surfactants, steam, and bitumen in high-temperature and high-pressure conditions. For this purpose, a real Athabasca oil sand composition is employed to assess the phase behavior of surfactant/steam/bitumen under in-situ steam-based bitumen recovery. Two different asphaltene architectures, archipelago and Island, are used to examine the effect of asphaltene type on bitumen's interfacial behavior. The influence of having sulfur heteroatoms in a resin structure and a benzene ring's effect in an anionic surfactant structure on surfactant-steam-bitumen interactions are investigated systematically. The outputs are supported by different analyses, including radial distribution functions (RDFs), mean squared displacement (MSD), radius of gyration, self-diffusion coefficient, solvent accessible surface area (SASA), interfacial thickness, and interaction energies. According to MD outputs, adding surfactant molecules to the steam phase improved the interaction energy between steam and bitumen. Moreover, surfactants can significantly improve steam emulsification capability by decreasing the interfacial tension (IFT) between bitumen and the steam phase. Asphaltene architecture has a considerable effect on the interfacial behavior in such systems. This study provides a better and more in-depth understanding of surfactant-steam-bitumen systems and spotlights the interactions between bitumen fractions and surfactant molecules under thermal recovery conditions.
| S-EPMC8490457 | biostudies-literature