Mechanical Performance of Graphene-Based Artificial Nacres under Impact Loads: A Coarse-Grained Molecular Dynamic Study.
Ontology highlight
ABSTRACT:
SUBMITTER: Liu N
PROVIDER: S-EPMC6432097 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Electrostatic interactions play a pivotal role in many biomolecular processes. The molecular organization and function in biological systems are largely determined by these interactions. Owing to the highly negative charge of RNA, the effect is expected to be more pronounced in this system. Moreover, RNA base pairing is dependent on the charge of the base, giving rise to alternative secondary and tertiary structures. The equilibrium between uncharged and charged bases is regulated by the solution pH, which is therefore a key environmental condition influencing the molecule's structure and behaviour. By means of constant-pH Monte Carlo simulations based on a fast proton titration scheme, coupled with the coarse-grained model HiRE-RNA, molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local pK a values for each nucleotide.
| S-EPMC6501344 | biostudies-literature
Project description:Graphene foams (GrFs) have been widely used as structural and/or functional materials in many practical applications. They are always assembled by thin and thick graphene sheets with multiple thicknesses; however, the effect of this basic structural feature has been poorly understood by existing theoretical models. Here, we propose a coarse-grained bi-modal GrF model composed of a mixture of 1-layer flexible and 8-layer stiff sheets to study the mechanical properties and deformation mechanisms based on the mesoscopic model of graphene sheets (Model. Simul. Mater. Sci. Eng. 2011, 19, 54003). It is found that the modulus increases almost linearly with an increased proportion of 8-layer sheets, which is well explained by the mixture rule; the strength decreases first and reaches the minimum value at a critical proportion of stiff sheets ~30%, which is well explained by the analysis of structural connectivity and deformation energy of bi-modal GrFs. Furthermore, high-stress regions are mainly dispersed in thick sheets, while large-strain areas mainly locate in thin ones. Both of them have a highly uneven distribution in GrFs due to the intrinsic heterogeneity in both structures and the mechanical properties of sheets. Moreover, the elastic recovery ability of GrFs can be enhanced by adding more thick sheets. These results should be helpful for us to understand and further guide the design of advanced GrF-based materials.
| S-EPMC8509715 | biostudies-literature
Project description:Tethered bilayer lipid membranes (tBLMs) provide a stable platform for modeling the dynamics and order of biological membranes where the tethers mimic the cytoskeletal supports present in biological cell membranes. In this paper coarse-grained molecular dynamics (CGMD) is applied to study the effects of tethers on lipid membrane properties. Using results from the CGMD model and the overdamped Fokker-Planck equation, we show that the diffusion tensor and particle density of water in the tBLM is spatially dependent. Further, it is shown that the membrane thickness, lipid diffusion, defect density, free energy of lipid flip-flop, and membrane dielectric permittivity are all dependent on the tether density. The numerically computed results from the CGMD model are in agreement with the experimentally measured results from tBLMs containing different tether densities and lipids derived from Archaebacteria. Additionally, using experimental measurements from Escherichia coli bacteria and Saccharomyces Cerevisiae yeast tethered membranes, we illustrate how previous molecular dynamics results can be combined with the proposed model to estimate the dielectric permittivity and defect density of these membranes as a function of tether density.
| S-EPMC5063460 | biostudies-literature
Project description:Many free-energy sampling and quantum mechanics/molecular mechanics (QM/MM) computations on protein complexes have been performed where, by necessity, a single component is studied isolated in solution while its overall configuration is kept in the complex-like state by either rigid restraints or harmonic constraints. A drawback in these studies is that the system's native fluctuations are lost, both due to the change of environment and the imposition of the extra potential. Yet, we know that having both accurate structure and fluctuations is likely crucial to achieving correct simulation estimates for the subsystem within its native larger protein complex context. In this work, we provide a new approach to this problem by drawing on ideas developed to incorporate experimental information into a molecular simulation by relative entropy minimization to a target system. We show that by using linear biases on coarse-grained (CG) observables (such as distances or angles between large subdomains within a protein), we can maintain the protein in a particular target conformation while also preserving the correct equilibrium fluctuations of the subsystem within its larger biomolecular complex. As an application, we demonstrate this algorithm by training a bias that causes an actin monomer (and trimer) in solution to sample the same average structure and fluctuations as if it were embedded within a much larger actin filament. Additionally, we have developed a number of algorithmic improvements that accelerate convergence of the on-the-fly relative entropy minimization algorithms for this type of application. Finally, we have contributed these methods to the PLUMED open source free energy sampling software library.
| S-EPMC5649387 | biostudies-literature
Project description:We propose a simple general framework to predict folding, native states, energy barriers, protein unfolding, as well as mutation induced diseases and other protein structural analyses. The model should not be considered as an alternative to classical approaches (Molecular Dynamics or Monte Carlo) because it neglects low scale details and rather focuses on global features of proteins and structural information. We aim at the description of phenomena that are out of the range of classical molecular modeling approaches due to the large computational cost: multimolecular interactions, cyclic behavior under variable external interactions, and similar. To demonstrate the effectiveness of the approach in a real case, we focus on the folding and unfolding behavior of tropoelastin and its mutations. Specifically, we derive a discrete mechanical model whose structure is deduced based on a coarse graining approach that allows us to group the amino acids sequence in a smaller number of `equivalent' masses. Nearest neighbor energy terms are then introduced to reproduce the interaction of such amino acid groups. Nearest and non-nearest neighbor energy terms, inter and intra functional blocks are phenomenologically added in the form of Morse potentials. As we show, the resulting system reproduces important properties of the folding-unfolding mechanical response, including the monotonic and cyclic force-elongation behavior, representing a physiologically important information for elastin. The comparison with the experimental behavior of mutated tropoelastin confirms the predictivity of the model. STATEMENT OF SIGNIFICANCE: Classical approaches to the study of phenomena at the molecular scale such as Molecular Dynamics (MD) represent an incredible tool to unveil mechanical and conformational properties of macromolecules, in particular for biological and medical applications. On the other hand, due to the computational cost, the time and spatial scales are limited. Focusing of the real case of tropoelastin, we propose a new approach based on a careful coarse graining of the system, able to describe the overall properties of the macromolecule and amenable of extension to larger scale effects (protein bundles, protein-protein interactions, cyclic loading). The comparison with tropoelastin behavior, also for mutations, is very promising.
| S-EPMC8542605 | biostudies-literature
Project description:Bone formation and deposition are initiated by sensory nerve infiltration in adaptive bone remodeling. Here, we focused on the role of Semaphorin 3A (Sema3A), expressed by sensory nerves, in mechanical loads-induced bone formation and nerve withdrawal using orthodontic tooth movement (OTM) model. Firstly, bone formation was activated after the 3rd day of OTM, coinciding with a decrease in sensory nerves and an increase in pain threshold. Sema3A, rather than nerve growth factor (NGF), highly expressed in both trigeminal ganglion and the axons of periodontal ligament following the 3rd day of OTM. Moreover, in vitro mechanical loads upregulated Sema3A in neurons instead of in human periodontal ligament cells (hPDLCs) within 24 hours. Furthermore, exogenous Sema3A restored the suppressed alveolar bone formation and the osteogenic differentiation of hPDLCs induced by mechanical overload. Mechanistically, Sema3A prevented overstretching of F-actin induced by mechanical overload through ROCK2 pathway, maintaining mitochondrial dynamics as mitochondrial fusion. Therefore, Sema3A exhibits dual therapeutic effects in mechanical loads-induced bone formation, both as a pain-sensitive analgesic and a positive regulator for bone formation.
| S-EPMC10796360 | biostudies-literature
Project description: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.
| S-EPMC7859260 | biostudies-literature
Project description:We examine the influence of steady shear on structural relaxation in a simulated coarse-grained unentangled polymer melt over a wide range of temperature and shear rates. Shear is found to progressively suppress the ?-relaxation process observed in the intermediate scattering function, leading ultimately to a purely inertially dominated ?-relaxation at high shear rates, a trend similar to increasing temperature. On the basis of a scaling argument emphasizing dynamic heterogeneity in cooled liquids and its alteration under material deformation, we deduce and validate a parameter-free scaling relation for both the structural relaxation time ?? from the intermediate scattering function and the "stretching exponent" ? quantifying the extent of dynamic heterogeneity over the entire range of temperatures and shear rates that we can simulate.
| S-EPMC7182423 | biostudies-literature
Project description:Transient pore formation on the membrane of red blood cells (RBCs) under high mechanical tensions is of great importance in many biomedical applications, such as RBC damage (hemolysis) and mechanoporation-based drug delivery. The dynamic process of pore formation, growth, and resealing is hard to visualize in experiments. We developed a mesoscale coarse-grained model to study the characteristics of transient pores on a patch of the lipid bilayer that is strengthened by an elastic meshwork representing the cytoskeleton. Unsteady molecular dynamics was used to study the pore formation and reseal at high strain rates close to the physiological ranges. The critical strain for pore formation, pore characteristics, and cytoskeleton effects were studied. Results show that the presence of the cytoskeleton increases the critical strain of pore formation and confines the pore growth. Moreover, the pore recovery process under negative strain rates (compression) is analyzed. Simulations show that pores can remain open for a long time during the high-speed tank-treading induced stretching and compression process that a patch of the RBC membrane usually experiences under high shear flow. Furthermore, complex loading conditions can affect the pore characteristics and result in denser pores. Finally, the effects of strain rate on pore formation are analyzed. Higher rate stretching of membrane patch can result in a significant increase in the critical areal strain and density of pores. Such a model reveals the dynamic molecular process of RBC damage in biomedical devices and mechanoporation that, to our knowledge, has not been reported before.
| S-EPMC7399477 | biostudies-literature
Project description:We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.
| S-EPMC5649594 | biostudies-literature