Size extensivity of elastic properties of alkane fragments.
Ontology highlight
ABSTRACT:
SUBMITTER: Radiom M
PROVIDER: S-EPMC5758687 | biostudies-literature | 2018 Jan
REPOSITORIES: biostudies-literature
Publications
Size extensivity of elastic properties of alkane fragments.
Radiom Milad M Maroni Plinio P Wesolowski Tomasz A TA
Journal of molecular modeling 20180108 1
Using MP2, CCSD, and B3LYP methods of computational chemistry, we show length dependence in the intrinsic elastic properties of short alkane fragments. For isolated alkane fragments of finite length in the gas phase and zero temperature, the intrinsic elasticity constants are found to vary with the number of carbon atoms and its parity. From extrapolation of the elasticity constants calculations to infinite chain length, and by comparing with in-situ elasticity constant of single poly(ethylene) ...[more]
Similar Datasets
Project description:We have performed sound velocity and unit cell volume measurements of three synthetic, ultrafine micro/nanocrystalline grossular samples up to 50 GPa using Brillouin spectroscopy and synchrotron X-ray diffraction. The samples are characterized by average grain sizes of 90 nm, 93 nm and 179 nm (hereinafter referred to as samples Gr90, Gr93, and Gr179, respectively). The experimentally determined sound velocities and elastic properties of Gr179 sample are comparable with previous measurements, but slightly higher than those of Gr90 and Gr93 under ambient conditions. However, the differences diminish with increasing pressure, and the velocity crossover eventually takes place at approximately 20-30 GPa. The X-ray diffraction peaks of the ultrafine micro/nanocrystalline grossular samples significantly broaden between 15-40 GPa, especially for Gr179. The velocity or elasticity crossover observed at pressures over 30 GPa might be explained by different grain size reduction and/or inhomogeneous strain within the individual grains for the three grossular samples, which is supported by both the pressure-induced peak broadening observed in the X-ray diffraction experiments and transmission electron microscopy observations. The elastic behavior of ultrafine micro/nanocrystalline silicates, in this case, grossular, is both grain size and pressure dependent.
| S-EPMC8602367 | biostudies-literature
Project description:At low micromolar concentrations, polyunsaturated fatty acids (PUFAs) alter the function of many membrane proteins. PUFAs exert their effects on unrelated proteins at similar concentrations, suggesting a common mode of action. Because lipid bilayers serve as the common "solvent" for membrane proteins, the common mechanism could be that PUFAs adsorb to the bilayer/solution interface to promote a negative-going change in lipid intrinsic curvature and, like other reversibly adsorbing amphiphiles, increase bilayer elasticity. PUFA adsorption thus would alter the bilayer deformation energy associated with protein conformational changes involving the protein/bilayer boundary, which would alter protein function. To explore the feasibility of such a mechanism, we used gramicidin (gA) analogues of different lengths together with bilayers of different thicknesses to assess whether docosahexaenoic acid (DHA) could exert its effects through a bilayer-mediated mechanism. Indeed, DHA increases gA channel appearance rates and lifetimes and decreases the free energy of channel formation. The appearance rate and lifetime changes increase with increasing channel-bilayer hydrophobic mismatch and are not related to differing DHA bilayer absorption coefficients. DHA thus alters bilayer elastic properties, not just lipid intrinsic curvature; the elasticity changes are important for DHA's bilayer-modifying actions. Oleic acid (OA), which has little effect on membrane protein function, exerts no such effects despite OA's adsorption coefficient being an order of magnitude greater than DHA's. These results suggest that DHA (and other PUFAs) may modulate membrane protein function by bilayer-mediated mechanisms that do not involve specific protein binding but rather changes in bilayer material properties.
| S-EPMC1887599 | biostudies-literature
Project description:Nanoscale carbon-based fillers are known to significantly alter the mechanical and electrical properties of polymers even at relatively low loadings. We report results from extensive molecular-dynamics simulations of mechanical testing of model polymer (high-density polyethylene) nanocomposites reinforced by nanocarbon fillers consisting of graphene flakes and fullerenes. By systematically varying filler concentration, morphology, and size, we identify clear trends in composite stiffness with reinforcement. To within statistical error, spherical fullerenes provide a nearly size-independent level of reinforcement. In contrast, two-dimensional graphene flakes induce a strongly size-dependent response: we find that flakes with radii in the 2-4 nm range provide appreciable enhancement in stiffness, which scales linearly with flake radius. Thus, with flakes approaching typical experimental sizes (~0.1-1 μm), we expect graphene fillers to provide substantial reinforcement, which also is much greater than what could be achieved with fullerene fillers. We identify the atomic-scale features responsible for this size- and morphology-dependent response, notably, ordering and densification of polymer chains at the filler-matrix interface, thereby providing insights into avenues for further control and enhancement of the mechanical properties of polymer nanocomposites.
| S-EPMC4992834 | biostudies-literature
Project description:The main motivation for studying damage in bone tissue is to better understand how damage develops in the bone tissue and how it progresses. Such knowledge may help in the surgical aspects of joint replacement, fracture fixation or establishing the fracture tolerance of bones to prevent injury. Currently, there are no standards that create a realistic bone model with anisotropic material properties, although several protocols have been suggested. This study seeks to retrospectively evaluate the damage of bone tissue with respect to patient demography including age, gender, race, body mass index (BMI), height, and weight, and their role in causing fracture. Investigators believe that properties derived from CT imaging data to estimate the material properties of bone tissue provides more realistic models. Quantifying and associating damage with in vivo conditions will provide the required information to develop mathematical equations and procedures to predict the premature failure and potentially mitigate problems before they begin. Creating a realistic model for bone tissue can predict the premature failure(s), provide preliminary results before getting the surgery, and optimize the design of orthopaedic implants. A comparison was performed between the proposed model and previous efforts, where they used elastic, hyper- elastic, or elastic-plastic properties. Results showed that there was a significant difference between the anisotropic material properties of bone when compared with unrealistic previous methods. The results showed that the density is 50% higher in male subjects than female subjects. Additionally, the results showed that the density is 47.91% higher in Black subjects than Mixed subjects, 53.27% higher than Caucasian subjects and 57.41% higher than Asian. In general, race should be considered during modeling implants or suggesting therapeutic techniques.
| S-EPMC8773132 | biostudies-literature
Project description:Several species of Gram-positive bacteria can avidly bind soluble and surface-associated fibrinogen (Fng), a property that is considered important in the pathogenesis of human infections. To gain insights into the mechanism by which group B Streptococcus (GBS), a frequent neonatal pathogen, interacts with Fng, we have screened two phage displayed genomic GBS libraries. All of the Fng-binding phage clones contained inserts encoding fragments of FbsA, a protein displaying multiple repeats. Since the functional role of this protein is only partially understood, representative fragments were recombinantly expressed and analyzed for Fng binding affinity and ability to induce immune protection against GBS infection. Maternal immunization with 6pGST, a fragment containing five repeats, significantly protected mouse pups against lethal GBS challenge and these protective effects could be recapitulated by administration of anti-6pGST serum from adult animals. Notably, a monoclonal antibody that was capable of neutralizing Fng binding by 6pGST, but not a non-neutralizing antibody, could significantly protect pups against lethal GBS challenge. These data suggest that FbsA-Fng interaction promotes GBS pathogenesis and that blocking such interaction is a viable strategy to prevent or treat GBS infections.
| S-EPMC3782484 | biostudies-literature
Project description:We present measurements of the bulk Young's moduli of early chick embryos at Hamburger-Hamilton stage 10. Using a micropipette probe with a force constant k approximately 0.025 N/m, we applied a known force in the plane of the embryo in the anterior-posterior direction and imaged the resulting tissue displacements. We used a two-dimensional finite-element simulation method to model the embryo as four concentric elliptical elastic regions with dimensions matching the embryo's morphology. By correlating the measured tissue displacements to the displacements calculated from the in-plane force and the model, we obtained the approximate short time linear-elastic Young's moduli: 2.4 +/- 0.1 kPa for the midline structures (notocord, neural tube, and somites), 1.3 +/- 0.1 kPa for the intermediate nearly acellular region between the somites and area pellucida, 2.1 +/- 0.1 kPa for the area pellucida, and 11.9 +/- 0.8 kPa for the area opaca.
| S-EPMC3212891 | biostudies-literature
Project description:The long wavelength, low-frequency modes of motion are the relevant motions for understanding the continuum mechanical properties of biomolecules. By examining these low-frequency modes, in the context of a spherical harmonic basis set, we identify four elastic moduli that are required to describe the two-dimensional elastic behavior of capsids. This is in contrast to previous modeling and theoretical studies on elastic shells, which use only the two-dimensional Young's modulus (Y) and the bending modulus (κ) to describe the system. Presumably, the heterogeneity of the structure and the anisotropy of the biomolecular interactions lead to a deviation from the homogeneous, isotropic, linear elastic shell theory. We assign functional relevance of the various moduli governing different deformation modes, including a mode primarily sensed in atomic force microscopy nanoindentation experiments. We have performed our analysis on the T = 3 cowpea chlorotic mottle virus and our estimate for the nanoindentation modulus is in accord with experimental measurements.
| S-EPMC3117158 | biostudies-literature
Project description:Microbial capsules are important for virulence, but their architecture and physical properties are poorly understood. The human pathogenic fungus Cryptococcus neoformans has a large polysaccharide capsule that is necessary for virulence and is the target of protective antibody responses. To study the C. neoformans capsule we developed what we believe is a new approach whereby we probed the capsular elastic properties by applying forces using polystyrene beads manipulated with optical tweezers. This method allowed us to determine the Young's modulus for the capsule in various conditions that affect capsule growth. The results indicate that the Young's modulus of the capsule decreases with its size and increases with the Ca(2+) concentration in solution. Also, capsular polysaccharide manifests an unexpected affinity for polystyrene beads, a property that may function in attachment to host cells and environmental structures. Bead probing with optical tweezers provides a new, nondestructive method that may have wide applicability for studying the effects of growth conditions, immune components, and drugs on capsular properties.
| S-EPMC2726329 | biostudies-literature
Project description:Neural precursor cells differentiate into several cell types that display distinct functions. However, little is known about how cell surface mechanics vary during the differentiation process. Here, by precisely measuring membrane tension and bending modulus, we map their variations and correlate them with changes in neural precursor cell morphology along their distinct differentiation fates. Both cells maintained in culture as neural precursors as well as those plated in neurobasal medium reveal a decrease in membrane tension over the first hours of culture followed by stabilization, with no change in bending modulus. During astrocyte differentiation, membrane tension initially decreases and then increases after 72 h, accompanied by consolidation of glial fibrillary acidic protein expression and striking actin reorganization, while bending modulus increases following observed alterations. For oligodendrocytes, the changes in membrane tension are less abrupt over the first hours, but their values subsequently decrease, correlating with a shift from oligodendrocyte marker O4 to myelin basic protein expressions and a remarkable actin reorganization, while bending modulus remains constant. Oligodendrocytes at later differentiation stages show membrane vesicles with similar membrane tension but higher bending modulus as compared to the cell surface. Altogether, our results display an entire spectrum of how membrane elastic properties are varying, thus contributing to a better understanding of neural differentiation from a mechanobiological perspective.
| S-EPMC7349228 | biostudies-literature
Project description:PurposeTo establish a continuous relationship between the size of various antibody fragments and their systemic clearance (CL) in mice.MethodsTwo different orthogonal approaches have been used to establish the relationship. First approach uses CL values estimated by non-compartmental analysis (NCA) to establish a correlation with protein size. The second approach simultaneously characterizes the PK data for all the proteins using a 2-compartment model to establish a relationship between protein size and pharmacokinetic (PK) parameters.ResultsSimple mathematical functions (e.g. sigmoidal, power law) were able to characterize the CL vs. protein size relationship generated using the investigated proteins. The relationship established in mouse was used to predict rat, rabbit, monkey, and human relationships using allometric scaling. The predicted relationships were found to capture the available spares data from each species reasonably well.ConclusionsThe CL vs. protein size relationship is important for establishing a robust quantitative structure-PK relationship (QSPKR) for protein therapeutics. The relationship presented here can help in a priori predicting plasma exposure of therapeutic proteins, and together with our previously established relationship between plasma and tissue concentrations of proteins, it can predict the tissue exposure of non-binding proteins simply based on molecular weight/radius and dose.
| S-EPMC5693627 | biostudies-literature