No Arabic abstract
Mechanotransduction, the biological response to mechanical stress, is often initiated by the activation of mechanosensitive (MS) proteins upon mechanically induced deformations of the cell membrane. A current challenge to fully understand this process is to predict how lipid bilayers deform upon application of mechanical stress. In this context, it is now well established that anionic lipids influence the function of many proteins. Here, we test the hypothesize that anionic lipids could indirectly modulate MS proteins by alteration of the lipid bilayer mechanical properties. Using all-atom molecular dynamics simulations, we computed the bilayer bending rigidity (K_C), the area compressibility (K_A), and the surface shear viscosity ({eta}_m) of phosphocholine (PC) lipid bilayers containing or not phosphatidylserine (PS) or phosphatidylinositol bisphosphate (PIP2) at physiological concentrations in the lower leaflet. Tensionless leaflets were first checked for each asymmetric bilayer model, and a formula for embedding an asymmetric channel in an asymmetric bilayer is proposed. Results from two different sized bilayers show consistently that the addition of 20% surface charge in the lower leaflet of PC bilayer by PIP2 has minimal impact on its mechanical properties, while PS reduced the bilayer bending rigidity by 22%. As a comparison, supplementing the PIP2-enriched PC membrane with 30% cholesterol, a known rigidifying steroid lipid, produces a significant increase in all three mechanical constants. Analysis of pairwise splay moduli suggests that the effect of anionic lipids on bilayer bending rigidity largely depends on the number of anionic lipid pairs formed during simulations. The potential implication of bilayer bending rigidity is discussed in the framework of mechanosensitive Piezo channels.
Triply Periodic Minimal Surfaces (TPMS) possess locally minimized surface area under the constraint of periodic boundary conditions. Different families of surfaces were obtained with different topologies satisfying such conditions. Examples of such families include Primitive (P), Gyroid (G) and Diamond (D) surfaces. From a purely mathematical subject, TPMS have been recently found in materials science as optimal geometries for structural applications. Proposed by Mackay and Terrones in 1991, schwarzites are 3D crystalline porous carbon nanocrystals exhibiting the shape of TPMS. Although their complex topology poses serious limitations on their synthesis with conventional nanoscale fabrication methods, such as Chemical Vapour Deposition (CVD), TPMS can be fabricated by Additive Manufacturing (AM) techniques, such as 3D Printing. In this work, we used an optimized atomic model of a schwarzite structure from the D family (D8bal) to generate a surface mesh that was subsequently used for 3D-printing through Fused Deposition Modelling (FDM). This D schwarzite was 3D-printed with thermoplastic PolyLactic Acid (PLA) polymer filaments. Mechanical properties under uniaxial compression were investigated for both the atomic model and the 3D-printed one. Fully atomistic Molecular Dynamics (MD) simulations were also carried out to investigate the uniaxial compression behavior of the D8bal atomic model. Mechanical testings were performed on the 3D-printed schwarzite where the deformation mechanisms were found to be similar to those observed in MD simulations. These results are suggestive of a scale-independent mechanical behavior that is dominated by structural topology.
Room Temperature Ionic Liquids (RTILs) have attracted much of the attention of the scientific community in the past decade due the their novel and highly customizable properties. Nonetheless their high viscosities pose serious limitations to the use of RTILs in practical applications. To elucidate some of the physical aspects behind transport properties of RTILs, extensive classical molecular dynamics (MD) calculations are reported. Bulk viscosities and ionic conductivities of butyl-methyl-imidazole based RTILs are presented over a wide range of temperatures. The dependence of the properties of the liquids on simulation parameters, e.g. system size effects and choice of the interaction potential, is analyzed.
Helical amorphous nanosprings have attracted particular interest due to their special mechanical properties. In this work we present a simple model, within the framework of the Kirchhoff rod model, for investigating the structural properties of nanosprings having asymmetric cross section. We have derived expressions that can be used to obtain the Youngs modulus and Poissons ratio of the nanospring material composite. We also address the importance of the presence of a catalyst in the growth process of amorphous nanosprings in terms of the stability of helical rods.
Schwarzites are porous crystalline structures with Gaussian negative curvature. In this work, we investigated the mechanical behavior and energy absorption properties of two carbon-based diamond schwarzites (D688 and D8bal). We carried out fully atomistic molecular dynamics (MD) simulations. The optimized MD atomic models were used to generate macro-scale models for 3D-printing (PolyLactic Acid (PLA) polymer filaments) through Fused Deposition Modelling (FDM). Mechanical properties under uniaxial compression were investigated for both the atomic models and the 3D-printed ones. Mechanical testings were performed on the 3D-printed schwarzites where the deformation mechanisms were found to be similar to those observed in MD simulations. These results are suggestive of a scale-independent mechanical behavior that is dominated by structural topology. The structures exhibit high specific energy absorption and crush force efficiency ~0.8, which suggest that the 3D-printed diamond schwarzites are good candidates as energy-absorbing materials.
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating the free energy of solid and liquid phases at a given temperature and reversible scaling for computing free energies over a wide range of temperatures, including the direct integration of $P$-$T$ coexistence lines. By changing the chemistry and the interatomic potential, alchemical and upscaling free energy calculations are possible. Several examples illustrate the accuracy and efficiency of our implementation.