No Arabic abstract
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of linkers in the solution modifies the effective inter-rod interaction and can lead to inter-filament attraction. Depending on the systems composition and physical properties such as linker binding energies, filaments will either orient perpendicular or parallel to each other, leading to network-like or bundled structures. We show that such a system can have one of three generic phase diagrams, one dominated by bundles, another by networks, and the third containing both bundle and network-like phases. The first two diagrams can be found over a wide range of interaction energies, while the third occurs only for a narrow range. These results provide theoretical understanding of the classification of linker proteins as bundling proteins or crosslinking proteins. In addition, they suggest possible mechanisms by which the cell may control cytoskeletal morphology.
The enhancement of mobility at the surface of an amorphous alloy is studied using a combination of molecular dynamic simulations and normal mode analysis of the non-uniform distribution of Debye-Waller factors. The increased mobility at the surface is found to be associated with the appearance of Arrhenius temperature dependence. We show that the transverse Debye-Waller factor exhibits a peak at the surface. Over the accessible temperature range, we find that the bulk and surface diffusion coefficients obey the same empirical relationship with the respective Debye-Waller factors. Extrapolating this relationship to lower T, we argue that the observed decrease in the constraint at the surface is sufficient to account for the experimentally observed surface enhancement of mobility.
The discrete element method constitutes a general class of modeling techniques to simulate the microscopic behavior (i.e. at the particle scale) of granular/soil materials. We present a contact dynamics method, accounting for the cohesive nature of fine powders and soils. A modification of the model adjusted to capture the essential physical processes underlying the dynamics of generation and collapse of loose systems is able to simulate quicksand behavior of a collapsing soil material, in particular of a specific type, which we call living quicksand. We investigate the penetration behavior of an object for varying density of the material. We also investigate the dynamics of the penetration process, by measuring the relation between the driving force and the resulting velocity of the intruder, leading to a power law behavior with exponent 1/2, i.e. a quadratic velocity dependence of the drag force on the intruder.
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each phase.
We explore quantitative descriptors that herald when a many-particle system in $d$-dimensional Euclidean space $mathbb{R}^d$ approaches a hyperuniform state as a function of the relevant control parameter. We establish quantitative criteria to ascertain the extent of hyperuniform and nonhyperuniform distance-scaling regimes n terms of the ratio $B/A$, where $A$ is volume coefficient and $B$ is surface-area coefficient associated with the local number variance $sigma^2(R)$ for a spherical window of radius $R$. To complement the known direct-space representation of the coefficient $B$ in terms of the total correlation function $h({bf r})$, we derive its corresponding Fourier representation in terms of the structure factor $S({bf k})$, which is especially useful when scattering information is available experimentally or theoretically. We show that the free-volume theory of the pressure of equilibrium packings of identical hard spheres that approach a strictly jammed state either along the stable crystal or metastable disordered branch dictates that such end states be exactly hyperuniform. Using the ratio $B/A$, the hyperuniformity index $H$ and the direct-correlation function length scale $xi_c$, we study three different exactly solvable models as a function of the relevant control parameter, either density or temperature, with end states that are perfectly hyperuniform. We analyze equilibrium hard rods and sticky hard-sphere systems in arbitrary space dimension $d$ as a function of density. We also examine low-temperature excited states of many-particle systems interacting with stealthy long-ranged pair interactions as the temperature tends to zero. The capacity to identify hyperuniform scaling regimes should be particularly useful in analyzing experimentally- or computationally-generated samples that are necessarily of finite size.
We develop the elastically collective nonlinear Langevin equation theory of bulk relaxation of glass-forming liquids to investigate molecular mobility under compression conditions. The applied pressure restricts more molecular motion and therefore significantly slows-down the molecular dynamics when increasing the pressure. We quantitatively determine the temperature and pressure dependence of the structural relaxation time. To validate our model, dielectric spectroscopy experiments for three rigid and non-polymeric supramolecules are carried out at ambient and elevated pressures. The numerical results quantitatively agree with experimental data.