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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 i
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 f
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 pha
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 ascert
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 si