Related papers: Coarse-grained protein-protein stiffnesses and dyn…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
In this study, one-dimensional systems of masses connected by springs, i.e., spring-chain systems, are investigated numerically. The average kinetic energy of chain-end particles of these systems is larger than that of other particles,…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
One great challenge of modeling granular systems lies in capturing the rheologic dependencies on scale. For example, there are marked differences between quasi-static, intermediate, and rapid flow regimes. In this study, we demonstrate that…
Athermal (i.e. zero-temperature) under-constrained systems are typically floppy, but they can be rigidified by the application of external strain, which is theoretically well understood. Here and in the companion paper, we extend this…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
When a dense monolayer of macroscopic slightly polydisperse spheres floats on chaotic capillary Faraday waves, a coexistence of large scale convective motion and caging dynamics typical for jammed systems is observed. We subtract the…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank…
An analytical theory is presented for the damping of low-frequency adsorbate vibrations via resonant coupling to the substrate phonons. The system is treated classically, with the substrate modeled as a semi-infinite elastic continuum and…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
Human joint dynamic stiffness plays an important role in the stability of performance augmentation exoskeletons. In this paper, we consider a new frequency domain model of the human joint dynamics which features a complex value stiffness.…
A variational model for epitaxially-strained thin films on rigid substrates is derived both by {\Gamma}-convergence from a transition-layer setting, and by relaxation from a sharp-interface description available in the literature for…
The model of a chain of springs and masses (CSM), originating from the works of Schr\"odinger (1914), and Pater (1974), is found suitable as an analytical description of the dynamics of layers in orientated FCC crystals. An analytical…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…