Related papers: Compounding formula approach to chromatin and acti…
Long, elastic filaments cross-linked and deformed by active molecular motors occur in various natural settings. The overall macroscopic mechanical response of such a composite network depends on the coupling between the active and the…
The motion of a tagged degree of freedom can give important insight in the interactions present in a complex environment. We investigate the dynamics of a tagged particle in two non-equilibrium systems that consist of interacting…
A coarse-graining strategy for dilute and semi-dilute solutions of interacting polymers, and of colloid polymer mixtures is briefly described. Monomer degrees of freedom are traced out to derive an effective, state dependent pair potential…
The dynamics of star polymers has been investigated via extensive Molecular- and Brownian Dynamics simulations for a large range of functionality $f$ and packing fraction $\eta$. The calculated isodiffusivity curves display both minima and…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
This paper presents a framework for abstracting uncertain or non-polynomial components of dynamical systems using polynomial constraints. This enables the application of polynomial-based analysis tools, such as sum-of-squares programming,…
We demonstrate how coupling nonlinear dynamical systems can reduce the effects of noise. For simplicity we investigate noisy coupled map lattices. Noise from different lattice nodes can diffuse across the lattice and lower the noise level…
A new approach is theoretically proposed to study the glass transition of active pharmaceutical ingredients and a glass-forming anisotropic molecular liquid at high pressures. We describe amorphous materials as a fluid of hard spheres.…
The dynamic structure factor of semiflexible polymers in solution is derived from the wormlike chain model. Special attention is paid to the rigid constraint of an inextensible contour and to the hydrodynamic interactions. For the cases of…
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the…
Active dynamic processes of cells are largely driven by the cytoskeleton, a complex and adaptable semiflexible polymer network, motorized by mechanoenzymes. Small dimensions, confined geome- tries and hierarchical structures make it…
Compositional Explanations is a method for identifying logical formulas of concepts that approximate the neurons' behavior. However, these explanations are linked to the small spectrum of neuron activations (i.e., the highest ones) used to…
We formulate the dynamical theory of nematic polymers, starting from a microscopic Poisson bracket approach. We find that the Poisson bracket between the nematic director and momentum depends on the (Maier-Saupe) order parameter of the…
An energy-based modeling framework for the nonlinear dynamics of spatial Cosserat rods undergoing large displacements and rotations is proposed. The mixed formulation features independent displacement, velocity and stress variables and is…
Pushing is a simple yet effective skill for robots to interact with and further change the environment. Related work has been mostly focused on utilizing it as a non-prehensile manipulation primitive for a robotic manipulator. However, it…
Active particles driven by colored noise can be approximately mapped onto a system that obeys detailed balance. The effective interactions which can be derived for such a system allow to describe the structure and phase behavior of the…
Preserving quantum coherence with the increase of a system's size and complexity is a major challenge. Molecules, with their diverse sizes and complexities and many degrees of freedom, are an excellent platform for studying the transition…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
A heterogeneous medium of constituents with vastly different mechanical properties, whose inhomogeneities are in close proximity to each other, is considered. The gradient of the solution to the corresponding problem exhibits singular…
The aim of this work is understanding the stretching mechanism of stochastic models of turbulence acting on a simple model of dilute polymers. We consider a turbulent model that is white noise in time and activates frequencies in a shell…