Related papers: A Solvable Model for Polymorphic Dynamics of Biofi…
In a mathematical model of interacting biological organisms, where external interventions may alter behavior over time, traditional models that assume fixed parameters usually do not capture the evolving dynamics. In oncology, this is…
A model for diffusion on a cubic lattice with a random distribution of traps is developed. The traps are redistributed at certain time intervals. Such models are useful for describing systems showing dynamic disorder, such as ion-conducting…
We consider the continuum limit of a recently-introduced model for discretized thick polymers, or tubes. We address both analytically and numerically how the polymer thickness influences the decay of tangent-tangent correlations and find…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Molecular dynamics simulations are performed to investigate heterogeneous dynamics in amorphous glassy materials under oscillatory shear strain. We consider three-dimensional binary Lennard-Jones mixture well below the glass transition…
The design of amorphous entangled systems, specifically from soft and active materials, has the potential to open exciting new classes of active, shape-shifting, and task-capable 'smart' materials. However, the global emergent mechanics…
We investigate the thermal and structural properties of knotted diblock copolymer rings using a coarse-grained lattice model in an implicit solvent. The system is studied by means of the Wang--Landau Monte Carlo algorithm, allowing us to…
We report on quantitative comparisons between simulation results of a bead-spring model and mode-coupling theory calculations for the structural and conformational dynamics of a supercooled, unentangled polymer melt. We find…
Filamentous bio-materials such as fibrin or collagen networks exhibit an enormous stiffening of their elastic moduli upon large deformations. This pronounced nonlinear behavior stems from a significant separation between the stiffnesses…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and experiments. A lot of important information which is not immediately accessible…
We describe simulations of a microscopic elastic filament immersed in a fluid and subject to a uniform external force. Our method accounts for the hydrodynamic coupling between the flow generated by the filament and the friction force it…
Magnetic bubbles are topologically spin textures that offering the interesting physics and great promise for next-generation information storage technologies. The main obstacles so far are that magnetic bubbles are generated with no field…
We develop a general analysis of the diffusive dynamics of polydisperse polymers in the presence of chemical potential gradients, within the context of the tube model (with all species entangled). We obtain a set of coupled dynamical…
We perform molecular-dynamics simulations for polymer melts of the coarse-grained polyvinyl alcohol model that crystallizes upon slow cooling. To establish the properties of its high temperature liquid state as a reference point, we…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
A quantitative theory of the buckling of a worm like chain based on a semi-classical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows to go beyond the…
In this paper a quantum mechanical description of the assembly/disassembly process for microtubules is proposed. We introduce creation and annihilation operators that raise or lower the microtubule length by a tubulin layer. Following that,…
The linear and non-linear dynamic response to an oscillatory shear flow of giant wormlike micelles consisting of Pb-Peo block copolymers is studied by means of Fourier transform rheology. Experiments are performed in the vicinity of the…