Related papers: Coarse-graining bistability with the Martini force…
There is growing interest in molecular structures that exhibit dynamics similar to bistable mechanical systems. These structures have the potential to be used as nanodevices with two distinct states. Particularly intriguing are structures…
The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing…
Nanometer-sized molecular structures exhibiting mechanical-like switching between discrete states are of great interest for their potential uses in nanotechnology and materials science. Designing such structures and understanding how they…
The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose long-term conformational dynamics are similar to the dynamics of bistable mechanical systems such as…
In soft matter systems the local displacement field can be accessed directly by video microscopy enabling one to compute local strain fields and hence the elastic moduli using a coarse-graining procedure. We study this process for a simple…
This paper presents an extended coarse-grained investigation of the elastic properties of polystyrene. In particular, we employ the well-known MARTINI force field and its modifications to perform extended molecular dynamics simulations at…
The paper constructs a coarse-grained model to investigate dry sliding friction of the body-centered-cubic Fe micron-scale system by smoothed particle hydrodynamics simulations and examines influences of the spring force on the characters…
The behavior of a bidisperse inelastic gas vertically shaken in a compartmentalized container is investigated using two different approaches: the first is a mean-field dynamical model, which treats the number of particles in the two…
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.…
We demonstrate how the dynamical coarse-graining approach can be systematically extended to higher orders in the coupling between system and reservoir. Up to second order in the coupling constant we explicitly show that dynamical…
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.…
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
Bi-stable objects that are pushed between states by an external field are often used as a simple model to study memory formation in disordered materials. Such systems, called hysterons, are typically treated quasistatically. Here, we…
Simple models have played an important role in the discussion of foundational issues in statistical mechanics. Among them the spin--echo system is of particular interest since it can be realized experimentally. This has led to inferences…
The stochastic trajectories of molecules in living cells, as well as the dynamics in many other complex systems, often exhibit memory in their path over long periods of time. In addition, these systems can show dynamic heterogeneities due…
Shape changes resulting from segmental flexibility are ubiquitous in molecular and biological systems, and are expected to affect both the diffusive motion and (biological) function of dispersed objects. The recent development of colloidal…
Our computer simulations have shown that the large-scale conformational dynamics of a short oligomeric fragment of thermoresponsive polymers resemble the mechanical movement of nonlinear bistable systems. The oligomers demonstrate…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
We study number density distribution and the behavior of time correlation functions in the density of grains for a quasi-two dimensional system of vibrated grains. We study the system at various packing fractions, from low to high. At low…
We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of…