Related papers: Nanosecond chain dynamics of single-stranded nucle…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
The dynamical response of metallic clusters up to $10^3$ atoms is investigated using the restricted molecular dynamics simulations scheme. Exemplarily, sodium like material is considered. Correlation functions are evaluated to investigate…
The purpose of this work is to expand the work of Streher (2017) in order to investigate the aeroelastic instabilities generated by the flow around a moving NACA0012 airfoil. The profile has a chord length of $c=0.1 m and is exposed to a…
The dynamic structure factor, vorticity and entropy density dynamic correlation functions are measured for Stochastic Rotation Dynamics (SRD), a particle based algorithm for fluctuating fluids. This allows us to obtain unbiased values for…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
We study the Single File Diffusion (SFD) of a cyclic chain of particles that cannot cross each other, in a thermal bath, with long ranged interactions, and arbitrary damping. We present simulations that exhibit new behaviors specifically…
Highly symmetric nano-shells are found in many biological systems, such as clathrin cages and viral shells. Several studies have shown that symmetric shells appear in nature as a result of the free energy minimization of a generic…
The recently obtained spin-crossover nanoparticles are possible candidates for applications in the recording media industry as materials for data storage, or as pressure and temperature sensors. For these applications the intermolecular…
We have used density functional perturbation theory to investigate the stiffness of interatomic bonds in small clusters of Si, Sn and Pb. As the number of atoms in a cluster is decreased, there is a marked shortening and stiffening of…
We investigate how the dynamics of a single chain influences the kinetics of early stage phase separation in a symmetric binary polymer mixture. We consider quenches from the disordered phase into the region of spinodal instability. On a…
We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…
Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a coarse-grained, low-dimensional representation of the…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
In recent years, fluorescence correlation spectroscopy has been increasingly applied for the study of polymer dynamics on the nanometer scale. The core idea is to extract, from a measured autocorrelation curve, an effective mean-square…
We report a detailed study of neuromorphic switching behaviour in inherently complex percolating networks of self-assembled metal nanoparticles. We show that variation of the strength and duration of the electric field applied to this…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded…
Coherent grazing-incidence small-angle X-ray scattering is used to investigate the average kinetics and the fluctuation dynamics during self-organized nanopatterning of silicon by Ar$^+$ bombardment at 65$^{\circ}$ polar angle. At early…