Related papers: Packaging stiff polymers in small containers: A mo…
We use numerical simulation to investigate and analyze the way that rigid disks and spheres arrange themselves when compressed next to incommensurate substrates. For disks, a movable set is pressed into a jammed state against an ordered…
What can cells gain by using disordered, rather than folded, proteins in the architecture of their skeleton? Disordered proteins take multiple co-existing conformations, and often contain segments which act as random-walk-shaped polymers.…
We suggest a geometrical mechanism for the ordering of slender filaments inside non-isotropic containers, using cortical microtubules in plant cells and packing of viral genetic material inside capsids as concrete examples. We show…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
DNA origami is a powerful method to achieve nanoscale folded structures. Despite rapid improvements in folding and purification methods, DNA origami objects are still often produced in small quantities and studied at single molecule scale.…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Via large-scale molecular dynamics simulations, we observe the melting of a topological glass of stiff ring polymers by incorporating flexible ring polymers, along an isobaric path. As more flexible ring polymers are introduced, cluster…
An external load on a particle packing is distributed internally through a heterogeneous network of particle contacts. This contact force distribution determines the stability of the particle packing and the resulting structure. Here, we…
We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
The close packing density of log-normal and bimodal distributed, surface-adsorbed particles or discs in 2D is studied by numerical simulation. For small spread in particle size, the system orders in a polycrystalline structure of hexagonal…
Using Langevin dynamics simulations, we study a system of transversely propelling filament and passive Brownian particles. We consider a polymer whose monomers experience a constant propulsion force perpendicular to the local tangent in the…
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this…
We study the adsorption of semiflexible polymers such as polyelectrolytes or DNA on planar and curved substrates, e.g., spheres or washboard substrates via short-range potentials using extensive Monte-Carlo simulations, scaling arguments,…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatic interaction between the positive charges on capsid proteins and the…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
Molecular packing, crystallinity, and texture of semiconducting polymers are often critical to performance. Although frame-works exist to quantify the ordering, interpretations are often just qualitative, resulting in imprecise and liberal…