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Motivated by recent experiments on colloidal systems with competing attractive and repulsive interactions, we simulate a two-dimensional system of colloids with competing interactions that can undergo fragmentation. In the absence of any…
The theory of elastic interaction of micron size axially symmetric colloidal particles immersed into confined nematic liquid crystal has been proposed. General formulas are obtained for the self energy of one colloidal particle and…
Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR…
Dynamics of two particles with short range repulsive or attractive interaction is studied numerically in the Harper model. It is shown that interaction leads to appearance of localized states and pure-point spectrum component in the case…
Effective electrostatic interactions between colloidal particles, coated with polyelectrolyte brushes and suspended in an electrolyte solvent, are described via linear response theory. The inner cores of the macroions are modeled as hard…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…
Contacts between particles in dense, sheared suspensions are believed to underpin much of their rheology. Roughness and adhesion are known to constrain the relative motion of particles, and thus globally affect the shear response, but an…
Recent literature indicates that attractive interactions between particles of a dense liquid play a secondary role in determining its bulk mechanical properties. Here we show that, in contrast with their apparent unimportance to the bulk…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
As the glass (in molecular fluids\cite{Donth}) or the jamming (in colloids and grains\cite{LiuNature1998}) transitions are approached, the dynamics slow down dramatically with no marked structural changes. Dynamical heterogeneity (DH) plays…
A binary mixture of oppositely charged components confined to a plane such as cationic and anionic lipid bilayers may exhibit local segregation. The relative strength of the net short range interactions, which favors macroscopic…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We explore phase separation and kinetic arrest in a model active colloidal system consisting of self-propelled, hard-core particles with nonconvex shapes. The passive limit of the model, namely cross-shaped particles on a square lattice,…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
In flat-band systems, destructive interference leads to the localization of non-interacting particles and forbids their motion through the lattice. However, in the presence of interactions the overlap between neighbouring single-particle…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…