Related papers: Twist-bend instability for toroidal DNA condensate…
The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…
Biomolecules are often very long with a definite chirality. DNA, xanthan and poly-gamma-benzyl-glutamate (PBLG) can all form columnar crystalline phases. The chirality, however, competes with the tendency for crystalline order. For chiral…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
We determine the phase diagram of DNA with inter- and intra-strand native-pair interactions that mimic the compaction of DNA. We show that DNA takes an overall sheet-like structure in the region where an incipient transition to a compact…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
We investigate morphologies of semiflexible polymer rings, such as circular DNA, which are adsorbed onto topographically or chemically structured substrate surfaces. We classify all equilibrium morphologies for two striped surface…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
Twisting two monolayers of a high-$T_c$ cuprate superconductor can engender a chiral topological state with spontaneously broken time reversal symmetry $\mathcal{T}$. A crucial ingredient required for the emergence of a gapped topological…
We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse…
We predict a diblock copolymer melt in the lamellar phase with added spherical nanoparticles that have an affinity for one block to have a lower tensile modulus than a pure diblock copolymer system. This weakening is due to the swelling of…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
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…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
Twisted bilayers of two-dimensional materials have emerged as a highly tunable platform for studying broken symmetry phases. While most interest has been focused on emergent states in systems whose constituent monolayers do not feature…
Topological winding and unwinding in a quasi-one-dimensional metastable Bose-Einstein condensate are shown to be manipulated by changing the strength of interaction or the frequency of rotation. Exact diagonalization analysis reveals that…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…