Related papers: Ion-dependent DNA Configuration in Bacteriophage C…

When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…

Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…

The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…

Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which…

Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…

Recently, Maassen et al. measured an appreciable pH difference between the bulk solution and the solution in the lumen of virus-like particles, self-assembled in an aqueous buffer solution containing the coat proteins of a simple plant…

In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…

In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming…

Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…

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.…

The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…

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…

Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of…

In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…

DNA is strong polyelectrolyte macromolecule making metal ions (counterions) condense to a cloud around the double helix. The counterions may be localized outside the macromolecule and inside the minor and major grooves of the double helix.…

Here we derive and experimentally test a free energy functional that captures the adhesion of DNA-coated emulsion droplets. Generalizing previous approaches, the theory combines important energetic and entropic effects of microscopic DNA…

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A…

DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…

We have functionalized the sides of fd bacteriophage virions with oligonucleotides to induce DNA hybridization driven self-assembly of high aspect ratio filamentous particles. Potential impacts of this new structure range from an entirely…

The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…