Related papers: Collapse and coexistence for a molecular braid wit…
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…
This is an archival document; the work contains theoretical development to be used in new publications and to stimulate further development. Here, we develop a statistical mechanical treatment of a braid formed of two molecules subject to…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
Strong short ranged positional correlations involving counterions can induce a net attractive force between negatively charged strands of DNA, and lead to the formation of ion pairs in dilute ionic solutions. But the long range of the…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
Previous theoretical, along with early simulation and experimental, studies have indicated that particles with a short-ranged attraction exhibit a range of new dynamical arrest phenomena. These include very pronounced reentrance in the…
This paper extends on a recent work where it was shown that forces dependent on the helical structure may cause two DNA molecules to spontaneously braid [R. Cortini et Al, Biophys. J. 101, 875 (2011)]. Here, bending fluctuations of DNA…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
Motivated by recent studies of colloidal particles in optical tweezer arrays, we study a two-dimensional model of a colloidal suspension in a periodic potential. The particles tend to stay near potential minima, approximating a lattice gas.…
Inspired by recent experiments on the dynamics of particles and polymers in artificial cytoskeletons and in cells, we introduce a modified Langevin equation for a particle in an environment that is a viscoelastic medium and that is brought…
The collapse and swelling behavior of a generic homopolymer is studied using implicit-solvent, explicit-cosolvent Langevin dynamics computer simulations for varying interaction strengths. The systematic investigation reveals that polymer…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
In solution, electrically like-charged particles can experience a strong and long-ranged attraction that leads to the formation of stable, slowly reorganizing clusters. The attractive force underpinning this spontaneous organization process…
Theoretical studies of self-assembly processes and condensed phases in colloidal systems are often based on effective inter-particle potentials. Here we show that developing an effective potential for particles interacting with a limited…
We derive formulae for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on…
Dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an…