Related papers: Nonlinear dynamics of damped DNA systems with long…
We study analytically the dynamics and the micro-structural changes of a host medium caused by a driven tracer particle moving in a confined, quiescent molecular crowding environment. Imitating typical settings of active micro-rheology…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
We explore a new type of discretizations of lattice dynamical models of the Klein-Gordon type relevant to the existence and long-term mobility of nonlinear waves. The discretization is based on non-holonomic constraints and is shown to…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
We show that in a gas of ultra cold atoms distance selective two-body loss can be engineered via the resonant laser excitation of atom pairs to interacting electronic states. In an optical lattice this leads to a dissipative Master equation…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
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…
We study a model in which a Hubbard Hamiltonian is coupled to the dispersive phonons in a classical nonlinear lattice. Our calculations are restricted to the case where we have only two quasi-particles of opposite spins, and we investigate…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
We present initial results regarding the existence, stability and interaction of linear and nonlinear vibrational modes in a system of two coupled, one dimensional lattices with unequal numbers of masses. The effects on these nonlinear…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as…
In this article we prove the existence of a new family of periodic solutions for discrete, nonlinear Schrodinger equations subject to spatially localized driving and damping. They provide an alternate description of the metastable behavior…
A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous…
Molecules at the air-water interface often form inhomogeneous layers in which domains of different densities are separated by sharp interfaces. Complex interfacial pattern formation may occur through the competition of short- and long-range…