Related papers: Statistical mechanics of columnar DNA assemblies
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
The dynamic behaviors of a mixed spin (1/2-1) hexagonal Ising nanowire (HIN) with core-shell structure in the presence of a time dependent magnetic field are investigated by using the effective-field theory with correlations based on the…
DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits…
The statistical mechanics of thermally excited vortex lines with columnar defects can be mapped onto the physics of interacting quantum particles with quenched random disorder in one less dimension. The destruction of the Bose glass phase…
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
We review here some general properties of antiferromagnetic Heisenberg spin chains, emphasizing and discussing the role of hidden symmetries in the classification of the various phases of the models. We present also some recent results that…
Homoclinic snaking is a widespread phenomenon observed in many pattern-forming systems. Demonstrating its occurrence in non-perturbative regimes has proven difficult, although a forcing theory has been developed based on the identification…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
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…
Phase transitions in a classical Heisenberg spin model of a chiral helimagnet with the Dzyaloshinskii--Moriya (DM) interaction in three dimensions are numerically studied. By using the event-chain Monte Carlo algorithm recently developed…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
Large spin systems can exhibit unconventional types of magnetic ordering different from the ferromagnetic or N\'eel-like antiferromagnetic order commonly found in spin 1/2 systems. Spin-nematic phases, for instance, do not break…
Machine-learning techniques have proved successful in identifying ordered phases of matter. However, it remains an open question how far they can contribute to the understanding of phases without broken symmetry, such as spin liquids. Here…
By utilizing the effective-field theory based on the Glauber-type stochastic dynamics, the dynamic behaviors of the hexagonal Ising nanowire (HIN) system in the presence of a time dependent magnetic field are obtained. The time variations…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
We study a spin-ice Kondo lattice model on a breathing pyrochlore lattice with classical localized spins. The highly efficient kernel polynomial expansion method, together with a classical Monte Carlo method, is employed in order to study…
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…
Recent work has shown that the honeycomb lattice spin-$1/2$ $J_1$-$J_3$ XY model, with nearest-neighbor ferromagnetic exchange $J_1$ and frustration induced by third-neighbor antiferromagnetic exchange $J_3$, may be relevant to a wide range…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…