Related papers: Models for energy and charge transport and storage…
Recent experimental evidence shows that the pi-orbitals along the stacking of base pairs can facilitate the long-range charge transfer in DNA. Proton motion in the base pair hydrogen bonds has also been found to affect the transfer rate. To…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
We report the results of a numerical study of nonequilibrium steady states for a class of Hamiltonian models. In these models of coupled matter-energy transport, particles exchange energy through collisions with pinned-down rotating disks.…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
The effects of the propagation of particles which have a finite life-time and an according broad distribution in their mass spectrum are discussed in the context of a transport descriptions. In the first part some example cases of mesonic…
Topological defects in low-dimensional non-linear systems feature a sliding-to-pinning transition of relevance for a variety of research fields, ranging from biophysics to nano- and solid-state physics. We find that the dynamics after a…
We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
We find that localized quantum N-body soliton states exist for a derivative nonlinear Schrodinger (DNLS) model within an extended range of coupling constant (\xi_q) given by 0 < | \xi_q | < 1/\hbar \tan [\pi/(N-1)]. We also observe that…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
Under certain conditions, the ionization of a molecule may create a superposition of electronic states, leading to ultrafast electron dynamics. If controlled, this motion could be used in attochemistry applications, but it has been shown…
Mixed feedback loops combining transcriptional and post-transcriptional regulations are common in cellular regulatory networks. They consist of two genes, encoding a transcription factor and a small non-coding RNA (sRNA), which mutually…
Nonlinear dynamics of two biomolecules is studied. These are a microtubule and DNA molecule. Two mathematical procedures are explained, yielding to three kinds of solitary waves moving through the systems. These waves are kinks, modulated…
Solitons - localized wave packets that travel without spreading - play a central role in understanding transport and properties of nonlinear systems, from optical fibers to fluid dynamics. In quantum many-body systems, however, such robust…
As a paradigm for heat conduction in 1 dimension, we propose a class of models represented by chains of identical cells, each one of which containing an energy storage device called a "tank". Energy exchange among tanks is mediated by…
Wave self-focusing in molecular systems subject to thermal effects, such as thin molecular films and long biomolecules, can be modeled by stochastic versions of the Discrete Self-Trapping equation of Eilbeck, Lomdahl and Scott, and this can…