Related papers: Models for energy and charge transport and storage…
Explicit energy-transport equations for the spinorial carrier transport in ferromagnetic semiconductors are calculated from a general spin energy-transport system that was derived by Ben Abdallah and El Hajj from a spinorial Boltzmann…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
We use an adiabatic approximation in terms of instantaneous resonances to study the steady-state and time-dependent transport properties of interacting electrons in biased resonant tunneling heterostructures. This approach leads, in a…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…
In the present study we revise the possible polaron contribution to the charge and energy transfer over long distances in biomolecules like DNA. The harmonic and the simple inharmonic ($U(x) = x^2/2 - \beta x^3/3$) lattices are considered.…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Recent papers have considered moving breathers (MBs) in DNA models including long range interaction due to the dipole moments of the hydrogen bonds. We have recalculated the value of the charge transfer when hydrogen bonds stretch using…
Uncompensated charges do not occur in Nature and any local charge should be a result of charge separation. Dissociable chemical groups at interfaces in contact with ions in solution, whose chemical equilibrium depends both on short-range…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
A closed set of coupled equations of motion for the description of time-dependent electron transport is derived. It provides the time evolution of energy-resolved quantities constructed from non-equilibrium Green functions. By means of an…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
A new statistical model for the combined effects of decoherence, energy redistribution and dissipation on electron transport in large quantum systems is introduced. The essential idea is to consider the electron phase information to be lost…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We consider the interaction of a nonlinear Schrodinger soliton with a localized (point) defect in the medium through which it travels. Using numerical simulations, we find parameter regimes under which the soliton may be reflected,…
The dynamics of models described by a one-dimensional discrete nonlinear Schr\"odinger equation is studied. The nonlinearity in these models appears due to the coupling of the electronic motion to optical oscillators which are treated in…
A model of a stable plasma formation, based on radial quantum oscillations of charged particles, is discussed. The given plasmoid is described with the help of the nonlinear Schr\"odinger equation. A new phenomenon of the effective…
We study the spreading of initially localized states in a nonlinear disordered lattice described by the nonlinear Schr\"odinger equation with random on-site potentials - a nonlinear generalization of the Anderson model of localization. We…