A new approach to microscopic modeling of a hole transfer in heteropolymer DNA

A review on nonlinear DNA physics

The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

Discrete-breather-assisted charge transport along DNA-like molecular wires

Mobile discrete breathers (MDBs) are here suggested as localized excitations underlying the trapping and transport of charged particles (electron or hole) along a DNA-like molecular wire with anchored ends such as attached to two electrodes. For illustration the Peyrard-Bishop-Dauxois-Holstein (PBDH) model is used. MDBs are excited by imposing appropriate disturbances to velocities or space positions of adjacent nucleotide pairs or lattice units of the wire. They can be directed either towards or away from the wire hence transverse to it. Numerical computer simulations show that a rather stable quasiparticle MDB + electron is possible when just a few of the nucleotide pairs near one of the fixed ends of the wire are excited. For the process to be effective, the charge, e.g., the electron, must be initially placed around the disturbed region of the molecule. Once the MDB + electron quasiparticle is formed it may be transported to quite a long distance up to ca. 60-70 nm in real space. Our findings show that such process does not demand intervention of an externally applied electric field and hence it may be considered as alternative to the polaron transport process.

Quantum-classical model of retinal photoisomerization reaction in visual pigment rhodopsin

A quantum-classical model of photoisomerization of the visual pigment rhodopsin chromophore is proposed. At certain (and more realistic) parameter value combinations, the model is shown to accurately reproduce a number of independent experimental data on the photoreaction dynamics: the quantum yield, the time to reach the point of conical intersection of potential energy surfaces, the termination time of the evolution of quantum subsystem, as well as the characteristic low frequencies of retinal molecular lattice fluctuations during photoisomerization. In addition, the model behavior is in good accordance with experimental data about coherence and local character of quantum transition.