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We study the coherent dynamics of excitations on vibrating chains. By applying an external field and matching the field strength with the oscillation frequency of the chain it is possible to obtain an (average) transport of an initial…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra- and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
We investigate charge dynamics in a two-electron double quantum dot. The quantum dot is manipulated by using a time-dependent external voltage that induces charge oscillations between the dots. We study the dependence of the charge dynamics…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
We analyze the time-evolution of a quantum dot which is proximized by a large-gap superconductor and weakly probed using the charge and heat currents into a wide-band metal electrode. We map out the full time dependence of these currents…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The dependence of electron transfer rates and yields in bridged molecular systems on the bridge length, and the dependence of the zero-bias conduction of molecular wires on wire length are discussed. Both phenomena are controlled by…
We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…
We study the current and the associated noise for the transport through a two-site molecule driven by an external oscillating field. Within a high-frequency approximation, the time-dependent Hamiltonian is mapped to a static one with…
In this work we investigate the electronic transport along model DNA molecules using an effective tight-binding approach that includes the backbone on site energies. The localization length and participation number are examined as a…
The influence of an external oscillating in time magnetic field on the dynamics of the Davydov's soliton is investigated. It is shown that it essentially depends not only on the amplitude and frequency of the magnetic field, but also on the…
We examine the spatial distribution of electrons generated by a fixed energy point source in uniform, parallel electric and magnetic fields. This problem is simple enough to permit analytic quantum and semiclassical solution, and it harbors…
Electron transfer (ET) at electrochemical interfaces is central to energy conversion and storage, yet its theoretical and computational modeling remain active research areas. This review elucidates key concepts and theories of ET kinetics,…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
We study a moving adsorbate interacting with a metal electrode immersed in a solvent using the time-dependent Newns-Anderson-Schmickler model Hamiltonian. We have adopted a semiclassical trajectory treatment of the adsorbate to discuss the…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…