Related papers: Electronic parameters for the hole transfer in DNA…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
Some recent results for a three--dimensional, semi--classical, tight--binding model for DNA show that there are two types of polarons, named radial and twist polarons, that can transport charge along the DNA molecule. However, the existence…
In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…
First-principles calculations are used to investigate the electronic properties of neutral and negatively charged n-pyrrole oligomers with n= 2-18. Chains of neutral oligomers are bent while the negatively charged oligomers become almost…
We present semiempirical tight binding calculations on thienylenevinylene oligomers up to the hexadecamer stage (n=16) and ab initio calculations based on the local density approximation up to n=8. The results correctly describe the…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
We investigate the localization property of an electron in the disordered two-chain system (ladder model) with long-range correlation as a simple model for electronic property in DNA sequence. The chains are constructed by repetition of the…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
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…
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
Electrical conductivity of DNA has been a controversial topic since it was first proposed in 1962. Disparities in the experimental results can often be explained by differences of the ambient or experimental conditions. We report the…
We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
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…