Related papers: Modelling DNA Response to THz Radiation
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
Near-zero magnetic fields, called hypomagnetic fields, are known to impact biological phenomena, including developmental processes, the circadian system, neuronal and brain activities, DNA methylation, calcium balance in cells, and many…
We suggest that the DNA molecules could form the cholesteric phase owing to an interaction mediated by the network of the hydrogen bonds (H-network) in the solvent. The model admits of the dependence of the optical activity of the solution…
We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…
We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
The emission properties of terahertz(THz) photoconductive antenna (PCA) have been numerically studied by three-dimensional finite-difference-time-domain method based on the full-wave model. The dependence of the THz radiation on various…
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
In this note, we discuss the low and high temperature contribution of Thermodynamic Bethe Ansatz (TBA) dressed excitations in the thermodynamics and energy-magnetization relaxation within the Generalized Hydrodynamics approach in the linear…
Recent papers that have studied variants of the Peyrard-Bishop model for DNA, have taken into account the long range interaction due to the dipole moments of the hydrogen bonds between base pairs. In these models the helicity of the double…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
In this work, we model the zero-bias conductance for the four different DNA strands that were used in conductance measurement experiment [A. K. Mahapatro, K. J. Jeong, G. U. Lee, and D. B. Janes, Nanotechnology 18, 195202 (2007)]. Our…
We report THz-pump / mid-infrared probe near-field studies on Si-doped GaAs-InGaAs core-shell nanowires utilizing THz radiation from the free-electron laser FELBE. Upon THz excitation of free carriers, we observe a red shift of the plasma…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Coherent phonon-polaritons have attracted a considerable amount of interest owing to their relevance to nonlinear optics and terahertz (THz)-wave emissions. Therefore, it is important to analyze the THz electric-fields of phonon-polaritons.…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…
To elucidate the mechanism by which THz radiation non-thermally affects living organisms, the lateral diffusion constants of lipid molecules in the cell membranes of HeLa cells were measured using fluorescence recovery after photobleaching…
Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy. While protons have been the predominant ion of choice in beam cancer therapy, heavier…
We extend, to include the effects of finite temperature, our earlier study of the interband dynamics of electrons with Markoffian dephasing under the influence of uniform static electric fields. We use a simple two-band tight-binding model…