Related papers: Modelling DNA Response to THz Radiation
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
The formation of hole pairs in the planar t-J model is studied in the presence of independent {\it dynamic} vibrations of the in-plane oxygen atoms. In-plane (breathing modes) and out-of-plane (buckling modes) displacements are considered.…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
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…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
The term two-dimensional coherent spectroscopy (2DCS) usually refers to experimental setups where a coherently generated electric field in a sample is recorded over many runs as a function of two time variables: the delay $\tau$ between two…
PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry and dynamics with the PDZ…
The effects of the highly damped modes in the energy and reaction rates in a plasma are discussed. These modes, with wavenumbers $k \gg k_{D}$, even being only weakly excited, with less than $k_{B}T$ per mode, make a significant…
We construct a comprehensive theory of the electrodynamic response of ferroelectric ultra-thin films containing periodic domain textures (PDT) with 180{\deg} polarization-oriented domains. The focal point of the theory is the…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Nearest-neighbor(NN) free energy parameters for DNA are well studied and reliable values of these parameters exist in the literature. They have been found to be very useful in studying DNA melting and DNA stabilization studies. In this…
In this paper we report direct measurement of large low frequency temperature fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation, which occurs only in the temperature range where the…
A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous…
Nonlinear THz-THz-Raman (TTR) liquid spectroscopy offers new possibilities for studying and understanding condensed-phase chemical dynamics. Although TTR spectra carry rich information about the systems under study, the response is encoded…
In complex oxides, the electrons under the influence of competing energetics are the cornerstone of coexistence (or phase-separation) of two or more electronic/magnetic phases in same structural configuration. Probing of growth and…
We demonstrate dynamic control of the lattice by THz light by exploiting the coupling of phonon modes. The low-energy sliding phonon modes in the spin-ladder system, Sr$_{14}$Cu$_{24}$O$_{41}$, are excited using THz radiation with high…