Related papers: Calculating the contribution of different binding …
We have investigated the binding interaction between the bacteriophage lambda repressor CI and its target DNA using total internal reflection fluorescence microscopy. Large, step-wise changes in the intensity of the red fluorescent protein…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
In previous work, we constructed a statistical framework for estimating the rate of clustered ionization from charged particle radiation in DNA. This model is extended to include contributions from secondary electrons. Using a simple…
We discuss the interplay of low-x physics and QCD scaling violations by extending the unified approach describing inclusive structure functions and diffractive production in $\gamma* p$ interactions proposed in previous papers, to large…
We study the interaction of berberine and sanguinarine (plant alkaloids) with DNA in aqueous solutions, by using optical spectroscopy methods (absorption and fluorescence). The dependencies of alkaloid spectral characteristics on the…
The effects of DNA on the fluorescence of silver phycocyanin complexes were investigated. It was shown, that the fluorescence intensity of phycocyanin decreases, when silver ions are added but the following DNA addition gives rise to…
Interest in studying the interaction of small molecules with DNA is caused by the need to develop new, highly effective, and low-toxic drugs for cancer treatment. The strong and highly specific binding of thionine with DNA makes it a…
The quark number density at finite imaginary chemical potential is investigated in the lattice QCD using the Dirac-mode expansion. We find the analytical formula of the quark number density in terms of the Polyakov loop in the large quark…
The investigation of small size embedded nanostructures, by a combination of complementary anomalous diffraction techniques, is reported. GaN Quantum Dots (QDs), grown by molecular beam epitaxy in a modified Stranski-Krastanow mode, are…
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
Quantitative fluorescence analysis is often used to derive chemical properties, including stoichiometries, of biomolecular complexes. One fundamental underlying assumption in the analysis of fluorescence data -- whether it be the…
Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
GaAsPN layers with a thickness of 30nm were grown on GaP substrates with metalorganic vapor phase epitaxy to study the feasibility of a single X-ray diffraction (XRD) measurement for full composition determination of quaternary layer…
The rates for diffractive quarkonium plus prompt-photon associated production at the LHC are estimated. The theoretical framework considered in the J/Psi (or Upsilon) production associated with a direct photon at the hadron collider is the…