Related papers: Quantitative transcription factor binding kinetics…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
We investigate the static and dynamical behavior of 1D interacting fermions in disordered Hubbard chains, contacted to semi-infinite leads. The chains are described via the repulsive Anderson-Hubbard Hamiltonian, using static and…
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through Position…
We consider heavy quark interactions in quenched and unquenched lattice QCD. In a region just above the deconfinement point, non-Abelian gluon polarization leads to a strong increase in the binding. Comparing quark-antiquark and quark-quark…
We demonstrate that the Configuration Interaction (CI) Approximation recaptures essential features of the exact (Bethe Ansatz) solution to the 1D Hubbard model. As such, it provides valuable route for describing effects which go beyond…
One of the major functions of RecA protein in the cell is to bind single-stranded DNA exposed upon damage, thereby triggering the SOS repair response.We present fluorescence anisotropy measurements at the binding onset, showing enhanced DNA…
To testify the validity of the perturbative QCD (pQCD) and investigate its application range, one should look for a suitable process to do the job. $B\to J/\psi D$ is a promising candidate. The linear momentum of the products is relatively…
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…
Intermittent photoluminescence of colloidal core/shell semiconductor nanocrystals of spherical and branched shape was studied under CW-laser excitation. Luminescent multichannel registration system was applied for the fluorescence detection…
We present a new quantum embedding theory called dynamical configuration interaction (DCI) that combines wave function and Green's function theories. DCI captures static correlation in a correlated subspace with configuration interaction…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
Biomolecular binding kinetics including the association (kon) and dissociation (koff) rates are critical parameters for therapeutic design of small-molecule drugs, peptides and antibodies. Notably, drug molecule residence time or…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
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…
The perturbative expression of the running strong coupling constant \alpha_{\rm s}(Q^{2}) has an unphysical singularity for Q^{2} = \Lambda^{2}_{\rm QCD}. Various modification have been proposed for the infrared region. The effect of some…