Related papers: Quantitative transcription factor binding kinetics…
In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of…
We employ various quantum-mechanical approaches for studying the impact of electric fields on both nonretarded and retarded noncovalent interactions between atoms or molecules. To this end, we apply perturbative and non-perturbative methods…
Transcription factors (TFs) are proteins that bind to specific sites on the DNA and regulate gene activity. Identifying where TF molecules bind and how much time they spend on their target sites is key for understanding transcriptional…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
We report fluorescence blinking statistics measured from single CdSe nanorods (NRs) of seven different sizes with aspect ratio ranging from 3 to 11. This study included core/shell CdSe/ZnSe NRs and core NRs with two different surface…
We study phase-dependent fluctuations of the resonance fluorescence of a single $\Lambda$-type three-level atom in the regime near coherent population trapping, i.e., alongside the two-photon detuning condition. To this end, we employ the…
We revisit previous determination of the strong coupling constant from moments of quarkonium correlators in (2+1)-flavor QCD. We use previously calculated moments obtained with Highly Improved Staggered Quark (HISQ) action for five…
Though QCD Factorization(QCDF) could produce sufficiently large $B\to K\pi$ branching ratios close to experiments, the predicted direct CP asymmetry in ${\bar B}^{0}\to K^{+}\pi^{-}$ decay is however still quite below experiment, even with…
Using data from e+e- annihilation into hadrons, taken with the OPAL detector at LEP at the Z pole between 1991 and 1995, we performed a simultaneous measurement of the colour factors of the underlying gauge group of the strong interaction,…
Recently, several studies have investigated the transcription process associated to specific genetic regulatory networks. In this work, we present a stochastic approach for analyzing the dynamics and effect of negative feedback loops (FBL)…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
Cells may control fluctuations in protein levels by means of negative autoregulation, where transcription factors bind DNA sites to repress their own production. Theoretical studies have assumed a single binding site for the repressor,…
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…
We analyze interacting one-dimensional bosons in the continuum, subject to a periodic sinusoidal potential of arbitrary depth. Variation of the lattice depth tunes the system from the Bose-Hubbard limit for deep lattices, through the…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors)…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
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…
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model…
We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…