Related papers: Quantitative transcription factor binding kinetics…
Determining the number of fluorescent entities that are coupled to a given molecule (DNA, protein, etc.) is a key point of numerous biological studies, especially those based on a single molecule approach. Reliable methods are important, in…
We report isovector form factors and low moments of isovector structure functions of nucleon from the coarse RIKEN-BNL-Columbia (RBC) and UKQCD joint dynamical (2+1)-flavor domain-wall fermions (DWF) ensembles. The lattice cut off is…
We investigate the time dependence of the quantum statistical model with $\lambda \phi^4/4!$ self-interaction and consider the resulting induced particle number density. For a special example in which the classical approximation exhibits…
Atomic Fermi gases provide an ideal platform for studying the pairing and superfluid physics, using a Feshbach resonance between closed channel molecular states and open channel scattering states. Of particular interest is the strongly…
The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…
Negative differential resistance remains an attractive but elusive functionality, so far only finding niche applications. Atom scale entities have shown promising properties, but viability of device fabrication requires fuller understanding…
Theoretical basics and experimental determinations of the coupling parameter of the Strong Interaction, $\alpha_s$, are reviewed. The world average value of $\alpha_s$, expressed at the energy scale of the rest mass of the $Z^0$ boson, is…
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 use an efficient projection scheme for the Fock operator to analyze the size dependence of silicon quantum dots (QDs) electronic properties. We compare the behavior of hybrid, screened hybrid and local density functionals as a function…
Quantum nonlinear interferometers (QNIs) can measure the infrared physical quantities of a sample by detecting visible photons. A QNI with Michelson geometry based on the spontaneous parametric down-conversion in a second-order nonlinear…
The binding of transcription factors (TFs) is essential for gene expression. One important characteristic is the actual occupancy of a putative binding site in the genome. In this study, we propose an analytical model to predict genomic…
A chain of connected genes with activation-repression links is analysed. It is shown that for various promoter activity functions (parametrised by Hill coefficient) the equations describing the concentrations of transcription factors, are…
We study the dynamics of a lattice hard-core boson gas released from a domain wall initial state in the presence of two weak links (defects). When the two defects are separated by a finite distance, the resulting density profile exhibits…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
We study the transport of a quantum particle through square lattices of various sizes by employing the tight-binding Hamiltonian from quantum percolation. Input and output semi-infinite chains are attached to the lattice either by diagonal…
We study the color correlation between static quark and antiquark ($q\bar q$) that is accompanied by gluonic excitations in the confined phase at $T=0$ by constructing reduced density matrices $\rho$ in color space. We perform quenched…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
After photo-excitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we…
It has been previously shown that a particular nonperturbative constituent-quark model of hadrons describes experimental measurements of electromagnetic form factors of light charged mesons through a small number of common phenomenological…