Search results

We investigate the translocation of a stiff polymer consisting of M monomersthrough a nanopore in a membrane, in the presence of binding particles(chaperones) that bind onto the polymer, and partially prevent backsliding ofthe polymer through the pore. The process is characterized by the rates: kfor the polymer to make a diffusive jump through the pore, q for unbinding ofa chaperone, and the rate

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in de

Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out

We investigate the dynamics of a single local denaturation zone in a DNA molecule, a so-called DNA bubble, in the presence of single-stranded DNA binding proteins (SSBs). In particular, we develop a dynamical description of the process in terms of a two-dimensional master equation for the time evolution of the probability distribution of having a bubble of size m with n bound SSBs, for the case wh

We derive an expression for the polarizability of an ellipsoidally shaped cell-like structure at field frequencies where membrane molecular resonances (vibrational and electronic) are important. We first present analytical results for the dielectric function of a flat, dipole coupled, bilayer consisting of molecules with one prominent resonance frequency. Due to the nature of the dipole coupling t

In this paper we study the response of an ellipsoidal particle with a dielectrically anisotropic coating (the coating dielectric function being different parallel and perpendicular to the coating normal) placed in a constant external electric field. For the coating region we find that potential can be written in terms of solutions to a one-dimensional Heun's equation which is derived from the thre

We investigate the vdrift velocity vdrift of ellipsoidal polarizable particles (ellipsoids and coated ellipsoids), driven through a viscous fluid by an electric or electromagnetic field intensity gradient. At low Reynolds number and in the dipole approximation vdrift is proportional to the square of the principal axis along the direction of motion multiplied by a form factor, which is weakly depen

We study the process of charged polymer translocation, driven by an external electric potential, through a narrow pore in a membrane. We assume that the number of polymer segments, m, having passed the entrance pore mouth, is a slow variable governing the translocation process. Outside the pore the probability that there is an end segment at the entrance pore mouth, is taken as the relevant parame

In the current study we evaluated the structure of positron emission tomography combined with computed tomography (PET/CT) diagnostics in the Russian Federation. Patient effective doses, organ doses and corresponding radiation risks for the most common PET/CT examinations were evaluated. Data was collected in 12 regions of the Russian Federation in the period 2012-2017 in 19 facilities (26 PET/CT

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA seque

If a leptoquark is produced at HERA as a narrow resonance, various effects tend to broaden the measurable mass distribution considerably. These effects are discussed here, with special emphasis on initial- and final-state QCD radiation. A proper understanding is important to assess the significance of data and to devise strategies for better mass reconstruction.

In computational fluid dynamic simulations of partially premixed combustion engines it is common to find simplifications of the in cylinder flow conditions in order to save computational cost. One common simplification is to start the simulation at the moment of intake valve closing with an assumed initial flow condition, rather than making a full scavenging simulation. Another common simplificati

Several distinct color flow topologies are possible in multiparton configurations. A method is proposed to find the correct topology, based on a minimization of the total transverse momentum of produced particles. This method is studied for three-jet [Formula presented] and four-jet [Formula presented] events. It is shown how the basic picture is smeared, especially by parton-shower activity. The

Low temperature combustion concepts used in compression ignition engines have shown to be able to produce simultaneous reduction of oxides of nitrogen and soot as well as generating higher gross indicated efficiencies compared to conventional diesel combustion. This is achieved by a combination of premixing, dilution and optimization of combustion phasing. Low temperature combustion can be comple

At HERA, the large flux of almost real photons accompanying the electron beam leads to the copious photoproduction of jets. Regions of small momentum fractions x of the incoming particles are explored, where the density of partons is high. As a result, the probability for more than one hard partonic scattering occurring in a single collision could become significant. It is well known that this eff