Facilitated diffusion of DNA-binding proteins

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.Comment: 4 pages, 2 figures Nov 22 2005 - accepted for PR

Multiscale entanglement in ring polymers under spherical confinement

The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length lk depends on the ring contour length, Lc and the radius of the confining sphere, Rc . In the no- and strong- confinement cases we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed by a simple scaling argument based on deflection theory. The same argument is used to rationalize the multiscale character of the entanglement that emerges with increasing confinement.Comment: 9 pages 9 figure

On the Limits of Analogy Between Self-Avoidance and Topology-Driven Swelling of Polymer Loops

The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops is described and shown to agree with simulation data. Contrast between this expression and the well known expression for excluded volume polymers leads to a graphical mapping of excluded volume to trivial knots, which may be useful for understanding where the analogy between the two physical forms is valid. The work also includes description of a new method for the computational generation of polymer loops via conditional probability. Although computationally intensive, this method generates loops without statistical bias, and thus is preferable to other loop generation routines in the region $N<N_0$.Comment: 10 pages, 5 figures, supplementary tex file and datafil

Observation of X-rays during heating a pyroelectric crystal by an infrared laser

A pyroelectric X-ray source is proposed, in which a lithium tantalate crystal is heated by an infrared laser with a wavelength of 10.6 μm. X-ray spectra measured during irradiation of the crystal with infrared radiation and during natural cooling of the crystal include characteristic X-ray radiation of atoms contained in the structural parts of the source, as well as bremsstrahlung of electrons with energies above 50 keV. An 8 mm sodium chloride window was used to inject 64 W infrared radiation into a vacuum chamber with the pyroelectric crystal installe

CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

X-ray generation during piezoelectric lighter operation in vacuum

The results of experimental studies on the generation of x-rays when operating a piezoelectric kitchen lighter in a vacuum are presented. For the first time, a new method for increasing the intensity of x-ray radiation in the piezoelectric effect in a high vacuum through the use of an additional electron emitter is proposed and demonstrated. The maximum energy of x-ray bremsstrahlung reaches 14 keV. This means that electrons are accelerated in vacuum in the field of a piezoelectric ceramic to energy of at least 14 ke

Lateral surface electrization of Z-cut lithium niobate during pyroelectric effect

The paper focuses on the surfaces electrization of Z-cut single-crystal lithium niobate during the pyroelectric effect. It is shown that the properties of the electric current passing through the surfaces of single-crystal lithium niobate depend on the ground circuit, the rate of temperature change, and orientation of polar axe

Investigation of neutron generation upon irradiation of deuterated crystalline structures with an electron beam

The possibility of neutron generation by irradiating deuterated crystalline structures with an electron beam with an energy of 20-40 keV was studied. As targets, the deuterated crystalline structures of palladium and textured CVD diamond were used. Measurements of neutron emission are presented, which were carried out by three independent methods-scintillation detectors, counters based on He-3, and track detectors CR-3

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.Comment: Book chapter to appear in The Bacterial Nucleoid, Methods and Protocols, Springer serie