Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev.

Characterization of Acylated Anthocyanins in Callus Induced From Storage Root of Purple-Fleshed Sweet Potato, Ipomoea batatas L

Four anthocyanins were isolated from a highly pigmented callus induced from the storage root of purple-fleshed sweet potato (Ipomoea batatas L) cultivar Ayamurasaki. The anthocyanins were respectively identified as cyanidin 3-O-(2-O-(6-O-(E)-caffeoyl-β-D-glucopyranosyl)-β-D-glucopyranoside) -5-O-β-D-glucopyranoside, cyanidin 3-O-(2-O-(6-O-(E)-p -coumaroyl-β-D-glucopyranosyl)-6-O-(E)-caffeoyl-β-D-glucopyranoside)-5-O-β-D-glucopyranoside, cyanidin 3-O-(2-O-(6-O-(E)-p -coumaroyl-β-D-glucopyranosyl)-6-O-(E)-p-coumaroyl-β-D-glucopyranoside)- 5-O-β-D-glucopyranoside, and peonidin 3-O-(2-O-(6-O-(E)-p -coumaroyl-β-D-glucopyranosyl)-6-O-(E)-p-coumaroyl-β-D-glucopyranoside)-5-O-β-D-glucopyranoside by chemical and spectroscopic analyses. These anthocyanins were examined with respect to the stability in neutral aqueous solution as well as the radical scavenging activity against the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. These acylated anthocyanins exhibited both higher stability and higher DPPH radical scavenging activity than corresponding nonacylated cyanidin and peonidin 3-O-sophoroside-5-O-glucosides

Radial distribution function of semiflexible polymers

We calculate the distribution function of the end--to--end distance of a semiflexible polymer with large bending rigidity. This quantity is directly observable in experiments on single semiflexible polymers (e.g., DNA, actin) and relevant to their interpretation. It is also an important starting point for analyzing the behavior of more complex systems such as networks and solutions of semiflexible polymers. To estimate the validity of the obtained analytical expressions, we also determine the distribution function numerically using Monte Carlo simulation and find good quantitative agreement.Comment: RevTeX, 4 pages, 1 figure. Also available at http://www.cip.physik.tu-muenchen.de/tumphy/d/T34/Mitarbeiter/frey.htm

Elasticity of Stiff Biopolymers

We present a statistical mechanical study of stiff polymers, motivated by experiments on actin filaments and the considerable current interest in polymer networks. We obtain simple, approximate analytical forms for the force-extension relations and compare these with numerical treatments. We note the important role of boundary conditions in determining force-extension relations. The theoretical predictions presented here can be tested against single molecule experiments on neurofilaments and cytoskeletal filaments like actin and microtubules. Our work is motivated by the buckling of the cytoskeleton of a cell under compression, a phenomenon of interest to biology.Comment: Submitted for publication, five pages, three figure

Quadrupole Susceptibility and Elastic Softening due to a Vacancy in Silicon Crystal

We investigate the electronic states around a single vacancy in silicon crystal by using the Green's function approach. The triply degenerate vacancy states within the band gap are found to be extended over a large distance $\sim20 {\rm \AA}$ from the vacancy site and contribute to the reciprocal temperature dependence of the quadrupole susceptibility resulting in the elastic softening at low temperture. The Curie constant of the quadrupole susceptibility for the trigonal mode ($O_{yz},O_{zx},O_{xy}$) is largely enhanced as compared to that for the tetragonal mode ($O_{2}^{0},O_{2}^{2}$). The obtained results are consistent with the recent ultrasonic experiments in silicon crystal down to 20 mK. We also calculate the dipole and octupole susceptibilities and find that the octupole susceptibilities are extremely enhannced for a specific mode.Comment: 6 pages, with 5 figure

Проблема конкуренції криінально-правових норм (кримінальних законів) у науці пострадянського (радянського) кримінального права та в науці кримінального права держав, які відносяться до романо-германської правової сім'ї

У статті проаналізовано наукові погляди на конкуренцію кримінально-правових норм (кримінальних законів) у теорії пострадянського (радянського) кримінального права та в теорії кримінального права держав, які відносяться до романо-германської правової сім'ї. Ключові слова: конкуренція кримінально-правових норм, конкуренція законів.В статье анализируются научные взгляды на конкуренцию уголовно-правовых норм (уголовных законов) в теории постсоветского (советского) уголовного права и в теории уголовного права государств, которые относятся к романо-германской правовой семье. Ключевые слова: конкуренция уголовно-правовых норм, конкуренция законов.In the article scientific looks are analyzed to the competition of criminal law norm’s (criminal laws) in the theory of post-soviet (soviet) criminal law and in the theory of criminal law of the states which behave to the legal system of civil law. Key words: competition of criminal law norm’s, competition of laws

Projectile Fragmentation of the Extremely Neutron-Rich Nucleus ^<11>Li at o.79 GeV/nucleon

Projectile fragmentations of ^Li, ^He, and ^He have been measured at 0.79 GeV/nucleon. Production cross sections and momentum distributions of the produced isotopes (Z≥2) are measured inclusively. Transverse-momentum distributions of ^Li from the fragmentation of ^Li show two Gaussian components of different widths. The width of the wide component is consistent with the values observed in the fragmentation of stable nuclei, whereas the other component shows an extremely narrow width reflecting the weak binding of the two outer neutrons in the ^Li nucleus

Bimodal distribution function of a 3d wormlike chain with a fixed orientation of one end

We study the distribution function of the three dimensional wormlike chain with a fixed orientation of one chain end using the exact representation of the distribution function in terms of the Green's function of the quantum rigid rotator in a homogeneous external field. The transverse 1d distribution function of the free chain end displays a bimodal shape in the intermediate range of the chain lengths ($1.3L_{p},...,3.5L_{p}$). We present also analytical results for short and long chains, which are in complete agreement with the results of previous studies obtained using different methods.Comment: 6 pages, 3 figure

Exact theory of kinkable elastic polymers

The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection angles, many rod systems exhibit a high-curvature softening. The signature behavior of these rod systems is a kinking transition in which the bending is localized. Recent DNA cyclization experiments by Cloutier and Widom have offered evidence that the linear-elastic bending theory fails to describe the high-curvature mechanics of DNA. Motivated by this recent experimental work, we develop a simple and exact theory of the statistical mechanics of linear-elastic polymer chains that can undergo a kinking transition. We characterize the kinking behavior with a single parameter and show that the resulting theory reproduces both the low-curvature linear-elastic behavior which is already well described by the Wormlike Chain model, as well as the high-curvature softening observed in recent cyclization experiments.Comment: Revised for PRE. 40 pages, 12 figure

The distribution function of a semiflexible polymer and random walks with constraints

In studying the end-to-end distribution function $G(r,N)$ of a worm like chain by using the propagator method we have established that the combinatorial problem of counting the paths contributing to $G(r,N)$ can be mapped onto the problem of random walks with constraints, which is closely related to the representation theory of the Temperley-Lieb algebra. By using this mapping we derive an exact expression of the Fourier-Laplace transform of the distribution function, $G(k,p)$, as a matrix element of an inverse of an infinite rank matrix. Using this result we also derived a recursion relation permitting to compute $G(k,p)$ directly. We present the results of the computation of $G(k,N)$ and its moments. The moments $$ of $$ can be calculated \emph{exactly} by calculating the (1,1) matrix element of $2n$-th power of a truncated matrix of rank $n+1$.Comment: 6 pages, 2 figures, added a referenc