Effects of Kinks on DNA Elasticity

We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of trans-gauche rotations in the backbone of the single-stranded DNA. The problem is solved both analytically and numerically by generalizing the well-known analogy to the Quantum Rotator. In the small stretching force regime, we find that the persistence length is renormalized due to the presence of the kinks. In the opposite regime, the response to the strong stretching is determined solely by the bare persistence length with exponential corrections due to the ``ideal gas of kinks''. This high-force behavior changes significantly in the limit of high bending rigidity of the chain. In that case, the leading corrections to the mechanical response are likely to be due to the formation of multi-kink structures, such as kink pairs.Comment: v1: 16 pages, 7 figures, LaTeX; submitted to Physical Review E; v2: a new subsection on soft kinks added to section Theory, sections Introduction and Conclusions expanded, references added, other minor changes; v3: a reference adde

Comment on ``Exact three-dimensional wave function and the on-shell t matrix for the sharply cut-off Coulomb potential: Failure of the standard renormalization factor''

The solutions analytically derived by Gloeckle et al. [Phys. Rev. C79, 044003 (2009)] for the three-dimensional wave function and on-shell t matrix in the case of scattering on a sharply cut-off Coulomb potential appear to be fallacious. And their renormalization factor lacks mathematical grounds.Comment: 5 page

Effects of Sequence Disorder on DNA Looping and Cyclization

Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of cyclization probabilities. For short DNA segments, the range of the distribution reaches several orders of magnitude for even completely random sequences. The ensemble averaged values of the cyclization probability are also calculated, and the connection to the recent experiments is discussed.Comment: 8 pages, 4 figures, LaTeX; accepted to Physical Review E; v2: a substantially revised version; v3: references added, conclusions expanded, minor editorial corrections to the text; v4: a substantially revised and expanded version (total number of pages doubled); v5: new Figure 4, captions expanded, minor editorial improvements to the tex

Core-based lipid nanoparticles as a nanoplatform for delivery of near-infrared fluorescent imaging agents.

Pyropheophorbide a (Pyro) is a near-infrared (NIR) fluorescent dye and photosensitizer with high quantum yield that makes the dye suitable for tumor treatment both as an imaging and therapy agent. We have designed and synthesized a series of a Pyro-based NIR probes, based on the conjugation of Pyro with lipids. The nature of our probes requires the use of a lipophilic carrier to deliver the probes to cancer cell membranes. To address this, we have utilized lipid-based nanoparticles (LNPs) consisting of PEGylated lipids, which form the nanoparticle shell, and a lipid core. To endow the LNPs with targeting properties, nitrilotriacetic acid (NTA) lipids were included in the composition that enables the non-covalent attachment of His-tag targeting proteins preserving their functional activity. We found that the nature of the core molecules influence the nanoparticle size, shelf-life and stability at physiological temperature. Two different Pyro-lipid conjugates were loaded either into the core or shell of the LNPs. The conjugates revealed differential ability to be accumulated in the cell membrane of the target cells with time. Thus, the modular organization of the core-shell LNPs allows facile adjustment of their composition with goal to fine tuning the nanoparticle properties for in vivo application

Potassium Ions are More Effective than Sodium Ions in Salt Induced Peptide Formation

Prebiotic peptide formation under aqueous conditions in the presence of metal ions is one of the plausible triggers of the emergence of life. The salt-induced peptide formation reaction has been suggested as being prebiotically relevant and was examined for the formation of peptides in NaCl solutions. In previous work we have argued that the first protocell could have emerged in KCl solution. Using HPLC-MS/MS analysis, we found that K(+) is more than an order of magnitude more effective in the L-glutamic acid oligomerization with 1,1'-carbonyldiimidazole in aqueous solutions than the same concentration of Na(+), which is consistent with the diffusion theory calculations. We anticipate that prebiotic peptides could have formed with K(+) as the driving force, not Na(+), as commonly believed

First results of the Kourovka Planet Search: discovery of transiting exoplanet candidates in the first three target fields

We present the first results of our search for transiting exoplanet candidates as part of the Kourovka Planet Search (KPS) project. The primary objective of the project is to search for new hot Jupiters which transit their host stars, mainly in the Galactic plane, in the $R_c$ magnitude range of 11 to 14 mag. Our observations were performed with the telescope of the MASTER robotic network, installed at the Kourovka astronomical observatory of the Ural Federal University (Russia), and the Rowe-Ackermann Schmidt Astrograph, installed at the private Acton Sky Portal Observatory (USA). As test observations, we observed three celestial fields of size $2\times2$ deg$^2$ during the period from 2012 to 2015. As a result, we discovered four transiting exoplanet candidates among the 39000 stars of the input catalogue. In this paper, we provide the description of the project and analyse additional photometric, spectral, and speckle interferometric observations of the discovered transiting exoplanet candidates. Three of the four transiting exoplanet candidates are most likely astrophysical false positives, while the nature of the fourth (most promising) candidate remains to be ascertained. Also, we propose an alternative observing strategy that could increase the project's exoplanet haul.Comment: 11 pages, 16 figures; Accepted for publication in Monthly Notices of the Royal Astronomical Society 201

Kinematically complete experimental study of Compton scattering at helium atoms near the ionization threshold

Compton scattering is one of the fundamental interaction processes of light with matter. Already upon its discovery [1] it was described as a billiard-type collision of a photon kicking a quasi-free electron. With decreasing photon energy, the maximum possible momentum transfer becomes so small that the corresponding energy falls below the binding energy of the electron. Then ionization by Compton scattering becomes an intriguing quantum phenomenon. Here we report a kinematically complete experiment on Compton scattering at helium atoms below that threshold. We determine the momentum correlations of the electron, the recoiling ion, and the scattered photon in a coincidence experiment finding that electrons are not only emitted in the direction of the momentum transfer, but that there is a second peak of ejection to the backward direction. This finding links Compton scattering to processes as ionization by ultrashort optical pulses [2], electron impact ionization [3,4], ion impact ionization [5,6], and neutron scattering [7] where similar momentum patterns occur.Comment: 7 pages, 4 figure