Full Lutz twist along the binding of an open book

Let T denote a binding component of an open book (S, f){(\Sigma, \phi)} compatible with a closed contact 3-manifold (M, ξ). We describe an explicit open book (S￠, f￠){(\Sigma', \phi')} compatible with (M, ζ), where ζ is the contact structure obtained from ξ by performing a full Lutz twist along T. Here, (S￠, f￠){(\Sigma', \phi')} is obtained from (S, f){(\Sigma, \phi)} by a local modification near the binding.     

Invariants of contact structures from open books

In this note we define three invariants of contact structures in terms of open books supporting the contact structures. These invariants are the support genus (which is the minimal genus of a page of a supporting open book for the contact structure), the binding number (which is the minimal number of binding components of a supporting open book for the contact structure with minimal genus pages) and the norm (which is minus the maximal Euler characteristic of a page of a supporting open book).

     

Analytic and asymptotic properties of non-symmetric Linnik's probability densities

The function

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

Time series analysis tools are employed on the principal modes obtained from the C(alpha) trajectories from two independent molecular-dynamics simulations of alpha-amylase inhibitor (tendamistat). Fluctuations inside an energy minimum (intraminimum motions), transitions between minima (interminimum motions), and relaxations in different hierarchical energy levels are investigated and compared with those encountered in vacuum by using different sampling window sizes and intervals. The low-frequency low-indexed mode relationship, established in vacuum, is also encountered in water, which shows the reliability of the important dynamics information offered by principal components analysis in water. It has been shown that examining a short data collection period (100 ps) may result in a high population of overdamped modes, while some of the low-frequency oscillations (<10 cm(-1)) can be captured in water by using a longer data collection period (1200 ps). Simultaneous analysis of short and long sampling window sizes gives the following picture of the effect of water on protein dynamics. Water makes the protein lose its memory: future conformations are less dependent on previous conformations due to the lowering of energy barriers in hierarchical levels of the energy landscape. In short-time dynamics (<10 ps), damping factors extracted from time series model parameters are lowered. For tendamistat, the friction coefficient in the Langevin equation is found to be around 40-60 cm(-1) for the low-indexed modes, compatible with literature. The fact that water has increased the friction and that on the other hand has lubrication effect at first sight contradicts. However, this comes about because water enhances the transitions between minima and forces the protein to reduce its already inherent inability to maintain oscillations observed in vacuum. Some of the frequencies lower than 10 cm(-1) are found to be overdamped, while those higher than 20 cm(-1) are slightly increased. As for the long-time dynamics in water, it is found that random-walk motion is maintained for approximately 200 ps (about five times of that in vacuum) in the low-indexed modes, showing the lowering of energy barriers between the higher-level minima.     

The elastic net algorithm and protein structure prediction

Predicting protein structures from their amino acid sequences is a problem of global optimization. Global optima (native structures) are often sought using stochastic sampling methods such as Monte Carlo or molecular dynamics, but these methods are slow. In contrast, there are fast deterministic methods that find near-optimal solutions of well-known global optimization problems such as the traveling salesman problem (TSP). But fast TSP strategies have yet to be applied to protein folding, because of fundamental differences in the two types of problems. Here, we show how protein folding can be framed in terms of the TSP, to which we apply a variation of the Durbin-Willshaw elastic net optimization strategy. We illustrate using a simple model of proteins with database-derived statistical potentials and predicted secondary structure restraints. This optimization strategy can be applied to many different models and potential functions, and can readily incorporate experimental restraint information. It is also fast; with the simple model used here, the method finds structures that are within 5-6 A all-Calpha-atom RMSD of the known native structures for 40-mers in about 8 s on a PC; 100-mers take about 20 s. The computer time tau scales as tau approximately n, where n is the number of amino acids. This method may prove to be useful for structure refinement and prediction.     

Optical absorption of isotopically enriched Li2B4O7 single crystals irradiated by thermal neutrons

Induced absorption spectra in the range 200–900 nm at 77 and 290 K for Li₂B₄O₇ single crystals, isotopically Li and B enriched are presented after irradiation of these crystals by thermal neutrons with fluence 1.8×10¹⁶ cm⁻². The dependence of induced absorption spectra on the isotope composition was revealed: for ⁶Li₂¹⁰B₄O₇ and ⁷Li₂¹⁰B₄O₇ crystals intensive band in the region of 280–294 nm was observed. Under substitution of ⁷Li isotope by ⁶Li in the lithium tetraborate lattice no changes in the absorption spectra were observed. The nuclear reaction ¹⁰B(n,)⁷Li is proposed to be the main mechanism of formation of the radiation defects.     

Explicit horizontal open books on some Seifert fibered 3-manifolds

We describe explicit horizontal open books on some Seifert fibered 3-manifolds. We show that the contact structures compatible with these horizontal open books are Stein fillable and horizontal as well. Moreover we draw surgery diagrams for some of these contact structures.     

Generation of spatial solitons using non-linear guided modes

We investigate how two-dimensional spatial optical solitons can be generated in a non-linear Kerr medium using the non-linear guided modes of a weakly-guiding slab waveguide with a linear core and a non-linear cladding as the source of excitation. Symmetric, antisymmetric and asymmetric non-linear modes are considered, from which we determine the parameters of single solitons, oscillating two-soliton bound states, and two repelling solitons, respectively. Both the beam propagation method and inverse scattering transform are used.     

Mixed norm estimates for certain generalized Radon transforms

We obtain essentially optimal local mixed norm inequalities for certain generalized Radon transforms defined by integration over curves.