Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins

Evaluating the availability of molecular oxygen (O₂) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and excited states related to 11-cis-retinal and the O₂ accessibility to the β-ionone ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O₂ pathways within rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis, and implicit ligand sampling while retinal energetic properties are investigated through density functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions reveal that an amino acid substitution can lead to enough energy and O₂ accessibility in the core hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which can be useful in understanding retinal degeneration mechanisms and in designing blue-lighting-absorbing proteic photosensitizers.     

Discrete and selective absorption in crystalline molecular nanofilms

Recent research in nano-optical engineering and in nanomedicine as well, seeks for methods of construction of various types of nano-markers, nano-carriers, and ways to deliver drugs to the exactly determined regions of body. In this process it is important to find methods of recognition of certain types of molecules. It is obvious that optical recognition would be the easiest and the most effective way to do it. Our research presents a model of a molecular ultrathin crystalline film and generated exciton system inside it and corresponding methodology of analysis of their optical characteristics. Properties of these spatially very restricted structures are very sensitive to their surrounding surfaces. Using the two-time Green’s functions adapted for crystalline structures with symmetry breaking, and graphical-numerical software, we have calculated the energy spectra and possible exciton states. We have shown that the appearance and the presence of localized states on the surfaces and in the boundary layers of the film depend on the thickness of the film and the film surroundings, presented through the perturbation of parameters on surfaces. Optical properties in these structures demonstrate discrete and very selective resonant absorption spectra, depending on the perturbation on their surfaces.     

“Locus” and “Trace” in Cabrigéomètre: relationships between geometric and functional aspects in a study of transformations

The present text describes and characterises the tools “Locus” and “Trace” of Cabri-géomètre II, in relations to a study of geometric transformation, more precisely, the passage from the notion of transformation of figures to the notion of applications¹ that map points on the plane onto the plane itself. In particular it discusses how the conception of image of a figure under a transformation can evolve—through interaction in a “milieu” organised around Cabri-géomètre—such that students move from views of figure-images as undecomposible entities to see them as sets of image-points. Moreover, the study allowed the identification that the notion of trajectory (in a dynamic interpretation) has an important role in this conceptually difficult passage and that dynamic geometry environment renovate this notion.     

Poincaré series of resolutions of surface singularities

Let be a resolution of singularities of a normal surface singularity , with integral exceptional divisors . We consider the Poincaré series

where

We show that if has characteristic zero and is a semi-abelian variety, then the Poincaré series is rational. However, we give examples to show that this series can be irrational if either of these conditions fails.

     

Interplay of Antiferromagnetic Coupling and Spin Crossover in Dinuclear Iron(II) Complexes

This article reports on the study of the interplay between magnetic coupling and spin transition in 2,2′-bipyrimidine (bpym)-bridged iron(II) dinuclear compounds. Coexistence of both phenomena has been observed in [Fe(bpym)(NCS)₂]₂bpym, [Fe(bpym)(NCSe)₂]₂bpym and [Fe(bt)(NCS)₂]₂bpym (bpym = 2,2′-bipyrimidine, bt = 2,2′-bithiazoline) by the action of external physical factors namely pressure or electromagnetic radiation. Competition between magnetic exchange and spin crossover has been studied in [Fe(bpym)(NCS)₂]₂bpym at 6.3 kbar. LIESST experiments carried out in [Fe(bpym)(NCSe)₂]₂bpym and [Fe(bt)(NCS)₂]₂bpym at 4.2 K have shown that is possible to achieve dinuclear molecules with different spin states in this class of compounds. This revised version was published online in August 2006 with corrections to the Cover Date.     

Real

The famous problem involves applying two maps: and to positive integers. If is even, one applies , if it is odd, one applies . The conjecture states that each trajectory of the system arrives to the periodic orbit . In this paper, instead of choosing each time which map to apply, we allow ourselves more freedom and apply both and independently of . That is, we consider the action of the free semigroup with generators and on the space of positive real numbers. We prove that this action is minimal (each trajectory is dense) and that the periodic points are dense. Moreover, we give a full characterization of the group of transformations of the real line generated by and .

     

Presmoothing the transition probabilities in the illness-death model

One major goal in clinical applications of multi-state models is the estimation of transition probabilities. In a recent paper, Meira-Machado et al. (2006) introduce a substitute for the Aalen-Johansen estimator in the case of a non-Markov illness-death model. The idea behind their estimator is to weight the data by the Kaplan-Meier weights pertaining to the distribution of the total survival time of the process. In this paper we propose a modification of Meira-Machado et al. (2006) estimator based on presmoothing. Consistency is established. We investigate the finite sample performance of the new estimator through simulations. Data from a study on colon cancer are used for illustration purposes.     

Self-inverse Sheffer sequences and Riordan involutions

In this short note, we focus on self-inverse Sheffer sequences and involutions in the Riordan group. We translate the results of Brown and Kuczma on self-inverse sequences of Sheffer polynomials to describe all involutions in the Riordan group.     

Exceedance probability of the integral of a stochastic process

Let X={X(s)}_s∈S be an almost sure continuous stochastic process (S compact subset of R^d) in the domain of attraction of some max-stable process, with index function constant over S. We study the tail distribution of ∫_SX(s)ds, which turns out to be of Generalized Pareto type with an extra ‘spatial’ parameter (the areal coefficient from Coles and Tawn (1996) [3]). Moreover, we discuss how to estimate the tail probability P(∫_SX(s)ds>x) for some high value x, based on independent and identically distributed copies of X. In the course we also give an estimator for the areal coefficient. We prove consistency of the proposed estimators. Our methods are applied to the total rainfall in the North Holland area; i.e. X represents in this case the rainfall over the region for which we have observations, and its integral amounts to total rainfall.The paper has two main purposes: first to formalize and justify the results of Coles and Tawn (1996) [3]; further we treat the problem in a non-parametric way as opposed to their fully parametric methods.