Specific and nonspecific collapse in protein folding funnels

Experiments with fast folding proteins are beginning to address the relationship between collapse and folding. We investigate how different scenarios for folding can arise depending on whether the folding and collapse transitions are concurrent or whether a nonspecific collapse precedes folding. Many earlier studies have focused on the limit in which collapse is fast compared to the folding time; in this work we focus on the opposite limit where, at the folding temperature, collapse and folding occur simultaneously. Real proteins exist in both of these limits. The folding mechanism varies substantially in these two regimes. In the regime of concurrent folding and collapse, nonspecific collapse now occurs at a temperature below the folding temperature (but slightly above the glass transition temperature).     

The semiclassical limit of a quantum Fermi accelerator

A classical Fermi accelerator model (FAM) is known to show chaotic behavior. The FAM is defined by a free particle bouncing elastically from two rigid walls, one fixed and the other oscillating periodically in time. The central aim of this paper is to connect the quantum and the classical solutions to the FAM in the semiclassical limit. This goal is accomplished using a finite inverted parametric oscillator (FIPO), confined to a box withfixed walls, as an alternative representation of the FAM. In the FIPO representation, an explicit correspondence between classical and quantum limits is accomplished using a Husimi representation of the quasienergy eigenfunctions.     

On the polynomial τ-functions for the KP hierarchy and the bispectral property

We show that the -functions obtained from Schur polynomials lead to wave functions w(x ₁, x ₂, ... ; k) that possess the following bispectral property: There exists a differential operator B{k,_k}, independent of x ₁ , such that B{k,_k}w = {x ₁}w, where {x ₁} is independent of k. This extends for the KP hierarchy some earlier results of J. J. Duistermaat and F. A. Grünbaum for the rational solutions of KdV and of P. Wright for certain rational solutions of the generalized KdV equations.     

Edge linking and image segmentation by combining optical and digital methods

We present a hybrid method for segmentation of intensity images, which combines an optical contouring technique and digital algorithms for linking edge points or image segmentation. In a first stage, the digital image to be processed is displayed in a twisted-nematic liquid-crystal display (LCD), which is placed between a polarizer–analyzer pair at 45 deg (instead of 90 deg as occurs in standard LCDs). It is not difficult to demonstrate that the proposed setup produces a resultant image with very pronounced dark contours at middle intensity. After the optical preprocessing, two different digital algorithms are applied: an edge linking algorithm (modified chain code) and a simple thresholding technique for image segmentation. The proposed procedure works well with monochromatic and color images. The method could be useful as a robust technique for segmentation of large images in real-time, which presents potential applications in medical and biological imaging.     

Free-space fluorescence molecular tomography utilizing 360 degrees geometry projections

Fluorescence tomography of diffuse media can yield optimal three-dimensional imaging when multiple projections over 360 degrees geometries are captured, compared with limited projection angle systems such as implementations in the slab geometry. We demonstrate how it is possible to perform noncontact, 360 degrees projection fluorescence tomography of mice using CCD-camera-based detection in free space, i.e., in the absence of matching fluids. This approach achieves high spatial sampling of photons propagating through tissue and yields a superior information content data set compared with fiber-based 360 degrees implementations. Reconstruction feasibility using 36 projections in 10 degrees steps is demonstrated in mice.     

Energetic and structural characterization of 2‐R‐3‐methylquinoxaline‐1,4‐dioxides (R = benzoyl or tert‐butoxycarbonyl): experimental and computational studies

The gaseous standard molar enthalpies of formation of two 2‐R‐3‐methylquinoxaline‐1,4‐dioxides (R = benzoyl or tert‐butoxycarbonyl), at T = 298.15 K, were derived using the values for the enthalpies of formation of the compounds in the condensed phase, measured by static bomb combustion calorimetry, and for the enthalpies of sublimation, measured by Knudsen effusion, using a quartz crystal oscillator. The three dimensional structure of 2‐tert‐butoxycarbonyl‐3‐methylquinoxaline‐1,4‐dioxide has been obtained by X‐ray crystallography showing that the two N? O bond lengths in this compound are identical. The experimentally determined geometry in the crystal is similar to that obtained in the gas‐phase after computations performed at the B3LYP/6‐311 + G(2d,2p) level of theory. The experimental and computational results reported allow to extend the discussion about the influence of the molecular structure on the dissociation enthalpy of the N? O bonds for quinoxaline 1,4‐dioxide derivatives. As found previously, similar N? O bond lengths in quinoxaline‐1,4‐dioxide compounds are not linked with N? O bonds having the same strength. Copyright © 2007 John Wiley & Sons, Ltd.     

Quantum scalar field in quantum gravity: the propagator and Lorentz invariance in the spherically symmetric case

We recently studied gravity coupled to a scalar field in spherical symmetry using loop quantum gravity techniques. Since there are local degrees of freedom one faces the “problem of dynamics”. We attack it using the “uniform discretization technique”. We find the quantum state that minimizes the value of the master constraint for the case of weak fields and curvatures. The state has the form of a direct product of Gaussians for the gravitational variables times a modified Fock state for the scalar field. In this paper we do three things. First, we verify that the previous state also yields a small value of the master constraint when one polymerizes the scalar field in addition to the gravitational variables. We then study the propagators for the polymerized scalar field in flat space-time using the previously considered ground state in the low energy limit. We discuss the issue of the Lorentz invariance of the whole approach. We note that if one uses real clocks to describe the system, Lorentz invariance violations are small. We discuss the implications of these results in the light of Hořava’s Gravity at the Lifshitz point and of the argument about potential large Lorentz violations in interacting field theories of Collins et al.     

EPR spectroscopy of protein microcrystals oriented in a liquid crystalline polymer medium

Correlation of the g-tensor of a paramagnetic active center of a protein with its structure provides a unique experimental information on the electronic structure of the metal site. To address this problem, we made solid films containing metalloprotein (Desulfovibrio gigas cytochrome c(3)) microcrystals. The microcrystals in a liquid crystalline polymer medium (water/hydroxypropylcellulose) were partially aligned by a shear flow. A strong orientation effect of the metalloprotein was observed by EPR spectroscopy and polarizing optical microscopy. The EPR spectra of partially oriented samples were simulated, allowing for molecular orientation distribution function determination. The observed effect results in enhanced sensitivity and resolution of the EPR spectra and provides a new approach towards the correlation of spectroscopic data, obtained by EPR or some other technique, with the three-dimensional structure of a protein or a model compound.     

Macrocycle-Derived Functional Xanthenes and Progress Towards Concurrent Detection of Glucose and Fructose

The detection of saccharides in biological media is of great current importance for the monitoring of disease states. We have previously reported that solutions of boronic acid-functionalized macrocycles form acyclic oligomeric materials in situ. The oligomers contain fluorescent xanthene moieties. Current efforts are aimed at modulating the spectroscopic responses of these materials for the analysis of specific sugars. We describe conditions whereby the xanthene boronic acids exhibit high colorimetric fructose selectivity. In contrast, at physiological levels selective glucose monitoring can be achieved via fluorescence. Additionally, we describe a method which exhibits promise for detecting both glucose and fructose at dual wavelengths in the UV-Vis region. Mechanistic rationale for each of these findings is presented.