Spectral measurement of absorption by spectroscopic frequency-domain optical coherence tomography

A new method of measurement that essentially combines Fourier-domain optical coherence tomography with spectroscopy is introduced. By use of a windowed Fourier transform it is possible to obtain, in addition to the object structure, spectroscopic information such as the absorption properties of materials. The feasibility of this new method for performing depth-resolved spectroscopy is demonstrated with a glass filter plate. The results are compared with theoretically calculated spectra by use of the well-known spectral characteristics of the light source and the filter plate.     

Reducing belief simpliciter to degrees of belief

Is it possible to give an explicit definition of belief (simpliciter) in terms of subjective probability, such that believed propositions are guaranteed to have a sufficiently high probability, and yet it is neither the case that belief is stripped of any of its usual logical properties, nor is it the case that believed propositions are bound to have probability 1? We prove the answer is ‘yes’, and that given some plausible logical postulates on belief that involve a contextual “cautiousness” threshold, there is but one way of determining the extension of the concept of belief that does the job. The qualitative concept of belief is not to be eliminated from scientific or philosophical discourse, rather, by reducing qualitative belief to assignments of resiliently high degrees of belief and a “cautiousness” threshold, qualitative and quantitative belief turn out to be governed by one unified theory that offers the prospects of a huge range of applications. Within that theory, logic and probability theory are not opposed to each other but go hand in hand.     

Unequal siblings: Adverse characteristics of naphtalene‐based hoveyda‐type second generation initiators in ring opening metathesis polymerization

A family of four different Hoveyda‐type initiators bearing a π‐extended carbene ligand was characterized regarding the activity in ring opening metathesis polymerization. One of the initiators shows high activity at ambient temperature, similar to the second generation Hoveyda–Grubbs catalyst and is even suited for the controlled polymerization of certain norbornene derivatives. The other family members exhibit a pronounced latency at room temperature, and polymerization can be triggered by heat. The scope of these initiators in the thermally triggered polymerizations of norbornene derivatives in general and dicyclopentadiene in particular was disclosed. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.     

Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: a molecular dynamics study

In this study, molecular dynamics simulations were carried out on Lys- and Arg-containing Ala-based peptides (i.e. Ace-(AAAAK)(n)A-NH(2) and Ace-(AAAAR)(n)A-NH(2), where n=1-4), in order to explore and characterize their folding processes. For the oligopeptides, the evolution of α-helical structure with regard to the whole conformation, as well as to each residue was investigated, and the helix-forming propensities were characterized. On the basis of the helicity curves, representing the alteration of average helicity as a function of time, the typical time values describing the folding processes and subprocesses were identified. In the case of each peptide, the evolution and role of helix-stabilizing, non-local and side-chain-to-backbone H-bonds were examined. The appearing i←i+4 H-bonds pointed out the role of these interactions in the stabilization of α-helical conformations, while the occurring i←i+3 H-bonds indicated the presence of β-turn or 3(10)-helical structures. Studying the formation and role of non-local and side-chain-to-backbone H-bonds led to the observation that these types of interactions produced an effect on the evolution of helical conformations, as well as on the folding processes.     

Determination of interface properties by spatial echo distribution processing

Echo amplitudes, detected by present ultrasonic pulse echo methods, are determined to a great part by the properties of the echo producing interfaces. Quantitative analysis by digital signal processing or sophisticated monitoring, especially by amplitude colour coding, appears to be advantageous only if these unwanted echo amplitude distortions can be avoided or compensated for.A promising way to achieve this aim may be the processing of the spatial echo distributions produced by reflection at the echo producing interfaces. In this paper it is shown by mathematical and experimental examination how interface properties can affect the spatial echo distributions.     

Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives

Phosphotyrosine (pTyr) is an essential component of biological signaling, often being a determinant of protein-protein interactions. Accordingly, a number of drug discovery efforts targeting signal transduction pathways have included phosphotyrosine and analogues as essential components of the lead compounds. Toward the goal of improved biological efficacy, the phosphonate and difluoro phosphonate analogues of pTyr have been employed in inhibitor design because of their stability to hydrolysis and enhanced binding affinity in certain cases. To quantitate the contribution of aqueous solubility of pTyr, phosphonomethyl phenylalanine (Pmp), and difluorophosphonomethyl phenylalanine (F(2)Pmp) to their relative binding affinities, free energy perturbation calculations were undertaken on the mimetics phenol phosphate (PP), benzyl phosphonate (BP), and difluorobenzyl phosphonate (F(2)BP), including development of empirical force field parameters compatible with the CHARMM all-atom force fields. Notably, it is shown that the most favorably solvated compound of the series is BP, followed by PP, with F(2)BP the least favorably solvated for both the mono- and dianionic forms of the compounds. The molecular origin of this ordering is shown to be due to changes in charge distribution, in the comparatively larger size of the fluorine atoms, as well as in differences of local solvation between PP and BP. The implications of the differences in aqueous solubility toward the relative binding potencies of pTyr-, Pmp-, and F(2)Pmp-containing peptide ligands are discussed. Our results indicate that one general principle explaining the efficacy of selective fluorination to enhance binding affinities may lie in the ability of fluorine atoms to increase the hydrophobicity of a ligand while maintaining its capability to form hydrogen bonds.     

Alchemical free energy calculations and multiple conformational substates

Thermodynamic integration (TI) was combined with (adaptive) umbrella sampling to improve the convergence of alchemical free energy simulations in which multiple conformational substates are present. The approach, which we refer to as non-Boltzmann TI (NBTI), was tested by computing the free energy differences between three five-atomic model systems, as well as the free energy difference of solvation between leucine and asparagine. In both cases regular TI failed to give converged results, whereas the NBTI results were free from hysteresis and had standard deviations well below +/-0.7 kcal/mole. We also present theoretical considerations that make it possible to compute free energy differences between simple molecules, such as the five-atomic model systems, by numerical integration of the partition functions at the respective end points.     

In-line reference-delayed digital holography using a low-coherence light source

We present a holographic imaging device with a low-coherence light source that uses the reflection of the objective lens as reference illumination. This results in a simple setup and allows applications to microscopy with only small modifications of the setup for aberration measurements. In addition, it opens the prospects to in vivo ophthalmic imaging. We present in vitro experiments using a resolution test target to quantify the system performance. We demonstrate that we can achieve diffraction-limited resolution and show the possibility of aberration correction. We also present preliminary results using a scattering sample.     

Spatial relationships between the pharmacophores of endomorphin-2: a comparative study of stereoisomers

The spatial relationships between the pharmacophore elements were investigated in the case of four different stereoisomeric forms of opioid tetrapeptide, endomorphin-2, taking into account the L-D and cis-trans isomerisms. On the basis of distances and angles measured between the pharmacophoric points, a comparative analysis of conformational distributions was performed, applying a variety of distance-angle maps. The results obtained by this theoretical study indicated that the stereoisomers of endomorphin-2 could be distinguished from one another, based on the comparative analysis of distance-angle maps. Nevertheless, it could be concluded that this method proved to be suitable to examine the effects of L-D and cis-trans isomerisms on the spatial relationships of the pharmacophores of tetrapeptide.      

Extended focus depth for Fourier domain optical coherence microscopy

We report on a new detection scheme for Fourier domain optical coherence microscopy that exhibits high transverse resolution along an axially extended focal range. Nearly constant transverse resolution of approximately 1.5 microm along a focal range of 200 microm is experimentally verified with a maximum sensitivity of 105 dB. A broad-bandwidth Ti:sapphire laser allowed for an axial resolution of 3 microm in air.