Distance and exposure dependent effective dielectric function.

In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (D(eff)) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of D(eff) versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the "exposure"). The D(eff) values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of D(eff) from 30 to 80.

Facile Pd-catalyzed cross-coupling of 2'-deoxyguanosine O6-arylsulfonates with arylboronic acids.

[reaction: see text]. The O6-(2-mesitylenesulfonyl) derivative of 2'-deoxyguanosine undergoes a facile palladium-mediated C-C cross-coupling with arylboronic acids. Demonstrating the general applicability of this method, the synthesis of a previously undescribed class of 2-amino-6-arylpurine 2'-deoxynucleosides has been accomplished.

Two-dimensional model of phase segregation in liquid binary mixtures.

The hydrodynamic effects on the late stage kinetics of phase separation in liquid mixtures is studied using the model H. Mass and momentum transport are coupled via a nonequilibrium body force, which is proportional to the Peclet number alpha, i.e.

Diffusiophoresis of two-dimensional liquid droplets in a phase-separating system.

The motion of phase-separating liquid drops was simulated in two dimensions following the model H, where convection and diffusion are coupled via a body force, expressing the tendency of demixing systems to minimize their free energy. This driving force depends on the capillary number, i.e.

Solvent size vs cohesive energy as the origin of hydrophobicity.

Two main physical explanations of hydrophobicity seem to be currently competing. The classical, intuitive view attributes it to the fact that interactions between water molecules are much stronger than those between water and nonpolar groups. The second, "heretical" view attributes it to the small size of the water molecule which increases the entropic cost of opening up a cavity to accommodate the solute.

Palladium catalysis for the synthesis of hydrophobic C-6 and C-2 aryl 2'-deoxynucleosides. Comparison of C-C versus C-N bond formation as well as C-6 versus C-2 reactivity.

Suzuki-Miyaura cross-coupling of haloaromatic compounds with arylboronic acids provides a simple entry to biaryl systems. Despite its ease, to date, there are no detailed investigations of this procedure for deoxynucleoside modification. As shown in this study, a wide variety of C-6 arylpurine 2'-deoxyriboside (C-6 aryl 2'-deoxynebularine analogues) and C-2 aryl 2'-deoxyinosine analogues can be conveniently prepared via the Pd-mediated cross-coupling of arylboronic acids with the C-6 halonucleosides, 6-bromo- or 6-chloro-9[2-deoxy-3,5-bis-O-(tert-butyldimethylsilyl)-beta-D-erythro-pentofuranosyl]purine (1 and 2), and the C-2 halonucleoside, 2-bromo-O(6)-benzyl-3',5'-bis-O-(tert-butyldimethylsilyl)-2'-deoxyinosine (3).

Effective energy functions for protein structure prediction.

Protein structure prediction, fold recognition, homology modeling and design rely mainly on statistical effective energy functions. Although the theoretical foundation of such functions is not clear, their usefulness has been demonstrated in many applications. Molecular mechanics force fields, particularly when augmented by implicit solvation models, provide physical effective energy functions that are beginning to play a role in this area.

The circadian rhythm in intraocular pressure and its relation to diurnal ocular growth changes in chicks.

Recent investigations have shown that growing chicken eyes elongate during the day and shorten during the night. We asked whether the chick, like a number of other animals, exhibits a rhythm in intraocular pressure (IOP) and whether this rhythm might be associated with this rhythm in elongation. We find that the intraocular pressure in normal eyes is high during the day and low in the middle of the night, similar to the rhythm in ocular elongation.

Visual influences on diurnal rhythms in ocular length and choroidal thickness in chick eyes.

Recent investigations have raised the possibility that ocular diurnal rhythms might be involved in the regulation of eye growth. Specifically, the chick eye elongates with a daily rhythm, said to be absent in form-deprived eyes. The present study asks: (1) Which components of the eye have daily rhythms-only the overall eye size, or also choroidal thickness or anterior chamber depth? (2) Does the phase or amplitude of these rhythms differ in eyes growing either faster than normal (form-deprived eyes) or slower than normal (eyes recovering from form-deprivation myopia)? Using high-frequency A-scan ultrasonography that allowed fine (8-20 micron) resolution of anterior chamber depth, vitreous chamber depth, choroidal thickness and axial length, we measured normal eyes, form-deprived eyes and eyes recovering from form-deprivation myopia at 6 hour intervals for 5 days and 4 nights.

Compensation for spectacle lenses involves changes in proteoglycan synthesis in both the sclera and choroid.

Purpose: It has been demonstrated that chick eye growth compensates for defocus imposed by spectacle lenses: the eye elongates in response to hyperopic defocus imposed by negative lenses and slows its elongation in response to myopic defocus imposed by positive lenses. We ask whether the synthesis of scleral extracellular matrix, specifically glycosaminoglycans, changes in parallel with the changes in ocular elongation. In addition, there is a choroidal component to compensation for spectacle lenses; the choroid thickens in response to myopic defocus and thins in response to hyperopic defocus.

Modelling the structural pathways for transcapillary exchange.

The ultrastructural pathways and mechanisms whereby endothelial cells and the clefts between the cells modulate capillary permeability to water and solutes have been a central unresolved question in microvessel transport since the early 1950s. Freeze-fracture studies and ultrathin serial sections have demonstrated that endothelial cells are joined by an array of junctional strands which are interrupted at intervals, allowing for the passage of water and solutes, whereas cytochemical studies have indicated that the endothelial surface and portions of the wide part of the cleft contain matrix components. Neither constricted slit models based on the classic pore theory nor fiber matrix models are able to explain the large body of existing permeability measurements.

The elasticity of synthetic phospholipid vesicles obtained by photon correlation spectroscopy.

Osmotic-swelling experiments were conducted on a variety of preparations of "uniform" unilamellar vesicle systems. The synthetic lipid preparations included both vesicles produced by extrusion through polycarbonate ultrafiltration membranes and vesicles produced by the pH-adjustment method. The vesicles were monitored by photon correlation spectroscopy during swelling as the osmolarity of the external solution was decreased.

Local ocular compensation for imposed local refractive error.

Chicks were raised in a low-ceiling environment to find out if their eye growth could compensate for locally imposed hyperopic refractive errors. These chicks became selectively more myopic in the upper visual field than chicks raised in a high-ceiling environment. The vitreous chamber in the low-ceiling birds showed a selective elongation in the ventral region that was not seen in the eyes of the high-ceiling birds.

Deviatoric and hydrostatic mode interaction in hard and soft tissue.

It has been established that many hard and soft tissues have anisotropic material symmetry. It is noted here that the deviatoric and hydrostatic modes interact with each other in a general anisotropic elastic material. In the special case of isotropic, linear elastic, materials these modes are non-interactive.