552 research outputs found
Many-body interactions and melting of colloidal crystals
We study the melting behavior of charged colloidal crystals, using a
simulation technique that combines a continuous mean-field Poisson-Boltzmann
description for the microscopic electrolyte ions with a Brownian-dynamics
simulation for the mesoscopic colloids. This technique ensures that many-body
interactions between the colloids are fully taken into account, and thus allows
us to investigate how many-body interactions affect the solid-liquid phase
behavior of charged colloids. Using the Lindemann criterion, we determine the
melting line in a phase-diagram spanned by the colloidal charge and the salt
concentration. We compare our results to predictions based on the established
description of colloidal suspensions in terms of pairwise additive Yukawa
potentials, and find good agreement at high-salt, but not at low-salt
concentration. Analyzing the effective pair-interaction between two colloids in
a crystalline environment, we demonstrate that the difference in the melting
behavior observed at low salt is due to many-body interactions
Dual role of benzophenone enables a fast and scalable C-4 selective alkylation of pyridines in flow
The efficient C-4 selective modification of pyridines is a major challenge for the synthetic community. Current strategies are plagued with at least one drawback regarding functional group-tolerant electronic activation of the heteroarene, mild generation of the required alkyl radicals, regioselectivity, safety and/or scalability. Herein, we describe a fast, safe and scalable flow process which allows preparation of said C-4 alkylated pyridines. The process involves a photochemical hydrogen atom transfer (HAT) event to generate the carbon-centered radicals needed to alkylate the C-2 blocked pyridine. In a two-step streamlined flow process, this light-mediated alkylation step is combined with a nearly instantaneous inline removal of the blocking group. Notably, cheap benzophenone plays a dual role in the pyridine alkylation mechanism by activating the hydrocarbon feedstock reagents via a HAT mechanism, and by acting as a benign, terminal oxidant. The key role of benzophenone in the operative reaction mechanism has also been revealed through a combination of experimental and computational studies
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Survey of Materials for Nanoskiving and Influence of the Cutting Process on the Nanostructures Produced
This paper examines the factors that influence the quality of nanostructures fabricated by sectioning thin films with an ultramicrotome (ânanoskivingâ). It surveys different materials (metals, ceramics, semiconductors, and conjugated polymers), deposition techniques (evaporation, sputter deposition, electroless deposition, chemical-vapor deposition, solution-phase synthesis, and spin-coating), and geometries (nanowires or two-dimensional arrays of rings and crescents). It then correlates the extent of fragmentation of the nanostructures with the composition of the thin films, the methods used to deposit them, and the parameters used for sectioning. There are four major conclusions. (i) Films of soft and compliant metals (those that have bulk values of hardness less than or equal to those of palladium, or â€500 MPa) tend to remain intact upon sectioning, whereas hard and stiff metals (those that have values of hardness greater than or equal to those of platinum, or â„500 MPa) tend to fragment. (ii) All conjugated polymers tested form intact nanostructures. (iii) The extent of fragmentation is lowest when the direction of cutting is perpendicular to the exposed edge of the embedded film. (iv) The speed of cuttingâfrom 0.1 to 8 mm/sâhas no effect on the frequency of defects. Defects generated during sectioning include scoring from defects in the knife, delamination of the film from the matrix, and compression of the matrix. The materials tested were: aluminum, titanium, nickel, copper, palladium, silver, platinum, gold, lead, bismuth, germanium, silicon dioxide (), alumina (), tin-doped indium oxide (ITO), lead sulfide nanocrystals, the semiconducting polymers poly(2-methoxy-5-(2âČ-ethyl-hexyloxy)-1,4-phenylene vinylene) (MEH-PPV), poly(3-hexylthiophene) (P3HT), and poly(benzimidazobenzophenanthroline ladder) (BBL), and the conductive polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS).Chemistry and Chemical Biolog
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Predicting visual function from the measurements of retinal nerve fiber layer structure
Purpose: To develop and validate a method for predicting visual function from retinal nerve fibre layer (RNFL) structure in glaucoma.
Methods: RNFL thickness (RNFLT) measurements from GDxVCC scanning laser polarimetry (SLP) and visual field (VF) sensitivity from standard automated perimetry were made available from 535 eyes from three centres. In a training dataset, structure-function relationships were characterized using linear regression and a type of neural network: Radial Basis Function customised under a Bayesian framework (BRBF). These two models were used in a test dataset to 1) predict sensitivity values at individual VF locations from RNFLT measurements and 2) predict the spatial relationship between VF locations and positions at a peripapillary RNFLT measurement annulus. Predicted spatial relationships were compared with a published anatomical structure-function map.
Results: Compared with linear regression, BRBF yielded a nearly two-fold improvement (P<0.001; paired t-test) in performance of predicting VF sensitivity in the test dataset (mean absolute prediction error of 2.9dB (standard deviation (SD) 3.7dB) versus 4.9dB (SD 4.0dB)). The predicted spatial structure-function relationship accorded better (P<0.001; paired t-test) with anatomical prior knowledge when the BRBF was compared with the linear regression (median absolute angular difference of 15° versus 62°).
Conclusions: The BRBF generates clinically useful relationships that relate topographical maps of RNFL measurement to VF locations and allows the VF sensitivity to be predicted from structural measurements. This method may allow clinicians to evaluate structural and functional measures in the same domain. It could also be generalized to use other structural measures
Progression Detection of Glaucoma from Polarimetric Images
Detecting glaucoma progression is crucial for assessing the effectivity of the treatment. This paper describes three methods for detecting progression related changes in polarimetric images of the retinal nerve fiber layer (NFL), both on a global and on a local scale. Detecting global changes proved not to be feasible due to poor reproducibility of the measurements at the pixel level. Local progression on the other hand could be detected. A distribution based approach did not work, but locating specific areas with minimum size and minimum NFL decrease did give relevant results. The described algorithm yielded a TPR of 0.42 and an FPR of 0.095 on our datasets. It proved to be able to outline suspect areas that show NFL reductio
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Smart Libraries: Best SQE Practices for Libraries with an Emphasis on Scientific Computing
As scientific computing applications grow in complexity, more and more functionality is being packaged in independently developed libraries. Worse, as the computing environments in which these applications run grow in complexity, it gets easier to make mistakes in building, installing and using libraries as well as the applications that depend on them. Unfortunately, SQA standards so far developed focus primarily on applications, not libraries. We show that SQA standards for libraries differ from applications in many respects. We introduce and describe a variety of practices aimed at minimizing the likelihood of making mistakes in using libraries and at maximizing users' ability to diagnose and correct them when they occur. We introduce the term Smart Library to refer to a library that is developed with these basic principles in mind. We draw upon specific examples from existing products we believe incorporate smart features: MPI, a parallel message passing library, and HDF5 and SAF, both of which are parallel I/O libraries supporting scientific computing applications. We conclude with a narrative of some real-world experiences in using smart libraries with Ale3d, VisIt and SAF
Effective Interactions and Volume Energies in Charged Colloids: Linear Response Theory
Interparticle interactions in charge-stabilized colloidal suspensions, of
arbitrary salt concentration, are described at the level of effective
interactions in an equivalent one-component system. Integrating out from the
partition function the degrees of freedom of all microions, and assuming linear
response to the macroion charges, general expressions are obtained for both an
effective electrostatic pair interaction and an associated microion volume
energy. For macroions with hard-sphere cores, the effective interaction is of
the DLVO screened-Coulomb form, but with a modified screening constant that
incorporates excluded volume effects. The volume energy -- a natural
consequence of the one-component reduction -- contributes to the total free
energy and can significantly influence thermodynamic properties in the limit of
low-salt concentration. As illustrations, the osmotic pressure and bulk modulus
are computed and compared with recent experimental measurements for deionized
suspensions. For macroions of sufficient charge and concentration, it is shown
that the counterions can act to soften or destabilize colloidal crystals.Comment: 14 pages, including 3 figure
The osmotic pressure of charged colloidal suspensions: A unified approach to linearized Poisson-Boltzmann theory
We study theoretically the osmotic pressure of a suspension of charged
objects (e.g., colloids, polyelectrolytes, clay platelets, etc.) dialyzed
against an electrolyte solution using the cell model and linear
Poisson-Boltzmann (PB) theory. From the volume derivative of the grand
potential functional of linear theory we obtain two novel expressions for the
osmotic pressure in terms of the potential- or ion-profiles, neither of which
coincides with the expression known from nonlinear PB theory, namely, the
density of microions at the cell boundary. We show that the range of validity
of linearization depends strongly on the linearization point and proof that
expansion about the selfconsistently determined average potential is optimal in
several respects. For instance, screening inside the suspension is
automatically described by the actual ionic strength, resulting in the correct
asymptotics at high colloid concentration. Together with the analytical
solution of the linear PB equation for cell models of arbitrary dimension and
electrolyte composition explicit and very general formulas for the osmotic
pressure ensue. A comparison with nonlinear PB theory is provided. Our analysis
also shows that whether or not linear theory predicts a phase separation
depends crucially on the precise definition of the pressure, showing that an
improper choice could predict an artificial phase separation in systems as
important as DNA in physiological salt solution.Comment: 16 pages, 5 figures, REVTeX4 styl
On the fluid-fluid phase separation in charged-stabilized colloidal suspensions
We develop a thermodynamic description of particles held at a fixed surface
potential. This system is of particular interest in view of the continuing
controversy over the possibility of a fluid-fluid phase separation in aqueous
colloidal suspensions with monovalent counterions. The condition of fixed
surface potential allows in a natural way to account for the colloidal charge
renormalization. In a first approach, we assess the importance of the so called
``volume terms'', and find that in the absence of salt, charge renormalization
is sufficient to stabilize suspension against a fluid-fluid phase separation.
Presence of salt, on the other hand, is found to lead to an instability. A very
strong dependence on the approximations used, however, puts the reality of this
phase transition in a serious doubt. To further understand the nature of the
instability we next study a Jellium-like approximation, which does not lead to
a phase separation and produces a relatively accurate analytical equation of
state for a deionized suspensions of highly charged colloidal spheres. A
critical analysis of various theories of strongly asymmetric electrolytes is
presented to asses their reliability as compared to the Monte Carlo
simulations
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