Topological "Shape" in Micellar Dynamics.

For micelles, "shape" is prominent in rheological computations of fluid flow, but this "shape" is often expressed too informally to be useful for rigorous analyses. We formalize topological "shape equivalence" of micelles, both and , to enable visualization of computational fluid dynamics. Although topological methods in visualization provide significant insights into fluid flows, this opportunity has been limited by the known difficulties in creating representative geometry.

Protocols to Dissolve Amorphous Urate Crystals in Urine.

Objective: Amorphous urate crystals can obscure significant findings during a routine urinalysis. There is no standardized protocol to minimize their effect.

Materials And Methods: We tested 210 urine specimens.

The Role of Chemical Heterogeneity in Surfactant Adsorption at Solid-Liquid Interfaces.

Chemical heterogeneity of solid surfaces disrupts the adsorption of surfactants from the bulk liquid. While its presence can hinder the performance of some formulations, bespoke chemical patterning could potentially facilitate controlled adsorption for nanolithography applications. Although some computational studies have investigated the impact of regularly patterned surfaces on surfactant adsorption, in reality, many interesting surfaces are expected to be stochastically disordered and this is an area unexplored via simulations.

Model for the Simulation of the CE Nonionic Surfactant Family Derived from Recent Experimental Results.

Using a comprehensive set of recently published experimental results for training and validation, we have developed computational models appropriate for simulations of aqueous solutions of poly(ethylene oxide) alkyl ethers, an important class of micelle-forming nonionic surfactants, usually denoted CE. These models are suitable for use in simulations that employ a moderate amount of coarse graining and especially for dissipative particle dynamics (DPD), which we adopt in this work. The experimental data used for training and validation were reported earlier and produced in our laboratory using dynamic light scattering (DLS) measurements performed on 12 members of the CE compound family yielding micelle size distribution functions and mass-weighted mean aggregation numbers at each of several surfactant concentrations.

Efficient Algorithm for the Topological Characterization of Worm-like and Branched Micelle Structures from Simulations.

Many surfactant-based formulations are utilized in industry as they produce desirable viscoelastic properties at low concentrations. These properties are due to the presence of worm-like micelles (WLMs), and as a result, understanding the processes that lead to WLM formation is of significant interest. Various experimental techniques have been applied with some success to this problem but can encounter issues probing key microscopic characteristics or the specific regimes of interest.

Challenge to Reconcile Experimental Micellar Properties of the CnEm Nonionic Surfactant Family.

We wished to compile a data set of results from the experimental literature to support the development and validation of accurate computational models (force fields) for an important class of micelle-forming nonionic surfactant compounds, the poly(ethylene oxide) alkyl ethers, usually denoted C E . However, careful examination of the experimental literature exposed a striking degree of variation in values reported for critical micelle concentrations (cmc) and mean aggregation numbers ( N). This variation was so large that it masked important trends known to exist within this family of molecules, thereby rendering most of the literature data to be of limited utility for force field development.

Toward a Standard Protocol for Micelle Simulation.

In this paper, we present protocols for simulating micelles using dissipative particle dynamics (and in principle molecular dynamics) that we expect to be appropriate for computing micelle properties for a wide range of surfactant molecules. The protocols address challenges in equilibrating and sampling, specifically when kinetics can be very different with changes in surfactant concentration, and with minor changes in molecular size and structure, even using the same force field parameters. We demonstrate that detection of equilibrium can be automated and is robust, for the molecules in this study and others we have considered.

Does race alter the relationship between Hba1c and glucose in type 2 diabetes?

Objective: Hemoglobin Alc (HbAlc) is the standard measurement of glycemic control, and the HbAlc value can be used to estimate average glucose using a formula. Several studies suggest that the relationship between average glucose and HbAlc may be different for Blacks. This project enrolled non-Hispanic black and white individuals with type 2 diabetes and evaluated the relationship between HbAlc and blood glucose.

Toward fast determination of protein stability maps: experimental and theoretical analysis of mutants of a Nocardiopsis prasina serine protease.

The stability of serine proteases is of major importance for their application in industrial processes. Here we study the determinants of the stability of a Nocardiopsis prasina serine protease using fast residual activity assays, a feature classification algorithm, and structure-based energy calculation algorithms for 121 micropurified mutant enzyme clones containing multiple point mutations. Using a multivariate regression analysis, we deconvolute the data for the mutant clones and find that mutations of residues Asn47 and Pro124 are deleterious to the stability of the enzyme.

A collaborative environment for developing and validating predictive tools for protein biophysical characteristics.

The exchange of information between experimentalists and theoreticians is crucial to improving the predictive ability of theoretical methods and hence our understanding of the related biology. However many barriers exist which prevent the flow of information between the two disciplines. Enabling effective collaboration requires that experimentalists can easily apply computational tools to their data, share their data with theoreticians, and that both the experimental data and computational results are accessible to the wider community.

Integrated prediction of the effect of mutations on multiple protein characteristics.

Site-directed mutagenesis is routinely used in modern biology to elucidate the functional or biophysical roles of protein residues, and plays an important role in the field of rational protein design. Over the past decade, a number of computational tools have been developed that can predict the effect of point mutations on a protein's biophysical characteristics. However, these programs usually provide predictions for only a single characteristic.

Microbial antagonists of Escherichia coli O157:H7 on fresh-cut lettuce and spinach.

Fresh-cut lettuce and spinach can become contaminated with pathogens at numerous points from the field to the retail market. Natural microflora present on fresh produce may help reduce the pathogen load. The objective of this study was to isolate natural microflora from fresh-cut iceberg lettuce and baby spinach and to determine whether these bacteria were antagonistic toward Escherichia coli O157:H7.

Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.

Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community.