Cells are organized on length scales ranging from Angstroms to microns. However, the mechanisms by which Angstrom-scale molecular properties are translated to micron-scale macroscopic properties are not well understood. Here we show that interactions between diverse, synthetic multivalent macromolecules (including multi-domain proteins and RNA) produce sharp, liquid-liquid demixing phase separations, generating micron-sized liquid droplets in aqueous solution. This macroscopic transition corresponds to a molecular transition between small complexes and large, dynamic supramolecular polymers. The concentrations needed for phase transition are directly related to valency of the interacting species. In the case of the actin regulatory protein, neuronal Wiskott-Aldrich Syndrome Protein (N-WASP) interacting with its established biological partners Nck and phosphorylated nephrin1, the phase transition corresponds to a sharp increase in activity toward the actin nucleation factor, Arp2/3 complex. The transition is governed by the degree of phosphorylation of nephrin, explaining how this property of the system can be controlled to regulatory effect by kinases. The widespread occurrence of multivalent systems suggests that phase transitions are likely used to spatially organize and biochemically regulate information throughout biology.

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, the RooFit package allows the user to perform complex data modeling and fitting while the RooStats library provides abstractions and implementations for advanced statistical tools. Multivariate classification methods based on machine learning techniques are available via the TMVA package. A central piece in these analysis tools are the histogram classes which provide binning of one-and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using onthe-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks -e.g. data mining in HEP -by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way. Antcheva et al. / Computer Physics Communications 180 (2009) [2499][2500][2501][2502][2503][2504][2505][2506][2507][2508][2509][2510][2511][2512] Program summary

The properties of dilute solutions of poly(oxy-1,4-phenyleneoxy-1,4-phenylenecarbonyl-l,4-phenylene) (PEEK) in strong acids such as HzS04 and HS03C1 have been investigated by static and dynamic light scattering, absorption spectroscopy, and viscometry. Chemical modification of the original polymer has been found to occur when it is dissolved in some acids. This modification has implications with respect to both the process of dissolution itself and the solution properties observed.

Fluorescence photobleaching recovery (FPR) was used to measure the probe self-diffusion coefficients, D" of eight labeled dextrans with different molecular weights in aqueous solutions of the semirigid polymer (hydroxypropyl)cellulose (HPC). With added measurements of free dye and a single dye-labeled polymeric latex, the probe hydrodynamic radius, Ri,, spanned 5-551 A. For dextrans, the dependence of D" upon M obeys D, ~M--5 with /3 ~V2 in water. In the most concentrated HPC solution studied, @ 1. Small probes show strong deviations from the Stokes-Einstein relation. The effect was less severe as probe size increased. Most of the diffusion data fit the Langevin-Rondelez equation,where Do and ijo are respectively the diffusion coefficient in and viscosity of pure solvent, £ is the correlation length, and b a parameter. Exceptions to the Langevin-Rondelez relation were found for small probes in dilute solution CRh/l < 0.1). The data are also interpreted using the hydrodynamic scaling model advanced by Phillies and a cylindrical cell model developed by Johansson and co-workers. The effect of the molecular weight of the HPC matrix upon the diffusion of variously sized probes was also studied; small probes were relatively insensitive to matrix molecular weight, but the diffusion of larger probes did depend on the molecular weight of the HPC. Analytical applications of FPR are considered. HPC selectively retards dextrans according to molecular weight, the effect becoming stronger as HPC concentration is increased. The FPR signal for a mixture of two dextrans with different molecular weights can be markedly biexponential in HPC solution, even if it is not pure water. This expansion of the recovery time distribution by the polymer matrix suggests that FPR in a polymer matrix can serve as a medium-resolution method to detect macromolecular polydispersity, similar in spirit to analytical gel electrophoresis but applicable to uncharged polymers, suitably labeled. A preliminary evaluation is promising.

Amine-functionalized colloidal silica finds use in a variety of applications and fundamental investigations. To explore convenient methods of synthesis and characterization of research-grade materials in relatively large quantities, nearly monodisperse colloidal silica particles were prepared by base-catalyzed hydrolysis of reagent-grade tetraethyl orthosilicate (TEOS) without the traditional time- and energy-consuming distillation step. Radius was varied reliably from 30 to 125 nm by changing the water/TEOS ratio. Asymmetric flow field flow fractionation (AF4) methods with online light scattering detection proved effective in assessing the uniformity of the various preparations. Even highly uniform commercial standards were resolved by AF4. The surface of the colloidal silica was decorated with amino groups using (3-aminopropyl) trimethoxysilane and spacer methyl groups from methyl-trimethoxysilane. The surface density of amino groups was quantified spectrophotometrically after reaction with ninhydrin; the nature of this analysis avoids interference from sample turbidity. As an alternative to the ninhydrin test, an empirical relationship between surface density of amino groups and zeta potential at low pH was found. The size of the colloidal silica was predictably decreased by etching with HF; this method will be effective for some preparations, despite a modest reduction in size uniformity.