Multiple time scales in diffraction measurements of diffusive surface relaxation

We grew SrTiO3 on SrTiO3(001) by pulsed laser deposition, using x-ray scattering to monitor the growth in real time. The time-resolved small-angle scattering exhibits a well-defined length scale associated with the spacing between unit-cell high surface features. This length scale imposes a discrete spectrum of Fourier components and rate constants upon the diffusion equation solution, evident in multiple exponential relaxation of the "anti-Bragg" diffracted intensity. An Arrhenius analysis of measured rate constants confirms that they originate from a single activation energy.     

Microfluidic assembly of homogeneous and Janus colloid-filled hydrogel granules

The microfluidic assembly of colloid-filled hydrogel granules of varying shape and composition is described. First, drops are formed by shearing a concentrated colloidal microsphere-acrylamide suspension in a continuous oil phase using a sheath-flow device. Both homogeneous and Janus (hemispherically distinct) spheres and disks are produced by confining the assembled drops in microchannels of varying geometry. Next, photopolymerization is carried out shortly after drop breakup to preserve their morphology. Representative wet and dried granules are characterized using fluorescence and scanning electron microscopy, respectively. Our approach offers a facile route for assembling colloid-filled hydrogel granules with controlled shape and composition.     

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide-MHC binding affinity. The ISC-PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide-MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms--q2, SEP, and NC--ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).     

Detection and Analysis of Low‐Abundance Cell‐Surface Biomarkers Using Enzymatic Amplification in Microfluidic Droplets

Finding the few : Cell‐surface proteins are useful disease biomarkers, but current high‐throughput methods are limited to detecting cells expressing more than several hundred proteins. Enzymatic amplification in microfluidic droplets (see picture) is a high‐throughput method for detection and analysis of cell‐surface biomarkers expressed at very low levels on individual human cells. Droplet optical labels allow concurrent analysis of several samples.

     

A Luminescent Microporous Metal–Organic Framework for the Fast and Reversible Detection of High Explosives

Sensors and sensitivity : A highly luminescent microporous metal–organic framework, [Zn₂(bpdc)₂(bpee)] (bpdc=4,4′‐biphenyldicarboxylate; bpee=1,2‐bipyridylethene), is capable of very fast and reversible detection of the vapors of the nitroaromatic explosive 2,4‐dinitrotoluene and the plastic explosive taggant 2,3‐dimethyl‐2,3‐dinitrobutane, through redox fluorescence quenching with unprecedented sensitivity (see spectra).

     

Adaptive numerical algorithms in space weather modeling

Space weather describes the various processes in the Sun–Earth system that present danger to human health and technology. The goal of space weather forecasting is to provide an opportunity to mitigate these negative effects. Physics-based space weather modeling is characterized by disparate temporal and spatial scales as well as by different relevant physics in different domains. A multi-physics system can be modeled by a software framework comprising several components. Each component corresponds to a physics domain, and each component is represented by one or more numerical models. The publicly available Space Weather Modeling Framework (SWMF) can execute and couple together several components distributed over a parallel machine in a flexible and efficient manner. The framework also allows resolving disparate spatial and temporal scales with independent spatial and temporal discretizations in the various models.Several of the computationally most expensive domains of the framework are modeled by the Block-Adaptive Tree Solarwind Roe-type Upwind Scheme (BATS-R-US) code that can solve various forms of the magnetohydrodynamic (MHD) equations, including Hall, semi-relativistic, multi-species and multi-fluid MHD, anisotropic pressure, radiative transport and heat conduction. Modeling disparate scales within BATS-R-US is achieved by a block-adaptive mesh both in Cartesian and generalized coordinates. Most recently we have created a new core for BATS-R-US: the Block-Adaptive Tree Library (BATL) that provides a general toolkit for creating, load balancing and message passing in a 1, 2 or 3 dimensional block-adaptive grid. We describe the algorithms of BATL and demonstrate its efficiency and scaling properties for various problems.BATS-R-US uses several time-integration schemes to address multiple time-scales: explicit time stepping with fixed or local time steps, partially steady-state evolution, point-implicit, semi-implicit, explicit/implicit, and fully implicit numerical schemes. Depending on the application, we find that different time stepping methods are optimal. Several of the time integration schemes exploit the block-based granularity of the grid structure.The framework and the adaptive algorithms enable physics-based space weather modeling and even short-term forecasting.     

Revealing Excited-State Trajectories on Potential Energy Surfaces with Atomic Resolution in Real Time

Photoexcited molecular trajectories on potential energy surfaces (PESs) prior to thermalization are intimately connected to the photochemical reaction outcome. The excited-state trajectories of a diplatinum complex featuring photo-activated metal–metal σ-bond formation and associated Pt−Pt stretching motions were detected in real time using femtosecond wide-angle X-ray solution scattering. The observed motions correspond well with coherent vibrational wavepacket motions detected by femtosecond optical transient absorption. Two key coordinates for intersystem crossing have been identified, the Pt−Pt bond length and the orientation of the ligands coordinated with the platinum centers, along which the excited-state trajectories can be projected onto the calculated PESs of the excited states. This investigation has gleaned novel insight into electronic transitions occurring on the time scales of vibrational motions measured in real time, revealing ultrafast nonadiabatic or non-equilibrium processes along excited-state trajectories involving multiple excited-state PESs.     

The role of monomer in the chain transfer reaction in cobaloxime‐mediated free‐radical polymerization

The role of monomer in catalytic chain transfer polymerization was studied by determination of the chain transfer constants of the tetraphenyl derivative of cobaloxime boron fluoride (COPhBF) in methyl methacrylate at 60°C varying the monomer concentration instead of the COPhBF concentration as is common practice. Toluene and tert‐butyl acetate were used as diluents in these studies and it was found that the chain transfer constants obtained in the present studies were not significantly different from those observed in conventional experiments. These results suggest the absence of a direct participation of monomer molecules in the hydrogen abstraction step in catalytic chain transfer.