Parallel processing of large datasets from NanoLC-FTICR-MS measurements

A new approach for automatic parallel processing of large mass spectral datasets in a distributed computing environment is demonstrated to significantly decrease the total processing time. The implementation of this novel approach is described and evaluated for large nanoLC-FTICR-MS datasets. The speed benefits are determined by the network speed and file transfer protocols only and allow almost real-time analysis of complex data (e.g., a 3-gigabyte raw dataset is fully processed within 5 min). Key advantages of this approach are not limited to the improved analysis speed, but also include the improved flexibility, reproducibility, and the possibility to share and reuse the pre- and postprocessing strategies. The storage of all raw data combined with the massively parallel processing approach described here allows the scientist to reprocess data with a different set of parameters (e.g., apodization, calibration, noise reduction), as is recommended by the proteomics community. This approach of parallel processing was developed in the Virtual Laboratory for e-Science (VL-e), a science portal that aims at allowing access to users outside the computer research community. As such, this strategy can be applied to all types of serially acquired large mass spectral datasets such as LC-MS, LC-MS/MS, and high-resolution imaging MS results.     

On the Absence of Ferromagnetism in Typical 2D Ferromagnets

We consider the Ising systems in d dimensions with nearest-neighbor ferromagnetic interactions and long-range repulsive (antiferromagnetic) interactions that decay with power s of the distance. The physical context of such models is discussed; primarily this is d = 2 and s = 3 where, at long distances, genuine magnetic interactions between genuine magnetic dipoles are of this form. We prove that when the power of decay lies above d and does not exceed d + 1, then for all temperatures the spontaneous magnetization is zero. In contrast, we also show that for powers exceeding d + 1 (with d ≥ 2) magnetic order can occur.     

Labeled Nanoparticles Based on Pharmaceutical EUDRAGIT® S 100 Polymers

The pharmaceutically important polymer P(MAA–r–MMA)_1:2 (EUDRAGIT ^® S100) was investigated concerning its behavior to form nanoparticles via nanoprecipitation. The particles obtained were characterized regarding their size, shape, and characteristics using DLS, SEM, and AUC. Furthermore, the P(MAA–r–MMA)_1:2 copolymer was modified with different markers in order to achieve polymer‐based nanocarrier systems, which are detectable and may be useful for controlled drug delivery devices to monitor the drug pathways. The particles were labeled by physical entrapment as well as by covalent attachment of various markers, e.g., radicals, fluorescent‐, and near‐infrared dyes, to the polymer. Physical entrapment of radicals into the polymeric units was performed by co‐nanoprecipitation of P(MAA–r–MMA)_1:2 and a radical marker. By means of covalent binding of the markers to the polymer, a stable and more defined labeling of the particles was also performed, leading only to a low degree of modification of the pharmaceutical polymer. After nanoprecipitation, the resulting labeled particles were characterized by SEM and DLS, whereas their biocompatibility was proven by in vitro studies. In order to ensure the possibility of detection of the particles inside the body for drug delivery‐, sensor‐, and imaging applications, the polymeric carriers were also investigated by electron spin resonance, fluorescence, as well as near‐infrared spectroscopy.

     

Bioconjugation via azide-Staudinger ligation: an overview

Bioconjugation techniques using organic azides are compared in this critical review. A particular focus is on chemical ligation reactions and their application to chemical biology (179 references).     

Isoperimetry in Two‐Dimensional Percolation

We study isoperimetric sets, i.e., sets with minimal boundary for a prescribed volume, on the unique infinite connected component of supercritical bond percolation on the square lattice. In the limit of the volume tending to infinity, properly scaled isoperimetric sets are shown to converge (in the Hausdorff metric) to the solution of an isoperimetric problem in ?² with respect to a particular norm. As part of the proof we also show that the anchored isoperimetric profile as well as the Cheeger constant of the giant component in finite boxes scale to deterministic quantities. This settles a conjecture of Itai Benjamini for the square lattice. © 2015 Wiley Periodicals, Inc.     

Sharp asymptotic for the chemical distance in long‐range percolation

We consider instances of long‐range percolation on and , where points at distance r get connected by an edge with probability proportional to r^?s, for s ∈ (d,2d), and study the asymptotic of the graph‐theoretical (a.k.a. chemical) distance D(x,y) between x and y in the limit as |x ? y|→∞. For the model on we show that, in probability as |x|→∞, the distance D(0,x) is squeezed between two positive multiples of , where for γ: = s/(2d). For the model on we show that D(0,xr) is, in probability as r→∞ for any nonzero , asymptotic to for φ a positive, continuous (deterministic) function obeying φ(r^γ) = φ(r) for all r > 1. The proof of the asymptotic scaling is based on a subadditive argument along a continuum of doubly‐exponential sequences of scales. The results strengthen considerably the conclusions obtained earlier by the first author. Still, significant open questions remain.     

Quantum Spin Systems at Positive Temperature

We develop a novel approach to phase transitions in quantum spin models based on a relation to their classical counterparts. Explicitly, we show that whenever chessboard estimates can be used to prove a phase transition in the classical model, the corresponding quantum model will have a similar phase transition, provided the inverse temperature β and the magnitude of the quantum spins satisfy . From the quantum system we require that it is reflection positive and that it has a meaningful classical limit; the core technical estimate may be described as an extension of the Berezin-Lieb inequalities down to the level of matrix elements. The general theory is applied to prove phase transitions in various quantum spin systems with . The most notable examples are the quantum orbital-compass model on and the quantum 120-degree model on which are shown to exhibit symmetry breaking at low-temperatures despite the infinite degeneracy of their (classical) ground state.     

Graph diameter in long‐range percolation

We study the asymptotic growth of the diameter of a graph obtained by adding sparse “long” edges to a square box in ${\mathbb Z}^dWe study the asymptotic growth of the diameter of a graph obtained by adding sparse “long” edges to a square box in ${\mathbb Z}^d$. We focus on the cases when an edge between x and y is added with probability decaying with the Euclidean distance as |x ? y|^?s+o(1) when |x ? y| → ∞. For s ∈ (d, 2d) we show that the graph diameter for the graph reduced to a box of side L scales like (log L)^Δ+o(1) where Δ^?1 := log₂(2d/s). In particular, the diameter grows about as fast as the typical graph distance between two vertices at distance L. We also show that a ball of radius r in the intrinsic metric on the (infinite) graph will roughly coincide with a ball of radius exp{r^1/Δ+o(1)} in the Euclidean metric. © 2010 Wiley Periodicals, Inc. Random Struct. Alg., 39, 210‐227, 2011     

A Central Limit Theorem for the Effective Conductance: Linear Boundary Data and Small Ellipticity Contrasts

Given a resistor network on ${\mathbb{Z}^d}$ with nearest-neighbor conductances, the effective conductance in a finite set with a given boundary condition is the minimum of the Dirichlet energy over functions with the prescribed boundary values. For shift-ergodic conductances, linear (Dirichlet) boundary conditions and square boxes, the effective conductance scaled by the volume of the box converges to a deterministic limit as the box-size tends to infinity. Here we prove that, for i.i.d. conductances with a small ellipticity contrast, also a (non-degenerate) central limit theorem holds. The proof is based on the corrector method and the Martingale Central Limit Theorem; a key integrability condition is furnished by the Meyers estimate. More general domains, boundary conditions and ellipticity contrasts will be addressed in a subsequent paper.