Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com      

Electrospray as a tool for drug micro- and nanoparticle patterning

Carbamazepine (CBZ) microparticles of different sizes and shapes, including spheres, q-tips, elongated spheres, and tear-shaped particles, were formed by electrospraying solutions of different CBZ concentrations. The particle characteristics were determined by the interplay between jet formation, droplet breakup, solvent evaporation, and eventual particle solidification. The average particle size increased with increasing CBZ concentration, with particles of different shapes being observed for different CBZ concentrations. The cascade of sizes and shapes observed was interpreted in terms of Rayleigh instability theory as applied to charged jets and droplets, with the final sizes depending upon the time needed to evaporate the solvent sufficiently for CBZ to solidify; the lower the initial concentration of CBZ, the smaller the final droplets/particles that are formed.     

Particle transport and acceleration in a time-varying electromagnetic field with a multi-scale structure

We present the results of a numerical study of particle transport and acceleration by an ensemble of electromagnetic waves with a multi-scale spatio-temporal structure. We explore the dependence of acceleration and transport on the properties of turbulence. We found that an initially Maxwellian distribution of particle velocities evolves into a heavy-tailed distribution, which resembles the ubiquitous kappa-distribution, often used in non-thermal plasma phenomenology. The results of this study may be used to explain plasma heating and energization in turbulent current sheets such as the current sheets often observed in the Earth's magnetotail and discussed in relation to solar corona.     

Microscopic origin of low-frequency flux noise in josephson circuits

We analyze the data and discuss their implications for the microscopic origin of the low-frequency flux noise in superconducting circuits. We argue that this noise is produced by spins at superconductor insulator boundary whose dynamics is due to RKKY interaction. We show that this mechanism explains size independence of the noise, different frequency dependences of the spectra reported in large and small SQUIDs, and gives the correct intensity for realistic parameters.     

Analytical estimates of the contact zone area for a pressurized flat-oval cylindrical shell placed between two parallel rigid plates

The paper presents an analytical estimate for an area of contact for a thin-walled noncircular cylindrical shell placed between two parallel rigid plates with an initial gap and then pressurized hydrostatically up to the contact appearance. The Euler–Bernoulli beam is used to model the shell deformation under the plane strain assumption. Such a simplification allows one to obtain the simplest closed-form estimate for the contact zone area. The first approximation is obtained neglecting the deformation of the curvilinear segments of the flat oval shell cross-section while the solution for the curved beam loaded by the homogeneous pressure is considered as a second approximation. The accuracy of the proposed analytical solutions as well as their usability in the preliminary design of thin-walled elements of various cooling systems is validated by the results of both numerical simulations and experimental tests.     

Synthesis and conformational analysis of a small meta‐cyclophane,bis(5‐carbomethoxy‐1,3‐phenylene)‐14‐crown‐4

A small cyclophane, bis(5‐carbometh‐oxy‐1,3‐phenylene)‐14‐crown‐4 (BCMP14C4, 3 ) and its diacid, bis(5‐carboxy‐1,3‐phenylene)‐14‐crown‐4 ( 4 ), were synthesized and characterized. The solid‐state molecular structures of 3 and 4 were determined by X‐ray crystallography as ladder or stepped conformations in which the two aromatic rings are antiparallel to each other without overlap and the ethylene tethers both take trans‐conformations. Diester 3 is formed in the lowest cyclization yield (under the same reaction conditions) and exhibits the highest melting point compared to its larger ring (20‐, 26‐ and 32‐membered) analogs. In CD₂Cl₂ solution, diester 3 exists predominantly as a nonplanar gauche–gauche structure as deduced by H NMR studies. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:48–54, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20393     

Synthesis of “living” chains of polyvinylpyridine and their application to the construction of homo- and hybrid polymer with complex architecture

Experimental conditions ensuring the formation of living poly(2- and 4-vinyl pyridine) chains in the vinyl pyridine - allyl derivatives of chromium, molybdenum and tungsten systems are described. Variation of the reagents nature, polarity of the solvent permits to obtain polymers differing in their structural and molecular parameters. Synthesized polymers contain block and graft sequences, as well as macrocyclic fragments. Living chains under consideration were applied for polymerization of different monomers. Hybrid polymers obtained by this way were studied in detail by the same methods as the homopolymers.     

Tensor rank bounds and explicit QTT representations for the inverses of circulant matrices

In this paper, we are concerned with the inversion of circulant matrices and their quantized tensor-train (QTT) structure. In particular, we show that the inverse of a complex circulant matrix $A$, generated by the first column of the form ${(a_0,\dots ,a_{m-1},0,\dots ,0,a_{-n},\dots ,a_{-1})}^{\top }$ admits a QTT representation with the QTT ranks bounded by $(m+n)$. Under certain assumptions on the entries of $A$, we also derive an explicit QTT representation of $A^{-1}$. The latter can be used, for instance, to overcome stability issues arising when numerically solving differential equations with periodic boundary conditions in the QTT format.