On the codimension growth of almost nilpotent Lie algebras

We study codimension growth of infinite dimensional Lie algebras over a field of characteristic zero. We prove that if a Lie algebra L is an extension of a nilpotent algebra by a finite dimensional semisimple algebra then the PI-exponent of L exists and is a positive integer.     

On 2-Systoles of Hyperbolic 3-Manifolds

We investigate the geometry of π ₁-injective surfaces in closed hyperbolic 3-manifolds. First we prove that for any ${\epsilon > 0}$ , if the manifold M has sufficiently large systole sys₁(M), the genus of any such surface in M is bounded below by ${{\rm exp}((\frac{1}{2} - \epsilon){\rm sys}_1(M))}$ . Using this result we show, in particular, that for congruence covers M _i → M of a compact arithmetic hyperbolic 3-manifold we have: (a) the minimal genus of π ₁-injective surfaces satisfies ${{\rm log} \, {\rm sysg}(M_i) \gtrsim \frac{1}{3} {\rm log} \, {\rm vol}(M_i) ; (b)}$ there exist such sequences with the ratio Heegard ${{\rm genus}(M_i)/{\rm sysg}(M_i) \gtrsim {\rm vol}(M_i)^{1/2}}$ ; and (c) under some additional assumptions π ₁(M _i ) is k-free with ${{\rm log} \, k \gtrsim \frac{1}{3}{\rm sys}_1(M_i)}$ . The latter resolves a special case of a conjecture of Gromov.     

Conformationally locked chromophores as models of excited-state proton transfer in fluorescent proteins

Members of the green fluorescent protein (GFP) family form chromophores by modifications of three internal amino acid residues. Previously, many key characteristics of chromophores were studied using model compounds. However, no studies of intermolecular excited-state proton transfer (ESPT) with GFP-like synthetic chromophores have been performed because they either are nonfluorescent or lack an ionizable OH group. In this paper we report the synthesis and photochemical study of two highly fluorescent GFP chromophore analogues: p-HOBDI-BF2 and p-HOPyDI:Zn. Among known fluorescent compounds, p-HOBDI-BF(2) is the closest analogue of the native GFP chromophore. These irrreversibly (p-HOBDI-BF(2)) and reversibly (p-HOPyDI:Zn) locked compounds are the first examples of fully planar GFP chromophores, in which photoisomerization-induced deactivation is suppressed and protolytic photodissociation is observed. The photophysical behavior of p-HOBDI-BF2 and p-HOPyDI:Zn (excited state pK(a)'s, solvatochromism, kinetics, and thermodynamics of proton transfer) reveals their high photoacidity, which makes them good models of intermolecular ESPT in fluorescent proteins. Moreover, p-HOPyDI:Zn is a first example of "super" photoacidity in metal-organic complexes.     

Universal behavior in the scattering of heavy, weakly interacting dark matter on nuclear targets

Particles that are heavy compared to the electroweak scale (M?mW), and that are charged under electroweak SU(2) gauge interactions display universal properties such as a characteristic fine structure in the mass spectrum induced by electroweak symmetry breaking, and an approximately universal cross section for scattering on nuclear targets. The heavy particle effective theory framework is developed to compute these properties. As illustration, the spin independent cross section for low-velocity scattering on a nucleon is evaluated in the limit M?mW, including complete leading-order matching onto quark and gluon operators, renormalization analysis, and systematic treatment of perturbative and hadronic-input uncertainties.     

Tracking of Pacific walruses in the Chukchi Sea using a single hydrophone

The vocal repertoire of Pacific walruses includes underwater sound pulses referred to as knocks and bell-like calls. An extended acoustic monitoring program was performed in summer 2007 over a large region of the eastern Chukchi Sea using autonomous seabed-mounted acoustic recorders. Walrus knocks were identified in many of the recordings and most of these sounds included multiple bottom and surface reflected signals. This paper investigates the use of a localization technique based on relative multipath arrival times (RMATs) for potential behavior studies. First, knocks are detected using a semi-automated kurtosis-based algorithm. Then RMATs are matched to values predicted by a ray-tracing model. Walrus tracks with vertical and horizontal movements were obtained. The tracks included repeated dives between 4.0 m and 15.5 m depth and a deep dive to the sea bottom (53 m). Depths at which bell-like sounds are produced, average knock production rate and source levels estimates of the knocks were determined. Bell sounds were produced at all depths throughout the dives. Average knock production rates varied from 59 to 75 knocks/min. Average source level of the knocks was estimated to 177.6 ± 7.5 dB re 1 μPa peak @ 1 m.     

Laser welding of structural steels: Influence of the edge roughness level

Laser welding continues to become more extensively used in many industrial applications and in the last 10 years an increasing number of studies have examined ways to increase the efficiency of the process. This study investigates the influence of joint edge surface roughness on weld quality and penetration depth. The characteristics are investigated of welded samples of two low alloyed steels, S355 and St 3, of 20 mm thickness with various joint edge surface roughness levels in butt joint configuration. Welding was performed with different fiber lasers with a wavelength of 1070 nm at power levels from 10 to 15 kW. The absorption characteristics were evaluated at 10 kW power level using a calorimeter. There was a significant positive correlation between edge surface roughness level and the penetration depth. Optimum roughness levels to provide maximum penetration depth are presented. The highest penetration depth at power levels of 14 and 10 kW was achieved at R_a=6.3 μm.     

Thermodiffusion motion of electrically charged nanoparticles

The present work deals with experimental studies to examine the theoretical model of thermodiffusion of electrically charged nanoparticles. Three different ionic magnetic colloid samples have been synthesized and profoundly analyzed. The theoretical model is a classical one, based on the calculation of the temperature and the electric potential distribution around nanoparticles. The discrepancy between experimental data and theory turns out not to exceed 20%. We focus on applying different approximations between calculated electrical double layer in the theoretical model and experimental determination of the surface charge density of colloidal particles. We assume this is the main reason for obtained discrepancy.     

Limitation of predictive 2-D liquid chromatography in reducing the database search space in shotgun proteomics: in silico studies

A two-dimensional (2-D) liquid chromatography (LC) separation of complex peptide mixtures that combines a normal phase utilizing hydrophilic interactions and a reversed phase offers reportedly the highest level of 2-D LC orthogonality by providing an even spread of peptides across multiple LC fractions. Matching experimental peptide retention times to those predicted by empirical models describing chromatographic separation in each LC dimension leads to a significant reduction in a database search space. In this work, we calculated the retention times of tryptic peptides separated in the C18 reversed phase at different separation conditions (pH 2 and pH 10) and in TSK gel Amide-80 normal phase. We show that retention times calculated for different 2-D LC separation schemes utilizing these phases start to correlate once the mass range of peptides under analysis becomes progressively narrow. This effect is explained by high degree of correlation between retention coefficients in the considered phases.     

On the utility of predictive chromatography to complement mass spectrometry based intact protein identification

The amino acid sequence determines the individual protein three-dimensional structure and its functioning in an organism. Therefore, “reading” a protein sequence and determining its changes due to mutations or post-translational modifications is one of the objectives of proteomic experiments. The commonly utilized approach is gradient high-performance liquid chromatography (HPLC) in combination with tandem mass spectrometry. While serving as a way to simplify the protein mixture, the liquid chromatography may be an additional analytical tool providing complementary information about the protein structure. Previous attempts to develop “predictive” HPLC for large biomacromolecules were limited by empirically derived equations based purely on the adsorption mechanisms of the retention and applicable to relatively small polypeptide molecules. A mechanism of the large biomacromolecule retention in reversed-phase gradient HPLC was described recently in thermodynamics terms by the analytical model of liquid chromatography at critical conditions (BioLCCC). In this work, we applied the BioLCCC model to predict retention of the intact proteins as well as their large proteolytic peptides separated under different HPLC conditions. The specific aim of these proof-of-principle studies was to demonstrate the feasibility of using “predictive” HPLC as a complementary tool to support the analysis of identified intact proteins in top-down, middle-down, and/or targeted selected reaction monitoring (SRM)-based proteomic experiments.     

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.