Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

Capture on High Curvature Region: Aggregation of Colloidal Particle Bound to Giant Phospholipid Vesicles

A very recent observation on the membrane mediated attraction and ordered aggregation of colloidal particles bound to giant phospholipid vesicles (I. Koltover, J. O. R\"{a}dler, C. R. Safinya, Phys. Rev. Lett. {\bf 82}, 1991(1999)) is investigated theoretically within the frame of Helfrich curvature elasticity theory of lipid bilayer fluid membrane. Since the concave or waist regions of the vesicle possess the highest local bending energy density, the aggregation of colloidal beads on these places can reduce the elastic energy in maximum. Our calculation shows that a bead in the concave region lowers its energy $\sim 20 k_B T$. For an axisymmetrical dumbbell vesicle, the local curvature energy density along the waist is equally of maximum, the beads can thus be distributed freely with varying separation distance.Comment: 12 pages, 2 figures. REVte

Wavelet transforms of meteorological parameters and gravity waves

The main purpose of this paper is to analyze some characteristics of gravity waves (GWs), and seasonal variations of atmospheric waves over Istanbul by using wavelet techniques. Daily radiosonda data of Istanbul in the troposphere and lower stratosphere (1000hPa-30hPa) between 1993 and 1997 have been considered. Wavelet analysis based on a computer simulation of data is generally close to the real data when Daubechies wavelet series are used. Daily, monthly, seasonal and annual variations of pressure heights, air temperature and deviations from mean values have been analyzed. Variations show the effects of gravity waves for different pressure levels in the troposphere. These waves lead to the meso-scale wave-form structures in spring, autumn and winter. As a result of this study, wavelet series and transforms for data construction, definition of some discontinuities and the local effects on the signal have been compared with the results of previous studies. The most similar structure between temperature, turbulence parameters and geo-potential height deviations has been defined at the 500-hPa pressure level

On bulk singularities in the random normal matrix model

We extend the method of rescaled Ward identities of Ameur-Kang-Makarov to study the distribution of eigenvalues close to a bulk singularity, i.e. a point in the interior of the droplet where the density of the classical equilibrium measure vanishes. We prove results to the effect that a certain "dominant part" of the Taylor expansion determines the microscopic properties near a bulk singularity. A description of the distribution is given in terms of a special entire function, which depends on the nature of the singularity (a Mittag-Leffler function in the case of a rotationally symmetric singularity).Comment: This version clarifies on the proof of Theorem

Large deformation of spherical vesicle studied by perturbation theory and Surface evolver

With tangent angle perturbation approach the axial symmetry deformation of a spherical vesicle in large under the pressure changes is studied by the elasticity theory of Helfrich spontaneous curvature model.Three main results in axial symmetry shape: biconcave shape, peanut shape, and one type of myelin are obtained. These axial symmetry morphology deformations are in agreement with those observed in lipsome experiments by dark-field light microscopy [Hotani, J. Mol. Biol. 178, (1984) 113] and in the red blood cell with two thin filaments (myelin) observed in living state (see, Bessis, Living Blood Cells and Their Ultrastructure, Springer-Verlag, 1973). Furthermore, the biconcave shape and peanut shape can be simulated with the help of a powerful software, Surface Evolver [Brakke, Exp. Math. 1, 141 (1992) 141], in which the spontaneous curvature can be easy taken into account.Comment: 16 pages, 6 EPS figures and 2 PS figure

Experimental entanglement verification and quantification via uncertainty relations

We report on experimental studies on entanglement quantification and verification based on uncertainty relations for systems consisting of two qubits. The new proposed measure is shown to be invariant under local unitary transformations, by which entanglement quantification is implemented for two-qubit pure states. The nonlocal uncertainty relations for two-qubit pure states are also used for entanglement verification which serves as a basic proposition and promise to be a good choice for verification of multipartite entanglement.Comment: 5 pages, 3 figures and 2 table

Numerical observation of non-axisymmetric vesicles in fluid membranes

By means of Surface Evolver (Exp. Math,1,141 1992), a software package of brute-force energy minimization over a triangulated surface developed by the geometry center of University of Minnesota, we have numerically searched the non-axisymmetric shapes under the Helfrich spontaneous curvature (SC) energy model. We show for the first time there are abundant mechanically stable non-axisymmetric vesicles in SC model, including regular ones with intrinsic geometric symmetry and complex irregular ones. We report in this paper several interesting shapes including a corniculate shape with six corns, a quadri-concave shape, a shape resembling sickle cells, and a shape resembling acanthocytes. As far as we know, these shapes have not been theoretically obtained by any curvature model before. In addition, the role of the spontaneous curvature in the formation of irregular crenated vesicles has been studied. The results shows a positive spontaneous curvature may be a necessary condition to keep an irregular crenated shape being mechanically stable.Comment: RevTex, 14 pages. A hard copy of 8 figures is available on reques

500 KW Rüzgar Türbini İçin Ana Şaft Tasarımı Ve Analizi

Konferans Bildirisi -- Teorik ve Uygulamalı Mekanik Türk Milli Komitesi, 2013Conference Paper -- Theoretical and Applied Mechanical Turkish National Committee, 2013Bu çalışmada, 500 kW güç üreten bir rüzgar türbinin ana şaftının tasarımı ve yapısal analizleri yapılmıştır. Ana şaftın boyutlandırılmasında yorulma kriterlerinin esas alınması gerekmektedir. Ana şaftın yorulmaya ait yük durumu ise literatürde bulunan ampirik formüller kullanılarak hesaplanmıştır. Yorulma analizlerinde şaftı çevrimsel yüklerle zorlayan rotor ağırlığının yanında rüzgar kesmesi ve kule blokaj etkisi vb. sebeplerle ortaya çıkan değişken eğilme momenti ve tork değerleri de hesaba katılmıştır. Ana şaftın kritik kesitlerindeki çap hesabı, ASME Eliptik yorulma kriteri kullanılarak sonsuz ömre göre yapılmıştır. Ana şaftın tasarımındaki kritik bölgeler şaftın yataklandığı bölge ve şaftın dişli kutusuna bağlandığı bölgedir. Ayrıca, kontrol amaçlı olarak Uluslararası Elektroteknik Komisyonu’nun (International Electrotechnical Commision) yayınlamış olduğu IEC 64100-1 standardında belirtilen yükleme şartları için ana şaftın statik analizleri ANSYS 14.5 sonlu elemanlar yazılımı kullanılarak gerçekleştirilmiştir. Şaftın sonlu eleman modeli SOLID185 elemanlar kullanılarak oluşturulmuştur. Ayrıca, ana şaft - göbek bağlantı elemanlarının analizi de bu çalışma kapsamında yapılmıştır. Sayısal ve analitik yöntemler kullanılarak elde edilen deformasyon ve gerilme sonuçları karşılaştırılmış ve iyi bir uyum olduğu görülmüştür.In this paper, the main shaft which is one of the important structural parts for a 500 kW wind turbine has been designed. The fatigue criteria has been based on sizing the main shaft. The main shafts critic desing loads have been calculated by empirical formulas which are on the literatures. Oscillation moments of the torque and the flexural moments which is created by wind share, and effect of tower, etc. have been envisaged for analytical and numerical studies. In this study, the main shaft has been designed for infinite life using with ASME Elliptic criteria. There are two critic areas which are supported and connected to the gear box. In addition Iternational Electrotechnical Commision (IEC) 64100-1 standards have been based on the critic design load cases. The main shaft and the fasteners are modeled using the finite element method. The finite element model of the shaft is designed using with SOLID185 elements. Its static analysis have been achieved with using ANSYS 14.5 software. Also a comparison of two different approximations have been mentioned in this paper. The values of analitic and numerical of deplacement and stress are compared each