563 research outputs found
Electrostatic Interactions in Strongly-Coupled Soft Matter
Charged soft-matter systems--such as colloidal dispersions and charged
polymers--are dominated by attractive forces between constituent like-charged
particles when neutralizing counterions of high charge valency are introduced.
Such counter-intuitive effects indicate strong electrostatic coupling between
like-charged particles, which essentially results from electrostatic
correlations among counterions residing near particle surfaces. In this paper,
the attraction mechanism and the structure of counterionic correlations are
discussed in the limit of strong coupling based on recent numerical and
analytical investigations and for various geometries (planar, spherical and
cylindrical) of charged objects.Comment: 26 pages, 13 figure
A European Pathogenic Microorganism Proteome Database: Construction and Maintenance
A relational database structure based on MS-Access and MySQL to store and manage
proteomics data was established. This system may be used to publish two-dimensional
electrophoretic proteomics data, and also may be accessed by external users who want to
compare their own data with those in the databases. The maintenance of the database is
managed centrally. The producers of proteomics data do not need to construct a database
themselves. Users can introduce mass spectra into the database, which allows the searching
of peptide mass fingerprints against their own protein sequence databases. The first release
published in January 2002 contains data from Mycobacterium tuberculosis, Helicobacter
pylori, Borrelia garinii, Francisella tularensis, Chlamydia pneumoniae, Mycoplasma pneumoniae,
Jurkat T-cells and mouse mammary gland projects (http://www.mpiib-berlin.
mpg.de/2D-PAGE/)
Mapping the spin-dependent electron reflectivity of Fe and Co ferromagnetic thin films
Spin Polarized Low Energy Electron Microscopy is used as a spin dependent
spectroscopic probe to study the spin dependent specular reflection of a
polarized electron beam from two different magnetic thin film systems:
Fe/W(110) and Co/W(110). The reflectivity and spin-dependent
exchange-scattering asymmetry are studied as a function of electron kinetic
energy and film thickness, as well as the time dependence. The largest value of
the figure of merit for spin polarimetry is observed for a 5 monolayer thick
film of Co/W(110) at an electron kinetic energy of 2eV. This value is 2 orders
of magnitude higher than previously obtained with state of the art Mini-Mott
polarimeter. We discuss implications of our results for the development of an
electron-spin-polarimeter using the exchange-interaction at low energy.Comment: 5 pages, 4 figure
Depletion induced isotropic-isotropic phase separation in suspensions of rod-like colloids
When non-adsorbing polymers are added to an isotropic suspension of rod-like
colloids, the colloids effectively attract each other via depletion forces. We
performed Monte Carlo simulations to study the phase diagram of such
rod-polymer mixture. The colloidal rods were modelled as hard spherocylinders;
the polymers were described as spheres of the same diameter as the rods. The
polymers may overlap with no energy cost, while overlap of polymers and rods is
forbidden.
Large amounts of depletant cause phase separation of the mixture. We
estimated the phase boundaries of isotropic-isotropic coexistence both, in the
bulk and in confinement. To determine the phase boundaries we applied the grand
canonical ensemble using successive umbrella sampling [J. Chem. Phys. 120,
10925 (2004)], and we performed a finite-size scaling analysis to estimate the
location of the critical point. The results are compared with predictions of
the free volume theory developed by Lekkerkerker and Stroobants [Nuovo Cimento
D 16, 949 (1994)]. We also give estimates for the interfacial tension between
the coexisting isotropic phases and analyse its power-law behaviour on approach
of the critical point
A European focus on proteomics
A report on the First International Symposium of the Austrian Proteomics Platform, Seefeld, Austria, 26-29 January 2004
Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis
Identification of protein translation start sites is largely a bioinformatics exercise, with relatively few confirmed by N-terminal sequencing. Translation start site determination is critical for defining both the protein sequence and the upstream DNA which may contain regulatory motifs. It is demonstrated here that translation start sites can be determined during routine protein identification, using MALDI-MS and MS/MS data to select the correct N-terminal sequence from a list of alternatives generated in silico. Applying the method to 13 proteins from Mycobacterium tuberculosis, 11 predicted translational start sites were confirmed, and two reassigned. The authors suggest that these data (be they confirmation or reassignments) are important for the annotation of both this genome and those of organisms with related genes. It was also shown that N-acetylation, reported to be rare in prokaryotes, was present in three of the 13 proteins (23 %), suggesting that in the mycobacteria this modification may be common, and an important regulator of protein function, although more proteins need to be analysed. This method can be performed with little or no additional experimental work during proteomics investigations
The speciation of the proteome
<p>Abstract</p> <p>Introduction</p> <p>In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function.</p> <p>Discussion</p> <p>Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function.</p> <p>Conclusion</p> <p>To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today.</p
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