Optical fluid and biomolecule transport with thermal fields

A long standing goal is the direct optical control of biomolecules and water for applications ranging from microfluidics over biomolecule detection to non-equilibrium biophysics. Thermal forces originating from optically applied, dynamic microscale temperature gradients have shown to possess great potential to reach this goal. It was demonstrated that laser heating by a few Kelvin can generate and guide water flow on the micrometre scale in bulk fluid, gel matrices or ice without requiring any lithographic structuring. Biomolecules on the other hand can be transported by thermal gradients, a mechanism termed thermophoresis, thermal diffusion or Soret effect. This molecule transport is the subject of current research, however it can be used to both characterize biomolecules and to record binding curves of important biological binding reactions, even in their native matrix of blood serum. Interestingly, thermophoresis can be easily combined with the optothermal fluid control. As a result, molecule traps can be created in a variety of geometries, enabling the trapping of small biomolecules, like for example very short DNA molecules. The combination with DNA replication from thermal convection allows us to approach molecular evolution with concurrent replication and selection processes inside a single chamber: replication is driven by thermal convection and selection by the concurrent accumulation of the DNA molecules. From the short but intense history of applying thermal fields to control fluid flow and biological molecules, we infer that many unexpected and highly synergistic effects and applications are likely to be explored in the future

Studies in t)le Sphingolipids Series. XII. Structure of the Cerebrin Anhydro Base of Yeast (C20 - Phytosphingosine Anhydro Base)

It was confirmed that the cerebrin anhydro base from yeast (Ila) isolated according to the procedure established by Reindel et ai.2 ,a h as a C20 -structure rather than C1 s-structure as one might conclude erroneously by simple comparison of physical constants \u27C/f both bases. The tetrahydrofuran structure was a lso d emonstrated by means of the IR spectroscopy. For this purpose following new compounds derived from C20 -anhydro b ase were prepared: N,0-diacetyl (lib), N,0-ditosyl (Ile), 0-acetyl-N-benzoyl (!Id) and Nphthaloyl derivative (III);· in addition, 2-hexadecyl-3 ,4-dihydroxytetrahydrofuran(IV) - a deamination product of the base was described

Strain and structure driven complex magnetic ordering of a CoO overlayer on Ir(100)

We have investigated the magnetic ordering in the ultrathin c(10$\times$2) CoO(111) film supported on Ir(100) on the basis of ab-initio calculations. We find a close relationship between the local structural properties of the oxide film and the induced magnetic order, leading to alternating ferromagnetically and anti-ferromagnetically ordered segments. While the local magnetic order is directly related to the geometric position of the Co atoms, the mismatch between the CoO film and the Ir substrate leads to a complex long-range order of the oxide.Comment: 5 pages, 4 figure

Mol. Cell. Proteomics

Post-translational modification of proteins by ubiquitin is a fundamentally important regulatory mechanism. However, proteome-wide analysis of endogenous ubiquitylation remains a challenging task, and almost always has relied on cells expressing affinity tagged ubiquitin. Here we combine single-step immunoenrichment of ubiquitylated peptides with peptide fractionation and high-resolution mass spectrometry to investigate endogenous ubiquitylation sites. We precisely map 11,054 endogenous putative ubiquitylation sites (diglycine-modified lysines) on 4,273 human proteins. The presented data set covers 67% of the known ubiquitylation sites and contains 10,254 novel sites on proteins with diverse cellular functions including cell signaling, receptor endocytosis, DNA replication, DNA damage repair, and cell cycle progression. Our method enables site-specific quantification of ubiquitylation in response to cellular perturbations and is applicable to any cell type or tissue. Global quantification of ubiquitylation in cells treated with the proteasome inhibitor MG-132 discovers sites that are involved in proteasomal degradation, and suggests a nonproteasomal function for almost half of all sites. Surprisingly, ubiquitylation of about 15% of sites decreased more than twofold within four hours of MG-132 treatment, showing that inhibition of proteasomal function can dramatically reduce ubiquitylation on many sites with non-proteasomal functions. Comparison of ubiquitylation sites with acetylation sites reveals an extensive overlap between the lysine residues targeted by these two modifications. However, the crosstalk between these two post-translational modifications is significantly less frequent on sites that show increased ubiquitylation upon proteasome inhibition. Taken together, we report the largest site-specific ubiquitylation dataset in human cells, and for the first time demonstrate proteome-wide, site-specific quantification of endogenous putative ubiquitylation sites

Adlayer core-level shifts of random metal overlayers on transition-metal substrates

We calculate the difference of the ionization energies of a core-electron of a surface alloy, i.e., a B-atom in a A_(1-x) B_x overlayer on a fcc-B(001)-substrate, and a core-electron of the clean fcc-B(001) surface using density-functional-theory. We analyze the initial-state contributions and the screening effects induced by the core hole, and study the influence of the alloy composition for a number of noble metal-transition metal systems. Data are presented for Cu_(1-x)Pd_x/Pd(001), Ag_(1-x) Pd_x/Pd(001), Pd_(1-x) Cu_x/Cu(001), and Pd_(1-x) Ag_x/Ag(001), changing x from 0 to 100 %. Our analysis clearly indicates the importance of final-state screening effects for the interpretation of measured core-level shifts. Calculated deviations from the initial-state trends are explained in terms of the change of inter- and intra-atomic screening upon alloying. A possible role of alloying on the chemical reactivity of metal surfaces is discussed.Comment: 4 pages, 2 figures, Phys. Rev. Letters, to appear in Feb. 199

Potential, core-level and d band shifts at transition metal surfaces

We have extended the validity of the correlation between the surface 3d-core-level shift (SCLS) and the surface d band shift (SDBS) to the entire 4d transition metal series and to the neighboring elements Sr and Ag via accurate first-principles calculations. We find that the correlation is quasilinear and robust with respect to the differencies both between initial and final-state calculations of the SCLS's and two distinct measures of the SDBS's. We show that despite the complex spatial dependence of the surface potential shift (SPS) and the location of the 3d and 4d orbitals in different regions of space, the correlation exists because the sampling of the SPS by the 3d and 4d orbitals remains similar. We show further that the sign change of the SCLS's across the transition series does indeed arise from the d band-narrowing mechanism previously proposed. However, while in the heavier transition metals the predicted increase of d electrons in the surface layer relative to the bulk arises primarily from transfers from s and p states to d states within the surface layer, in the lighter transition metals the predicted decrease of surface d electrons arises primarily from flow out into the vacuum.Comment: RevTex, 22 pages, 5 figures in uufiles form, to appear in Phys.Rev.

Exhaustive generation of kk-critical H\mathcal H-free graphs

We describe an algorithm for generating all $k$-critical $\mathcal H$-free graphs, based on a method of Ho\`{a}ng et al. Using this algorithm, we prove that there are only finitely many $4$-critical $(P_7,C_k)$-free graphs, for both $k=4$ and $k=5$. We also show that there are only finitely many $4$-critical graphs $(P_8,C_4)$-free graphs. For each case of these cases we also give the complete lists of critical graphs and vertex-critical graphs. These results generalize previous work by Hell and Huang, and yield certifying algorithms for the $3$-colorability problem in the respective classes. Moreover, we prove that for every $t$, the class of 4-critical planar $P_t$-free graphs is finite. We also determine all 27 4-critical planar $(P_7,C_6)$-free graphs. We also prove that every $P_{10}$-free graph of girth at least five is 3-colorable, and determine the smallest 4-chromatic $P_{12}$-free graph of girth five. Moreover, we show that every $P_{13}$-free graph of girth at least six and every $P_{16}$-free graph of girth at least seven is 3-colorable. This strengthens results of Golovach et al.Comment: 17 pages, improved girth results. arXiv admin note: text overlap with arXiv:1504.0697

Photon pressure induced test mass deformation in gravitational-wave detectors

A widely used assumption within the gravitational-wave community has so far been that a test mass acts like a rigid body for frequencies in the detection band, i.e. for frequencies far below the first internal resonance. In this article we demonstrate that localized forces, applied for example by a photon pressure actuator, can result in a non-negligible elastic deformation of the test masses. For a photon pressure actuator setup used in the gravitational wave detector GEO600 we measured that this effect modifies the standard response function by 10% at 1 kHz and about 100% at 2.5 kHz

Analysis of OPM potentials for multiplet states of 3d transition metal atoms

We apply the optimized effective potential method (OPM) to the multiplet energies of the 3d$^n$ transition metal atoms, where the orbital dependence of the energy functional with respect to orbital wave function is the single-configuration HF form. We find that the calculated OPM exchange potential can be represented by the following two forms. Firstly, the difference between OPM exchange potentials of the multiplet states can be approximated by the linear combination of the potentials derived from the Slater integrals $F^2({\rm 3d,3d})$ and $F^4({\rm 3d,3d})$ for the average energy of the configuration. Secondly, the OPM exchange potential can be expressed as the linear combination of the OPM exchange potentials of the single determinants.Comment: 15 pages, 6 figures, to be published in J. Phys.