A Development Environment for Visual Physics Analysis

The Visual Physics Analysis (VISPA) project integrates different aspects of physics analyses into a graphical development environment. It addresses the typical development cycle of (re-)designing, executing and verifying an analysis. The project provides an extendable plug-in mechanism and includes plug-ins for designing the analysis flow, for running the analysis on batch systems, and for browsing the data content. The corresponding plug-ins are based on an object-oriented toolkit for modular data analysis. We introduce the main concepts of the project, describe the technical realization and demonstrate the functionality in example applications

MALT1 Phosphorylation Controls Activation of T Lymphocytes and Survival of ABC-DLBCL Tumor Cells

The CARMA1/CARD11-BCL10-MALT1 (CBM) complex bridges T and B cell antigen receptor (TCR/BCR) ligation to MALT1 protease activation and canonical nuclear factor kappa B (NF-kappa B) signaling. Using unbiased mass spectrometry, we discover multiple serine phosphorylation sites in the MALT1 C terminus after T cell activation. Phospho-specific antibodies reveal that CBM-associated MALT1 is transiently hyper-phosphorylated upon TCR/CD28 co-stimulation. We identify a dual role for CK1 alpha as a kinase that is essential for CBM signalosome assembly as well as MALT1 phosphorylation. Although MALT1 phosphorylation is largely dispensable for protease activity, it fosters canonical NF-kappa B signaling in Jurkat and murine CD4 T cells. Moreover, constitutive MALT1 phosphorylation promotes survival of activated B cell-type diffuse large B cell lymphoma (ABC-DLBCL) cells addicted to chronic BCR signaling. Thus, MALT1 phosphorylation triggers optimal NF-kappa B activation in lymphocytes and survival of lymphoma cells

Statistical Mechanics of Canonical-Dissipative Systems and Applications to Swarm Dynamics

We develop the theory of canonical-dissipative systems, based on the assumption that both the conservative and the dissipative elements of the dynamics are determined by invariants of motion. In this case, known solutions for conservative systems can be used for an extension of the dynamics, which also includes elements such as the take-up/dissipation of energy. This way, a rather complex dynamics can be mapped to an analytically tractable model, while still covering important features of non-equilibrium systems. In our paper, this approach is used to derive a rather general swarm model that considers (a) the energetic conditions of swarming, i.e. for active motion, (b) interactions between the particles based on global couplings. We derive analytical expressions for the non-equilibrium velocity distribution and the mean squared displacement of the swarm. Further, we investigate the influence of different global couplings on the overall behavior of the swarm by means of particle-based computer simulations and compare them with the analytical estimations.Comment: 14 pages incl. 13 figures. v2: misprints in Eq. (40) corrected, ref. updated. For related work see also: http://summa.physik.hu-berlin.de/~frank/active.htm

Collective Dynamics of Deformable Self-Propelled Particles with Repulsive Interaction

We investigate dynamics of deformable self-propelled particles with a repulsive interaction whose magnitude depends on the relative direction of elongation of a pair of particles. A collective motion of the particles appears in two dimensions. However this ordered state becomes unstable when the particle density exceeds a certain critical threshold and the dynamics becomes disorder. We show by a mean field analysis that this novel transition characteristic to deformability occurs due to a saddle-node bifurcation.Comment: 4 pages, 6 figure

Dynamics of the Volterra-type integral and differentiation operators on generalized Fock spaces

[EN] Various dynamical properties of the differentiation and Volterra-type integral operators on generalized Fock spaces are studied. We show that the differentiation operator is always supercyclic on these spaces. We further characterize when it is hypercyclic, power bounded and uniformly mean ergodic. We prove that the operator satisfies the Ritt's resolvent condition if and only if it is power bounded and uniformly mean ergodic. Some similar results are obtained for the Volterra-type and Hardy integral operators.J. Bonet was partially supported by the research projects MTM2016-76647-P and GV Prometeo 2017/102 (Spain). M. Worku is supported by ISP project, Addis Ababa University, Ethiopia.Bonet Solves, JA.; Mengestie, T.; Worku, M. (2019). Dynamics of the Volterra-type integral and differentiation operators on generalized Fock spaces. Results in Mathematics. 74(4):1-15. https://doi.org/10.1007/s00025-019-1123-7S115744Abanin, A.V., Tien, P.T.: Differentiation and integration operators on weighted Banach spaces of holomorphic functions. Math. Nachr. 290(8–9), 1144–1162 (2017)Atzmon, A., Brive, B.: Surjectivity and invariant subspaces of differential operators on weighted Bergman spaces of entire functions, Bergman spaces and related topics in complex analysis, Contemp. Math., vol. 404, Amer. Math. Soc., Providence, RI, pp. 27–39 (2006)Bayart, F., Matheron, E.: Dynamics of Linear Operators, Cambridge Tracts in Math, vol. 179. Cambridge Univ. Press, Cambridge (2009)Bermúdez, T., Bonilla, A., Peris, A.: On hypercyclicity and supercyclicity criteria. Bull. Austral. Math. Soc. 70, 45–54 (2004)Beltrán, M.J.: Dynamics of differentiation and integration operators on weighted space of entire functions. Studia Math. 221, 35–60 (2014)Beltrán, M.J., Bonet, J., Fernández, C.: Classical operators on weighted Banach spaces of entire functions. Proc. Am. Math. Soc. 141, 4293–4303 (2013)Bès, J., Peris, A.: Hereditarily hypercyclic operators. J. Funct. Anal. 167, 94–112 (1999)Bonet, J.: Dynamics of the differentiation operator on weighted spaces of entire functions. Math. Z. 26, 649–657 (2009)Bonet, J.: The spectrum of Volterra operators on weighted Banach spaces of entire functions. Q. J. Math. 66, 799–807 (2015)Bonet, J., Bonilla, A.: Chaos of the differentiation operator on weighted Banach spaces of entire functions. Complex Anal. Oper. Theory 7, 33–42 (2013)Bonet, J., Taskinen, J.: A note about Volterra operators on weighted Banach spaces of entire functions. Math. Nachr. 288, 1216–1225 (2015)Constantin, O., Persson, A.-M.: The spectrum of Volterra-type integration operators on generalized Fock spaces. Bull. Lond. Math. Soc. 47, 958–963 (2015)Constantin, O., Peláez, J.-Á.: Integral operators, embedding theorems and a Littlewood–Paley formula on weighted Fock spaces. J. Geom. Anal. 26, 1109–1154 (2016)De La Rosa, M., Read, C.: A hypercyclic operator whose direct sum is not hypercyclic. J. Oper. Theory 61, 369–380 (2009)Dunford, N.: Spectral theory. I. Convergence to projections. Trans. Am. Math. Soc. 54, 185–217 (1943)Grosse-Erdmann, K.G., Peris Manguillot, A.: Linear Chaos. Springer, New York (2011)Harutyunyan, A., Lusky, W.: On the boundedness of the differentiation operator between weighted spaces of holomorphic functions. Studia Math. 184, 233–247 (2008)Krengel, U.: Ergodic Theorems. Walter de Gruyter, Berlin (1985)Lyubich, Yu.: Spectral localization, power boundedness and invariant subspaces under Ritt’s type condition. Studia Mathematica 143(2), 153–167 (1999)Mengestie, T.: A note on the differential operator on generalized Fock spaces. J. Math. Anal. Appl. 458(2), 937–948 (2018)Mengestie, T.: Spectral properties of Volterra-type integral operators on Fock–Sobolev spaces. J. Kor. Math. Soc. 54(6), 1801–1816 (2017)Mengestie, T.: On the spectrum of volterra-type integral operators on Fock–Sobolev spaces. Complex Anal. Oper. Theory 11(6), 1451–1461 (2017)Mengestie, T., Ueki, S.: Integral, differential and multiplication operators on weighted Fock spaces. Complex Anal. Oper. Theory 13, 935–95 (2019)Mengestie, T., Worku, M.: Isolated and essentially isolated Volterra-type integral operators on generalized Fock spaces. Integr. Transf. Spec. Funct. 30, 41–54 (2019)Nagy, B., Zemanek, J.A.: A resolvent condition implying power boundedness. Studia Math. 134, 143–151 (1999)Nevanlinna, O.: Convergence of iterations for linear equations. Lecture Notes in Mathematics. ETH Zürich, Birkhäuser, Basel (1993)Ritt, R.K.: A condition that $$\lim _{n\rightarrow \infty } n^{-1}T^n =0$$. Proc. Am. Math. Soc. 4, 898–899 (1953)Ueki, S.: Characterization for Fock-type space via higher order derivatives and its application. Complex Anal. Oper. Theory 8, 1475–1486 (2014)Yosida, K.: Functional Analysis. Springer, Berlin (1978)Yosida, K., Kakutani, S.: Operator-theoretical treatment of Marko’s process and mean ergodic theorem. Ann. Math. 42(1), 188–228 (1941

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

PMCID: PMC3410907This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Ionometric sensor for ammonium ions control in sewage waters

Цель работы заключалась в создании измерительного датчика для автоматизированного потенциометрического контроля содержания ионов аммония в проточных условиях. В результате исследования разработана конструкция электрода сравнения измерительного датчика, представляющая собой ионоселективный электрод, опущенный в буферную систему с катионитом. В работе представлен потенциометрический анализ модельных растворов ионов аммония, изучено мешающее влияние температуры, а также определена стабильность предложенной системы. The purpose of the work was to create a sensor for automated potentiometric monitoring of the ammonium ions content in flowing conditions. As a result of the study, the reference electrode design was developed. This is an ion-selective electrode lowered into a buffer system with cation exchanger. The work presents a potentiometric analysis of ammonium ions model solutions, the study of temperature interfering effect, and system's stability determination

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

Persistent Cell Motion in the Absence of External Signals: A Search Strategy for Eukaryotic Cells

Eukaryotic cells are large enough to detect signals and then orient to them by differentiating the signal strength across the length and breadth of the cell. Amoebae, fibroblasts, neutrophils and growth cones all behave in this way. Little is known however about cell motion and searching behavior in the absence of a signal. Is individual cell motion best characterized as a random walk? Do individual cells have a search strategy when they are beyond the range of the signal they would otherwise move toward? Here we ask if single, isolated, Dictyostelium and Polysphondylium amoebae bias their motion in the absence of external cues. We placed single well-isolated Dictyostelium and Polysphondylium cells on a nutrient-free agar surface and followed them at 10 sec intervals for ~10 hr, then analyzed their motion with respect to velocity, turning angle, persistence length, and persistence time, comparing the results to the expectation for a variety of different types of random motion. We find that amoeboid behavior is well described by a special kind of random motion: Amoebae show a long persistence time (~10 min) beyond which they start to lose their direction; they move forward in a zig-zag manner; and they make turns every 1-2 min on average. They bias their motion by remembering the last turn and turning away from it. Interpreting the motion as consisting of runs and turns, the duration of a run and the amplitude of a turn are both found to be exponentially distributed. We show that this behavior greatly improves their chances of finding a target relative to performing a random walk. We believe that other eukaryotic cells may employ a strategy similar to Dictyostelium when seeking conditions or signal sources not yet within range of their detection system.Comment: 15 pages, 11 figures, accepted for publication in PLOS On

Multi-Jet Event Rates in Deep Inelastic Scattering and Determination of the Strong Coupling Constant

Jet event rates in deep inelastic ep scattering at HERA are investigated applying the modified JADE jet algorithm. The analysis uses data taken with the H1 detector in 1994 and 1995. The data are corrected for detector and hadronization effects and then compared with perturbative QCD predictions using next-to-leading order calculations. The strong coupling constant alpha_S(M_Z^2) is determined evaluating the jet event rates. Values of alpha_S(Q^2) are extracted in four different bins of the negative squared momentum transfer~\qq in the range from 40 GeV2 to 4000 GeV2. A combined fit of the renormalization group equation to these several alpha_S(Q^2) values results in alpha_S(M_Z^2) = 0.117+-0.003(stat)+0.009-0.013(syst)+0.006(jet algorithm).Comment: 17 pages, 4 figures, 3 tables, this version to appear in Eur. Phys. J.; it replaces first posted hep-ex/9807019 which had incorrect figure 4