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Search Results: 1 - 10 of 308232 matches for " Johannes F. G. Vliegenthart "
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In silico Study on Sulfated and Non-Sulfated Carbohydrate Chains from Proteoglycans in Cnidaria and Interaction with Collagen  [PDF]
Thomas Eckert, Sabine St?tzel, Monika Burg-Roderfeld, Judith Sewing, Thomas Lütteke, Nikolay E. Nifantiev, Johannes F. G. Vliegenthart, Hans-Christian Siebert
Open Journal of Physical Chemistry (OJPC) , 2012, DOI: 10.4236/ojpc.2012.22017
Abstract: Proteoglycans and collagen molecules are interacting with each other thereby forming various connective tissues. The sulfation pattern of proteoglycans differs depending on the kind of tissue and/or the degree of maturation. Tissues from Cnidaria are suitable examples for exploration of the effects in relation to the presence and the absence of sulfate groups, when studying characteristic fragments of the long proteoglycan carbohydrate chains in silico. It has been described that a non-sulfated chondroitin appears as a scaffold in early morphogenesis of all nematocyst types in Hydra. On the other hand, sulfated glucosaminoglycans play an important role in various developmental processes of Cnidaria. In order to understand this biological phenomenon on a sub-molecular level we have analysed the structures of sulfated and non-sulfated proteoglycan carbohydrate chains as well as the structure of diverse collagen molecules with computational methods including quantum chemical calculations. The strong interactions between the sulfate groups of the carbohydrates moieties in proteoglycans and positively charged regions of collagen are essential in stabilizing various Cnidaria tissues but could hinder the nematocyst formation and its proper function. The results of our quantum chemical calculations show that the sulfation pattern has a significant effect on the conformation of chondroitin structures under study.
Kinetics of depletion interactions
G. A. Vliegenthart,P. Van Der Schoot
Physics , 2002, DOI: 10.1209/epl/i2003-00393-0
Abstract: Depletion interactions between colloidal particles dispersed in a fluid medium are effective interactions induced by the presence of other types of colloid. They are not instantaneous but build up in time. We show by means Brownian dynamics simulations that the fluctuations in the depletion force between two guest particles in a host dispersion of differently sized colloids do not decay exponentially with time, but show a power-law dependence. A simple scaling theory accurately describes the dependence of the magnitude of these fluctuations on time, on the inter-particle distance and on the size ratio of guest and host particles. The consequences in particular for the dynamics of colloidal mixtures are discussed.
The fractal structure of cellular automata on Abelian groups
Johannes Gütschow,Vincent Nesme,Reinhard F. Werner
Computer Science , 2010,
Abstract: It is well-known that the spacetime diagrams of some cellular automata have a fractal structure: for instance Pascal's triangle modulo 2 generates a Sierpinski triangle. Explaining the fractal structure of the spacetime diagrams of cellular automata is a much explored topic, but virtually all of the results revolve around a special class of automata, whose typical features include irreversibility, an alphabet with a ring structure, a global evolution that is a ring homomorphism, and a property known as (weakly) p-Fermat. The class of automata that we study in this article has none of these properties. Their cell structure is weaker, as it does not come with a multiplication, and they are far from being p-Fermat, even weakly. However, they do produce fractal spacetime diagrams, and we explain why and how.
Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger
Mayken W Wadman, Ronald P de Vries, Stefanie IC Kalkhove, Gerrit A Veldink, Johannes FG Vliegenthart
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-59
Abstract: The current study shows experimentally that A. niger produces the oxylipins 8,11-dihydroxy octadecadienoic acid (8,11-diHOD), 5,8-dihydroxy octadecadienoic acid (5,8-diHOD), lactonized 5,8-diHOD, 8-hydroxy octadecadienoic acid (8-HOD), 10-hydroxy octadecadienoic acid (10-HOD), small amounts of 8-hydroxy octadecamonoenoic acid (8-HOM), 9-hydroxy octadecadienoic acid (9-HOD) and 13-hydroxy octadecadienoic acid (13-HOD). Importantly, this study shows that the A. niger genome contains three putative dioxygenase genes, ppoA, ppoC and ppoD. Expression analysis confirmed that all three genes are indeed expressed under the conditions tested.A. niger produces the same oxylipins and has similar dioxygenase genes as A. nidulans. Their presence could point towards the existence of sexual reproduction in A. niger or a broader role for the gene products in physiology, than just sexual development.The fungal kingdom comprises a large group of organisms (estimated to consist of over 1.5 million species) with only 5% identified thus far. Fungal species can survive in virtually all biotopes on earth, as they have been identified in water and soil, and on plants and animals. Part of their success comes from the ability to use different reproductive strategies, which provide increased flexibility for diverse environmental requirements. Fungal species can produce sexual cells and/or asexual cells in distinct reproductive structures. Some fungi are able to reproduce both sexually and asexually depending on the circumstances, while others display one mode of reproduction, only. Sexual reproduction and recombination allows the repair of naturally occurring mutations and results in new genotypes and phenotypes that allow for natural selection [5]. On the other hand, asexual reproduction provides the ability to disperse numerous genetically identical mitospores, without the metabolic costs of sexual reproduction [5].Aspergillus niger is an ascomycetous fungus that is considered to reproduce
The Significance of Solutions Obtained from Ill-Posed Systems of Linear Equations Constituted by Synchrotron Radiation Based Anomalous Small-Angle X-Ray Scattering  [PDF]
Günter Johannes Goerigk
Advances in Linear Algebra & Matrix Theory (ALAMT) , 2018, DOI: 10.4236/alamt.2018.81007
Abstract: Synchrotron radiation based experimental techniques known as Anomalous Small-Angle X-ray Scattering (ASAXS) provide deep insight into the nanostructure of uncountable material systems in condensed matter research i.e. solid state physics, chemistry, engineering and life sciences thereby rendering the origin of the macroscopic functionalization of the various materials via correlation to its structural architecture on a nanometer length scale. The techniques constitute a system of linear equations, which can be treated by matrix theory. The study aims to analyze the significance of the solutions of the stated matrix equations by use of the so-called condition numbers first introduced by A. Turing, J. von Neumann and H. Goldstine. Special attention was given for the comparison with direct methods i.e. the Gaussian elimination method. The mathematical roots of ill-posed ASAXS equations preventing matrix inversion have been identified. In the framework of the theory of von Neumann and Goldstine the inversion of certain matrices constituted by ASAXS gradually becomes impossible caused by non-definiteness. In Turing’s theory which starts from more general prerequisites, the principal minors of the same matrices approach singularity thereby imposing large errors on inversion. In conclusion both theories recommend for extremely ill-posed ASAXS problems avoiding inversion and the use of direct methods for instance Gaussian elimination.
Intravenous magnesium in subarachnoid hemorrhage
Wilson F Abdo, Cornelia W Hoedemaekers, Johannes G van der Hoeven
Critical Care , 2011, DOI: 10.1186/cc10221
Abstract: First, the authors did not mention a (non-blinded) randomized placebo-controlled trial conducted by Akdemir and colleagues and published in 2009 [2]. Although this study would probably not pass Wong and colleagues' method of scrutiny, we believe that it should be mentioned alongside two other studies the authors described but did not include in the data analysis.Second, the study by Westermaier and colleagues [3] should not be included in the data analysis. These authors, in contrast to those of the other included studies in which magnesium was used as an add-on therapy, did not use nimodipine in any of the included patients. Wong and colleagues exclude the study by Schmid-Elsaesser and colleagues [4] because nimodipine was not used in the magnesium group but omit doing the same for the study by Westermaier and colleagues.Third, Figure 3 [1] shows that the number of control subjects in 'Veyna 2002' was 20. However, in that study, the outcome data in the control group were present for only 16 patients (4 of the 20 patients were withdrawn because study requirements were not met) [5]. Accordingly, the risk ratios in Figure 3 should be adjusted.Fourth, given Wong and colleagues' definition of delayed cerebral ischemia, we wonder why the studies of Veyna and colleagues [5], Muroi and colleagues [6], and their own study in 2006 [7] were not included in Figure 1[1]. In the study by Veyna and colleagues [5], the outcome measure 'clinical vasospasm' was defined as a 'new focal neurological deficit that could not be accounted for by other causes'. Although the time frame in which this was scored is not mentioned, this was during the patients' stay in the intensive care unit and therefore would be clinically relevant to include in Figure 1[1]. The same applies to the outcome measures 'delayed ischemic neurological deficit' in the study by Muroi and colleagues [6] and 'symptomatic vasospasm' in their own study in 2006 [7].George KC Wong and Wai S PoonWe thank Abdo and colleague
Levantilides A and B, 20-Membered Macrolides from a Micromonospora Strain Isolated from the Mediterranean Deep Sea Sediment
Andrea G?rtner,Birgit Ohlendorf,Dirk Schulz,Heidi Zinecker,Jutta Wiese,Johannes F. Imhoff
Marine Drugs , 2011, DOI: 10.3390/md9010098
Abstract: Two new 20-membered macrolides, levantilide A and B, were isolated from the Micromonospora strain M71-A77. Strain M71-A77 was recovered from an Eastern Mediterranean deep-sea sediment sample and revealed to produce the levantilides under in situ salinity of 38.6‰. The chemical structures of the levantilides were elucidated on the basis of different one- and two- dimensional NMR experiments. Levantilide A exhibits a moderate antiproliferative activity against several tumor cell lines.
Time Asymptotics and Entanglement Generation of Clifford Quantum Cellular Automata
Johannes Gütschow,Sonja Uphoff,Reinhard F. Werner,Zoltán Zimborás
Physics , 2009, DOI: 10.1063/1.3278513
Abstract: We consider Clifford Quantum Cellular Automata (CQCAs) and their time evolution. CQCAs are an especially simple type of Quantum Cellular Automata, yet they show complex asymptotics and can even be a basic ingredient for universal quantum computation. In this work we study the time evolution of different classes of CQCAs. We distinguish between periodic CQCAs, fractal CQCAs and CQCAs with gliders. We then identify invariant states and study convergence properties of classes of states, like quasifree and stabilizer states. Finally we consider the generation of entanglement analytically and numerically for stabilizer and quasifree states.
Particle Learning and Smoothing
Carlos M. Carvalho,Michael S. Johannes,Hedibert F. Lopes,Nicholas G. Polson
Statistics , 2010, DOI: 10.1214/10-STS325
Abstract: Particle learning (PL) provides state filtering, sequential parameter learning and smoothing in a general class of state space models. Our approach extends existing particle methods by incorporating the estimation of static parameters via a fully-adapted filter that utilizes conditional sufficient statistics for parameters and/or states as particles. State smoothing in the presence of parameter uncertainty is also solved as a by-product of PL. In a number of examples, we show that PL outperforms existing particle filtering alternatives and proves to be a competitor to MCMC.
Trains, tails and loops of partially adsorbed semi-flexible filaments
D. Welch,M. P. Lettinga,M. Ripoll,Z. Dogic,G. A. Vliegenthart
Physics , 2015,
Abstract: Polymer adsorption is a fundamental problem in statistical mechanics that has direct relevance to diverse disciplines ranging from biological lubrication to stability of colloidal suspensions. We combine experiments with computer simulations to investigate depletion induced adsorption of semi-flexible polymers onto a hard-wall. Three dimensional filament configurations of partially adsorbed F-actin polymers are visualized with total internal reflection fluorescence microscopy. This information is used to determine the location of the adsorption/desorption transition and extract the statistics of trains, tails and loops of partially adsorbed filament configurations. In contrast to long flexible filaments which primarily desorb by the formation of loops, the desorption of stiff, finite-sized filaments is largely driven by fluctuating filament tails. Simulations quantitatively reproduce our experimental data and allow us to extract universal laws that explain scaling of the adsorption-desorption transition with relevant microscopic parameters. Our results demonstrate how the adhesion strength, filament stiffness, length, as well as the configurational space accessible to the desorbed filament can be used to design the characteristics of filament adsorption and thus engineer properties of composite biopolymeric materials.
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