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Search Results: 1 - 10 of 9866 matches for " Stefan Kempa "
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ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii
Patrick May, Jan-Ole Christian, Stefan Kempa, Dirk Walther
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-209
Abstract: In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de webcite.The unicellular green alga Chlamydomonas reinhardtii (for brevity, in the following referred to as Chlamydomonas) is an important eukaryotic model organism for the study of photosynthesis and chloroplast development in higher plants as well as flagella development and other cellular processes, and has recently attracted substantial interest in the context of bio-fuel and hydrogen production [1,2]. Because of its unique evolutionary position – it diverged from land-plants over a billion years ago – the genome and its gene catalogue have received much attention, especially since the recent publication of the draft genome [2]. The genome of Chlamydomonas currently (version 3.1) contains about 14,500 protein-coding genes. Additionally, the mitochondrial and plastid genomes have been fully sequenced.Although the Chlamydomonas genome is far from being completely annotated, e.g., there are more than 150,000 alternative gene models of unclear validity available in addition to the currently annotated genes, there is a fast growing need for a better understan
A Central Role of Abscisic Acid in Stress-Regulated Carbohydrate Metabolism
Stefan Kempa, Julia Krasensky, Silvia Dal Santo, Joachim Kopka, Claudia Jonak
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003935
Abstract: Background Abiotic stresses adversely affect plant growth and development. The hormone abscisic acid (ABA) plays a central role in the response and adaptation to environmental constraints. However, apart from the well established role of ABA in regulating gene expression programmes, little is known about its function in plant stress metabolism. Principal Findings Using an integrative multiparallel approach of metabolome and transcriptome analyses, we studied the dynamic response of the model glyophyte Arabidopsis thaliana to ABA and high salt conditions. Our work shows that salt stress induces complex re-adjustment of carbohydrate metabolism and that ABA triggers the initial steps of carbon mobilisation. Significance These findings open new perspectives on how high salinity and ABA impact on central carbohydrate metabolism and highlight the power of iterative combinatorial approaches of non-targeted and hypothesis-driven experiments in stress biology.
Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii
Guido Mastrobuoni, Susann Irgang, Matthias Pietzke, Markus Wenzel, Heike E Assmus, Waltraud X Schulze, Stefan Kempa
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-215
Abstract: To study de novo protein synthesis an arginine auxotroph Chlamydomonas strain was cultivated in presence of stable isotope-labeled arginine for 24 hours. From the time course experiment in 3 salt concentrations we could identify more than 2500 proteins and their H/L ratio in at least one experimental condition; for 998 protiens at least 3 ratio counts were detected in the 24?h time point (0?mM NaCl). After fractionation we could identify 3115 proteins and for 1765 of them we determined their de novo synthesis rate. Consistently with previous findings we showed that RuBisCO is among the most prominent proteins in the cell; and similar abundance and turnover for the small and large RuBisCO subunit could be calculated. The D1 protein was identified among proteins with a high synthesis rates. A global median half-life of 45?h was calculated for Chlamydomonas proteins under the chosen conditions.To investigate the temporal co-regulation of the proteome and metabolome, we applied salt stress to Chlamydomonas and studied the time dependent regulation of protein expression and changes in the metabolome. The main metabolic response to salt stress was observed within the amino acid metabolism. In particular, proline was up-regulated manifold and according to that an increased carbon flow within the proline biosynthetic pathway could be measured. In parallel the analysis of abundance and de novo synthesis of the corresponding enzymes revealed that metabolic rearrangements precede adjustments of protein abundance.
Duality of the collective and single particle responses in simple metals in the extreme long wavelength limit
K. Kempa
Physics , 2014,
Abstract: It is demonstrated that the collective and single particle responses of simple metals in the extreme long wavelength limit become identical. When applied to alternative models of a metallic slab, this duality proves equivalence of the plasma frequency and the surface energy barrier, which confines electrons inside the metal. This in-turn proves also a simple, yet powerful formula, which expresses the work function of a metals as a difference between its free-electron plasmon and Fermi energies, and which has been shown to be more accurate (even for complex metals) than the best available simulations.
Controlling phonon emission with plasmonic metamaterials
Krzysztof Kempa
Physics , 2012,
Abstract: It is shown, that plasmonic metamaterial nanostructures could be used to reduce the electron-phonon scattering rate, by providing an alternative, fast electron-plasmon scattering channel. Since the plasmon-phonon and plasmon-photon scattering processes are relatively slow, this provides a mechanism for a hot-electron plasmonic protection against the phonon emission. The stored/protected energy can be returned to the single particle channel by processes similar to the Rabi oscillations, plasmon resonance energy transfer (PERT), or formation of plasmarons. This effect could be used to control phonon scattering in various electron systems, such as solar cells or high Tc-superconductors.
Negative refraction of photonic and polaritonic waves in periodic structures
K. Kempa , A. Rose
Bulletin of the Polish Academy of Sciences: Technical Sciences , 2009, DOI: 10.2478/v10175-010-0102-7
Abstract: Negative refraction can be achieved in photonic crystals. We briefly summarize recent studies in this field, and show that such effects are also possible in polaritonic and plasmonic structures, such as the dipole crystal. We propose a practical realization of this crystal, a periodic lattice of dielectric spheres. We study its mode structure, and preliminary results demonstrate the negative refraction on a polaritonic band.
On departure process in the batch arrival queue with single vacation and setup time
Wojciech M. Kempa
Annales UMCS, Informatica , 2010, DOI: 10.2478/v10065-010-0040-x
Abstract: A single-server queueing system of MX/G/1 type with unlimited buffer size is considered. Whenever the system becomes empty, the server takes a single compulsory vacation that is independent of the arrival process. The service of the first customer after the vacation is preceded by a random setup time. We distinguish two cases of the evolution of the system: when the setup time begins after the vacation only, or if it begins at once when the first group of customers enters. In the paper we investigate the departure process h(t) that at any fixed moment t takes on a random value equal to the number of customers completely served before t. An explicit representation for Laplace Transform of probability generating function of departure process is derived and written down by means of transforms of four crucial "input" distributions of the system and factors of a certain factorization identity connected with them. The results are obtained using the method consisting of two main stages: first we study departure process on a single vacation cycle for an auxiliary system and direct the analysis to the case of the system without vacations, applying the formula of total probability; next we use the renewal-theory approach to obtain a general formula.
On time to buffer saturation in a GI/M/1/N-type queue
Wojciech Michal Kempa
International Journal of Advances in Telecommunications, Electrotechnics, Signals and Systems , 2012, DOI: 10.11601/ijates.v1i2-3.15
Abstract: A GI/M/1/N-type queueing system with independent and generally distributed interarrival times and exponential service times is investigated. A system of equations for conditional distributions of the time to the first buffer saturation is built. The solution is written using a special-type sequence defined by ``input'' distributions of the system. The formula of total probability is used to derive a representation for the distribution of the time to the $k$th buffer saturation for k>=2. Moreover, special cases of the Poisson arrival process and the system with one-place buffer are discussed. Sample numerical results for the 3-Erlang and deterministic distributions of interarrival times are attached as well.
A Field-Effect-Transistor from Graphite: No Effect of Low Gate Fields
H. Kempa,P. Esquinazi
Physics , 2003,
Abstract: Inspired by the striking similarities between the metal-insulator transitions in graphite and Si-MOSFET's and the recent attention to charge doping in carbon-based materials, we have made attempts to fabricate a field-effect transistor based on graphite. A relatively thick layer of boron nitride turned out to be able to serve as a gate dielectric. This, however, limits the achievable electric gate field, which might be the reason for our observation of no charge-doping effect.
Negative Refraction and Subwavelength Lensing in a Polaritonic Crystal
X. Wang,K. Kempa
Physics , 2004, DOI: 10.1103/PhysRevB.71.233101
Abstract: We show that a two-dimensional polaritonic crystal, made of metallic rods that support well defined plasmon oscillations, can act in a narrow frequency range as a medium in which a negative refraction and subwavelength lensing can occur. We show that surface modes are excited on the surface of the lens, and that they facilitate restoration of the evanescent waves, which carry the subwavelength image information. We demonstrate that this can occur in the visible frequency range, for a wide range of materials, including silver and aluminum rods, and carbon nanotubes. This flexibility should allow for an experimental demonstration of this phenomenon in the visible frequency range.
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