32 results on '"Stephan Knapek"'
Search Results
2. Direct neural pathways convey distinct visual information to Drosophila mushroom bodies
- Author
-
Katrin Vogt, Yoshinori Aso, Toshihide Hige, Stephan Knapek, Toshiharu Ichinose, Anja B Friedrich, Glenn C Turner, Gerald M Rubin, and Hiromu Tanimoto
- Subjects
learning and memory ,neural circuit ,physiology ,behavior ,anatomy ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Previously, we demonstrated that visual and olfactory associative memories of Drosophila share mushroom body (MB) circuits (Vogt et al., 2014). Unlike for odor representation, the MB circuit for visual information has not been characterized. Here, we show that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. We identified two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects.
- Published
- 2016
- Full Text
- View/download PDF
3. Shared mushroom body circuits underlie visual and olfactory memories in Drosophila
- Author
-
Katrin Vogt, Christopher Schnaitmann, Kristina V Dylla, Stephan Knapek, Yoshinori Aso, Gerald M Rubin, and Hiromu Tanimoto
- Subjects
associative memory ,dopamine neuron ,visual learning ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
In nature, animals form memories associating reward or punishment with stimuli from different sensory modalities, such as smells and colors. It is unclear, however, how distinct sensory memories are processed in the brain. We established appetitive and aversive visual learning assays for Drosophila that are comparable to the widely used olfactory learning assays. These assays share critical features, such as reinforcing stimuli (sugar reward and electric shock punishment), and allow direct comparison of the cellular requirements for visual and olfactory memories. We found that the same subsets of dopamine neurons drive formation of both sensory memories. Furthermore, distinct yet partially overlapping subsets of mushroom body intrinsic neurons are required for visual and olfactory memories. Thus, our results suggest that distinct sensory memories are processed in a common brain center. Such centralization of related brain functions is an economical design that avoids the repetition of similar circuit motifs.
- Published
- 2014
- Full Text
- View/download PDF
4. Versorgungsrealität von Patienten mit sekundär-progredienter Multipler Sklerose in Deutschland
- Author
-
Thekla Hemstedt, Stephan Knapek, Santiago Beier, Marie Groth, and Markus Heibel
- Subjects
Neurology (clinical) ,Family Practice - Abstract
ZUSAMMENFASSUNG Hintergrund Der Übergang von der schubförmig-remittierenden Multiplen Sklerose (RRMS) zur sekundär-progredienten MS (SPMS) verläuft sehr heterogen und ist nicht einfach festzustellen. Bisher fehlen für die SPMS einheitliche diagnostische Abgrenzungskriterien und Handlungsempfehlungen. Im Vorfeld der Zulassung von Siponimod wurde die hier vorliegende Studie zur Versorgungssituation von SPMS-Patienten in Deutschland durchgeführt, um die Ist-Situation der entsprechenden Diagnosekriterien im Praxisalltag zu erfassen. Methodik Zwischen März 2019 und Februar 2020 wurden Neurologen (n = 72) und MS-Schwestern (n = 25) mittels eines Online-Fragebogens zum Umfang der MS-Patientenversorgung und in qualitativen Interviews zu Kriterien der SPMS-Diagnose und Therapie in der Praxisroutine befragt. Ergebnisse Die meistgenannten Faktoren für eine SPMS-Diagnose waren eine RRMS-Vorerkrankung, eine schubunabhängige Progression, der EDSS-Score und der progrediente Anstieg des Behinderungsgrades innerhalb von 6 Monaten. Häufigster Grund, trotz Verdacht die SPMS-Diagnose nicht zu stellen, waren die im Umfragezeitraum fehlenden Therapieoptionen. Die Zeit zwischen Verdacht und definitiver SPMS-Diagnose betrug in der Vergangenheit 16,1±9,6 Monate (Praxis) bzw. 14,5±9,6 Monate (Klinik). Der SPMS-Verdacht wurde am häufigsten durch verringerte Gehstrecke (58 %), schubunabhängige Behinderungsprogression (35 %) und kognitive Defizite (29 %) ausgelöst. EDSS und Gehstrecke waren die Tests, die von 86,1 % und 83,3 % der Ärzte häufig oder sehr häufig bei Patienten mit Verdacht auf SPMS erfasst wurden. Etwa jeder zweite Arzt hat bereits in der Vergangenheit regelmäßige Tests zu Fatigue und Kognition durchgeführt (58,4 %; 50 %). Etwa 80 % der Ärzte gab an, zusätzliche Tests zu empfehlen, diese jedoch aus Zeitgründen nicht durchführen zu können. Diskussion Zur Vermeidung einer diagnostischen Verzögerung sollten in der neurologischen Praxis früh Symptome und Befunde erhoben werden, die über den Teilaspekt der motorischen Fähigkeiten hinausgehen und den Verdacht auf eine SPMS-Konversion begründen bzw. erhärten können.
- Published
- 2022
- Full Text
- View/download PDF
5. Optimized general sparse grid approximation spaces for operator equations.
- Author
-
Michael Griebel and Stephan Knapek
- Published
- 2009
- Full Text
- View/download PDF
6. Integral Operators on Sparse Grids.
- Author
-
Stephan Knapek and Frank Koster
- Published
- 2002
- Full Text
- View/download PDF
7. Matrix-Dependent Multigrid Homogenization for Diffusion Problems.
- Author
-
Stephan Knapek
- Published
- 1998
- Full Text
- View/download PDF
8. Functional dissociation in sweet taste receptor neurons between and within taste organs of Drosophila
- Author
-
Ayako Abe, Vladimiros Thoma, Hiroshi Kohsaka, Marion Hartl, Stephan Knapek, Shogo Arai, Koichi Hashimoto, Pudith Sirigrivatanawong, and Hiromu Tanimoto
- Subjects
0301 basic medicine ,Taste ,Sensory Receptor Cells ,Science ,General Physics and Astronomy ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Taste receptor ,medicine ,Melanogaster ,Animals ,Drosophila Proteins ,Thoracic ganglia ,Receptor ,Appendage ,Mouth ,Multidisciplinary ,digestive, oral, and skin physiology ,General Chemistry ,Anatomy ,Feeding Behavior ,biology.organism_classification ,030104 developmental biology ,medicine.anatomical_structure ,nervous system ,Drosophila ,Neuroscience ,Drosophila Protein - Abstract
Finding food sources is essential for survival. Insects detect nutrients with external taste receptor neurons. Drosophila possesses multiple taste organs that are distributed throughout its body. However, the role of different taste organs in feeding remains poorly understood. By blocking subsets of sweet taste receptor neurons, we show that receptor neurons in the legs are required for immediate sugar choice. Furthermore, we identify two anatomically distinct classes of sweet taste receptor neurons in the leg. The axonal projections of one class terminate in the thoracic ganglia, whereas the other projects directly to the brain. These two classes are functionally distinct: the brain-projecting neurons are involved in feeding initiation, whereas the thoracic ganglia-projecting neurons play a role in sugar-dependent suppression of locomotion. Distinct receptor neurons for the same taste quality may coordinate early appetitive responses, taking advantage of the legs as the first appendages to contact food., Locating food sources is essential for the survival of animals. Here, the authors identify two functionally and anatomically distinct classes of sweet taste receptor neurons in Drosophila legs, involved in feeding initiation and sugar-dependent suppression of locomotion.
- Published
- 2016
9. Bidding Complexities in the Combinatorial Clock Auction
- Author
-
Vitali Gretschko, Stephan Knapek, and Achim Wambach
- Subjects
TheoryofComputation_MISCELLANEOUS ,Combinatorial auction ,Microeconomics ,Opportunity cost ,Profit (real property) ,Economics ,TheoryofComputation_GENERAL ,Common value auction ,Competitor analysis ,Bidding ,Auction algorithm ,Price discovery - Abstract
Introduction The Combinatorial Clock Auction (CCA) is an innovative auction design that has been used in many recent auctions of spectrum for telecommunication use. The CCA is based on ideas from modern microeconomic theory and combines package bidding with dynamic price discovery in a two-stage design. In the clock phase , bidders express their demands at increasing prices in each of the auctioned categories of spectrum lots until the indicated demand matches the available supply. In the supplementary phase, bidders can improve their bids from the clock phase and submit additional bids for other desired combinations of lots. To induce truthful bidding in the clock phase, bids in the supplementary phase are constrained by a cap that is based on the clock bids. To determine winnings and prices all bids of a particular bidder are treated as mutually exclusive package bids and the combination of packages that maximizes the value as expressed by the bids is the winning allocation. The prices are determined through (a variant of) the Vickrey (second-price) rule by calculating the opportunity cost imposed by each bidder on her competitors. In general, there exist many more additional details like reserve prices, caps, or activity rules that have to be considered when designing a CCA. While the design is quite complex, the promise of the CCA is that bidding is simple. Regulators argue that in a CCA truthful bidding is close to optimal independent of the bidding strategy of the competitors. Regulators claim that the CCA “allows bidders to use a simple strategy” and “allows the participants to evaluate the spectrum without […] shadow bids.” If truthful bidding is indeed close to optimal independent of the competitors’ behavior, this would be useful for the participants. In this case there is no need for strategizing and bidders could simply quote on the packages that lead to largest profit in the clock phase. In particular, bidders could focus their resources on determining the correct valuations and would not need to worry about the preferences of the competitors or their potentially erratic or spiteful behavior.
- Published
- 2017
- Full Text
- View/download PDF
10. Short Neuropeptide F Acts as a Functional Neuromodulator for Olfactory Memory in Kenyon Cells ofDrosophilaMushroom Bodies
- Author
-
Åsa M. E. Winther, Lily Kahsai, Stephan Knapek, Dick R. Nässel, and Hiromu Tanimoto
- Subjects
Male ,Appetite ,Neuropeptide ,Biology ,Animals, Genetically Modified ,Memory ,RNA interference ,Conditioning, Psychological ,medicine ,Animals ,Drosophila Proteins ,Olfactory memory ,Receptor ,Mushroom Bodies ,Anesthesia-resistant memory ,Neurotransmitter Agents ,Gene knockdown ,Behavior, Animal ,General Neuroscience ,Neuropeptides ,Articles ,Smell ,Drosophila melanogaster ,medicine.anatomical_structure ,Odorants ,Mushroom bodies ,Female ,Neuroscience ,Neuroanatomy - Abstract
In insects, many complex behaviors, including olfactory memory, are controlled by a paired brain structure, the so-called mushroom bodies (MB). InDrosophila, the development, neuroanatomy, and function of intrinsic neurons of the MB, the Kenyon cells, have been well characterized. Until now, several potential neurotransmitters or neuromodulators of Kenyon cells have been anatomically identified. However, whether these neuroactive substances of the Kenyon cells are functional has not been clarified yet. Here we show that a neuropeptide precursor gene encoding four types of short neuropeptide F (sNPF) is required in the Kenyon cells for appetitive olfactory memory. We found that activation of Kenyon cells by expressing a thermosensitive cation channel (dTrpA1) leads to a decrease in sNPF immunoreactivity in the MB lobes. Targeted expression of RNA interference against the sNPF precursor in Kenyon cells results in a highly significant knockdown of sNPF levels. This knockdown of sNPF in the Kenyon cells impairs sugar-rewarded olfactory memory. This impairment is not due to a defect in the reflexive sugar preference or odor response. Consistently, knockdown of sNPF receptors outside the MB causes deficits in appetitive memory. Altogether, these results suggest that sNPF is a functional neuromodulator released by Kenyon cells.
- Published
- 2013
- Full Text
- View/download PDF
11. Author response: Direct neural pathways convey distinct visual information to Drosophila mushroom bodies
- Author
-
Toshihide Hige, Katrin Vogt, Stephan Knapek, Hiromu Tanimoto, Toshiharu Ichinose, Anja B. Friedrich, Gerald M. Rubin, Glenn C. Turner, and Yoshinori Aso
- Subjects
biology ,Mushroom bodies ,Drosophila (subgenus) ,biology.organism_classification ,Neuroscience - Published
- 2016
- Full Text
- View/download PDF
12. Structural Long-Term Changes at Mushroom Body Input Synapses
- Author
-
Florian Leiss, Peter Kloppenburg, Gaia Tavosanis, Till F. M. Andlauer, Stephan J. Sigrist, Frauke Christiansen, Friedrich Forstner, Moritz Paehler, Stephan Knapek, and Malte C. Kremer
- Subjects
Potassium Channels ,Recombinant Fusion Proteins ,Action Potentials ,Sensory system ,Cellular level ,Neurotransmission ,Biology ,Synaptic Transmission ,General Biochemistry, Genetics and Molecular Biology ,Calyx ,Postsynaptic potential ,Animals ,Drosophila Proteins ,Active zone ,Mushroom Bodies ,Neurons ,Agricultural and Biological Sciences(all) ,Biochemistry, Genetics and Molecular Biology(all) ,fungi ,Anatomy ,Smell ,Brain region ,nervous system ,Synapses ,Mushroom bodies ,Drosophila ,General Agricultural and Biological Sciences ,Neuroscience - Abstract
SummaryHow does the sensory environment shape circuit organization in higher brain centers? Here we have addressed the dependence on activity of a defined circuit within the mushroom body of adult Drosophila. This is a brain region receiving olfactory information and involved in long-term associative memory formation [1]. The main mushroom body input region, named the calyx, undergoes volumetric changes correlated with alterations of experience [2–5]. However, the underlying modifications at the cellular level remained unclear. Within the calyx, the clawed dendritic endings of mushroom body Kenyon cells form microglomeruli, distinct synaptic complexes with the presynaptic boutons of olfactory projection neurons [6, 7]. We developed tools for high-resolution imaging of pre- and postsynaptic compartments of defined calycal microglomeruli. Here we show that preventing firing of action potentials or synaptic transmission in a small, identified fraction of projection neurons causes alterations in the size, number, and active zone density of the microglomeruli formed by these neurons. These data provide clear evidence for activity-dependent organization of a circuit within the adult brain of the fly.
- Published
- 2010
- Full Text
- View/download PDF
13. Synapsin is selectively required for anesthesia-sensitive memory
- Author
-
Bertram Gerber, Hiromu Tanimoto, and Stephan Knapek
- Subjects
Cognitive Neuroscience ,Mutant ,Animals, Genetically Modified ,Adenylyl cyclase ,Cellular and Molecular Neuroscience ,chemistry.chemical_compound ,Feedback, Sensory ,Memory ,Encoding (memory) ,Animals ,Learning ,Anesthesia ,Habituation ,Olfactory memory ,Habituation, Psychophysiologic ,biology ,Synapsin ,Synapsins ,biology.organism_classification ,Cold Temperature ,Smell ,Memory, Short-Term ,Neuropsychology and Physiological Psychology ,nervous system ,chemistry ,Drosophila ,Drosophila melanogaster ,Psychology ,Neuroscience ,Function (biology) - Abstract
Odor-shock memory in Drosophila melanogaster consists of heterogeneous components each with different dynamics. We report that a null mutant for the evolutionarily conserved synaptic protein Synapsin entails a memory deficit selectively in early memory, leaving later memory as well as sensory motor function unaffected. Notably, a consolidated memory component remaining after cold-anesthesia is not impaired, suggesting that only anesthesia-sensitive memory [ASM] depends on Synapsin. The lack of Synapsin does not further impair the memory deficit of mutants for the rutabaga gene encoding the type I adenylyl cyclase. This suggests that cAMP signaling, through a Synapsin-dependent mechanism, may underlie the formation of a labile memory component.
- Published
- 2010
- Full Text
- View/download PDF
14. Direct neural pathways convey distinct visual information to Drosophila mushroom bodies
- Author
-
Gerald M. Rubin, Toshiharu Ichinose, Anja B. Friedrich, Stephan Knapek, Yoshinori Aso, Toshihide Hige, Glenn C. Turner, Katrin Vogt, and Hiromu Tanimoto
- Subjects
0301 basic medicine ,anatomy ,Visual perception ,genetic structures ,QH301-705.5 ,Science ,Sensory system ,neural circuit ,General Biochemistry, Genetics and Molecular Biology ,Calyx ,03 medical and health sciences ,Memory ,ddc:570 ,Neural Pathways ,Animals ,Biology (General) ,Drosophila (subgenus) ,Mushroom Bodies ,Neurons ,D. melanogaster ,General Immunology and Microbiology ,biology ,behavior ,General Neuroscience ,Sensory memory ,Optic Lobe, Nonmammalian ,General Medicine ,Anatomy ,Olfactory Perception ,biology.organism_classification ,eye diseases ,030104 developmental biology ,Odor ,physiology ,Mushroom bodies ,Visual Perception ,Olfactory stimulation ,Medicine ,Drosophila ,learning and memory ,Research Advance ,Neuroscience - Abstract
Previously, we demonstrated that visual and olfactory associative memories of Drosophila share mushroom body (MB) circuits (Vogt et al., 2014). Unlike for odor representation, the MB circuit for visual information has not been characterized. Here, we show that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. We identified two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects.
- Published
- 2016
15. Integral Operators on Sparse Grids
- Author
-
Frank Koster and Stephan Knapek
- Subjects
Laplace's equation ,Numerical Analysis ,Applied Mathematics ,Mathematical analysis ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,MathematicsofComputing_NUMERICALANALYSIS ,Sparse grid ,Integral equation ,Computational Mathematics ,symbols.namesake ,Tensor product ,Kernel (statistics) ,Dirichlet boundary condition ,Biorthogonal system ,symbols ,Biorthogonal wavelet ,Mathematics - Abstract
In this paper we are concerned with the construction and use of wavelet approximation spaces for the fast evaluation of integral expressions. The spaces are based on biorthogonal anisotropic tensor product wavelets. We introduce sparse grid (hyperbolic cross) approximation spaces which are adapted not only to the smoothness of the kernel but also to the norm in which the error is measured. Furthermore, we introduce compression schemes for the corresponding discretizations. Numerical examples for the Laplace equation with Dirichlet boundary conditions and an additional integral term with a smooth kernel demonstrate the validity of our theoretical results.
- Published
- 2002
- Full Text
- View/download PDF
16. Author response: Shared mushroom body circuits underlie visual and olfactory memories in Drosophila
- Author
-
Kristina V. Dylla, Katrin Vogt, Yoshinori Aso, Hiromu Tanimoto, Gerald M. Rubin, Christopher Schnaitmann, and Stephan Knapek
- Subjects
Mushroom bodies ,Biology ,Drosophila (subgenus) ,biology.organism_classification ,Neuroscience - Published
- 2014
- Full Text
- View/download PDF
17. Optimized Tensor-Product Approximation Spaces
- Author
-
Stephan Knapek and Michael Griebel
- Subjects
Pure mathematics ,General Mathematics ,Topological tensor product ,Mathematical analysis ,Hilbert space ,Hardy space ,Sobolev space ,Computational Mathematics ,symbols.namesake ,Tensor product ,symbols ,Interpolation space ,Birnbaum–Orlicz space ,Lp space ,Analysis ,Mathematics - Abstract
This paper is concerned with the construction of optimized grids and approximation spaces for elliptic differential and integral equations. The main result is the analysis of the approximation of the embedding of the intersection of classes of functions with bounded mixed derivatives in standard Sobolev spaces. Based on the framework of tensor-product biorthogonal wavelet bases and stable subspace splittings, the problem is reduced to diagonal mappings between Hilbert sequence spaces. We construct operator adapted finite element subspaces with a lower dimension than the standard full-grid spaces. These new approximation spaces preserve the approximation order of the standard full-grid spaces, provided that certain additional regularity assumptions are fulfilled. The form of the approximation spaces is governed by the ratios of the smoothness exponents of the considered classes of functions. We show in which cases the so-called curse of dimensionality can be broken. The theory covers elliptic boundary value problems as well as boundary integral equations.
- Published
- 2000
- Full Text
- View/download PDF
18. Strategic Complexities in the Combinatorial Clock Auction
- Author
-
Vitali Gretschko, Stephan Knapek, and Achim Wambach
- Subjects
TheoryofComputation_MISCELLANEOUS ,combinatorial clock auction ,TheoryofComputation_GENERAL ,jel:D44 ,jel:L96 - Abstract
In recent years, regulatory bodies in Europe and around the world implemented Combinatorial Clock Auctions (CCA) to allocate scarce and valuable spectrum frequencies usage rights. Although the auction design is complex, the promise is that bidding becomes simple. More precisely, bidders may bid on the profit-maximizing package (truthful bidding) during the clock phase and submit bids that are equal to their valuations on only a handful of relevant packages (truncated bidding) in the supplementary phase. While this might be correct with the ideal implementation of the CCA for perfectly rational, profit-maximizing bidders with private values, our experience with consulting bidders shows that practical implementations of the CCA and the concerns of the bidders lead to severe complexities in determining the right bidding behavior. We provide simple examples that illustrate how "truthful and truncated" bidding may be harmful to bidders and thereby illustrate the complexities bidders face in preparing for a CCA.
- Published
- 2012
19. Bruchpilot, A Synaptic Active Zone Protein for Anesthesia-Resistant Memory
- Author
-
Stephan J. Sigrist, Hiromu Tanimoto, and Stephan Knapek
- Subjects
Anesthesia-resistant memory ,Gene knockdown ,General Neuroscience ,Presynaptic Terminals ,Stimulation ,Synapsin ,Articles ,Biology ,Animals, Genetically Modified ,Smell ,Drosophila melanogaster ,Memory ,Mushroom bodies ,Odorants ,Synapses ,Avoidance Learning ,Animals ,Drosophila Proteins ,Anesthesia ,Female ,Active zone ,Olfactory memory ,Neuroscience ,Presynaptic active zone - Abstract
InDrosophila, aversive associative memory of an odor consists of heterogeneous components with different stabilities. Here we report that Bruchpilot (Brp), a ubiquitous presynaptic active zone protein, is required for olfactory memory. Brp was shown before to facilitate efficient vesicle release, particularly at low stimulation frequencies. Transgenic knockdown in the Kenyon cells of the mushroom body, the second-order olfactory interneurons, revealed that Brp is required for olfactory memory. We further demonstrate that Brp in the Kenyon cells preferentially functions for anesthesia-resistant memory. Another presynaptic protein, Synapsin, was shown previously to be required selectively for the labile anesthesia-sensitive memory, which is less affected inbrpknockdown. Thus, consolidated and labile components of aversive olfactory memory can be dissociated by the function of different presynaptic proteins.
- Published
- 2011
20. Das Linked-Cell-Verfahren für kurzreichweitige Potentiale
- Author
-
Gerhard Zumbusch, Michael Griebel, Attila Caglar, and Stephan Knapek
- Abstract
In Kapitel 1 haben wir das Partikelmodell, erste Potentiale sowie den Basisalgorithmus vorgestellt. Weitere Potentiale haben wir in Abschnitt 2.2.4 kennengelernt. Offene Fragen sind dabei die schnelle Auswertung der Potentiale beziehungsweise der daraus resultierenden Krafte an den Partikelpositionen und die Wahl eines geeigneten Integrationsverfahrens. Diesen Problemen sind die folgenden Kapitel des Buches gewidmet. Die verschiedenen Verfahren und Algorithmen fur die Auswertung der Krafte sind dabei stark von der Art der verwendeten Potentiale abhangig. Wir beginnen die Diskussion in diesem Kapitel mit der Herleitung eines Algorithmus fur kurzreichweitige Wechselwirkungen, die sich jeweils nur auf die nachsten geometrischen Nachbarn eines Partikels beschranken lassen. Man beachte jedoch, das der hier vorgestellte Algorithmus auch die Basis fur die in den Kapiteln 7 und 8 diskutierten Verfahren fur Probleme mit langreichweitigen Wechselwirkungen darstellt.
- Published
- 2004
- Full Text
- View/download PDF
21. Erweiterung auf kompliziertere Potentiale und Moleküle
- Author
-
Michael Griebel, Gerhard Zumbusch, Stephan Knapek, and Attila Caglar
- Abstract
In den bisherigen Anwendungen traten nur Paarpotentiale auf. In diesem Kapitel betrachten wir nun einige Anwendungen mit komplizierteren Potentialen und diskutieren die dafur notwendigen Anderungen in den Algorithmen. Wir beginnen mit drei Beispielen fur Mehrkorperpotentiale, dem Potential von Finnis-Sinclair [230, 326, 584], dem EAM-Potential [64, 172, 173] und dem Potential von Brenner [122]. Das Potential von Finnis-Sinclair und das EAM-Potential beschreiben Bindungen in Metallen. Wir verwenden diese Potentiale zur Simulation von Mikrorissen und Strukturumwandlungen in metallischen Materialien. Das Potential von Brenner beschreibt Kohlenwasserstoffbindungen. Wir setzen es zur Simulation von Kohlenstoff-Nanorohren und sogenannten Kohlenstoff-Buckyballen ein. Anschliesend erweitern wir unseren Code auf Potentiale mit festen Nachbarschaftsstrukturen. Damit konnen wir auch einfache Netze aus Atomen und lineare Molekulketten wie Alkane und Polymere simulieren. Zuletzt geben wir einen Ausblick auf die Implementierung von komplizierteren Biomolekulen und Proteinen.
- Published
- 2004
- Full Text
- View/download PDF
22. Zeitintegrationsverfahren
- Author
-
Michael Griebel, Stephan Knapek, Gerhard Zumbusch, and Attila Caglar
- Published
- 2004
- Full Text
- View/download PDF
23. Anwendungen aus Biochemie und Biophysik
- Author
-
Attila Caglar, Gerhard Zumbusch, Michael Griebel, and Stephan Knapek
- Abstract
Gentechnik und Biotechnologie sind im letzen Jahrzehnt ein immer wichtigeres und aktuelles Thema geworden. Deswegen wollen wir in diesem Kapitel einen Ausblick auf die Vielfalt von Fragestellungen aus dem Bereich Biochemie und Biophysik geben, die mit den bisher entwickelten Molekuldynamik-Methoden behandelt und untersucht werden konnen. Die Anwendungen gehen dabei von der Dynamik von Proteinen (Eiweisen) uber die Strukturuntersuchung von Membranen, der Bestimmung der Bindungsenergien zwischen Inhibitoren und Liganden, bis hin zur Untersuchung von Konformationsanderungen und Fragen der (Ent-)Faltung von Peptiden, Proteinen und Nucleinsauren.
- Published
- 2004
- Full Text
- View/download PDF
24. Baumverfahren für langreichweitige Potentiale
- Author
-
Attila Caglar, Stephan Knapek, Michael Griebel, and Gerhard Zumbusch
- Abstract
In Kapitel 7 haben wir am Beispiel des Coulomb- und des Gravitationspotentials gitterbasierte Verfahren fur die Behandlung langreichweitiger Wechselwirkungen zwischen Partikeln beschrieben. Dieser Zugang stutzt sich auf eine Darstellung des Potentials Ф als Losung der Poisson-Gleichung (7.5). Er funktioniert gut solange wir Potentiale vom Typ l/r betrachten und die Teilchen in etwa uniform verteilt sind. Im Falle nicht-uniformer Verteilungen, wenn sich also die Partikel in einem Teil des Simulationsgebietes haufen, verringert sich die Effizienz der gitterbasierten Methoden stark. Das zu verwendende Gitter mus namlich fein genug gewahlt sein, um die inhomogenen Partikelverteilungen aufzulosen. Solche inhomogenen Partikelverteilungen treten insbesondere in der Astrophysik haufig auf, kommen aber auch in vielfaltiger Form bei biochemischen Molekuldynamik-Simulationen vor.
- Published
- 2004
- Full Text
- View/download PDF
25. Computersimulation — eine Schlüsseltechnologie
- Author
-
Attila Caglar, Stephan Knapek, Gerhard Zumbusch, and Michael Griebel
- Abstract
Experiment, Modellbildung und numerische Simulation. In den Naturwissenschaften ist man bestrebt, die komplexen Vorgange in der Natur moglichst genau zu modellieren. Der erste Schritt in diese Richtung ist dabei die Naturbeschreibung. Sie dient zunachst dazu, ein geeignetes Begriffssystem zu bilden. Die reine Beobachtung eines Vorganges erlaubt es allerdings in den meisten Fallen nicht, die ihm zugrundeliegenden Gesetzmasigkeiten zu finden. Dazu sind diese zu kompliziert und lassen sich von anderen sie beeinflussenden Vorgangen nicht exakt trennen. Nur in seltenen Ausnahmefallen konnen aus reiner Beobachtung Gesetzmasigkeiten abgeleitet werden, wie dies beispielsweise bei der Entdeckung der Gesetze der Planetenbewegung durch Kepler der Fall war. Statt dessen schafft sich der Wissenschaftler (soweit dies moglich ist) die Bedingungen unter denen der zu beobachtende Vorgang ablaufen soll selbst, das heist, er fuhrt ein Experiment durch. Dieses Vorgehen erlaubt es, Abhangigkeiten des beobachteten Ergebnisses von den im Experiment gewahlten Bedingungen herauszufinden und so Ruckschlusse auf die Gesetzmasigkeiten zu ziehen, denen das untersuchte System unterliegt. Das Ziel ist dabei die mathematische Formulierung der beobachteten Gesetzmasigkeiten, also eine Theorie der untersuchten Naturerscheinungen. Meist beschreibt man dabei mit Hilfe von Differential- und Integralgleichungen, wie sich bestimmte Grosen in Abhangigkeit von anderen verhalten und sich unter bestimmten Bedingungen uber die Zeit andern. Die resultierenden Gleichungen zur Beschreibung des Systems beziehungsweise des Prozesses bezeichnet man als mathematisches Modell.
- Published
- 2004
- Full Text
- View/download PDF
26. Ausblick
- Author
-
Michael Griebel, Stephan Knapek, Gerhard Zumbusch, and Attila Caglar
- Published
- 2004
- Full Text
- View/download PDF
27. Numerische Simulation in der Moleküldynamik
- Author
-
Attila Caglar, Michael Griebel, Stephan Knapek, and Gerhard Zumbusch
- Subjects
Physics - Published
- 2004
- Full Text
- View/download PDF
28. Von der Schrödingergleichung zur Moleküldynamik
- Author
-
Michael Griebel, Attila Caglar, Stephan Knapek, and Gerhard Zumbusch
- Abstract
In Partikelmethoden werden die Gesetze der klassischen Mechanik [48. 367] verwendet, insbesondere das zweite Gesetz von Newton. In diesem Abschnitt gehen wir nun der Frage nach, wieso es uberhaupt sinnvoll ist, die Gesetze der klassischen Mechanik anzuwenden, da eigentlich die Gesetze der Quantenmechanik benutzt werden musten. Leser, die mehr an der algorithmischen Seite beziehungsweise der Implementierung der Algorithmen in der Molekuldynamik interessiert sind, konnen diesen Abschnitt uberspringen.
- Published
- 2004
- Full Text
- View/download PDF
29. Gitterbasierte Methoden für langreichweitige Potentiale
- Author
-
Gerhard Zumbusch, Michael Griebel, Attila Caglar, and Stephan Knapek
- Abstract
In den Kapiteln 3 und 5 haben wir sogenannte kurzreichweitige Potentiale wie das Lennard-Jones-Potential (3.27), das Potential von Finnis-Sinclair (5.2), das EAM-Potential (5.14) und das Potential von Brenner (5.17) betrachtet. Die daraus resultierenden Wechselwirkungen zwischen den Partikeln waren dabei auf nahe beieinander liegende Partikel beschrankt. Neben diesen kurzreichweitigen Potentialen gibt es aber auch Typen von Potentialen, bei denen Wechselwirkungen mit weiter entfernten Partikeln fur die Entwicklung des betrachteten Partikelsystems relevant sind. In drei Dimensionen bezeichnet man Potentiale, die in r schneller als l / r3 abfallen, als kurzreich weit ig. 1 Damit gehoren das Gravitationspotential (2.42) und das Coulomb-Potential (2.43) zu den langsam abfallenden, langreichweitigen Potentialen.
- Published
- 2004
- Full Text
- View/download PDF
30. A Multigrid-Homogenization Method
- Author
-
Stephan Knapek and Michael Griebel
- Subjects
Renormalization ,Multigrid method ,Effective diffusion coefficient ,Applied mathematics ,Galerkin method ,Grid ,Computer Science::Numerical Analysis ,Homogenization (chemistry) ,Mathematics::Numerical Analysis ,Mathematics - Abstract
For problems with strongly varying or discontinuous diffusion coefficients, we present a method to approximately determine the effective diffusion coefficient on the coarse scale level. It is based on techniques used also in multigrid, i.e. matrix-dependent prolongations and the construction of coarse grid operators by means of the Galerkin approximation. In numerical experiments, we compare our multigrid-homogenization method with homogenization, renormalization and averaging approaches.
- Published
- 1997
- Full Text
- View/download PDF
31. Numerical Simulation in Molecular Dynamics : Numerics, Algorithms, Parallelization, Applications
- Author
-
Michael Griebel, Stephan Knapek, Gerhard Zumbusch, Michael Griebel, Stephan Knapek, and Gerhard Zumbusch
- Subjects
- Physical chemistry, Computer simulation, Mathematics—Data processing, Numerical analysis, Chemometrics, Mathematical physics
- Abstract
Particle models play an important role in many applications in physics, chemistry and biology. They can be studied on the computer with the help of molecular dynamics simulations. This book presents in detail both the necessary numerical methods and techniques (linked-cell method, SPME-method, tree codes, multipole technique) and the theoretical background and foundations. It illustrates the aspects modelling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. Furthermore, detailed explanations are given to the different steps of numerical simulation, and code examples are provided. With the description of the algorithms and the presentation of the results of various simulations from the areas material science, nanotechnology, biochemistry and astrophysics, the reader of this book will be able to write his own programs for molecular dynamics step by step and to run successful experiments.
- Published
- 2007
32. Suppression of Conditioned Odor Approach by Feeding Is Independent of Taste and Nutritional Value in Drosophila
- Author
-
Koichiro Matsuo, Franz Andreas Gruber, Igor Siwanowicz, Teiichi Tanimura, Nao Shinzato, Lasse B. Bräcker, Stephan Knapek, Michiko Fujita, and Hiromu Tanimoto
- Subjects
Male ,medicine.medical_specialty ,Taste ,Conditioning, Classical ,Stimulation ,Energy homeostasis ,General Biochemistry, Genetics and Molecular Biology ,Reward ,Internal medicine ,Hemolymph ,medicine ,Animals ,Adipokinetic hormone ,Drosophila ,Motivation ,Osmotic concentration ,Agricultural and Biological Sciences(all) ,biology ,Biochemistry, Genetics and Molecular Biology(all) ,Taste Perception ,Feeding Behavior ,Sweetness ,Olfactory Perception ,biology.organism_classification ,Neurosecretory Systems ,Pyrrolidonecarboxylic Acid ,Drosophila melanogaster ,Glucose ,Endocrinology ,Odor ,Insect Hormones ,Female ,Current (fluid) ,General Agricultural and Biological Sciences ,Nutritive Value ,Oligopeptides ,Neuroscience ,Value (mathematics) - Abstract
SummaryMotivation controls behavior [1]. A variety of food-related behaviors undergo motivational modulation by hunger, satiety, and other states [2–4]. Here we searched for critical satiation factors modulating approach to an odor associated with sugar reward in Drosophila melanogaster. We selectively manipulated different parameters associated with feeding, such as internal glucose levels, and determined which are required for suppressing conditioned odor approach. Surprisingly, glucose levels in the hemolymph, nutritional value, sweetness of the food, and ingested volume (above a minimal threshold) did not influence behavior suppression. Instead, we found that the total osmolarity of ingested food is a critical satiation factor. In parallel, we found that conditioned approach is transiently suppressed by artificial stimulation of adipokinetic hormone (AKH) expressing corpora cardiaca cells, which causes elevation of hemolymph carbohydrate and lipid concentrations [5, 6]. This result implies that a rise in hemolymph osmolarity, without the experience of feeding, is sufficient to satiate conditioned odor approach. AKH stimulation did not affect innate sugar preference, suggesting that multiple satiation signals control different sets of appetitive behaviors.
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.