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Search Results: 1 - 10 of 53256 matches for " David ?afránek "
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On Expressing and Monitoring Oscillatory Dynamics
Petr Dluho?,Lubo? Brim,Davidafránek
Electronic Proceedings in Theoretical Computer Science , 2012, DOI: 10.4204/eptcs.92.6
Abstract: To express temporal properties of dense-time real-valued signals, the Signal Temporal Logic (STL) has been defined by Maler et al. The work presented a monitoring algorithm deciding the satisfiability of STL formulae on finite discrete samples of continuous signals. The logic has been used to express and analyse biological systems, but it is not expressive enough to sufficiently distinguish oscillatory properties important in biology. In this paper we define the extended logic STL* in which STL is augmented with a signal-value freezing operator allowing us to express (and distinguish) detailed properties of biological oscillations. The logic is supported by a monitoring algorithm prototyped in Matlab. The monitoring procedure of STL* is evaluated on a biologically-relevant case study.
Robustness Analysis of Stochastic Biochemical Systems
Milan ?eska, Davidafránek, Sven Dra?an, Lubo? Brim
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0094553
Abstract: We propose a new framework for rigorous robustness analysis of stochastic biochemical systems that is based on probabilistic model checking techniques. We adapt the general definition of robustness introduced by Kitano to the class of stochastic systems modelled as continuous time Markov Chains in order to extensively analyse and compare robustness of biological models with uncertain parameters. The framework utilises novel computational methods that enable to effectively evaluate the robustness of models with respect to quantitative temporal properties and parameters such as reaction rate constants and initial conditions. We have applied the framework to gene regulation as an example of a central biological mechanism where intrinsic and extrinsic stochasticity plays crucial role due to low numbers of DNA and RNA molecules. Using our methods we have obtained a comprehensive and precise analysis of stochastic dynamics under parameter uncertainty. Furthermore, we apply our framework to compare several variants of two-component signalling networks from the perspective of robustness with respect to intrinsic noise caused by low populations of signalling components. We have successfully extended previous studies performed on deterministic models (ODE) and showed that stochasticity may significantly affect obtained predictions. Our case studies demonstrate that the framework can provide deeper insight into the role of key parameters in maintaining the system functionality and thus it significantly contributes to formal methods in computational systems biology.
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)
L. Brim,J. Fabriková,S. Dra?an,D. ?afránek
Electronic Proceedings in Theoretical Computer Science , 2011, DOI: 10.4204/eptcs.67.9
Abstract: In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect the imposed level of approximation provided that with increasing parameter value the approximation converges to the original continuous system. By employing this approximation technique, we present algorithms solving the reachability problem for biochemical dynamical systems. The presented method and algorithms are evaluated on several exemplary biological models and on a real case study.
Robustness Analysis for Value-Freezing Signal Temporal Logic
L. Brim,T. Vejpustek,D. ?afránek,J. Fabriková
Computer Science , 2013, DOI: 10.4204/EPTCS.125.2
Abstract: In our previous work we have introduced the logic STL*, an extension of Signal Temporal Logic (STL) that allows value freezing. In this paper, we define robustness measures for STL* by adapting the robustness measures previously introduced for Metric Temporal Logic (MTL). Furthermore, we present an algorithm for STL* robustness computation, which is implemented in the tool Parasim. Application of STL* robustness analysis is demonstrated on case studies.
Observations of vortex-like structure in the cusp-magnetosheath region during northward IMF orientation
O. Tkachenko, J. afránková, Z. Něme ek, J. im nek,L. P ech
Annales Geophysicae (ANGEO) , 2008,
Abstract: Two-point observations made by the Interball spacecraft pair unveiled a presence of a large vortex-like structure filled by slow and heated plasma in the outer cusp during periods of the positive BZ interplanetary magnetic field (IMF) component. We have observed the rotation of the magnetic field and the decrease of its magnitude connected with the presence of a hot plasma population inside the vortex. The structure starts with a clear reversal of the plasma flow caused by reconnection tailward of the cusp that turns a part of the magnetosheath plasma into the cusp. We compare the observations of two spacecraft in detail, discuss the differences between them and suggest the way of a formation such structure. Moreover, the statistical results have confirmed that this phenomenon is probably a regular feature of the high-altitude cusp, however, this relatively small structure cannot be observed too often. The alternative explanation of presented observations as a flapping of the magnetopause is taken into account and discussed.
Multifractal structure of turbulence in the magnetospheric cusp
Z. Něme ek, J. im nek, J. afránková,L. P ech
Annales Geophysicae (ANGEO) , 2004,
Abstract: Structured dispersion patterns of the ion precipitation in low- and mid-altitude cusp regions have been reported by many authors. These patterns are interpreted either as temporal features in terms of the pulsed reconnection model or as spatial changes caused by a combination of the particle velocity with the convection of magnetic field lines. It is generally expected that the spatial dispersion is predominantly observed in lower altitudes where the spacecraft crosses a wide range of geomagnetic coordinates in a short time, whereas the high-altitude spacecraft observes temporal changes because it stays nearly on the same field line for a long time. We have analyzed one pass of the INTERBALL-1/MAGION-4 satellite pair through the high-altitude cusp and found that both temporal and spatial dispersion effects are important even in the magnetopause vicinity. The analysis of the present event shows a spatial nature of the observed dispersion in the LLBL and in the plasma mantle. We have identified two sources of a mantle precipitation operating simultaneously. Our investigations suggest that besides already reported latitudinal dispersion, the longitudinal dispersion can be observed during intervals of sufficiently high east-west interplanetary magnetic field component. Full Article (PDF, 1077 KB) Special Issue Citation: Něme ek, Z., im nek, J., afránková, J., and P ech, L.: Spatial and temporal variations of the high-altitude cusp precipitation, Ann. Geophys., 22, 2441-2450, doi:10.5194/angeo-22-2441-2004, 2004. Bibtex EndNote Reference Manager XML
Formation and Stability of Cellular Carbon Foam Structures:An {\em Ab Initio} Study
Zhen Zhu,David Tománek
Physics , 2012, DOI: 10.1103/PhysRevLett.109.135501
Abstract: We use ab initio density functional calculations to study the formation and structural as well as thermal stability of cellular foam-like carbon nanostructures. These systems with a mixed $sp^2/sp^3$ bonding character may be viewed as bundles of carbon nanotubes fused to a rigid contiguous 3D honeycomb structure that can be compressed more easily by reducing the symmetry of the honeycombs. The foam may accommodate the same type of defects as graphene, and its surface may be be stabilized by terminating caps. We postulate that the foam may form under non-equilibrium conditions near grain boundaries of a carbon-saturated metal surface.
Spatial variations of b-values in the subduction zone of Central America
David A. Monterroso,Ota Kulhánek
Geofísica internacional , 2003,
Abstract: Frequency-magnitude distribution along the Mid-American Trench (MAT) has been studied by means of 2345 earthquakes during the period 1964-1994. We used the regional MIDAS catalogue with a magnitude of completeness of 4.2. To resolve the b-value as a function of depth (one dimensional approach), we applied vertically sliding windows containing a constant number of events. To obtain more details in the b distribution, we projected catalogue hypocenters in three selected regions (approximately Guatemala and El Salvador, Nicaragua, Costa Rica), onto planes perpendicular to the trench. The b-values were calculated in sliding cylindrical volumes (two-dimensional approach) containing a constant number of earthquakes and centered at nodes of a 5 km x 5 km grid. The b-value varies significantly along a large part of MAT. High b-values were identified in the upper part of the slab at depths of 80-110 km beneath Guatemala-El Salvador and at depths 130-170 km beneath Nicaragua. Anomalous (high) b-values in the lower part of the slab were located at depths of 50-90 km and 50-160 km beneath Guatemala-El Salvador and Nicaragua, respectively. Anomalies observed at the upper part of the slab may be related to dehydration and successive increase in pore pressure in the down-going lithosphere, which may generate volcanism above the anomalies in the upper part of the slab. Anomalies on the lower surface of the Wadati-Benioff zone are likely to be associated with high thermal gradients between the slab and mantle.
Phase coexistence and metal-insulator transition in few-layer phosphorene: A computational study
Jie Guan,Zhen Zhu,David Tománek
Physics , 2014, DOI: 10.1103/PhysRevLett.113.046804
Abstract: Based on {\em ab initio} density functional calculations, we propose $\gamma$-P and $\delta$-P as two additional stable structural phases of layered phosphorus besides the layered $\alpha$-P (black) and $\beta$-P (blue) phosphorus allotropes. Monolayers of some of these allotropes have a wide band gap, whereas others, including $\gamma$-P, show a metal-insulator transition caused by in-layer strain or changing the number of layers. An unforeseen benefit is the possibility to connect different structural phases at no energy cost. This becomes particularly valuable in assembling heterostructures with well-defined metallic and semiconducting regions in one contiguous layer.
Designing electrical contacts to MoS$_2$ monolayers: A computational study
Igor Popov,Gotthard Seifert,David Tománek
Physics , 2012, DOI: 10.1103/PhysRevLett.108.156802
Abstract: Studying the reason, why single-layer molybdenum disulfide (MoS$_2$) appears to fall short of its promising potential in flexible nanoelectronics, we found that the nature of contacts plays a more important role than the semiconductor itself. In order to understand the nature of MoS$_2$/metal contacts, we performed ab initio density functional theory calculations for the geometry, bonding and electronic structure of the contact region. We found that the most common contact metal (Au) is rather inefficient for electron injection into single-layer MoS$_2$ and propose Ti as a representative example of suitable alternative electrode materials.
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