TY - GEN A1 - Zaourar, Naima A1 - Hamoudi, Mohamed A1 - Mandea, Mioara A1 - Balasis, Georgios A1 - Holschneider, Matthias T1 - Wavelet-based multiscale analysis of geomagnetic disturbance T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The dynamics of external contributions to the geomagnetic field is investigated by applying time-frequency methods to magnetic observatory data. Fractal models and multiscale analysis enable obtaining maximum quantitative information related to the short-term dynamics of the geomagnetic field activity. The stochastic properties of the horizontal component of the transient external field are determined by searching for scaling laws in the power spectra. The spectrum fits a power law with a scaling exponent β, a typical characteristic of self-affine time-series. Local variations in the power-law exponent are investigated by applying wavelet analysis to the same time-series. These analyses highlight the self-affine properties of geomagnetic perturbations and their persistence. Moreover, they show that the main phases of sudden storm disturbances are uniquely characterized by a scaling exponent varying between 1 and 3, possibly related to the energy contained in the external field. These new findings suggest the existence of a long-range dependence, the scaling exponent being an efficient indicator of geomagnetic activity and singularity detection. These results show that by using magnetogram regularity to reflect the magnetosphere activity, a theoretical analysis of the external geomagnetic field based on local power-law exponents is possible. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 947 KW - geomagnetic field KW - magnetosphere KW - geomagnetic storm KW - multiscale analysis KW - spectral exponent Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436912 SN - 1866-8372 VL - 65 IS - 12 SP - 1525 EP - 1540 ER - TY - GEN A1 - Van Bel, Michiel A1 - Proost, Sebastian A1 - Van Neste, Christophe A1 - Deforce, Dieter A1 - Van de Peer, Yves A1 - Vandepoele, Klaas T1 - TRAPID BT - an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 900 KW - gene ontology KW - gene family KW - functional annotation KW - reference database KW - reference proteomes Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436409 SN - 1866-8372 IS - 900 ER - TY - GEN A1 - Molahajloo, Shahla A1 - Pirhayati, Mohammad T1 - Traces of pseudo-differential operators on compact and Hausdorff groups T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - We give a characterization of and a trace formula for trace class pseudo-differential operators on compact Hausdorff groups. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 893 KW - pseudo-differential operators KW - compact groups Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436371 SN - 1866-8372 IS - 893 SP - 361 EP - 369 ER - TY - GEN A1 - Karpuz, Eylem Guzel A1 - Çevik, Ahmet Sinan A1 - Koppitz, Jörg A1 - Cangul, Ismail Naci T1 - Some fixed-point results on (generalized) Bruck-Reilly ∗-extensions of monoids T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In this paper, we determine necessary and sufficient conditions for Bruck-Reilly and generalized Bruck-Reilly ∗-extensions of arbitrary monoids to be regular, coregular and strongly π-inverse. These semigroup classes have applications in various field of mathematics, such as matrix theory, discrete mathematics and p-adic analysis (especially in operator theory). In addition, while regularity and coregularity have so many applications in the meaning of boundaries (again in operator theory), inverse monoids and Bruck-Reilly extensions contain a mixture fixed-point results of algebra, topology and geometry within the purposes of this journal. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 942 KW - Bruck-Reilly extension KW - generalized Bruck-Reilly ∗-extension KW - π -inverse monoid KW - regular monoid Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432701 SN - 1866-8372 IS - 942 ER - TY - GEN A1 - Goychuk, Igor A1 - Kharchenko, Vasyl O. T1 - Rocking subdiffusive ratchets BT - origin, optimization and efficiency T2 - Mathematical Modelling of Natural Phenomena N2 - We study origin, parameter optimization, and thermodynamic efficiency of isothermal rocking ratchets based on fractional subdiffusion within a generalized non-Markovian Langevin equation approach. A corresponding multi-dimensional Markovian embedding dynamics is realized using a set of auxiliary Brownian particles elastically coupled to the central Brownian particle (see video on the journal web site). We show that anomalous subdiffusive transport emerges due to an interplay of nonlinear response and viscoelastic effects for fractional Brownian motion in periodic potentials with broken space-inversion symmetry and driven by a time-periodic field. The anomalous transport becomes optimal for a subthreshold driving when the driving period matches a characteristic time scale of interwell transitions. It can also be optimized by varying temperature, amplitude of periodic potential and driving strength. The useful work done against a load shows a parabolic dependence on the load strength. It grows sublinearly with time and the corresponding thermodynamic efficiency decays algebraically in time because the energy supplied by the driving field scales with time linearly. However, it compares well with the efficiency of normal diffusion rocking ratchets on an appreciably long time scale. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 622 KW - anomalous Brownian motion KW - generalized Langevin equation KW - memory effects KW - viscoelasticity KW - ratchet transport KW - stochastic Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-416138 SN - 1866-8372 IS - 622 ER - TY - GEN A1 - Green, Lucie M. A1 - Kliem, Bernhard T1 - Observations of flux rope formation prior to coronal mass ejections T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Understanding the magnetic configuration of the source regions of coronal mass ejections (CMEs) is vital in order to determine the trigger and driver of these events. Observations of four CME productive active regions are presented here, which indicate that the pre-eruption magnetic configuration is that of a magnetic flux rope. The flux ropes are formed in the solar atmosphere by the process known as flux cancellation and are stable for several hours before the eruption. The observations also indicate that the magnetic structure that erupts is not the entire flux rope as initially formed, raising the question of whether the flux rope is able to undergo a partial eruption or whether it undergoes a transition in specific flux rope configuration shortly before the CME. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 607 KW - Sun: coronal mass ejections (CMEs) KW - Sun: activity Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-416103 SN - 1866-8372 IS - 607 ER - TY - GEN A1 - Kaminski, Roland A1 - Schaub, Torsten H. A1 - Siegel, Anne A1 - Videla, Santiago T1 - Minimal intervention strategies in logical signaling networks with ASP T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 596 KW - systems biology KW - transduction KW - circuits KW - models KW - sets Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415704 SN - 1866-8372 IS - 4-5 SP - 675 EP - 690 ER - TY - GEN A1 - Driel-Gesztelyi, L. van A1 - Baker, Daniel N. A1 - Török, Tibor A1 - Pariat, Etienne A1 - Green, L. M. A1 - Williams, D. R. A1 - Carlyle, J. A1 - Valori, G. A1 - Démoulin, Pascal A1 - Matthews, S. A. A1 - Kliem, Bernhard A1 - Malherbe, J.-M. T1 - Magnetic reconnection driven by filament eruption in the 7 June 2011 event T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - During an unusually massive filament eruption on 7 June 2011, SDO/AIA imaged for the first time significant EUV emission around a magnetic reconnection region in the solar corona. The reconnection occurred between magnetic fields of the laterally expanding CME and a neighbouring active region. A pre-existing quasi-separatrix layer was activated in the process. This scenario is supported by data-constrained numerical simulations of the eruption. Observations show that dense cool filament plasma was re-directed and heated in situ, producing coronal-temperature emission around the reconnection region. These results provide the first direct observational evidence, supported by MHD simulations and magnetic modelling, that a large-scale re-configuration of the coronal magnetic field takes place during solar eruptions via the process of magnetic reconnection. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 608 KW - MHD KW - instabilities KW - Sun: activity KW - magnetic fields KW - coronal mass ejections (CMEs) KW - filaments KW - methods: numerical KW - data analysis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415671 IS - 608 SP - 502 EP - 503 ER - TY - GEN A1 - Delikostidis, Ioannis A1 - Engel, Juri A1 - Retsios, Bas A1 - Elzakker, Corné P.J.M. van A1 - Kraak, Menno-Jan A1 - Döllner, Jürgen Roland Friedrich T1 - Increasing the usability of pedestrian navigation interfaces by means of landmark visibility analysis T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Communicating location-specific information to pedestrians is a challenging task which can be aided by user-friendly digital technologies. In this paper, landmark visibility analysis, as a means for developing more usable pedestrian navigation systems, is discussed. Using an algorithmic framework for image-based 3D analysis, this method integrates a 3D city model with identified landmarks and produces raster visibility layers for each one. This output enables an Android phone prototype application to indicate the visibility of landmarks from the user's actual position. Tested in the field, the method achieves sufficient accuracy for the context of use and improves navigation efficiency and effectiveness. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 599 KW - pedestrian navigation KW - landmark visibility KW - user-centred design KW - usability testing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415500 SN - 1866-8372 IS - 599 SP - 523 EP - 537 ER - TY - GEN A1 - Thomas, Philipp A1 - Matuschek, Hannes A1 - Grima, Ramon T1 - How reliable is the linear noise approximation of gene regulatory networks? T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Background: The linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first order reactions or for networks involving bimolecular reactions and large numbers of molecules. It is however well known that gene regulation involves bimolecular interactions with molecule numbers as small as a single copy of a particular gene. It is therefore questionable how reliable are the LNA predictions for these systems. Results: We implement in the software package intrinsic Noise Analyzer (iNA), a system size expansion based method which calculates the mean concentrations and the variances of the fluctuations to an order of accuracy higher than the LNA. We then use iNA to explore the parametric dependence of the Fano factors and of the coefficients of variation of the mRNA and protein fluctuations in models of genetic networks involving nonlinear protein degradation, post-transcriptional, post-translational and negative feedback regulation. We find that the LNA can significantly underestimate the amplitude and period of noise-induced oscillations in genetic oscillators. We also identify cases where the LNA predicts that noise levels can be optimized by tuning a bimolecular rate constant whereas our method shows that no such regulation is possible. All our results are confirmed by stochastic simulations. Conclusion: The software iNA allows the investigation of parameter regimes where the LNA fares well and where it does not. We have shown that the parametric dependence of the coefficients of variation and Fano factors for common gene regulatory networks is better described by including terms of higher order than LNA in the system size expansion. This analysis is considerably faster than stochastic simulations due to the extensive ensemble averaging needed to obtain statistically meaningful results. Hence iNA is well suited for performing computationally efficient and quantitative studies of intrinsic noise in gene regulatory networks. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 876 KW - Gene Regulatory Network KW - Stochastic Simulation KW - Bimolecular Reaction KW - Fano Factor KW - Reaction Rate Constant Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435028 SN - 1866-8372 IS - 876 ER - TY - GEN A1 - Bentele, Kajetan A1 - Saffert, Paul A1 - Rauscher, Robert A1 - Ignatova, Zoya A1 - Bluethgen, Nils T1 - Efficient translation initiation dictates codon usage at gene start T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5-10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 912 KW - codon usage KW - mRNA structure KW - translation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441337 SN - 1866-8372 IS - 912 ER - TY - GEN A1 - Chechkin, Aleksei V. A1 - Zaid, Irwin M. A1 - Lomholt, Michael A. A1 - Sokolov, Igor M. A1 - Metzler, Ralf T1 - Bulk-mediated surface diffusion on a cylinder in the fast exchange limit T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - In various biological systems and small scale technological applications particles transiently bind to a cylindrical surface. Upon unbinding the particles diffuse in the vicinal bulk before rebinding to the surface. Such bulk-mediated excursions give rise to an effective surface translation, for which we here derive and discuss the dynamic equations, including additional surface diffusion. We discuss the time evolution of the number of surface-bound particles, the effective surface mean squared displacement, and the surface propagator. In particular, we observe sub- and superdiffusive regimes. A plateau of the surface mean-squared displacement reflects a stalling of the surface diffusion at longer times. Finally, the corresponding first passage problem for the cylindrical geometry is analysed. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 593 KW - Bulk-mediated diffusion; KW - anomalous diffusion KW - Levy flights KW - stochastic processes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415480 SN - 1866-8372 IS - 593 SP - 114 EP - 126 ER - TY - GEN A1 - Banbara, Mutsunori A1 - Soh, Takehide A1 - Tamura, Naoyuki A1 - Inoue, Katsumi A1 - Schaub, Torsten H. T1 - Answer set programming as a modeling language for course timetabling T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The course timetabling problem can be generally defined as the task of assigning a number of lectures to a limited set of timeslots and rooms, subject to a given set of hard and soft constraints. The modeling language for course timetabling is required to be expressive enough to specify a wide variety of soft constraints and objective functions. Furthermore, the resulting encoding is required to be extensible for capturing new constraints and for switching them between hard and soft, and to be flexible enough to deal with different formulations. In this paper, we propose to make effective use of ASP as a modeling language for course timetabling. We show that our ASP-based approach can naturally satisfy the above requirements, through an ASP encoding of the curriculum-based course timetabling problem proposed in the third track of the second international timetabling competition (ITC-2007). Our encoding is compact and human-readable, since each constraint is individually expressed by either one or two rules. Each hard constraint is expressed by using integrity constraints and aggregates of ASP. Each soft constraint S is expressed by rules in which the head is the form of penalty (S, V, C), and a violation V and its penalty cost C are detected and calculated respectively in the body. We carried out experiments on four different benchmark sets with five different formulations. We succeeded either in improving the bounds or producing the same bounds for many combinations of problem instances and formulations, compared with the previous best known bounds. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 594 KW - answer set programming KW - educational timetabling KW - course timetabling Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415469 SN - 1866-8372 IS - 594 SP - 783 EP - 798 ER - TY - GEN A1 - Gschwind, Yves J. A1 - Kressig, Reto W. A1 - Lacroix, Andre A1 - Mühlbauer, Thomas A1 - Pfenninger, Barbara A1 - Granacher, Urs T1 - A best practice fall prevention exercise program to improve balance, strength/power, and psychosocial health in older adults BT - study protocol for a randomized controlled trial T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - Background: With increasing age neuromuscular deficits (e.g., sarcopenia) may result in impaired physical performance and an increased risk for falls. Prominent intrinsic fall-risk factors are age-related decreases in balance and strength / power performance as well as cognitive decline. Additional studies are needed to develop specifically tailored exercise programs for older adults that can easily be implemented into clinical practice. Thus, the objective of the present trial is to assess the effects of a fall prevention program that was developed by an interdisciplinary expert panel on measures of balance, strength / power, body composition, cognition, psychosocial well-being, and falls self-efficacy in healthy older adults. Additionally, the time-related effects of detraining are tested. Methods/Design: Healthy old people (n = 54) between the age of 65 to 80 years will participate in this trial. The testing protocol comprises tests for the assessment of static / dynamic steady-state balance (i.e., Sharpened Romberg Test, instrumented gait analysis), proactive balance (i.e., Functional Reach Test; Timed Up and Go Test), reactive balance (i.e., perturbation test during bipedal stance; Push and Release Test), strength (i.e., hand grip strength test; Chair Stand Test), and power (i.e., Stair Climb Power Test; countermovement jump). Further, body composition will be analysed using a bioelectrical impedance analysis system. In addition, questionnaires for the assessment of psychosocial (i.e., World Health Organisation Quality of Life Assessment-Bref), cognitive (i.e., Mini Mental State Examination), and fall risk determinants (i.e., Fall Efficacy Scale -International) will be included in the study protocol. Participants will be randomized into two intervention groups or the control / waiting group. After baseline measures, participants in the intervention groups will conduct a 12-week balance and strength / power exercise intervention 3 times per week, with each training session lasting 30 min. (actual training time). One intervention group will complete an extensive supervised training program, while the other intervention group will complete a short version (` 3 times 3') that is home-based and controlled by weekly phone calls. Post-tests will be conducted right after the intervention period. Additionally, detraining effects will be measured 12 weeks after program cessation. The control group / waiting group will not participate in any specific intervention during the experimental period, but will receive the extensive supervised program after the experimental period. Discussion: It is expected that particularly the supervised combination of balance and strength / power training will improve performance in variables of balance, strength / power, body composition, cognitive function, psychosocial well-being, and falls self-efficacy of older adults. In addition, information regarding fall risk assessment, dose-response-relations, detraining effects, and supervision of training will be provided. Further, training-induced health-relevant changes, such as improved performance in activities of daily living, cognitive function, and quality of life, as well as a reduced risk for falls may help to lower costs in the health care system. Finally, practitioners, therapists, and instructors will be provided with a scientifically evaluated feasible, safe, and easy-to-administer exercise program for fall prevention. KW - seniors KW - fall risk assessment KW - resistance training KW - postural stability Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-427104 SN - 1866-8364 IS - 604 ER -