Characteristics of the polymer transport in ratchet systems

Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover also deterministic potential switching mechanisms, energetic efficiency and non-uniform charge distributions. We also use currents in the non-equilibrium steady state to identify the dominating mechanisms that lead to polymer transportation and analyze the evolution of the macroscopic state (e.g., total and head-to-head lengths) of the polymers. Several numerical methods are used to solve the master equations and nonlinear optimization problems. The dominating transport mechanisms are found via graph optimization methods. The results show that small changes in the molecule structure and the environment variables can lead to large increases of the drift. The drift and the coherence can be amplified by using deterministic flashing potentials and customized polymer charge distributions. Identifying the dominating transport mechanism by graph analysis tools is found to give insight in how the molecule is transported by the ratchet effect.Comment: 35 pages, 17 figures, to appear in Phys. Rev.

Three-Body Halos. II. from Two- to Three-Body Asymptotics

The large distance behavior of weakly bound three-body systems is investigated. The Schr\"{o}dinger equation and the Faddeev equations are reformulated by an expansion in eigenfunctions of the angular part of a corresponding operator. The resulting coupled set of effective radial equations are then derived. Both two- and three-body asymptotic behavior are possible and their relative importance is studied for systems where subsystems may be bound. The system of two nucleons outside a core is studied numerically in detail and the character of possible halo structure is pointed out and investigated.Comment: 16 pages, compressed and uuencoded PosrScript file, IFA-94/3

Spin-dependent effective interactions for halo nuclei

We discuss the spin-dependence of the effective two-body interactions appropriate for three-body computations. The only reasonable choice seems to be the fine and hyperfine interactions known for atomic electrons interacting with the nucleus. One exception is the nucleon-nucleon interaction imposing a different type of symmetry. We use the two-neutron halo nucleus 11Li as illustration. We demonstrate that models with the wrong spin-dependence are basically without predictive power. The Pauli forbidden core and valence states must be consistently treated.Comment: TeX file, 6 pages, 3 postscript figure

From quantum graphs to quantum random walks

We give a short overview over recent developments on quantum graphs and outline the connection between general quantum graphs and so-called quantum random walks.Comment: 14 pages, 6 figure

Molecular tracing of viral diseases in aquaculture

Molecular Tracing of Viral Diseases in Aquaculture = Traçage Moléculaire des Maladies Virales en Aquaculture : Colloque, Montpellier (FRA), 2015/01/27-29International audienc

Parameterized Algorithms for Generalizations of Directed Feedback Vertex Set

The Directed Feedback Vertex Set (DFVS) problem takes as input a directed graph~$G$ and seeks a smallest vertex set~$S$ that hits all cycles in $G$. This is one of Karp's 21 $\mathsf{NP}$-complete problems. Resolving the parameterized complexity status of DFVS was a long-standing open problem until Chen et al. [STOC 2008, J. ACM 2008] showed its fixed-parameter tractability via a $4^kk! n^{\mathcal{O}(1)}$-time algorithm, where $k = |S|$. Here we show fixed-parameter tractability of two generalizations of DFVS: - Find a smallest vertex set $S$ such that every strong component of $G - S$ has size at most~$s$: we give an algorithm solving this problem in time $4^k(ks+k+s)!\cdot n^{\mathcal{O}(1)}$. This generalizes an algorithm by Xiao [JCSS 2017] for the undirected version of the problem. - Find a smallest vertex set $S$ such that every non-trivial strong component of $G - S$ is 1-out-regular: we give an algorithm solving this problem in time $2^{\mathcal{O}(k^3)}\cdot n^{\mathcal{O}(1)}$. We also solve the corresponding arc versions of these problems by fixed-parameter algorithms

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P < 2.2 × 10-7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent 'false leads' with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition

A Cognitive Model of an Epistemic Community: Mapping the Dynamics of Shallow Lake Ecosystems

We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices of the individual cognitive maps and the collective cognitive map produced by augmentation. The graph theoretical indices revealed internal cycles showing non-linear dynamics in the shallow lake ecosystem. The ecological processes were organized democratically without a top-down hierarchical structure. The steady state condition of the generic model was a characteristic turbid shallow lake ecosystem since there were no dynamic environmental changes that could cause shifts between a turbid and a clearwater state, and the generic model indicated that only a dynamic disturbance regime could maintain the clearwater state. The model developed herein captured the empirical behavior of shallow lakes, and contained the basic model of the Alternative Stable States Theory. In addition, our model expanded the basic model by quantifying the relative effects of connections and by extending it. In our expanded model we ran 4 simulations: harvesting submerged plants, nutrient reduction, fish removal without nutrient reduction, and biomanipulation. Only biomanipulation, which included fish removal and nutrient reduction, had the potential to shift the turbid state into clearwater state. The structure and relationships in the generic model as well as the outcomes of the management simulations were supported by actual field studies in shallow lake ecosystems. Thus, fuzzy cognitive mapping methodology enabled us to understand the complex structure of shallow lake ecosystems as a whole and obtain a valid generic model based on tacit knowledge of experts in the field.Comment: 24 pages, 5 Figure