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Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care
No full textReplica exchange MD simulations of Two-Dimensional Water in Graphene Nanocapillaries: Rhombic Versus Square Structures, Proton Ordering, and Phase Transitions
No full textHydrogen bond patterns, proton ordering, and phase transitions of monolayer ice in two-dimensional hydrophobic confinement are fundamentally different from those found for bulk ice. To investigate the behavior of quasi-2D ice, we perform molecular dynamics simulations of water confined between fixed graphene plates at a distance of 0.65 nm. While experimental results are still limited and theoretical investigations are often based on a single force field model, this work presents a systematic study using different water force fields, i.e. SPCE, TIP3P, TIP4P, TIP4P/ICE, TIP5P. The water-graphene interaction is modeled by effective Lennard-Jones potentials previously derived from high-level ab initio CCSD(T) calculations of water adsorbed on graphene [Phys. Chem. Chem. Phys. 15, 4995 (2013)]. The water occupancy of the graphene capillary at a pressure of 1000 MPa is determined to be between 13.5 and 13.9 water molecules per square nanometer, depending on the choice of the water force field. Based on these densities, we explore the structure and dynamics of quasi-2D water for temperatures ranging from 200 K to about 600 K for each of the five force fields. To ensure complete sampling of the configurational space and to overcome barriers separating metastable structures, these simulations are based on the replica exchange molecular dynamics technique. We report different tetragonal hydrogen bond patterns which are classified as nearly square or as rhombic. While many of these arrangements are flat, in some cases puckered arrangements are found, too.
Also the proton ordering of the quasi-2D water structures is considered, allowing to identify them as ferroelectric, ferrielectric or antiferroelectric. For temperatures between 200 K and 400 K we find several second-order phase transitions from one ice structure to another, changing in many cases both the arrangements of the oxygen atoms and the proton ordering.
For temperatures between 400 K and 600 K there are melting-like transitions from a monolayer of ice to a monolayer of liquid water. These first-order phase transitions have a latent heat between 3.4 and 4.0 kJ/mol. Both the values of the transition temperatures and of the latent heats display considerable model dependence for the five different water models investigated here
A semi-implicit compressible model for atmospheric flows with seamless access to soundproof and hydrostatic dynamics
Get PDFWe introduce a second-order numerical scheme for compressible atmospheric motions at small to planetary scales. The collocated finite volume method treats the advection of mass, momentum, and mass-weighted potential temperature in conservation form while relying on Exner pressure for the pressure gradient term. It discretises the rotating compressible equations by evolving full variables rather than perturbations around a background state, and operates with time steps constrained by the advection speed only. Perturbation variables are only used as auxiliary quantities in the formulation of the elliptic problem. Borrowing ideas on forward-in-time differencing, the algorithm reframes the authors' previously proposed schemes into a sequence of implicit midpoint, advection, and implicit trapezoidal steps that allows for a time integration unconstrained by the internal gravity wave speed. Compared with existing approaches, results on a range of benchmarks of nonhydrostatic- and
hydrostatic-scale dynamics are competitive. The test suite includes a new planetary-scale inertia-gravity wave test highlighting the properties of the scheme and its large time step capabilities. In the hydrostatic-scale cases the model is run in pseudo-incompressible and hydrostatic mode with simple switching within a uniform discretization framework. The differences with the compressible runs return expected relative magnitudes. By providing seamless access to soundproof and hydrostatic dynamics, the developments represent a necessary step towards an all-scale blended multimodel solver
Creep on seismogenic faults: Insights from analogue earthquake experiments
Get PDFTectonic faults display a range of slip behaviors including continuous and episodic slip covering rates of more than 10 orders of magnitude (m/s). The physical control of such kinematic observations remains ambiguous. To gain insight into the slip behavior of brittle faults we performed laboratory stick-slip experiments using a rock analogue, granular material. We realized conditions under which our seismogenic fault analogue shows a variety of slip behaviors ranging from slow, quasi continuous creep to episodic slow slip to dynamic rupture controlled by a limited number of parameters. We explore a wide parameter space by varying loading rate from those corresponding to interseismic to postseismic rates and normal loads equivalent to hydrostatic to lithostatic conditions at seismogenic depth. The experiments demonstrate that significant interseismic creep and earthquakes may not be mutually exclusive phenomena and that creep signals vary systematically with the fault’s seismic potential. Accordingly, the transience of interseismic creep scales with fault strength and seismic coupling as well as with the maturity of the seismic cycle. Loading rate independence of creep signals suggests that mechanical properties of faults (e.g. seismic coupling) can be inferred from shortterm observations (e.g. aftershock sequences). Moreover, we observe the number and size of small episodic slip events to systematically increase towards the end of the seismic cycle providing an observable proxy of the relative shear stress state on seismogenic faults. Modelling the data suggest that for very weak faults in a late stage of their seismic cycle, the observed creep systematics may lead to the chimera of a perennially creeping fault releasing stress by continuous creep and/or transient slow slip instead of large earthquakes
Orthogonality of fluxes in general nonlinear reaction networks
No full textWe consider the chemical reaction networks and study currents in these systems. Reviewing recent decompo- sition of rate functionals from large deviation theory for Markov processes, we adapt these results for reaction networks. In particular, we state a suitable generalisation of orthogonality of forces in these systems, and derive an inequality that bounds the free energy loss and Fisher information by the rate functional
Flow Structures and Scale Interactions in Stable Atmospheric Boundary Layer Turbulence
No full textAtmospheric boundary layer turbulence in stably stratified conditions is characterised by an intermittent, unsteady behaviour. The intermittency can result from localised flow acceleration due to non-turbulent motions, which can exhibit structures such as ramp-cliff convective patterns, waves or microfronts. Based on a timeseries clustering method, we characterise interactions between scales of motion in a dataset of near-surface stable boundary layer turbulence. Individual flow structures are investigated in two weak-wind flow regimes exhibiting distinct scale interaction properties. The signature of flow structures differs despite comparable wind and stability properties
Using the concept of the Dynamic State Index for a scale-dependent analysis of atmospheric blocking
No full textThe present study investigates the phenomenon of atmospheric blocking using a cascade of Dynamic State Indices. The different DSI variants signalize model dependent aspects of atmospheric blockings, which allows for a scale-dependent analysis of the corresponding flow pattern. Starting from the primitive equations, approximations lead to the reduced equations of the quasi-geostrophic model and the further approximated barotropic Rossby model. For each model a corresponding Dynamic State Index can be derived. All DSI variants underlie the same concept, such that the three variants capture the stationary and adiabatic state as well as their local deviations. The DSI variants are investigated in the framework of a case study of the atmospheric blocking phenomenon over the European part of Russia in summer 2010. Two main results are presented: (i) The anticyclone of the block is characterized by a large area with nearly vanishing DSI values in all three models. In contrast, the typical DSI dipoles along the jet that surrounds the block differ, dependent on the level of the model reduction, not only in the spatial extent but also in the amplitude. (ii) The DSI variants shows the difference of the impact of the diabatic processes related to precipitation concerning the back and front side of the high. The amplitudes of the negative mean of DSI values on the back side of the high, respectively the amplitudes of the positive DSI mean on the front side, is larger for the primitive equations than for the quasi-geostrophic model. Thus, the DSI is a unified concept for atmospheric dynamics designed to diagnose the scale-dependent footprints of the steady and adiabatic conditions as well as non-steady and diabatic processes depending on the level of the model reduction
Approximate String Matching - Improving Data Structures and Algorithms
No full textThis thesis addresses important algorithms and data structures used in sequence analysis for applications such as read mapping. First, we give an overview on state-of-the-art FM indices and present the latest improvements. In particular, we will introduce a recently published FM index based on a new data structure: EPR dictionaries. This rank data structures allows search steps in constant time for unidirectional and bidirectional FM indices. To our knowledge this is the first and only constant-time implementation of a bidirectional FM index at the time of writing. We show that its running time is not only optimal in theory, but currently also outperforms all available FM index implementations in practice.
Second, we cover approximate string matching in bidirectional indices. To improve the running time and make higher error rates suitable for index-based searches, we introduce an integer linear program for finding optimal search strategies. We show that it is significantly faster than other search strategies in indices and cover additional improvements such as hybrid approaches of index-based searches with in-text verification, i.e., at some point the partially matched string is located and verified directly in the text.
Finally, we present a yet unpublished algorithm for fast computation of the mappability of genomic sequences. Mappability is a measure for the uniqueness of a genome by counting how often each -mer of the sequence occurs with a certain error threshold in the genome itself. We suggest two applications of mappability with prototype implementations: First, a read mapper incorporating the mappability information to improve the running time when mapping reads that match highly repetitive regions, and second, we use the mappability information to identify phylogenetic markers in a set of similar strains of the same species by the example of E. coli. Unique regions allow identifying and distinguishing even highly similar strains using unassembled sequencing data.
The findings in this thesis can speed up many applications in bioinformatics as we demonstrate for read mapping and computation of mappability, and give suggestions for further research in this field
Network measures of mixing
Get PDFABSTRACT
Transport and mixing processes in fluid flows can be studied directly from Lagrangian trajectory data, such as those obtained from particle tracking experiments. Recent work in this context highlights the application of graph-based approaches, where trajectories serve as nodes and
some similarity or distance measure between them is employed to build a (possibly weighted) network, which is then analyzed using spectral
methods. Here, we consider the simplest case of an unweighted, undirected network and analytically relate local network measures such as
node degree or clustering coeffient to flow structures. In particular, we use these local measures to divide the family of trajectories into groups
of similar dynamical behavior via manifold learning methods
Discretization error estimates for penalty formulations of a linearized Canham-Helfrich-type energy
Get PDFThis article is concerned with minimization of a fourth-order linearized Canham–Helfrich energy subject
to Dirichlet boundary conditions on curves inside the domain. Such problems arise in the modeling of
the mechanical interaction of biomembranes with embedded particles. There, the curve conditions result
from the imposed particle–membrane coupling. We prove almost-H. 5. 2 regularity of the solution and then
consider two possible penalty formulations. For the combination of these penalty formulations with a
Bogner–Fox–Schmit finite element discretization, we prove discretization error estimates that are optimal
in view of the solution’s reduced regularity. The error estimates are based on a general estimate for linear
penalty problems in Hilbert spaces. Finally, we illustrate the theoretical results by numerical computations.
An important feature of the presented discretization is that it does not require the particle boundary to be
resolved. This is crucial to avoid re-meshing if the presented problem arises as a subproblem in a model
where particles are allowed to move or rotate