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Analogue modelling of basin inversion: a review and future perspectives
No full textBasin inversion involves the reversal of subsidence in a basin due to compressional tectonic forces, leading to uplift of the basin’s sedimentary infill. A thorough understanding of basin inversion is of great importance for scientific, societal and economic reasons. Analogue tectonic modelling forms a key part our efforts to improve our understanding of basin inversion processes, and researchers have conducted numerous studies on this topic. In this review paper we recap the advances in knowledge of basin inversion tectonics acquired through analogue modelling studies, providing an up-to-date summary of the state of analogue modelling of basin inversion. We describe the different definitions of basin inversion that are being applied by researchers, why basin inversion has been historically an important research topic, and what the general mechanics involved in basin inversion are. We subsequently treat the wide range of different experimental approaches used for basin inversion modelling, with attention to the various materials, set-ups and techniques used for monitoring and analysing the model results. Our new systematic overviews of generalized results reveal the diversity of model results, depending greatly on the chosen set-up, model layering and (oblique) kinematics of inversion, as well as 3D along-strike structural and kinematic variations in the system. We show how analogue modelling results are in good agreement with numerical models, and how these results help to better understand natural examples of basin inversion. In addition to reviewing the past efforts in the field of analogue modelling, we also shed light on future modelling challenges and identify a number of opportunities for follow-up research. These include the testing of force-boundary conditions, adding geological processes such as sedimentation, transport and erosion, applying state-of-the-art modelling and quantification techniques, and establishing best modelling practices. We also suggest expanding the scope of basin inversion modelling beyond the traditional upper crustal "North Sea style" of inversion, which may contribute to the on-going search for clean energy resources. It follows that basin inversion modelling can bring valuable new insights, providing a great incentive to continue our efforts in this field. We therefore hope that this review paper will form an inspiration for future analogue modelling studies of basin inversion
Critical Assessment of Metagenome Interpretation - the second round of challenges
No full textEvaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ∼1,700 novel and known microbial genomes, as well as ∼600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results.
Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.
Competing Interest Statement:
A.E.D. co-founded Longas Technologies Pty Ltd, a company aimed at development of synthetic long-read sequencing technologies
Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations
No full textWe generalise the two-sided Bogoliubov inequality for classical particles (Delle Site et al. in J Stat Mech Theory Exp 083201, 2017 to systems of quantum particles. As in the classical set-up, the inequality leads to upper and lower bounds for the free energy difference associated with the partitioning of a large system into smaller, independent subsystems. From a thermodynamic modelling point of view, the free energy difference determines the finite size correction needed to consistently treat a small system as a representation of a large system. Applications of the bounds to quantify finite size effects are ubiquitous in physics, chemistry, material science, or biology, to name just a few; in particular, it is relevant for molecular dynamics simulations in which a small portion of a system is usually taken as representative of the idealized large system
Quantum dynamics using path integral coarse-graining
No full textThe vibrational spectra of condensed and gas-phase systems are influenced by thequantum-mechanical behavior of light nuclei. Full-dimensional simulations of approximate quantum dynamics are possible thanks to the imaginary time path-integral (PI) formulation of quantum statistical mechanics, albeit at a high computational cost which increases sharply with decreasing temperature. By leveraging advances in machine-learned coarse-graining, we develop a PI method with the reduced computational cost of a classical simulation. We also propose a simple temperature elevation scheme to significantly attenuate the artifacts of standard PI approaches as well as eliminate the unfavorable temperature scaling of the computational cost. We illustrate the approach, by calculating vibrational spectra using standard models of water molecules and bulk water, demonstrating significant computational savings and dramatically improved accuracy compared to more expensive reference approaches. Our simple, efficient, and accurate method has prospects for routine calculations of vibrational spectra for a wide range of molecular systems - with an explicit treatment of the quantum nature of nuclei
Markovian embedding of generalized Langevin equations with a nonlinear friction kernel and configuration-dependent mass
No full textWe consider a generalized Langevin equation (GLE) in which the deterministic force, the mass and
the friction kernel are configuration-dependent, i.e. general nonlinear functions of the reaction coordinate. We
introduce a projection operator that allows for a self-consistent Markovian embedding of such GLEs. Selfconsistency
means that trajectories generated by the Markovian embedding are described by a GLE with the
same configuration-dependent deterministic force, mass and friction kernel. Using the projection operator, we
derive a closed-form relation between the parameters of the Markovian embedding Langevin equations and the
parameters of the GLE. This is accomplished by applying the projection operator formalism to the system of
Markovian embedding stochastic equations
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences
No full textBackground
The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software.
Results
We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version.
Conclusions
With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases
Strain signals governed by frictional-elastoplastic interaction of the upper plate and shallow subduction megathrust interface over seismic cycles
No full textUnderstanding the behavior of the shallow portion of the subduction zone, which generates the largest earthquakes and devastating tsunamis, is a vital step forward in earthquake geoscience. Monitoring only a fraction of a single megathrust earthquake cycle and the offshore location of the source of these earthquakes are the foremost reasons for the insufficient understanding. The frictional-elastoplastic interaction between the interface and its overlying wedge causes variable surface strain signals such that the wedge strain patterns may reveal the mechanical state of the interface. We employ Seismotectonic Scale Modeling and simplify elastoplastic megathrust subduction, generate hundreds of analog seismic cycles at laboratory scale, and monitor the surface strain signals over the model's forearc over high to low temporal resolutions. We establish two coseismically compressional and extensional wedge configurations to explore the mechanical and kinematic interaction between the shallow wedge and the interface. Our results demonstrate that this interaction can partition the wedge into different segments such that the anlastic extensional segment overlays the seismogenic zone at depth. Moreover, the different segments of the wedge may switch their state from compression/extension to extension/compression domains. We highlight that a more segmented upper plate represents megathrust subduction that generates more characteristic and periodic events. Additionally, the strain time series reveals that the strain state may remain quasi-stable over a few seismic cycles in the coastal zone and then switch to the opposite mode. These observations are crucial for evaluating earthquake-related morphotectonic markers (i.e., marine terraces) and short-term interseismic GPS time-series onshore (coastal region)
Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA
No full textNext-Generation Sequencing technologies generate a vast and exponentially increasing amount of sequence data. The Interleaved Bloom Filter (IBF) is a novel indexing data structure which is state-of-the-art for distributing approximate queries with an in-memory data structure. With it, a main task of sequence analysis pipelines, (approximately) searching large reference data sets for sequencing reads or short sequence patterns like genes, can be significantly accelerated. To meet performance and energy-efficiency requirements, we chose a co-design approach of the IBF data structure on the FPGA platform. Further, our OpenCL-based implementation allows a seamless integration into the widely used SeqAn C++ library for biological sequence analysis. Our algorithmic design and optimization strategy takes advantage of FPGA-specific features like shift register and the parallelization potential of many bitwise operations. We designed a well-chosen schema to partition data across the different memory domains on the FPGA platform using the Shared Virtual Memory concept. We can demonstrate significant improvements in energy efficiency of up to 19 times and in performance of up to 5.6 times, respectively, compared to a well-tuned, multithreaded CPU reference
An Interactive Approach for Identifying Structure Definitions
Get PDFOur ability to grasp and understand complex phenomena is essentially based on recognizing
structures and relating these to each other. For example, any meteorological description of
a weather condition and explanation of its evolution recurs to meteorological structures,
such as convection and circulation structures, cloud fields and rain fronts. All of these
are spatiotemporal structures, defined by time-dependent patterns in the underlying fields.
Typically, such a structure is defined by a verbal description that corresponds to the more or
less uniform, often somewhat vague mental images of the experts.
However, a precise, formal definition of the structures or, more generally, concepts is often
desirable, e.g., to enable automated data analysis or the development of phenomenological
models. Here, we present a systematic approach and an interactive tool to obtain formal
definitions of spatiotemporal structures. The tool enables experts to evaluate and compare
different structure definitions on the basis of data sets with time-dependent fields that
contain the respective structure. Since structure definitions are typically parameterized, an
essential part is to identify parameter ranges that lead to desired structures in all time steps.
In addition, it is important to allow a quantitative assessment of the resulting structures
simultaneously. We demonstrate the use of the tool by applying it to two meteorological
examples: finding structure definitions for vortex cores and center lines of temporarily
evolving tropical cyclones.
Ideally, structure definitions should be objective and applicable to as many data sets as
possible. However, finding such definitions, e.g., for the common atmospheric structures
in meteorology, can only be a long-term goal. The proposed procedure, together with the
presented tool, is just a first systematic approach aiming at facilitating this long and arduous
way.
Keywords: Visual data analysis; Coherent and persistent structures; Atmospheric vortices;
Tropical storms;
Diffraction of shock waves through a non-quiescent medium
No full textAn investigation of shock diffraction through a non-quiescent background medium is presented using both experimental and numerical techniques. Unlike diffracting shocks in quiescent media, a spatial distortion of the shock front occurs, producing a region of constant shock angle. An example of this process arises in the exhaust from a pulse-detonation combustor. As the background velocity is increased, such as through the inclusion of a converging nozzle at the exhaust, the spatial distortion becomes more apparent. Numerical simulations using a compressible Euler solver demonstrate that the distortion is not due to the geometrical influence of the nozzle, but rather is a function of the magnitude of the background flow velocity. The distortion is studied using a modified geometrical shock dynamics formulation which includes the background flow and is validated against experiments. A simple model is presented to predict the shock distortion angle in the weak-shock limit. Finally, the axial decay behaviour of the shock is investigated and it is shown that the advection of the shock by the background flow delays the arrival of the head and tail of the expansion characteristic at the centreline. This leads to an increase in the rate of decay of the shock Mach number as the background flow velocity is increased