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Future changes in North Atlantic winter cyclones in CESM-LE – Part 2: A Lagrangian analysis
No full textFuture changes in extratropical cyclone structure and dynamics may lead to important impacts but are not yet fully understood. In the first part of this study, we have applied a composite approach together with potential vorticity (PV) inversion to study such changes in the dynamics of North Atlantic cyclones. Here, this is complemented with the help of a Lagrangian perspective, making use of air parcel trajectories to investigate the causes of altered PV anomalies as well as the role that cyclone airstreams play in shaping these changes. Intense cyclones in the extended winter seasons of two periods, 1990–2000 and 2091–2100, are studied in Community Earth System Model Large Ensemble (CESM-LE) simulations, and backward trajectories are calculated from the cyclone area as a basis to construct cyclone-centered composites of Lagrangian tendencies and their projected future changes. Our results show that diabatic processes on a timescale of 24 h shape the cyclones' low-level PV distribution and corroborate that the increasing moisture content along with enhanced ascent in warm conveyor belts leads to amplified latent heat release and larger low- and mid-level PV anomalies near the cyclone center in a warmer climate. In contrast, projected upper-level PV changes are due to a combination of several processes. These processes include cloud diabatic PV changes, anomalous PV advection, and likely also radiative PV generation in the lower stratosphere above the cyclone center. For instance, enhanced poleward advection is the primary reason for a projected decrease in upper-level PV anomalies south of the cyclone center. Warm conveyor belt outflow regions are projected to shift upward, but there is not robust change in the associated upper-level PV anomalies due to compensation between enhanced low-level PV generation and upper-level PV destruction. In summary, our two-part study points to future changes in the relative importance of different processes for the dynamics of intense North Atlantic cyclones in a warming climate, with important consequences for the near-surface wind pattern. In particular, a larger role of cloud diabatic processes is projected, affecting the cyclones through PV production in the lower troposphere. The role of other mechanisms, in particular radiative changes near the tropopause, should be investigated in more detail in future studies
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences
No full textMotivation
Local alignments of query sequences in large databases represent a core part of metagenomic studies and facilitate homology search. Following the development of NCBI Blast, many applications aimed to provide faster and equally sensitive local alignment frameworks. Most applications focus on protein alignments, while only few also facilitate DNA-based searches. None of the established programs allow searching DNA sequences from bisulfite sequencing experiments commonly used for DNA methylation profiling, for which specific alignment strategies need to be implemented.
Results
Here, we introduce Lambda3, a new version of the local alignment application Lambda. Lambda3 is the first solution that enables the search of protein, nucleotide as well as bisulfite-converted nucleotide query sequences. Its protein mode achieves comparable performance to that of the highly optimized protein alignment application Diamond, while the nucleotide mode consistently outperforms established local nucleotide aligners. Combined, Lambda3 presents a universal local alignment framework that enables fast and sensitive homology searches for a wide range of use-cases.
Availability and implementation
Lambda3 is free and open-source software publicly available at https://github.com/seqan/lambda/
Exponential Stability of the Flow for a Generalized Burgers Equation on a Circle
No full textThe paper deals with the problem of stability for the flow of the 1D Burgers equation on a circle. Using some ideas from the theory of positivity preserving semigroups, we establish the strong contraction in the L1 norm. As a consequence, it is proved that the equation with a bounded external force possesses a unique bounded solution on R, which is exponentially stable in H1 as t → +∞. In the case of a random external force, we show that the difference between two trajectories goes to zero with probability 1
A Λ-Fleming-Viot type model with intrinsically varying population size
No full textWe propose an extension of the classical Λ-Fleming-Viot model to intrinsically varying population sizes. During events, instead of replacing a proportion of the population, a random mass dies and a, possibly different, random mass of new individuals is added. The model can also incorporate a (deterministic) drift term, representing infinitesimally small, but frequent events. We investigate elementary properties of the model, analyse its relation to the Λ-Fleming-Viot model and describe a duality relationship. Through the lookdown framework, we provide a forward-in-time analysis of fixation and coming down from infinity. A visual introduction to this paper can be found at youtube.com/watch?v=v59motZWQcY
Towards More Effective Table-to-Text Generation: Assessing In-Context Learning and Self-Evaluation with Open-Source Models
No full textTable processing, a key task in natural language processing, has significantly benefited from recent advancements in language models (LMs). However, the capabilities of LMs in table-to-text generation, which transforms structured data into coherent narrative text, require an in-depth investigation, especially with current open-source models. This study explores the effectiveness of various in-context learning strategies in LMs across benchmark datasets, focusing on the impact of providing examples to the model. More importantly, we examine a real-world use case, offering valuable insights into practical applications. To complement traditional evaluation metrics, we employ a large language model (LLM) self-evaluation approach using chain-of-thought reasoning and assess its correlation with human-aligned metrics like BERTScore. Our findings highlight the significant impact of examples in improving table-to-text generation and suggest that, while LLM self-evaluation has potential, its current alignment with human judgment could be enhanced. This points to the need for more reliable evaluation methods
Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal
No full textModern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studying chemical reactions remains uncertain due to the high and sharp energy barriers and complex reaction coordinates involved. This study focuses on the thermal cis-trans isomerization in retinal, employing molecular simulations and comparing rate constant estimates based on one-dimensional rate theories with those based on sampling transitions and grid-based models for low-dimensional collective variable spaces. Even though each individual method to estimate the rate passes its quality tests, the rate constant estimates exhibit considerable disparities. Rate constant estimates based on one-dimensional reaction coordinates prove challenging to converge, even if the reaction coordinate is optimized. However, consistent estimates of the rate constant are achieved by sampling transitions and by multi-dimensional grid-based models
Quasi-Monte Carlo and Discontinuous Galerkin
No full textIn this study, we consider the development of tailored quasi-Monte Carlo (QMC) cubatures for non-conforming discontinuous Galerkin (DG) approximations of elliptic partial differential equations (PDEs) with random coefficients. We consider both the affine and uniform and the lognormal models for the input random field and investigate the use of QMC cubatures to approximate the expected value of the PDE response subject to input uncertainty. In particular, we prove that the resulting QMC convergence rate for DG approximations behaves in the same way as if continuous finite elements were chosen. Notably, the parametric regularity bounds for DG, which are developed in this work, are also useful for other methods such as sparse grids. Numerical results underline our analytical findings
Graph convex hull bounds as generalized Jensen inequalities
No full textJensen's inequality is ubiquitous in measure and probability theory, statistics, machine learning, information theory and many other areas of mathematics and data science. It states that, for any convex function f:K→R defined on a convex domain K⊆Rd and any random variable X taking values in K, E[f(X)]⩾f(E[X]). In this paper, sharp upper and lower bounds on E[f(X)], termed ‘graph convex hull bounds’, are derived for arbitrary functions f on arbitrary domains K, thereby extensively generalizing Jensen's inequality. The derivation of these bounds necessitates the investigation of the convex hull of the graph of f, which can be challenging for complex functions. On the other hand, once these inequalities are established, they hold, just like Jensen's inequality, for any K$K
Scaling law for the size dependence of a finite-range quantum gas
No full textIn a recent work [Reible et al., Phys. Rev. Res. 5, 023156 (2023)], it was shown that the mean particle-particle interaction across an ideal surface that divides a system into two parts can be employed to estimate the size dependence for the thermodynamic accuracy of the system. In this work we propose its application to systems with finite-range interactions that model dense quantum gases and derive an approximate size-dependence scaling law. In addition, we show that the application of the criterion is equivalent to the determination of a free-energy response to a perturbation. The latter result confirms the complementarity of the criterion to other estimates of finite-size effects based on direct simulations and empirical structure or energy convergence criteria