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The Soundproof Model of an Acoustic–internal Waves System with Low Stratification
No full textThis work is devoted to investigating a compressible fluid system with low stratification, which is driven by fast acoustic waves and internal waves. The approximation using a soundproof model is justified. More precisely, the soundproof model captures the dynamics of both the non-oscillating mean flows and the oscillating internal waves, while filters out the fast acoustic waves, of the compressible system with or without initial acoustic waves. Moreover, the fast-slow oscillation structure is investigated
GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms
No full textTwo of the most widely used Langevin integrators for molecular dynamics simulations are the GROMACS Stochastic Dynamics (GSD) integrator and the splitting method BAOAB. In this letter, we show that the GROMACS Stochastic Dynamics integrator is equal to the less frequently used splitting method BAOA. It immediately follows that GSD and BAOAB sample the same configurations and have the same high configurational accuracy. Our numerical results indicate that GSD/BAOA has higher kinetic accuracy than BAOAB
Kernel autocovariance operators of stationary processes: Estimation and convergence
Get PDFWe consider autocovariance operators of a stationary stochastic
process on a Polish space that is embedded into a reproducing kernel Hilbert
space. We investigate how empirical estimates of these operators converge
along realizations of the process under various conditions. In particular, we
examine ergodic and strongly mixing processes and prove several asymptotic
results as well as finite sample error bounds with a detailed analysis for the
Gaussian kernel. We provide applications of our theory in terms of consistency
results for kernel PCA with dependent data and the conditional mean
embedding of transition probabilities. Finally, we use our approach to examine
the nonparametric estimation of Markov transition operators and highlight
how our theory can give a consistency analysis for a large family of spectral
analysis methods including kernel-based dynamic mode decomposition
What is in my Sample? Challenges and Approaches for Unveiling the Hidden Diversity in Plankton Samples
No full textThe goal of this work is to deploy a primer search tool (PriSeT) suitable for taxonomically broad, sparse, and uncurated datasets of reference sequences. I discuss the theoretical and practical challenges when sequence datasets are large. Uncurated online reference databases are often the only source available when designing new primer sequences, studying the effectiveness, and for species identification. As a case study, two different identification methods for planktonic microorganisms from freshwater samples are presented: identification via light microscopy and DNA sequencing. The sequencing approach will replace the manual method to a large extent, but still needs to be improved and requires many costly trial-and-error iterations. The robust primer search tool PriSeT is here developed and designed to shorten the optimization time and to facilitate new types of in silico analyses. I evaluate PriSeT on 18S rRNA genes from all major plankton clades and on whole RNA genomes. The resulting primer sequences are compared to published primer pairs. Finally, the workflow of an academic research group planning and conducting metabarcoding experiments is critically reviewed. I present a database schema designed to summarize key information and enable researchers to be more productive in less time. The scheme also alleviates new types of meta-analysis that are not possible when data are scattered, such as quantitative and qualitative comparisons between different studies
Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems
No full textThe adaptive resolution simulation (AdResS) technique couples regions with different molecular resolutions and allows the exchange of molecules between different regions in an adaptive fashion. The latest development of the technique allows to abruptly couple the atomistically resolved region with a region of non‐interacting point‐like particles. The abrupt set‐up is derived having in mind the idea of the atomistically resolved region as an open system embedded in a large reservoir at a given macroscopic state. In this work, starting from the idea of open systems, the authors derive thermodynamic relations for AdResS which justify conceptually and numerically the claim of AdResS as a technique for simulating open systems. In particular, the relation between the chemical potential of the AdResS set‐up and that of its reference fully atomistic simulation is derived. The implication of this result is that the grand potential of AdResS can be explicitly written and thus, from a statistical mechanics point of view, the atomistically resolved region of AdResS can be identified with a well‐defined open system
Nonequilibrium Induced by Reservoirs: Physico-Mathematical Models and Numerical Tests
Get PDFIn a recently proposed computational model of open molecular systems out of
equilibrium the action of different reservoirs enters as a linear sum into the
Liouville-type evolution equations for the open system’s statistics. The
linearity of the coupling is common to different mathematical models of open
systems and essentially relies on neglecting the feedback of the system onto
the reservoir due to their interaction. In this paper, the range of applicability of
the computational model is tested with a linear coupling to two different
reservoirs, which induces a nonequilibrium situation. To this end, the density
profiles of Lennard–Jones liquids in large thermal gradients are studied using
nonequilibrium molecular dynamics simulations with open boundaries. The
authors put in perspective the formulation of an extension of the
mathematical model that can account for nonlinear effects
Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence
Get PDFAbstract We introduce two new concepts of convergence of gradient systems (Q, Eε,Rε) to a limiting gradient
system (Q, E0,R0). These new concepts are called ‘EDP convergence with tilting’ and ‘contact–EDP
convergencewith tilting.’ Both are based on the energy-dissipation-principle (EDP) formulation of solutions of
gradient systems and can be seen as refinements of the Gamma-convergence for gradient flows first introduced
by Sandier and Serfaty. The two newconcepts are constructed in order to avoid the ‘unnatural’ limiting gradient
structures that sometimes arise as limits in EDP convergence. EDP convergence with tilting is a strengthening
of EDP convergence by requiring EDP convergence for a full family of ‘tilted’ copies of (Q, Eε,Rε). It
avoids unnatural limiting gradient structures, but many interesting systems are non-convergent according to
this concept. Contact–EDP convergence with tilting is a relaxation of EDP convergence with tilting and still
avoids unnatural limits but applies to a broader class of sequences (Q, Eε,Rε). In this paper, we define these
concepts, study their properties, and connect them with classical EDP convergence.We illustrate the different
concepts on a number of test problems.
Continuum Mech. Thermodyn. (2021) 33:611–637
https://doi.org/10.1007/s00161-020-00932-
On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir
No full textKinematics of footwall exhumation at oceanic detachment faults: solid-block rotation and apparent unbending
No full textAbstract
Seafloor spreading at slow rates can be accommodated on large-offset oceanic detachment faults (ODFs), that exhume lower crustal and mantle rocks in footwall domes termed oceanic core complexes (OCCs). Footwall rock experiences large rotation during exhumation, yet important aspects of the kinematics - particularly the relative roles of rigid block rotation and flexure - are not clearly understood. Using a high-resolution numerical model, we explore the exhumation kinematics in the footwall beneath an emergent ODF/OCC. A key feature of the models is that footwall motion is dominated by solid rotation, accommodated by the concave-down ODF. This is attributed to a system behaviour in which the accumulation of distributed plastic strain is minimized. A consequence of these kinematics is that curvature measured along the ODF is representative of a neutral stress configuration, rather than a 'bent' one. Instead, it is in the subsequent process of `apparent unbending’ that significant flexural stresses are developed in the model footwall. The brittle strain associated with apparent unbending is produced dominantly in extension, beneath the OCC, consistent with earthquake clustering observed in the Trans-Atlantic Geotraverse at the Mid-Atlantic Ridge
Lithium influences whole‐organism metabolic rate in Drosophila subobscura
No full textLithium is widely used to treat bipolar disorder. However, the efficacy and vulnerability as to its side effects are known to differ. Although the specific biochemical mechanism of action is still elusive, lithium may influence mitochondrial function, and consequently, metabolism. Lithium exposure in this study was conducted on a unique set of mito-nuclear introgression lines of Drosophila subobscura to disentangle the independent effects of mitochondrial DNA (mtDNA) against a common nuclear DNA background. The study addressed three issues: (a) whether lithium has a dose-dependent effect on whole-organism metabolic rate, (b) whether mtDNA haplotypes show divergent metabolic efficiency measured by metabolic rate to lithium exposure and (c) whether lithium influences the whole-organism metabolic rate across sexes. The results confirm that lithium influenced the whole-organism metabolic rate, showing a subtle balance between efficacy and adverse effects within a narrow dose range. In addition, lithium exposure was found to influence metabolism differently based on mtDNA haplotypes and sex. This preliminary research may have a range of biological implications for the role of mitochondrial variability in psychiatric disease and treatment by contributing to the understanding and predicting of the lithium treatment response and risk for toxic side effects