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On a thermodynamic framework for developing boundary conditions for Korteweg-type fluids
Get PDFWe provide a derivation of several classes of boundary conditions for fluids of Korteweg- type using a simple and transparent thermodynamic approach that automatically guaran- tees that the derived boundary conditions are compatible with the second law of thermo- dynamics. The starting assumption of our approach is to describe the boundary of the do- main as the membrane separating two different continua, one inside the domain, and the other outside the domain. With this viewpoint one may employ the framework of con- tinuum thermodynamics involving singular surfaces. This approach allows us to identify, for various classes of surface Helmholtz free energies, the corresponding surface entropy production mechanisms. By establishing the constitutive relations that guarantee that the surface entropy production is non-negative, we identify a new class of boundary condi- tions, which on one hand generalizes in a nontrivial manner the Navier’s slip boundary conditions, and on the other hand describes dynamic and static contact angle conditions. We explore the general model in detail for a particular case of a Korteweg fluid where the Helmholtz free energy in the bulk is that of a van der Waals fluid. We perform a series of numerical experiments to document the basic qualitative features of the novel boundary conditions and their practical applicability to model phenomena such as the contact angle hysteresis
How to calculate pH-dependent binding rates for receptor–ligand systems based on thermodynamic simulations with different binding motifs
No full textAbstract
Molecular simulations of ligand–receptor interactions are a computational challenge, especially when their association- (‘on’-rate) and dissociation- (‘off’-rate) mechanisms are working on vastly differing timescales. One way of tackling this multiscale problem is to compute the free-energy landscapes, where molecular dynamics (MD) trajectories are used to only produce certain statistical ensembles. The approach allows for deriving the transition rates between energy states as a function of the height of the activation-energy barriers. In this article, we derive the association rates of the opioids fentanyl and N-(3-fluoro-1-phenethylpiperidin-4-yl)-N-phenyl propionamide (NFEPP) in a μ-opioid receptor by combining the free-energy landscape approach with the square-root-approximation method (SQRA), which is a particularly robust version of Markov modelling. The novelty of this work is that we derive the association rates as a function of the pH level using only an ensemble of MD simulations. We also verify our MD-derived insights by reproducing the in vitro study performed by the Stein Lab
Dynamical reweighting methods for Markov models
No full textConformational dynamics is essential to biomolecular
processes. Markov State Models (MSMs) are widely used to
elucidate dynamic properties of molecular systems from
unbiased Molecular Dynamics (MD). However, the
implementation of reweighting schemes for MSMs to analyze
biased simulations is still at an early stage of development.
Several dynamical reweighing approaches have been
proposed, which can be classified as approaches based on (i)
Kramers rate theory, (ii) rescaling of the probability density flux,
(iii) reweighting by formulating a likelihood function, (iv) path
reweighting. We present the state-of-the-art and discuss the
methodological differences of these methods, their limitations
and recent applications
Predicting Imminence of Analog Megathrust Earthquakes With Machine Learning: Implications for Monitoring Subduction Zones
No full textAbstract
Subduction zones are monitored using space geodesy with increasing resolution, with the aim of better capturing the deformation accompanying the seismic cycle. Here, we investigate data characteristics that maximize the performance of a machine learning binary classifier predicting slip‐event imminence. We overcome the scarcity of recorded instances from real subduction zones using data from a seismotectonic analog model monitored with a spatially dense, continuously recording onshore geodetic network. We show that a 70–85 km‐wide coastal swath recording interseismic deformation gives the most important information on slip imminence. Prediction performances are mainly influenced by the alarm duration (amount of time that we consider an event as imminent), with density of stations and record length playing a secondary role. The techniques developed in this study are most likely applicable in regions of slow earthquakes, where stick‐slip‐like failures occur at time intervals of months to years
Variations in runout of rock avalanches controlled by fragmentation, not basal friction
No full textRock avalanches are large rockslides consisting of highly fragmented materials that display exceptionally long runouts, which are found to correlate with their volume. Such volume-dependent runouts are conventionally attributed to dynamic lowering of the effective basal friction. However, even for similar volumes, the runouts are seen to span several orders of magnitude suggesting additional controlling factors. Here, we perform analogue models of fragmenting rockslides and compare them to natural rock avalanches. We show that for a given low basal friction, the runout of rock avalanches varies over two orders of magnitude and is determined by their degree of fragmentation. The fragmentation is observed to cause spreading, but also to increased mechanical interactions between fragments. Consequently, the runout’s dependence on fragmentation appears to be determined by the competition between spreading and internal friction. This shows that variation in degree of fragmentation can explain the large variation of runout of rock avalanches
Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping
No full textZoonotic pathogens that can be transmitted via food to humans have a high potential for large-scale emergencies, comprising severe effects on public health, critical infrastructures, and the economy. In this context, the development of laboratory methods to rapidly detect zoonotic bacteria in the food supply chain, including high-resolution mass spectrometry proteotyping are needed. In this work, an optimized sample preparation method for liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteome profiling was established for Francisella isolates, and a cluster analysis, as well as a phylogenetic tree, was generated to shed light on evolutionary relationships. Furthermore, this method was applied to tissues of infected hare carcasses from Germany. Even though the non-informative data outnumbered by a manifold the information of the zoonotic pathogen in the resulting proteome profiles, the standardized evaluation of MS data within an established automated analysis pipeline identified Francisella (F.) tularensis and, thus, could be, in principle, an applicable method to monitor food supply chains
Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures
Get PDFFriction in liquids arises from conservative forces between molecules and atoms. Although the
hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest
in the non-Markovian dynamics of single molecules and solutes, the emergence of friction from
the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequencyresolved
friction data from high-precision simulations of three prototypical liquids, including
water. Combining with rigorous theoretical arguments, we show that friction in liquids is
non-local in time and emerges abruptly at a characteristic frequency, beyond which viscous
liquids appear as non-dissipative, elastic solids. At the same time, the molecules experience
Brownian forces that display persistent correlations and long-lasting memory. A critical test
of the generalised Stokes–Einstein relation, mapping the friction of single molecules to the
viscoelastic response of the macroscopic sample, disproves the relation for Newtonian fluids,
but substantiates it exemplarily for a supercooled liquid. The employed approach is suitable
to yield novel insights into vitrification mechanisms and the intriguing mechanical properties
of soft materials
Atmospheric blocking types: Frequencies and transitions
Get PDFAbstract. Stationary, long-lasting blocked weather patterns can lead to extreme conditions such as very high temperatures or heavy rainfall. They are defined by a persistent high pressure system in combination with one or two low pressure systems. The mechanisms for the onset of such weather patterns are still not fully understood. Using a novel method based on the kinematic vorticity number we distinguish between two blocking types, namely High-over-Low and Omega block, in previously-identified blocking periods. Our main goal of this work is to study the temporal evolution of the occurrence probability and the onset, offset, and transition probabilities of blocking on the northern hemisphere. We analyze NCEP-DOE Reanalysis 2 data over the30 year period from 1990 to 2019 in two regions: Euro-Atlantic sector (40° W–30° E) and half northern hemisphere (90° W–90° E). First, we use logistic regression to investigate the temporal development of blocking probabilities depending on years, seasons and months. We find no significant difference in blocking numbers over the 30 year period. But we find large differences in the occurrence probabilities on a monthly basis with strongest increases over the 30 year period in February and March that are compensated by a decrease in December and autumn. Second, we use a Markov model to calculate the transition probabilities for two models: One is composed of two states blocking and no blocking, and another Markov model (three states) that additionally distinguishes between the specific blocking types High-over-Low and Omega blocking as well as of the state no blocking. The description with Markov theory reduces the probability to change from one weather regime to another or to stay within the same regime to a dependency only on the previous time step. Over the 30 year period, we found the largest changes in transition probabilities in the summer season, where the transition probability to Omega blocks increase strongly, while the unblocked state becomes less probable. Hence, Omega blocks become more frequent and stable in summer at the expense of the other states. As a main result, we show that Omega blocking is more likely to occur and more persistent than the High-over-Low blocking pattern
Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks
Get PDFThe small-deformation limit of finite elasticity is considered in presence of a given crack. The rescaled finite energies with the constraint of global injectivity are shown to Γ-converge to the linearized elastic energy with a local constraint of non-interpenetration along the crack
Generalized modulation theory for nonlinear gravity waves in a compressible atmosphere
No full textThis study investigates nonlinear gravity waves in the compressible atmosphere from the Earth's surface to the deep atmosphere. These waves are effectively described by Grimshaw's dissipative modulation equations which provide the basis for finding stationary solutions such as mountain lee waves and testing their stability in an analytic fashion. Assuming energetically consistent boundary and far-field conditions, that is no energy flux through the surface, free-slip boundary, and finite total energy, general wave solutions are derived and illustrated in terms of realistic background fields. These assumptions also imply that the wave-Reynolds number must become less than unity above a certain height. The modulational stability of admissible, both non-hydrostatic and hydrostatic, waves is examined. It turns out that, when accounting for the self-induced mean flow, the wave-Froude number has a resonance condition. If it becomes 1/2–√, then the wave destabilizes due to perturbations from the essential spectrum of the linearized modulation equations. However, if the horizontal wavelength is large enough, waves overturn before they can reach the modulational stability condition.
Mathematics of Climate and Weather Forecasting, vol. 6, no. 1, 2020, pp