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We establish here the local-in-time well-posedness of strong solutions with large initial data to a system coupling compressible atmospheric dynamics with a refined moisture model introduced in Hittmeir and Klein (Theor. Comput. Fluid Dyn. 32:137--164, 2018). This micro-physics moisture model is a refinement of the one communicated by Klein and Majda (Theor. Comput. Fluid Dyn. 20:525--551, 2006), which serves as a foundation of multi-scale asymptotic expansions for moist deep convection in the atmosphere. Specifically, we show, in this paper, that the system of compressible Navier--Stokes equations coupled with the moisture dynamics is well-posed. In particular, the micro-physics of moisture model incorporates the phase changes of water in moist air.

The ``Shockless Explosion Combustion" (SEC) concept for gas turbine combustors, introduced in 2014, approximates constant volume combustion (CVC) by harnessing acoustic confinement of autoigniting gas packets. The resulting pressure waves simultaneously transmit combustion energy to a turbine plenum and facilitate the combustor's recharging against an average pressure gain. Challenges in actualizing an SEC-driven gas turbine include i) the creation of charge stratifications for nearly homogeneous autoignition, ii) protecting the turbo components from combustion-induced pressure fluctuations, iii) providing evidence that efficiency gains comparable to those of CVC over deflagrative combustion can be realized, and iv) designing an effective one-way intake valve. This work addresses challenges i)-iii) utilizing computational engine models incorporating a quasi-one-dimensional combustor, zero- and two-dimensional compressor and turbine plena, and quasi-stationary turbo components. Two SEC operational modes are identified which fire at roughly one and two times the combustors' acoustic frequencies. Results for SEC-driven gas turbines with compressor pressure ratios of 6:1 and 20:1 reveal 1.5-fold mean pressure gains across the combustors. Assuming ideally efficient compressors and turbines, efficiency gains over engines with deflagration-based combustors of 30% and 18% are realized, respectively. With absolute values of 52% and 66%, the obtained efficiencies are close to the theoretical Humphrey cycle efficiencies of 54% and 65% for the mentioned pre-compression ratios. Detailed thermodynamic cycle analyses for individual gas parcels suggest that there is room for further efficiency gains through optimized plenum and combustor designs.

A model for the motion of slender vortex filaments is extended to include the effect of gravity. The model, initially introduced by Callegari and Ting (SIAM, J. of App. Math., (1978), vol. 35, pp. 148-175), is based on a matched asymptotic expansion in which the outer solution, given by the Biot-Savart law, is matched with the inner solution derived from the Navier-Stokes equations. Building on recent work by Harikrishnan et al (Phys. of Fluids, (2023), vol. 35) the Boussinesq approximation is applied such that the density variations only enter in the gravity term. However, unlike Harikrishnan et al. (2023) the density variation enters at a lower order in the asymptotic expansion, and thus has a more significant impact on the self-induced velocity of the vortex filament. In this regime, which corresponds to the regime studied by Chang and Smith (J. of Fl. Mech., (2018), vol. 857), the effect of gravity is given by an alteration of the core constant, which couples the motion of the filament to the motion within the vortical core, in addition to a change in the compatability conditions (evolution equations) which determine the leading order azimuthal and tangential velocity fields in the vortex core. The results are used to explain certain properties of bouyant vortex rings, as well as qualitatively explore the impact of gravity on tornado type atmospheric vorticies., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in "Physics of Fluids 1 May 2024; 36 (5): 056604", and may be found at https://doi.org/10.1063/5.0205028

In this paper, we investigate the boundary layer arising from the fast internal waves in the Boussinesq equations with the Brunt-Vais\"al\"a frequency of order $ \mathcal O(1/\varepsilon) $. For the homogeneous-in-height stratification, previous work by \emph{Desjardins, Lannes, Saut, 3(1):153--192, Water Waves, 2021} establishes uniform-in-$\epsilon$ estimates locally in time, with additional constraints on the boundary data initially, which essentially restricts the dynamics in the spatially periodic domain. Removing such constraints, our goal is to investigate the general near-boundary behavior. We observe that the fast internal waves will give rise to large growth of the spatial derivatives in the normal direction of the solutions in the vicinity of the boundary. To capture this phenomenon, we introduce an inviscid boundary layer using a natural scaling. In addition, we investigate the well-posedness of such a boundary layer system in the space of analytic functions.

A recent work of Harikrishnan et al. [arXiv:2110.02253 (2021)] has revealed an abundance of hairpin-like vortex structures, oriented in a similar direction, in the turbulent patches of a stably stratified Ekman flow. The Ekman flow over a smooth wall is a simplified configuration of the Atmospheric Boundary Layer (ABL) where effects of both stratification and rotation are present. In this study, hairpin-like structures are investigated by treating them as slender vortex filaments, i.e., a vortex filament whose diameter $d$ is small when compared to its radius of curvature $R$. The corrected thin-tube model of Klein and Knio [J. Fluid Mech. (1995)] is used to compute the motion of these filaments with the ABL as a background flow. The influence of the mean background flow on the filaments is studied for two stably stratified cases and a neutrally stratified case. Our results suggest that the orientation of the hairpin filament in the spanwise direction is linked to its initial starting height under stable stratification whereas no such dependency can be observed with the neutrally stratified background flow. An improved feature tracking scheme based on spatial overlap for tracking $Q$-criterion vortex structures on the Direct Numerical Simulation (DNS) data is also developed. It overcomes the limitation of using a constant threshold in time by dynamically adjusting the thresholds to accommodate the growth or deterioration of a feature. A comparison between the feature tracking and the filament simulation reveals qualitatively similar temporal developments. Finally, an extension of the asymptotic analysis of Callegari and Ting [J. App. Math (1978)] is carried out to include the effect of gravity. The results show that, in the regime considered here, a contribution from the gravity term occurs only when the tail of an infinitely long filament is tilted at an angle relative to the wall.

WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only. The Python package is centered around tensor train (TT, or matrix product) format representations of Hamiltonian operators and (stationary or time-evolving) state vectors. It builds on the Python tensor train toolbox Scikit-tt, which provides efficient construction methods and storage schemes for the TT format. Its solvers for eigenvalue problems and linear differential equations are used in WaveTrain for the time-independent and time-dependent Schroedinger equations, respectively. Employing efficient decompositions to construct low-rank representations, the tensor-train ranks of state vectors are often found to depend only marginally on the chain length N. This results in the computational effort growing only slightly more than linearly with N, thus mitigating the curse of dimensionality. As a complement to the classes for full quantum mechanics, WaveTrain also contains classes for fully classical and mixed quantum-classical (Ehrenfest or mean field) dynamics of bipartite systems. The graphical capabilities allow visualization of quantum dynamics on the fly, with a choice of several different representations based on reduced density matrices. Even though developed for treating quasi one-dimensional excitonic energy transport in molecular solids or conjugated organic polymers, including coupling to phonons, WaveTrain can be used for any kind of chain-like quantum systems, with or without periodic boundary conditions, and with NN interactions only.

We investigate the use of tensor-train approaches to the solution of the time-dependent Schr\"odinger equation for chain-like quantum systems with on-site and nearest-neighbor interactions only. Using efficient low-rank tensor train representations, we aim at reducing the memory consumption as well as the computation costs. As an example, coupled excitons and phonons modeled in terms of Fr\"ohlich-Holstein type Hamiltonians are studied here. By comparing our tensor-train based results with semi-analytical results, we demonstrate the key role of the ranks of the quantum state vectors. Typically, an excellent quality of the solutions is found only when the maximum number of ranks exceed a certain value. One class of propagation schemes builds on splitting the Hamiltonian into two groups of interleaved nearest-neighbor interactions which commutate within each of the groups. In particular, the 4-th order Yoshida-Neri and the 8-th order Kahan-Li symplectic compositions are demonstrated to yield very accurate results, close to machine precision. However, due to the computational costs, currently their use is restricted to rather short chains. That also applies to propagations based on the time-dependent variational principle, typically used in the context of matrix product states. Yet another class of propagators involves explicit, time-symmetrized Euler integrators. Especially the 4-th order variant is recommended for quantum simulations of longer chains, even though the high precision of the splitting schemes cannot be reached. Moreover, the scaling of the computational effort with the dimensions of the local Hilbert spaces is much more favorable for the differencing than for the splitting or variational schemes.

In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the adaptive resolution scheme (AdResS), with non-interacting tracers as particles reservoir, is combined with a fluctuating hydrodynamics (FHD) solver. The resulting algorithm, supported by a solid mathematical model, allows for a physically consistent exchange of matter and energy between the particle domain and its fluctuating continuum reservoir. Numerical tests are performed to show the validity of the algorithm. Differently from previous algorithms of the same kind, the current approach allows for simulations where, in addition to density fluctuations, also thermal fluctuations can be accounted for, thus large complex molecular systems, as for example hydrated biological membranes in a thermal field, can now be efficiently treated., Comment: In press

Quasi-geostrophic (QG) theory is of fundamental importance in the study of large-scale atmospheric flows. In recent years, there has been growing interest in extending the classical QG plus Ekman friction layer model (QG-Ekman) to systematically include additional physical processes known to significantly contribute to real-life weather phenomena. This paper lays the foundation for combining two of these developments, namely Smith and Stechmann's family of \emph{Precipitating Quasi-Geostrophic} (PQG) models (J.\ Atmos.\ Sci, {\bfseries 74}, 3285--3303, 2017) on the one hand, and the extension of QG-Ekman for dry air by a strongly \emph{Diabatic Layer} (DL) of intermediate height (QG-DL-Ekman) in (J.\ Atmos.\ Sci, {\bfseries 79}, 887--905, 2022) on the other hand. To this end, Smith and Stechmann's PQG equations for sound-proof motions are first corroborated within a general asymptotic modeling framework starting from a full compressible flow model. The derivations show that the PQG model family is naturally embedded in the asymptotic hierarchy of scale-dependent atmospheric flow models introduced by one of the present authors in (Ann.\ Rev.\ Fluid Mech., {\bfseries 42}, 249--274). Particular emphasis is then placed on an asymptotic scaling regime for PQG that accounts for a generic Kessler-type bulk microphysics closure and is compatible with QG-DL-Ekman theory. The detailed derivation of a moist QG-DL-Ekman model is deferred to a future publication.

The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for reaction--diffusion processes. The CDME consists of an infinite ordered family of Fokker--Planck equations, where each level of the ordered family corresponds to a certain number of particles and each particle represents a molecule. The equations at each level describe the spatial diffusion of the corresponding set of particles, and they are coupled to each other via reaction operators --linear operators representing chemical reactions. These operators change the number of particles in the system, and thus transport probability between different levels in the family. In this work, we present three approaches to formulate the CDME and show the relations between them. We further deduce the non-trivial combinatorial factors contained in the reaction operators, and we elucidate the relation to the original formulation of the CDME, which is based on creation and annihilation operators acting on many-particle probability density functions. Finally we discuss applications to multiscale simulations of biochemical systems among other future prospects.

This 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.

In this work we study the global solvability of moisture dynamics with phase changes for warm clouds. We thereby in comparison to previous studies [Hittmeir-Klein-Li-Titi (2017)] take into account the different gas constants for dry air and water vapor as well as the different heat capacities for dry air, water vapor and liquid water, which leads to a much stronger coupling of the moisture balances and the thermodynamic equation. This refined thermodynamic setting has been demonstrated to be essential e.g. in the case of deep convective cloud columns in [Hittmeir-Klein (2017)]. The more complicated structure requires careful derivations of sufficient a priori estimates for proving global existence and uniqueness of solutions., Comment: arXiv admin note: text overlap with arXiv:1907.11199

The traditional approximation neglects the cosine components of the Coriolis acceleration, and this approximation has been widely used in the study of geophysical phenomena. However, the justification of the traditional approximation is questionable under a few circumstances. In particular, dynamics with substantial vertical velocities or geophysical phenomena in the tropics have non-negligible cosine Coriolis terms. Such cases warrant investigations with the non-traditional setting, i.e., the full Coriolis acceleration. In this manuscript, we study the effect of the non-traditional setting on an isothermal, hydrostatic and compressible atmosphere assuming a meridionally homogeneous flow. Employing linear stability analysis, we show that, given appropriate boundary conditions, i.e., a bottom boundary condition that allows for a vertical energy flux and non-reflecting boundary at the top, the atmosphere at rest becomes prone to a novel unstable mode. The validity of assuming a meridionally homogeneous flow is investigated via scale analysis. Numerical experiments were conducted, and Rayleigh damping was used as a numerical approximation for the non-reflecting top boundary. Our three main results are as follows. 1) Experiments involving the full Coriolis terms exhibit an exponentially growing instability, yet experiments subjected to the traditional approximation remain stable. 2) The experimental instability growth rate is close to the theoretical value. 3) A perturbed version of the unstable mode arises even under sub-optimal bottom boundary conditions. Finally, we conclude our study by discussing the limitations, implications, and remaining open questions. Specifically, the influence on numerical deep-atmosphere models and possible physical interpretations of the unstable mode are discussed., Comment: 39 pages, 12 figures

Long-lived flow patterns in the atmosphere such as weather fronts, mid-latitude blockings or tropical cyclones often induce extreme weather conditions. As a consequence, their description, detection, and tracking has received increasing attention in recent years. Similar objectives also arise in diverse fields such as turbulence and combustion research, image analysis, and medical diagnostics under the headlines of "feature tracking", "coherent structure detection" or "image registration" - to name just a few. A host of different approaches to addressing the underlying, often very similar, tasks have been developed and successfully used. Here, several typical examples of such approaches are summarized, further developed and applied to meteorological data sets. Common abstract operational steps form the basis for a unifying framework for the specification of "persistent structures" involving the definition of the physical state of a system, the features of interest, and means of measuring their persistence.

In a previous paper [Gholami et al. Adv.Th.Sim.4, 2000303 (2021)], we have identified a precise relation between the chemical potential of a fully atomistic simulation and the simulation of an open system in the adaptive resolution method (AdResS). The starting point was the equivalence derived from the statistical partition functions between the grand potentials, $\Omega$, of the open system and of the equivalent subregion in the fully atomistic simulation of reference. In this work, instead, we treat the identity for the grand potential based on the thermodynamic relation $\Omega=-pV$ and investigate the behaviour of the pressure in the coupling region of the adaptive resolution method (AdResS). We confirm the physical consistency of the method for determining the chemical potential described by the previous work and strengthen it further by identifying a clear numerical relation between the potential that couples the open system to the reservoir on the one hand and the local pressure of the reference fully atomistic system on the other hand. Such a relation is of crucial importance in the perspective of coupling the AdResS method for open system to the continuum hydrodynamic regime., Comment: 20 pages, 8 figures

Global intermittency is observed in the stably stratified Atmospheric Boundary Layer (ABL) and corresponds to having large nonturbulent flow regions to develop in an otherwise turbulent flow. In this paper, the differences between continuous and intermittent turbulence are quantified with the help of coherent structures. Eight classes of coherent structures are identified from literature, most of which are indicated by scalar criteria derived from velocity fields. A method is developed to geometrically classify structures into three categories: blob-like, tube-like or sheet-like. An alternate definition of the intermittency factor $\gamma$ based on coherent structures is introduced to separate turbulent and nonturbulent parts of a flow. Applying this conditioning technique and the geometrical characterization on direct numerical simulations (DNS) of an Ekman flow, we find the following: (i) structures with similar geometries (either tube-like or sheet-like) are found regardless of the strength of stratification; (ii) global intermittency affects all regions of the ABL - viscous sublayer, buffer layer, inner, and outer layer; (iii) for the highly stratified case, sweep/ejection pairs form well-separated clusters within the viscous sublayer which can possibly explain the abundance of hairpin-like vortices with a particular orientation; (iv) nonturbulent regions are occupied with streamwise velocity fluctuations and there is a switch between high- and low-speed streaks at a particular height for all stratified cases., Comment: This version of the document has been submitted to the Journal of Fluid Mechanics. Compared to the previous version, there are minor changes throughout the document

We demonstrate how to apply the tensor-train format to solve the time-independent Schr\"{o}dinger equation for quasi one-dimensional excitonic chain systems with and without periodic boundary conditions. The coupled excitons and phonons are modeled by Frenkel-Holstein type Hamiltonians with on-site and nearest-neighbor interactions only. We reduce the memory consumption as well as the computational costs significantly by employing efficient decompositions to construct low rank tensor-train representations, thus mitigating the curse of dimensionality. In order to compute also higher quantum states, we introduce an approach which directly incorporates the Wielandt deflation technique into the alternating linear scheme for the solution of eigenproblems. Besides systems with coupled excitons and phonons, we also investigate uncoupled problems for which (semi-)analytical results exist. There, we find that in case of homogeneous systems the tensor-train ranks of state vectors only marginally depend on the chain length which results in a linear growth of the storage consumption. However, the CPU time increases slightly faster with the chain length than the storage consumption because the alternating linear scheme adopted in our work requires more iterations to achieve convergence for longer chains and a given rank. Finally, we demonstrate that the tensor-train approach to the quantum treatment of coupled excitons and phonons makes it possible to directly tackle the phenomenon of mutual self-trapping. We are able to confirm the main results of the Davydov theory, i.e., the dependence of the wavepacket width and the corresponding stabilization energy on the exciton-phonon coupling strength, though only for a certain range of that parameter. In future work, our approach will allow calculations also beyond the restrictions of the Frenkel-Holstein type Hamiltonians.

The dynamic state index (DSI) is a scalar field that combines variational information on the total energy and enstrophy of a flow field with the second law of thermodynamics. Its magnitude is a combined local measure for non-stationarity, diabaticity, and dissipation in the flow, and it has been shown to provide good qualitative indications for the onset and presence of precipitation and the organization of storms. The index has been derived thus far for ideal fluid models only, however, so that one may expect more detailed insights from a revised definition of the quantity that includes more complex aerothermodynamics. The present paper suggests definitions of DSI-like indicators for flows of moist air with phase changes and precipitation. In this way, the DSI is generalized to signal deviations from a variety of different types of balanced states. A comparison of these indices evaluated with respect to one and the same flow field enables the user to test whether the flow internally balances any combination of the physical processes encoded in the generalized DSI-indices.

Quasi-geostrophic (QG) theory describes the dynamics of synoptic scale flows in the trophosphere that are balanced with respect to both acoustic and internal gravity waves. Within this framework, effects of (turbulent) friction near the ground are usually represented by Ekman Layer theory. The troposphere covers roughly the lowest ten kilometers of the atmosphere while Ekman layer heights are typically just a few hundred meters. However, this two-layer asymptotic theory does not explicitly account for substantial changes of the potential temperature stratification due to diabatic heating associated with cloud formation or with radiative and turbulent heat fluxes, which, in the middle latitudes, can be particularly important in about the lowest three kilometers. To address this deficiency, this paper extends the classical QG-Ekman layer model by introducing an intermediate, dynamically and thermodynamically active layer, called the "diabatic layer" (DL) from here on. The flow in this layer is also in acoustic, hydrostatic, and geostrophic balance but, in contrast to QG flow, variations of potential temperature are not restricted to small deviations from a stable and time independent background stratification. Instead, within the diabatic layer, diabatic processes are allowed to affect the leading-order stratification. As a consequence, the diabatic layer modifies the pressure field at the top of the Ekman layer, and with it the intensity of Ekman pumping seen by the quasi-geostrophic bulk flow. The result is the proposed extended quasi-geostrophic three-layer QG-DL-Ekman model for mid-latitude (dry and moist) dynamics., Comment: 12 pages, 5 figures

A challenge arising from the local Bayesian assimilation of data in an atmospheric flow simulation is the imbalances it may introduce. Acoustic fast-mode imbalances of the order of the slower dynamics can be negated by employing a blended numerical model with seamless access to the compressible and the soundproof pseudo-incompressible dynamics. Here, the blended modelling strategy by Benacchio et al., MWR, vol. 142 (2014) is upgraded in an advanced numerical framework and extended with a Bayesian local ensemble data assimilation method. Upon assimilation of data, the model configuration is switched to the pseudo-incompressible regime for one time-step. After that, the model configuration is switched back to the compressible model for the duration of the assimilation window. The switching between model regimes is repeated for each subsequent assimilation window. An improved blending strategy for the numerical model ensures that a single time-step in the pseudo-incompressible regime is sufficient to suppress imbalances coming from the initialisation and data assimilation. This improvement is based on three innovations: (i) the association of pressure fields computed at different stages of the numerical integration with actual time levels; (ii) a conversion of pressure-related variables between the model regimes derived from low Mach number asymptotics; and (iii) a judicious selection of the pressure variables used in converting numerical model states when a switch of models occurs. Idealised two-dimensional travelling vortex and buoyancy-driven bubble convection experiments show that acoustic imbalances arising from data assimilation can be eliminated by using this blended model, thereby achieving balanced analysis fields., Comment: 50 pages, 15 figures

The 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 was 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 system, we derive thermodynamic relations for AdResS which justify conceptually and numerically the claim of AdResS as a technique for simulating open systems. In particular, we derive the relation between the chemical potential of the AdResS set-up and that of its reference fully atomistic simulation. 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.

In a recently proposed computational model of open molecular systems out of equilibrium [Ebrahimi Viand et al. J.Chem.Phys. 153, 101102 (2020)], 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, we test the range of applicability of the computational model with a linear coupling to two different reservoirs, which induces a nonequilibrium situation. To this end, we studied the density profiles of Lennard-Jones liquids in large thermal gradients using nonequilibrium molecular dynamics simulations with open boundaries. We put in perspective the formulation of an extension of the mathematical model that can account for nonlinear effects.

Moist processes are among the most important drivers of atmospheric dynamics,and scale analysis and asymptotics are cornerstones of theoretical meteorology. Accounting for moist processes in systematic scale analyses therefore seems of considerable importance for the field. Klein & Majda (TCFD, 20, 525--552, (2006)) proposed a scaling regime for the incorporation of moist bulk microphysics closures in multiscale asymptotic analyses of tropical deep convection. This regime is refined here to allow for mixtures of ideal gases and to establish consistency with a more general multiple scales modelling framework for atmospheric flows. Deep narrow updrafts, so-called "hot towers", constitute principal building blocks of larger scale storm systems. They are analysed here in a sample application of the new scaling regime. A single quasi-onedimensional columnar cloud is considered on the vertical advective (or tower life cycle) time scale. The refined asymptotic scaling regime is essential for this example as it reveals a new mechanism for the self-sustainance of such updrafts. Even for strongly positive convectively available potential energy (CAPE), a vertical balance of buoyancy forces is found in the presence of precipitation. This balance induces a diagnostic equation for the vertical velocity and it is responsible for the generation of self-sustained balanced updrafts. The time dependent updraft structure is encoded in a Hamilton-Jacobi equation for the precipitation mixing ratio. Numerical solutions of this equation suggest that the self-sustained updrafts may strongly enhance hot tower life cycles.

We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution molecular dynamics technique (AdResS). We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with results obtained from the simulation of a larger, locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations., Comment: page 1-6 main manuscript with 3 figures, page 7-11 supplementary material with 4 figures

The dynamic evolution of a highly underexpanded transient supersonic jet at the exit of a pulse detonation engine is investigated via high-resolution time-resolved schlieren and numerical simulations. Experimental evidence is provided for the presence of a second triple shock configuration along with a shocklet between the reflected shock and the slipstream, which has no analogue in a steady-state underexpanded jet. A pseudo-steady model is developed, which allows for the determination of the post-shock flow condition for a transient propagating oblique shock. This model is applied to the numerical simulations to reveal the mechanism leading to the formation of the second triple point. Accordingly, the formation of the triple point is initiated by the transient motion of the reflected shock, which is induced by the convection of the vortex ring. While the vortex ring embedded shock move essentially as a translating strong oblique shock, the reflected shock is rotating towards its steady state position. This results in a pressure discontinuity that must be resolved by the formation of a shocklet.

In this work we study the global solvability of the primitive equations for the atmosphere coupled to moisture dynamics with phase changes for warm clouds, where water is present in the form of water vapor and in the liquid state as cloud water and rain water. This moisture model contains closures for the phase changes condensation and evaporation, as well as the processes of autoconversion of cloud water into rainwater and the collection of cloud water by the falling rain droplets. It has been used by Klein and Majda in \cite{KM} and corresponds to a basic form of the bulk microphysics closure in the spirit of Kessler \cite{Ke} and Grabowski and Smolarkiewicz \cite{GS}. The moisture balances are strongly coupled to the thermodynamic equation via the latent heat associated to the phase changes. In \cite{HKLT} we assumed the velocity field to be given and proved rigorously the global existence and uniqueness of uniformly bounded solutions of the moisture balances coupled to the thermodynamic equation. In this paper we present the solvability of a full moist atmospheric flow model, where the moisture model is coupled to the primitive equations of atmospherical dynamics governing the velocity field. For the derivation of a priori estimates for the velocity field we thereby use the ideas of Cao and Titi \cite{CT}, who succeeded in proving the global solvability of the primitive equations.

In this work we derive a mathematical model for an open system that exchanges particles and momentum with a reservoir from their joint Hamiltonian dynamics. The complexity of this many-particle problem is addressed by introducing a countable set of n-particle phase space distribution functions just for the open subsystem, while accounting for the reservoir only in terms of statistical expectations. From the Liouville equation for the full system we derive a set of coupled Liouville-type equations for the n-particle distributions by marginalization with respect to reservoir states. The resulting equation hierarchy describes the external momentum forcing of the open system by the reservoir across its boundaries, and it covers the effects of particle exchanges, which induce probability transfers between the n- and (n+1)-particle distributions. Similarities and differences with the Bergmann-Lebowitz model of open systems (P.G.Bergmann, J.L. Lebowitz, Phys.Rev., 99:578--587 (1955)) are discussed in the context of the implementation of these guiding principles in a computational scheme for molecular simulations.

We 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.

The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, we construct a combined, explicit reservoir by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed., Comment: accepted as communication in Advanced Theory and Simulations

WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum dynamics of closed and open systems, respectively, the present Part III adds fully classical and mixed quantum-classical propagations to WavePacket. In those simulations classical phase-space densities are sampled by trajectories which follow (diabatic or adiabatic) potential energy surfaces. In the vicinity of (genuine or avoided) intersections of those surfaces trajectories may switch between surfaces. To model these transitions, two classes of stochastic algorithms have been implemented: (1) J. C. Tully's fewest switches surface hopping and (2) Landau-Zener based single switch surface hopping. The latter one offers the advantage of being based on adiabatic energy gaps only, thus not requiring non-adiabatic coupling information any more. The present work describes the MATLAB version of WavePacket 6.0.2 which is essentially an object-oriented rewrite of previous versions, allowing to perform fully classical, quantum-classical and quantum-mechanical simulations on an equal footing, i.e., for the same physical system described by the same WavePacket input. The software package is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous worked-out demonstration examples with animated graphics are available.

The present study focuses on the interaction of gravity waves in the atmosphere with the tropopause. As the vertical extent of the latter is small compared to the density scale height, wave propagation is described by the Taylor-Goldstein equation as derived from the linearised Boussinesq approximation. Of particular interest in the construction of gravity wave parameterisations for the upper atmosphere are the transmission and reflection properties of the tropopause as these determine the upward fluxes of energy and momentum carried by internal waves. A method is presented that decomposes internal waves explicitly into upward and downward propagating contributions, thus giving direct access to transmission and reflection coefficients of finite regions of non-uniform stratification in a stationary atmosphere. The scheme utilizes a piecewise constant approximation for the background stratification and matches up- and downward propagating plane wave solutions in each layer through physically meaningful coupling conditions. As a result, transmission and reflection coefficients follow immediately.

We present a dimensionally split method for computing solutions to the compressible Navier-Stokes equations on Cartesian cut cell meshes. The method is globally second order accurate in the L1 norm, fully conservative, and allows the use of time steps determined by the regular grid spacing. We provide a description of the three-dimensional implementation of the method and evaluate its numerical performance by computing solutions to a number of test problems ranging from the nearly incompressible to the highly compressible flow regimes. All the computed results show good agreement with reference results from theory, experiment and previous numerical studies. To the best of our knowledge, this is the first presentation of a dimensionally split cut cell method for the compressible Navier-Stokes equations in the literature.

We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane models in preparation of calculations based on a large scale continuum model.

We present a dimensionally split method for solving hyperbolic conservation laws on Cartesian cut cell meshes. The approach combines local geometric and wave speed information to determine a novel stabilised cut cell flux, and we provide a full description of its three-dimensional implementation in the dimensionally split framework of Klein et al. [1]. The convergence and stability of the method are proved for the one-dimensional linear advection equation, while its multi-dimensional numerical performance is investigated through the computation of solutions to a number of test problems for the linear advection and Euler equations. When compared to the cut cell flux of Klein et al., it was found that the new flux alleviates the problem of oscillatory boundary solutions produced by the former at higher Courant numbers, and also enables the computation of more accurate solutions near stagnation points. Being dimensionally split, the method is simple to implement and extends readily to multiple dimensions.

A study on the application of the Tensor Train decomposition method to 3D direct numerical simulation data of channel turbulence flow is presented. The approach is validated with respect to compression rate and storage requirement. In tests with synthetic data, it is found that grid-aligned self-similar patterns are well captured, and also the application to non grid-aligned self-similarity yields satisfying results. It is observed that the shape of the input Tensor significantly affects the compression rate. Applied to data of channel turbulent flow, the Tensor Train format allows for surprisingly high compression rates whilst ensuring low relative errors.

P\"aschke et al. (JFM, 701, 137--170 (2012)) studied the nonlinear dynamics of strongly tilted vortices subject to asymmetric diabatic heating by asymptotic methods. They found, \ia, that an azimuthal Fourier mode~1 heating pattern can intensify or attenuate such a vortex depending on the relative orientation of tilt and heating asymmetries. The theory originally addressed the gradient wind regime which, asymptotically speaking, corresponds to vortex Rossby numbers of order unity in the limit. Formally, this restricts the applicability of the theory to rather weak vortices in the near equatorial region. It is shown below that said theory is, in contrast, uniformly valid for vanishing Coriolis parameter and thus applicable to vortices up to low hurricane strengths. In addition, the paper presents an extended discussion of the asymptotics as regards their physical interpretation and their implications for the overall vortex dynamics. The paper's second contribution is a series of three-dimensional numerical simulations examining the effect of different orientations of dipolar heat release on idealized tropical cyclones. Comparisons with numerical solutions of the asymptotic equations yield evidence that supports the original predictions. In addition, the influence of asymmetric diabatic heat release on the time evolution of centerline tilt is analysed further, and a steering mechanism based on the orientation of the heating dipole is revealed., Comment: 38 pages, 19 figures

Data assimilation algorithms are used to estimate the states of a dynamical system using partial and noisy observations. The ensemble Kalman filter has become a popular data assimilation scheme due to its simplicity and robustness for a wide range of application areas. Nevertheless, the ensemble Kalman filter also has limitations due to its inherent Gaussian and linearity assumptions. These limitations can manifest themselves in dynamically inconsistent state estimates. We investigate this issue in this paper for highly oscillatory Hamiltonian systems with a dynamical behavior which satisfies certain balance relations. We first demonstrate that the standard ensemble Kalman filter can lead to estimates which do not satisfy those balance relations, ultimately leading to filter divergence. We also propose two remedies for this phenomenon in terms of blended time-stepping schemes and ensemble-based penalty methods. The effect of these modifications to the standard ensemble Kalman filter are discussed and demonstrated numerically for two model scenarios. First, we consider balanced motion for highly oscillatory Hamiltonian systems and, second, we investigate thermally embedded highly oscillatory Hamiltonian systems. The first scenario is relevant for applications from meteorology while the second scenario is relevant for applications of data assimilation to molecular dynamics.

A qualitative explanation for the scaling of energy dissipation by high Reynolds number fluid flows in contact with solid obstacles is proposed in the light of recent mathematical and numerical results. Asymptotic analysis suggests that it is governed by a fast, small scale Rayleigh-Tollmien-Schlichting instability with an unstable range whose lower and upper bounds scale as $Re^{3/8}$ and $Re^{1/2}$, respectively. By linear superposition the unstable modes induce a boundary vorticity flux of order $Re^1$, a key ingredient in detachment and drag generation according to a theorem of Kato. These predictions are confirmed by numerically solving the Navier-Stokes equations in a two-dimensional periodic channel discretized using compact finite differences in the wall-normal direction, and a spectral scheme in the wall-parallel direction., Comment: 37 pages, 18 figures and 3 tables

Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in the way the change of molecular resolution is made in a buffer/transition region. In particular a central question concerns the possibility of the existence of a global Hamiltonian which, by describing the change of resolution, is at the same time physically consistent, mathematically well defined and numerically accurate. In this paper we present an asymptotic analysis of the adaptive process complemented by numerical results and show that under certain mathematical conditions a Hamiltonian, which is physically consistent and numerically accurate, may exist. Such conditions show that molecular simulations in the current computational implementation require systems of large size and thus a Hamiltonian approach as the one proposed, at this stage, would not be practical from the numerical point of view. However, the Hamiltonian proposed provides the basis for a simplification and generalization of the numerical implementation of adaptive resolution algorithms to other molecular dynamics codes., Comment: To appear in Physical Review E 2016

We study a moisture model for warm clouds that has been used by Klein and Majda as a basis for multiscale asymptotic expansions for deep convective phenomena. These moisture balance equations correspond to a bulk microphysics closure in the spirit of Kessler and of Grabowski and Smolarkiewicz, in which water is present in the gaseous state as water vapor and in the liquid phase as cloud water and rain water. It thereby contains closures for the phase changes condensation and evaporation, as well as the processes of autoconversion of cloud water into rainwater and the collection of cloud water by the falling rain droplets. Phase changes are associated with enormous amounts of latent heat and therefore provide a strong coupling to the thermodynamic equation. In this work we assume the velocity field to be given and prove rigorously the global existence and uniqueness of uniformly bounded solutions of the moisture model with viscosity, diffusion and heat conduction. To guarantee local well-posedness we first need to establish local existence results for linear parabolic equations, subject to the Robin boundary conditions on the cylindric type of domains under consideration. We then derive a priori estimates, for proving the maximum principle, using the Stampacchia method, as well as the iterative method by Alikakos to obtain uniform boundedness. The evaporation term is of power law type, with an exponent in general less or equal to one and therefore making the proof of uniqueness more challenging. However, these difficulties can be circumvented by introducing new unknowns, which satisfy the required cancellation and monotonicity properties in the source terms.

We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.