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With the escalating complexity and volume of genomic data, the capacity of biology institutions' HPC faces limitations. While the Cloud presents a viable solution for short-term elasticity, its intricacies pose challenges for bioinformatics users. Alternatively, serverless computing allows for workload scalability with minimal developer burden. However, porting a scientific application to serverless is not a straightforward process. In this article, we present a Variant Calling genomics pipeline migrated from single-node HPC to a serverless architecture. We describe the inherent challenges of this approach and the engineering efforts required to achieve scalability. We contribute by open-sourcing the pipeline for future systems research and as a scalable user-friendly tool for the bioinformatics community., Comment: 6 pages, published at 9th International Workshop on Serverless Computing (WoSC '23), December 11-15, 2023, Bologna, Italy

Accurate calibration of polarization dependent optical elements is often necessary in optical experiments. A versatile polarimeter device to measure the polarization state of light is a valuable tool in these experiments. Here we report a rotating waveplate-based polarimeter capable of complete Stokes vector analysis of collimated light. Calibration of the device allows accurate measurements over a range of wavelengths, with a bandwidth of >30 nm in this implementation. A photo-interrupter trigger system supplies the phase information necessary for full determination of the Stokes vector. An Arduino microcontroller performs rapid analysis and displays the results on a liquid crystal display. The polarimeter is compact and can be placed anywhere on an optical table on a single standard post. The components to construct the device are only a fraction of the cost of commercially available devices while the accuracy and precision of the measurements are of the same order of magnitude., Comment: 4 pages, 3 figures

Longstanding problems regarding the causality of the diffusion equation are resolved through a class of exact solutions. A universal differential solution for diffusive processes is derived that is causal and exact at any analytic point in the data, albeit infinite order in spatial derivatives. This is true for systems both relativistic and nonrelativistic and shows that the hyperbolic and other relativistic extensions of the heat equation are not valid. A similar effect is demonstrated for flow enhanced mixing of solutions but with a new nonanalytic feature. Viscous hydrodynamics of liquids have both features. Both Newtonian and non-Newtonian viscous liquids give a more important and confounding alteration of the N-S equations for nonstationary flows. A careful analysis of liquids in terms of microscopic constituents and Lagrangian paths show there is a well-defined unique microscopic decomposition of fluid deformations into rotation and two modes corresponding to organized layered flow that do not enhance mixing and a mode that induces mixing and preferred static orientations. The resulting equations are both infinite order in spatial derivatives almost everywhere and are divided into two disjoint classes by an essential nonanalytic hypersuface. These give important rheological effects coupling hydrodynamic flow to diffusion and reaction kinetics. Practical consequences include catalysis and reaction yield control by rheological means. Implications of this work should percolate through almost all of continuum mechanics.

The interaction of waves and flows is a challenging topic where a complete resolution has been frustrated by the essential nonlinear features in the hydrodynamic case. Even in the case of EM waves in flowing media, the results are subtle. For a simple shear flow of constant n fluid, incident radiation is shown to be reflected and refracted in an analogous manner to Snell's law. However, the beam intensities differ and the system has an asymmetry in that an internal reflection gap opens at steep incident angles nearly oriented with the shear. For EM waves these effects are generally negligible in real systems but they introduce the topic at a reduced level of complexity of the more interesting acoustic case. Acoustic streaming is suggested, both from theory and experimental data, to be associated with vorticity generation at the driver itself. Bounds on the vorticity in bulk and nonlinear effects demonstrate that the bulk sources, even with attenuation, cannot drive such a strong flow. A review of the velocity scales in the problem suggest that a variation of the Scholte wave at the driver-fluid interface with local cavitation on the decompression phase creates a lateral flow of fluid that generates the stream and imparts the vorticity from the driver plate. In the case of Darcy flow in sintered media, an analysis of data suggests that acoustically enhanced flow may be the result of surface effects that narrow channels that are cleared by ultrasonic cavitation.

Stokes drift has been as central to the history of wave theory as it has been distressingly absent from experiment. Neither wave tanks nor experiments in open bodies detect this without nearly canceling "eulerian flows." Acoustic waves have an analogous problem that is particularly problematic in the vorticity production at the edges of beams. Here we demonstrate that the explanation for this arises from subtle end-of-packet and wavetrain gradient effects such as microbreaking events and wave-flow decomposition subtleties required to conserve mass and momentum and avoid fictitious external forces. These losses occur at both ends of packets and can produce a significant nonviscous energy loss for translating and spreading surface wave packets and wavetrains. In contrast, monochromatic sound wave packets will be shown to asymmetrically distort to conserve momentum. This provides an interesting analogy to how such internal forces arise for gradients of electromagnetic wavetrains in media. Such examples show that the interactions of waves in media are so system dependent as to be completely nonuniversal. These give further examples of how boundary effects must be carefully considered for conservation laws especially when harmonic functions are involved. The induced flows in establishing surface waves are shown to be time changing and dependent on wave history and suggest that some classical work based on mass flux and wave interactions may need to be reconsidered.

Hydrodynamics of gases in the classical domain are examined from the perspective that the gas has a well-defined wavefunction description at all times. Specifically, the internal energy and volume exclusion of decorrelated vortex structures are included so that quantum corrections and modifications to Navier-Stokes behavior can be derived. This leads to a small deviation in rigid body rotation for a cylindrically bound gas and the internal energy changes associated with vorticity give deviations in the Reynolds' transport theorem. Some macroscopic observable features arising from this include variations in the specific heat, an anisotropic correction to thermal conductivity and a variation in optical scattering as a function of the declination from the axis of local vorticity. The improvements in magneto-optical traps suggests some interesting experiments to be done in higher temperature regimes where they are not usually employed. It is argued that the finite lifetime of observed vortices in ultracold bosonic gases is only apparent and these volume excluding structures persist in generating angular momentum and pressure in the cloud in a non-imageable form.

Previous approaches of emergent thermalization for condensed matter based on typical wavefunctions are extended to generate an intrinsically quantum theory of gases. Gases are fundamentally quantum objects at all temperatures, by virtue of rapid delocalization of their constituents. When there is a sufficiently broad spread in the energy of eigenstates, a well-defined temperature is shown to arise by photon production when the samples are optically thick. This produces a highly accurate approximation to the Planck distribution so that thermalization arises from the initial data as a consequence of purely quantum and unitary dynamics. These results are used as a foil for some common hydrodynamic theory of ultracold gases. It is suggested here that strong history dependence typically remains in these gases and so limits the validity of thermodynamics in their description. These problems are even more profound in the extension of hydrodynamics to such gases when they are optically thin, even when their internal energy is not low. We investigate rotation of elliptically trapped gases and consistency problems with deriving a local hydrodynamic approach. The presence of vorticity that is "hidden" from order parameter approaches is discussed along with some buoyancy intrinsically associated with vorticity that gives essential quantum corrections to gases in the regimes where standard perturbation approaches to the Boltzmann equations are known to fail to converge. These results suggest that studying of trapped gases in the far from ultracold regions may yield interesting results not described by classical hydrodynamics.

Here we propose a pair of experiments to distinguish the recently proposed "slicing theory" of quantum measurement, which gives a transient many worlds picture, and decoherence. Since these two theories are essentially "opposites" in their approach and both claim to arise from the many body Schr\"odinger equation itself, there is no chance of them being equivalent representations of the same reality. It will be explicitly shown that each theory gives very different answers to the questions of back reaction and revival of phase effects after measurement. We suggest that the kinds of isolated systems now possible in optical traps is now sufficient to generate a selective distinction between these two theories. In particular we show that the slicing theory gives examples of interference from "revival of histories" in controlled examples but no back reaction on the measurement devices whereas decoherence gives the opposite.

The problems with an emergent approach to quantum statistical mechanics are discussed and shown to follow from some of the same sources as those of quantum measurement. A wavefunction of an N atom solid is described in the ground and excited eigenstates with explicit modifications for phonons. Using the particular subclass of wavefunctions that can correspond to classical solids we investigate the localization properties of atomic centers of mass motion and contrast it with more general linear combinations of phonon states. The effectively large mass of longer modes means that localization present in the ground state persists on excitation of the material by macroscopic coherent disturbances. The "thermalization" that arises then follows from the long term well defined motion of these localized peaks in their 3N dimensional harmonic wells in the same fashion as that of a classical solid in phase space. Thermal production of photons then create an internal radiation field and provides the first dynamical derivation of the Planck distribution from material motions. Significantly, this approach resolves a long standing paradox of thermalization of many body quantum systems from Schr\"{o}dinger dynamics alone.

An emergent theory of quantum measurement arises directly by considering the particular subset of many body wavefunctions that can be associated with classical condensed matter and its interaction with delocalized wavefunctions. This transfers questions of the "strangeness" of quantum mechanics from the wavefunction to the macroscopic material itself. An effectively many-worlds picture of measurement results for long times and induces a natural arrow of time. The challenging part is then justifying why our macroscopic world is dominated by such far-from-eigenstate matter. Condensing cold mesoscopic clusters provide a pathway to a partitioning of a highly correlated many body wavefunction to long lasting islands composed of classical-like bodies widely separated in Fock space. Low mass rapidly delocalizing matter that recombines with the solids "slice" the system into a set of nearby yet very weakly interacting subsystems weighted according to the Born statistics and yields a kind of many worlds picture but with the possibility of revived phase interference on iterative particle desorption, delocalization and readsorption. A proliferation of low energy photons competes with such a possibility. Causality problems associated with correlated quantum measurement are resolved and conserved quantities are preserved for the overall many body function despite their failure in each observer's bifurcating "slice-path." The necessity of such a state for a two state logic and reliable discrete state machine suggests that later stages of the universe's evolution will destroy the physical underpinnings required for consciousness and the arrow of time even without heat-death or atomic destruction. Some exotic possibilities outside the domain of usual quantum measurement are considered such as measurement with delocalized devices and revival of information from past measurements.

The use of continuum mechanics and invariants built from the deviator as an adequate foundation for rheology has been recently disputed by this author. Here we give a specific example of the kind of parcel deformations that are uniquely decomposed by way of microscopic motions into a maximal rotation, a pure shear and an extension. The construction of these equations depends on only one free material parameter but they have no nice form in terms of the operations of vector and tensor calculus which may be why they were overlooked. Although the first order flow is often sufficient to give the rheological information, finite sized parcel deformations can give confusion because of boundary effects, the relevance of which are highly dependent on the global geometry of the experiment.

It is shown that electrostatic and diamagnetic forces can combine to give long lasting metastable bound dimers of macro and mesoscopically sized objects for a physically attainable material regime. This can be a large enough effect to support itself in a trap against Earth's gravity and they can stable at very high temperatures. For a more restricted material parameter set, we investigate the possibility of stable many particle collections that lose their identity as bound pairs and create a kind of plasma. These would constitute a kind of transitional state between fluids and granular materials but, unlike usual approaches, the fluid is a gas rather than a liquid.

We investigate the energy transfer from large waves to small ones through vertical acceleration and demonstrate that this is a much larger effect than that of the potential energy changes of the small waves moving over the larger ones. Rates of exponential growth for this process are given and limits on the stable size of small waves in the horizontal accelerations from the larger ones are derived. We discuss the possibility of this being a manifestation of the Benjamin-Feir instability.

The role of whitecapping losses of waves is investigated in a simple model based on conservation laws. It is shown that, for Airy waves, at least as much energy is lost in gradual reequilibration as is lost in the whitecapping events themselves. This model is based on the the notion that the waves and losses are small enough that some narrow spectrum of frequencies reappears over time.

The usual wavemaker theory hides an unjustified integration constant assumption that renders it invalid. We discuss some surprising subtleties of momentum flux in infinite waves, packets and some counterintuitive examples where "hidden" flux contributions can arise. From here, we construct an ideal wavemaker that builds Airy waves from a series of microjets that allows an exact calculation of the forces on boundaries. This allows us to also compute the fluxes of all conserved quantities directly and rule out some of these hidden contributions to momentum flux. We then discuss some realistic flapper wavemakers and the trouble vorticity sources can create in the resulting fluid motion. Along the way we present a completely local derivation of the group velocity using fluxes.

Inviscid hydrodynamics mediates forces through pressure and other, typically irrotational, external forces. Acoustically induced forces must be consistent with arising from such a pressure field. The use of "acoustic stress" is shown to have inconsistencies with such an analysis and generally arise from mathematical expediency but poor overall conceptualization of such systems. This contention is further supported by the poor agreement of experiment in many such approaches. The notion of momentum as being an intrinsic property of sound waves is similarly found to be paradoxical. Through an analysis that includes viscosity and attenuation, we conclude that all acoustic streaming must arise from vorticity introduced by viscous forces at the driver or other solid boundaries and that calculations with acoustic stress should be replaced with ones using a nonlinear correction to the overall pressure field.

We examine two means by which wind can impart energy to waves: sheltering and deposition of material upwards from windward surface shear. The shear driven deposition is shown to be the more efficient process. Lengthening of waves to match the wind speed is shown to be very inefficient and consume a large fraction of the energy imparted by the wind. The surface shear provides a low energy sink that absorbs most of the momentum from the wind. These produce bounds on the efficiency of wave growth. The results here are computed in a model independent and perturbation free fashion by a careful consideration of conservation laws. By combining these effects we can place bounds on the rates waves can grow in a given fetch and the relative amount of shear flow versus the, relatively small, Stokes drift that must arise.

We investigate the interaction of waves with surface flows by considering the full set of conserved quantities, subtle but important surface elevation changes induced by wave packets and by directly considering the necessary forces to prevent packet spreading in the deep water limit. Narrow surface shear flows are shown to exert strong localizing and stabilizing forces on wavepackets to maintain their strength and amplify their intensity even in the linear regime. Subtle packet scale nonlinear elevation changes from wave motion are crucial here and it suggest that popular notions of wave stress and action are naive. Quantitative bounds on the surface shear flow necessary to stabilize packets of any wave amplitude are given. One implication of this mechanism is that rogue wave stabilization must be due to a purely nonperturbative process.

The conservation laws of electromagnetism, and implicitly all theories built from quadratic Lagrangians, are extended to a continuum of nonlocal versions. These are associated with symmetries of a class of equal time field correlation functions and give results for both connected and disconnected branches of the general linear group of the space. It is generally assumed that manifestly covariant Lagrangians are the necessary starting point for physical theories. Here we show that the EOM derived from any of these can also follow from a broad class of nonlocal ones and each generally gives a different nonlocal Noether current. When the equations are put into a linear form and evaluated on a flat spacetime, a simple ansatz exists to give a class of conservation laws corresponding to all affine transformations of the underlying space. A general procedure is given to generate a class of nonlocal conservation laws for solutions to a very large class of nonlinear PDEs.

Through a discussion of some typical unsteady hydrodynamic flows, we argue that the time averaged hydrodynamic functions at each point give a rather sparse filling of the local jet space. This situation then suggests a set of time dependent probability functions that are shown to give evolution uniquely defined by the Navier-Stokes equations through a set of "differential distribution equations." The closure relations are therefore unique and have no ad hoc characteristics. Annealing methods are proposed as a way to arrive at the stable stationary solutions corresponding to time averaged fluid flow with constant driving forces and fixed boundary conditions. Some applications of this method to quantum statistical mechanics and kinetic theory to higher orders are suggested.

We present an exactly solvable model of a classical dielectric medium that gives an unambiguous local decomposition of field and charge motion and their contribution to the conserved quantities. The result is a set of four branches to the dispersion law that gives full independent freedom in the selection of initial data of the fields and charge motion, in contrast with constitutive laws. This is done with special care to the forces that exist at surfaces, coatings and the ends of packets. As a result the utility of a stress-tensor as a function of field strengths and dielectric response for deriving general forces is called into question. The Abraham-Minkowskii paradox is clarified from this point of view and the export of such notions to realistic media and metamaterials are discussed. One result of this model is a mathematically simpler and more intuitive understanding of causality in media than the Brillouin and Sommerfeld theories. Necessary elastic medium response is estimated and some implications of this picture for quantum effects are included based on conservation laws. This model can be extended to manifestly maintain these features as general nonlinear and time and space dependent changes in medium response are introduced. The extent to which this can provide a universal description for all dielectrics is discussed. A microscopic treatment of negative index materials from this point of view is included as an illustration of the extreme economy and simplicity of these methods.

The superrotation of the atmosphere of Venus requires a large torque on the up- per atmosphere. Mechanisms for providing a net balancing of this through waves or ionospheric motions to other parts of the atmosphere have been proposed but all have difficulties. Here we demonstrate that the albedo gradient from the day to night side of the cloud layer allows a gradient of light pressure that is sufficient to provide an external torque to drive this flow.

Surface tension of small grains and droplets makes them stable only at a much lower temperature than in bulk. This makes spontaneous nucleation unfavorable in many cases. Kinetic approaches are delicate in that one can easily generate models that do not agree with thermodynamics in the large N limit. Here it is shown that thermodynamics itself dictates a kind of temperature suppression inside each small cluster in any gas-cluster mixture. This gives a different perspective on the "translation-rotation" paradox in that this gives a time averaged steady state thermal inhomogeneity rather than just temporal fluctuations in the energy. This not only reduces the barrier to nucleation but also suggests a change in the thermal radiation spectrum from such a mixture that is not just a result of the inhibited radiation spectrum from Mie radiators. Either verification or refutation of this effect will be shown have important consequences for thermodynamics. An understanding of this effect will be essential to kinetic approaches to nucleation theory.

This article will use arguments derived from the deformation driven component of mixing, especially important for microfluidics, to show that the standard invariant based approaches to rheology are lacking. It is shown that the deviator, $D_{ij}$, after the process of symmetrization, loses microscopically determined information that distinguish rotation from shear and extension in a unique fashion. We recover this information through an analysis of the discrete processes that must underlie deformation driven mixing in highly correlated fluids. Without this we show there is no hope of ever deriving adequate general material parameters for rheology from microscopic dynamics. There is an unambiguous microscopic notion of the rotation rate for every parcel and we derive a general class of invariant rheological theories from it. We discuss some implications of higher order flows on solutions and suspensions including possibilities for driving and stabilization of nonuniform distributions using hydrodynamic forces alone.

In this short note, we discuss a mechanism for the transport of energy, momentum and dipole moment via transient neutral carriers in plasma. This gives a way to rapidly convert bulk hydrodynamic flow energy into thermal energy over a distance of several mean free paths. In the transition region of the solar corona we estimate various processes and their potential to introduce the high energies needed to to reach the 2 x10^6K observed there. It implies that kinetic methods may be essential for modeling the corona and that there are more gentle but still robust means than reconnection to relax magnetic fields in plasmas.

The geometric properties of General Relativity are reconsidered as a particular nonlinear interaction of fields on a flat background where the perceived geometry and coordinates are "physical" entities that are interpolated by a patchwork of observable bodies with a nonintuitive relationship to the underlying fields. This more general notion of gauge in physics opens an important door to put all fields on a similar standing but requires a careful reconsideration of tensors in physics and the conventional wisdom surrounding them. The meaning of the flat background and the induced conserved quantities are discussed and contrasted with the "observable" positive definite energy and probability density in terms of the induced physical coordinates. In this context, the Dirac matrices are promoted to dynamic proto-gravity fields and the keeper of "physical metric" information. Independent sister fields to the wavefunctions are utilized in a bilinear rather than a quadratic lagrangian in these fields. This construction greatly enlarges the gauge group so that now proving causal evolution, relative to the physical metric, for the gauge invariant functions of the fields requires both the stress-energy conservation and probability current conservation laws. Through a Higgs-like coupling term the proto-gravity fields generate a well defined physical metric structure and gives the usual distinguishing of gravity from electromagnetism at low energies relative to the Higgs-like coupling. The flat background induces a full set of conservation laws but results in the need to distinguish these quantities from those observed by recording devices and observers constructed from the fields.

Through an illuminating thought experiment we demonstrate that the nonsingular "continued collapse" picture of a black hole is the only consistent and physical one. We provide a class exact solutions on the boundary of the space of physical configurations. This will show that all the other known exact solutions are unphysical near the surface of the event horizon or in the interior. This will have important consequences for the no-hair conjecture and the kinds of persistent fields that can emerge from a black hole as well as the evolution during collisions and near grazing events. The interior of these holes are characterized by a limiting degenerate metric and these regions tend to well defined volumes and radii in contrast with what is inferred from singular solutions. Surprisingly, these depend on past history and not simply the mass or external fields of the body. It is shown that there is often a well defined "hidden" flat background that can be used to equivalently reformulate GR in terms of a classical nonlinear gravity field and gives local conservation laws. This has implications for unification efforts and numerical approaches to handle the degenerate metric regions reminiscent of the Rankine-Hugoniot conditions. Possible consistency problems with current numerical approaches to black hole dynamics are discussed.