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An explicit, energy-conserving particle-in-cell scheme

We present an explicit temporal discretization of particle-in-cell schemes for the non-relativistic Vlasov equation that results in exact energy conservation when combined with an appropriate spatial discretization. The scheme is inspired by a simple, second-order explicit scheme that conserves energy exactly in the Eulerian context. We show that direct translation to particle-in-cell does not result in strict conservation, but derive a simple correction based on an analytically solvable optimization problem that recovers conservation. While this optimization problem is not guaranteed to have a real solution for every particle, we provide a correction that makes imaginary values extremely rare and still admits $\mathcal{O}$(10 –12 ) fractional errors in energy for practical simulation parameters. We present the scheme in both electrostatic – where we use the Ampère formulation – and electromagnetic contexts. With an electromagnetic field solve, the field update is most naturally linearly implicit, but the more computationally intensive particle update remains fully explicit. Here, we also show how the scheme can be extended to use the fully explicit leapfrog and pseudospectral analytic time-domain (PSATD) field solvers. The scheme is tested on standard kinetic plasma problems, confirming its conservation properties.

Energy conservation↗

Quantifying the Impact of Lagged Hydrological Responses on the Effectiveness of Groundwater Conservation

Many irrigated agricultural areas seek to prolong the lifetime of their groundwater resources by reducing pumping. However, it is unclear how lagged responses, such as reduced groundwater recharge caused by more efficient irrigation, may impact the long-term effectiveness of conservation initiatives. Here, we use a variably saturated, simplified surrogate groundwater model to: 1) analyze aquifer responses to pumping reductions, 2) quantify time lags between reductions and groundwater level responses, and 3) identify the physical controls on lagged responses. We explore a range of plausible model parameters for an area of the High Plains Aquifer (USA) where stakeholder-driven conservation has slowed groundwater depletion. We identify two types of lagged responses that reduce the long-term effectiveness of groundwater conservation, recharge-dominated and lateral-flow-dominated, with vertical hydraulic conductivity (K Z ) the major controlling variable. When high K z allows percolation to reach the aquifer, more efficient irrigation reduces groundwater recharge. By contrast, when low K z impedes vertical flow, short term changes in recharge are negligible, but pumping reductions alter the lateral flow between the groundwater conservation area and the surrounding regions (lateral-flow-dominated response). For the modeled area, we found that a pumping reduction of 30% resulted in median usable lifetime extensions of 20 or 25 years, depending on the dominant lagged response mechanism (recharge- vs. lateral-flow-dominated). These estimates are far shorter than estimates that do not account for lagged responses. To conclude, results indicate that conservation-based pumping reductions can extend aquifer lifetimes, but lagged responses can create a sizable difference between the initially perceived and actual long-term effectiveness.

54 ENVIRONMENTAL SCIENCES↗

Energy conservation in real-time nuclear–electronic orbital Ehrenfest dynamics

Real-time nuclear–electronic orbital Ehrenfest (RT-NEO-Ehrenfest) dynamics methods provide a first-principles approach for describing nonadiabatic molecular processes with nuclear quantum effects. For an efficient description of proton transfer within RT-NEO-Ehrenfest dynamics, the basis function center associated with the quantum proton can be allowed to move classically. Here, this traveling proton basis (TPB) approach effectively captures proton quantum dynamics, although its energy conservation behavior is not yet fully satisfactory. Two recently proposed TPB approaches, in principle, conserve the extended energy, which includes both the system energy and the kinetic energy associated with the proton basis function center. Herein, a thermostatted TPB approach is proposed to improve the conservation of the system energy, excluding the kinetic energy associated with the proton basis function center. In this approach, the quantum proton dynamics are modulated by dynamically rescaling the proton momentum operator to maintain the system energy conservation. With the excited-state intramolecular proton transfer of o-hydroxybenzaldehyde as an example, this approach is shown to significantly improve the system energy conservation while preserving the accuracy of the quantum proton dynamics as achieved in the original TPB approach.

Ehrenfest dynamics↗

One hundred priority questions for advancing seagrass conservation in Europe

Societal Impact Statement Seagrass ecosystems are of fundamental importance to our planet and wellbeing. Seagrasses are marine flowering plants, which engineer ecosystems that provide a multitude of ecosystem services, for example, blue foods and carbon sequestration. Seagrass ecosystems have largely been degraded across much of their global range. There is now increasing interest in the conservation and restoration of these systems, particularly in the context of the climate emergency and the biodiversity crisis. The collation of 100 questions from experts across Europe could, if answered, improve our ability to conserve and restore these systems by facilitating a fundamental shift in the success of such work. Summary Seagrass meadows provide numerous ecosystem services including biodiversity, coastal protection, and carbon sequestration. In Europe, seagrasses can be found in shallow sheltered waters along coastlines, in estuaries & lagoons, and around islands, but their distribution has declined. Factors such as poor water quality, coastal modification, mechanical damage, overfishing, land‐sea interactions, climate change and disease have reduced the coverage of Europe’s seagrasses necessitating their recovery. Research, monitoring and conservation efforts on seagrass ecosystems in Europe are mostly uncoordinated and biased towards certain species and regions, resulting in inadequate delivery of critical information for their management. Here, we aim to identify the 100 priority questions, that if addressed would strongly advance seagrass monitoring, research and conservation in Europe. Using a Delphi method, researchers, practitioners, and policymakers with seagrass experience from across Europe and with diverse seagrass expertise participated in the process that involved the formulation of research questions, a voting process and an online workshop to identify the final list of the 100 questions. The final list of questions covers areas across nine themes: Biodiversity & Ecology; Ecosystem services; Blue carbon; Fishery support; Drivers, Threats, Resilience & Response; Monitoring & Assessment; Conservation & Restoration; Governance, Policy & Management; and Communication. Answering these questions will fill current knowledge gaps and place European seagrass onto a positive trajectory of recovery.

Nordlund, Lina Mtwana↗

Ecologically-Informed Precision Conservation: A framework for increasing biodiversity in intensively managed agricultural landscapes with minimal sacrifice in crop production

Conservation actions are urgently needed to tackle biodiversity loss in intensively managed agricultural landscapes. Production lands are usually heterogeneous and contain low-yield areas that can be set aside for biodiversity conservation without serious yield losses. Here, we introduce Ecologically-Informed Precision Conservation, a framework that integrates yield mapping and ecological theory to select the best areas to create new set-asides while ensuring high crop yields at the farm/landscape level. Long-term yield maps can be generated using globally available satellite data and basic information on field/farm crop yield from farmers. Ecological principles are then used to select the subset of areas with the highest potential for biodiversity conservation by prioritising those that increase connectivity, maximise habitat heterogeneity and decrease landscape grain size. Here, the created non-crop habitats can be permanent and thus ensure biodiversity support over time. In addition, agricultural management efficiency can be enhanced by improving field shapes. The framework provides the basis for a practical, user-friendly tool that informs all interested stakeholders on how to rationalise existing agricultural landscapes using already-existing farming systems and available technologies. High cost-effectiveness from an economic and conservation perspective, along with the creation of heterogeneous non-crop habitats, make our framework a promising solution to re-design agricultural landscapes.

Precision agriculture↗

A conservative implicit-PIC scheme for the hybrid kinetic-ion fluid-electron plasma model on curvilinear meshes

We report that the hybrid kinetic-ion fluid-electron plasma model is widely used to study challenging multi-scale problems in space and laboratory plasma physics. Here, a novel conservative scheme for this model employing implicit particle-in-cell techniques is extended to arbitrary coordinate systems via curvilinear maps from logical to physical space. The scheme features a fully non-linear electromagnetic formulation with a multi-rate time advance - including sub-cycling and orbit-averaging for the kinetic ions. By careful choice of compatible particle-based kinetic-ion and mesh-based fluid-electron discretizations in curvilinear coordinates, as well as particle-mesh interpolations and implicit midpoint time advance, the scheme is proven to conserve total energy for arbitrary curvilinear meshes. In the electrostatic limit, the method is also proven to conserve total momentum for arbitrary curvilinear meshes. Although momentum is not conserved for arbitrary curvilinear meshes in the electromagnetic case, it is for an important subset of Cartesian tensor-packed meshes. The scheme and its novel conservation properties are demonstrated for several challenging numerical problems using different curvilinear meshes, including a merging flux-rope simulation for a space weather application, and a helical m = 1 mode simulation for magnetic fusion energy application.

97 MATHEMATICS AND COMPUTING↗

Immunogenicity and protective efficacy of a rhesus adenoviral vaccine targeting conserved COVID-19 replication transcription complex

The COVID-19 pandemic marks the third coronavirus pandemic this century (SARS-CoV-1, MERS, SARS-CoV-2), emphasizing the need to identify and evaluate conserved immunogens for a pan-sarbecovirus vaccine. Here we investigate the potential utility of a T-cell vaccine strategy targeting conserved regions of the sarbecovirus proteome. We identified the most conserved regions of the sarbecovirus proteome as portions of the RNA-dependent RNA polymerase (RdRp) and Helicase proteins, both of which are part of the coronavirus replication transcription complex (RTC). Fitness constraints suggest that as SARS-CoV-2 continues to evolve these regions may better preserve cross-reactive potential of T-cell responses than Spike, Nucleocapsid, or Membrane proteins. We sought to determine if vaccine-elicited T-cell responses to the highly conserved regions of the RTC would reduce viral loads following challenge with SARS-CoV-2 in mice using a rhesus adenovirus serotype 52 (RhAd52) vector. The RhAd52.CoV.Consv vaccine generated robust cellular immunity in mice and led to significant reductions in viral loads in the nasal turbinates following challenge with a mouse-adapted SARS-CoV-2. These data suggest the potential utility of T-cell targeting of conserved regions for a pan-sarbecovirus vaccine.

60 APPLIED LIFE SCIENCES↗

Accuracy of the explicit energy-conserving particle-in-cell method for under-resolved simulations of capacitively coupled plasma discharges

The traditional explicit electrostatic momentum-conserving particle-in-cell algorithm requires strict resolution of the electron Debye length to deliver numerical stability and accuracy. The explicit electrostatic energy-conserving particle-in-cell algorithm alleviates this constraint with minimal modification to the traditional algorithm, retaining its simplicity, ease of parallelization, and acceleration on modern supercomputing architectures. In this article, we apply the algorithm to model a one-dimensional radio frequency capacitively coupled plasma discharge relevant to industrial applications. The energy-conserving approach closely matches the results from the momentum-conserving algorithm and retains accuracy even for cell sizes up to 8 times the electron Debye length. For even larger cells, the algorithm loses accuracy due to poor resolution of steep gradients within the radio frequency sheath. Accuracy can be recovered by adopting a non-uniform grid, which resolves the sheath and allows for cell sizes up to 32 times the electron Debye length in the quasi-neutral bulk of the discharge. The effect is an up to 8 times reduction in the number of required simulation cells, an improvement that can compound in higher-dimensional simulations. We therefore consider the explicit energy-conserving algorithm as a promising approach to significantly reduce the computational cost of full-scale device simulations and a pathway to delivering kinetic simulation capabilities of use to industry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Energy conserving and well-balanced discontinuous Galerkin methods for the Euler–Poisson equations in spherical symmetry

ABSTRACT This paper presents high-order Runge–Kutta (RK) discontinuous Galerkin methods for the Euler–Poisson equations in spherical symmetry. The scheme can preserve a general polytropic equilibrium state and achieve total energy conservation up to machine precision with carefully designed spatial and temporal discretizations. To achieve the well-balanced property, the numerical solutions are decomposed into equilibrium and fluctuation components that are treated differently in the source term approximation. One non-trivial challenge encountered in the procedure is the complexity of the equilibrium state, which is governed by the Lane–Emden equation. For total energy conservation, we present second- and third-order RK time discretization, where different source term approximations are introduced in each stage of the RK method to ensure the conservation of total energy. A carefully designed slope limiter for spherical symmetry is also introduced to eliminate oscillations near discontinuities while maintaining the well-balanced and total-energy-conserving properties. Extensive numerical examples – including a toy model of stellar core collapse with a phenomenological equation of state that results in core bounce and shock formation – are provided to demonstrate the desired properties of the proposed methods, including the well-balanced property, high-order accuracy, shock-capturing capability, and total energy conservation.

79 ASTRONOMY AND ASTROPHYSICS↗

Conservation law for electromagnetic fields in a space-time-varying medium and its implications

We discuss the propagation of electromagnetic waves in a space-time modulated medium, for which neither energy nor momentum remains conserved. We have found a new conservation law when modulation moves at a constant speed v in a traveling-wave fashion. We use this law to study how light is scattered inside such a medium. We consider both the subluminal (v < c) andsuperluminal (v > c) cases and find that they differ considerably in terms of what remains conserved. We show that the total number of photons is conserved in the subluminal case. In contrast, it is the difference between the forward and backward moving photons that remains conserved in the superluminal case. We also study the reciprocity issue for a space-time modulated medium and found that reciprocity holds in all situations. Here, we develop a quantum formulation of our scattering problem and show that the subluminal case is similar to the action of a beam splitter. In the superluminal case, photon pairs can be generated from vacuum in a fashion analogous to the two-mode frequency down-conversion process.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery

Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.

59 BASIC BIOLOGICAL SCIENCES↗

Entropy Stable Conservative Flux Form Neural Networks

We propose an entropy-stable conservative flux form neural network (CFN) to predict the dynamics of unknown governing conservation laws. The design of the network is based on the entropy-stable, second-order, and non-oscillatory Kurganov-Tadmor (KT) scheme. The proposed entropy-stable CFN, hereafter referred to as ESCFN, uses slope limiting as a denoising mechanism, ensuring accurate predictions in both noisy and sparse observation environments, as well as in both smooth and discontinuous regions. Importantly, our method is designed to predict long term dynamics of the unknown conservation law exclusively from a short temporal window of observed data, that is, without oracle knowledge of the PDE or later-time solution profiles. Numerical experiments demonstrate that the ESCFN achieves both stability and conservation while maintaining accuracy over extended time domains, and successfully predicts shock propagation speeds in long-term simulations. Furthermore, it is also robust to both noisy and sparse data environments.

Hyperbolic conservation laws↗

Path-Integrated Stereo X-Ray Digital Image Correlation: Resolving the Violation of Conservation of Intensity

In this study, x-ray imaging addresses many challenges with visible light imaging in extreme environments, where optical diagnostics such as digital image correlation (DIC) and particle image velocimetry (PIV) suffer biases from index of refraction changes and/or cannot penetrate visibly occluded objects. However, conservation of intensity—the fundamental principle of optical image correlation algorithms—may be violated if ancillary components in the X-ray path besides the surface or fluid of interest move during the test. The test series treated in this work sought to characterize the safe use of fiber-epoxy composites in aerospace and aviation industries during fire accident scenarios. Stereo X-ray DIC was employed to measure test unit deformation in an extreme thermal environment involving a visibly occluded test unit, incident surface heating to temperatures above 600°C, and flames and soot from combusting epoxy decomposition gasses. The objective of the current work is to evaluate two solutions to resolve the violation of conservation of intensity that resulted from both the test unit and the thermal chamber deforming during the test. The first solution recovered conservation of intensity by pre-processing the path-integrated X-ray images to isolate the DIC pattern of the test unit from the thermal chamber components. These images were then correlated with standard, optical DIC software. The second solution, called Path-Integrated Digital Image Correlation (PI-DIC), modified the fundamental matching criterion of DIC to account for multiple, independently-moving components contributing to the final image intensity. The PI-DIC algorithm was extended from a 2D framework to a stereo framework and implemented in a custom DIC software. Both solutions accurately measured the cylindrical shape of the undeformed test unit, recovering radii values of R = 76.20±0.12 mm compared to the theoretical radius of R theor = 76.20 mm. During the test, the test unit bulged asymmetrically as decomposition gasses pressurized the interior and eventually burned in a localized jet. Both solutions measured the heterogeneous radius of this bulge, which reached a maximum of approximately R = 91 mm, with a discrepancy of 2–3% between the two solutions. Two solutions that resolve the violation of conservation of intensity for path-integrated X-ray images were developed. Both were successfully employed in a stereo X-ray DIC configuration to measure deformation of an aluminum-skinned, fiber-epoxy composite test unit in a fire accident scenario.

47 OTHER INSTRUMENTATION↗

Performance Analysis of Speculative Parallel Adaptive Local Timestepping for Conservation Laws

Stable simulation of conservation laws, such as those used to model fluid dynamics and plasma physics applications, requires the satisfaction of the so-called Courant-Friedrichs-Lewy condition. By allowing regions of the mesh to advance with different timesteps that locally satisfy this stability constraint, significant work reduction can be attained when compared to a time integration scheme using a single timestep size. However, parallelizing this algorithm presents considerable difficulty. Since the stability condition depends on the state of the system, dependencies become dynamic and potentially non-local. In this article, we present an adaptive local timestepping algorithm using an optimistic (Timewarp-based) parallel discrete event simulation. We introduce waiting heuristics to limit misspeculation and a semi-static load balancing scheme to eliminate load imbalance as parts of the mesh require finer or coarser timesteps. Last, we outline an interface for separating the physics of the specific conservation law from the temporal integration allowing for productive adoption of our proposed algorithm. We present a misspeculation study for three conservation laws, demonstrating both the productivity of the local timestepping API, for which 74% of the lines of code are reused across different conservation laws, and the robustness of the waiting heuristics—at most 1.5% of element updates are rolled back. Our performance studies demonstrate up to a 2.8× speedup versus a baseline unoptimized local timestepping approach, a 4x improvement in per-node throughput compared to an MPI parallelization of synchronous timestepping, and scalability up to 3,072 cores on NERSC’s Cori Haswell partition.

97 MATHEMATICS AND COMPUTING↗

A pseudospectral implicit particle-in-cell method with exact energy and charge conservation

The standard particle-in-cell (PIC) method employs explicit finite-difference (FD) methods (e.g. the leap-frog scheme) for both spatial and temporal integrations. Here, we employ a pseudospectral method for solving the Poisson equation and a fully implicit time integration to achieve exact energy conservation. The advantage of a pseudospectral field solver is its spectral accuracy in solving field solutions. Earlier studies of implicit time integration of PIC FD equations can enforce exact energy exchange between field and particles, resulting in exact energy-conserving schemes. Here, we prove that the exact energy conservation property can be carried over to the pseudospectral scheme. Simultaneously, we provide a solution to ensure a pseudospectral charge continuity equation. We demonstrate the new scheme in a 2D electrostatic PIC code. In conclusion, theoretical results are confirmed via numerical examples.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A conservative Galerkin solver for the quasilinear diffusion model in magnetized plasmas

We propose a conservative Galerkin scheme for the quasilinear model in three-dimensional momentum space and three-dimensional spectral space, with cylindrical symmetry. We construct an unconditionally conservative weak form and use a discretization that preserves conservation properties independent of the wave emission probability. The discrete operators, combined with a consistent quadrature rule, preserve all the conservation laws rigorously. The proposed scheme is quite general: it works for both relativistic and non-relativistic systems, for both magnetized and unmagnetized plasmas, and even for problems with time-dependent dispersion relations. We represent the particle distribution by continuous basis functions and use discontinuous basis functions for the wave spectral energy density, which enables the application of a positivity-preserving technique. We adopt the marching simplex algorithm, designed initially for computer graphics, for numerical integration on the resonance manifold. Furthermore, the numerical examples with a bump-on-tail initial configuration show how the unstable waves produce strong momentum space diffusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Carbon-conserving bioproduction of malate in an E. coli -based cell-free system

Formate, a biologically accessible form of CO 2 , has attracted interest as a renewable feedstock for bioproduction. However, approaches are needed to investigate efficient routes for biological formate assimilation due to its toxicity and limited utilization by microorganisms. Cell-free systems hold promise due to their potential for efficient use of carbon and energy sources and compatibility with diverse feedstocks. However, bioproduction using purified cell-free systems is limited by costly enzyme purification, whereas lysate-based systems must overcome loss of flux to background reactions in the cell extract. Here, we engineer an E. coli-based system for an eight-enzyme pathway from DNA and incorporate strategies to regenerate cofactors and minimize loss of flux through background reactions. We produce the industrial di-acid malate from glycine, bicarbonate, and formate by engineering the carbon-conserving reductive TCA and formate assimilation pathways. We show that in situ regeneration of NADH drives metabolic flux towards malate, improving titer by 15-fold. Background reactions can also be reduced 6-fold by diluting the lysate following expression and introducing chemical inhibitors of competing reactions. Together, these results establish a carbon-conserving, lysate-based cell-free platform for malate production, producing 64 μM malate after 8 h. This system conserves 43 % of carbon otherwise lost as CO 2 through the TCA cycle and incorporates 0.13 mol CO 2 equivalents/mol glycine fed. Finally, techno-economic analysis of cell-free malate production from formate revealed that the high cost of lysate is a key challenge to the economic feasibility of the process, even assuming efficient cofactor recycling. This work demonstrates the capabilities of cell-free expression systems for both the prototyping of carbon-conserving pathways and the sustainable bioproduction of platform chemicals.

60 APPLIED LIFE SCIENCES↗

Momentum conservation in current drive and alpha-channeling-mediated rotation drive

Alpha channeling uses waves to extract hot ash from a fusion plasma, transferring energy from the ash to the wave. It has been proposed that this process could create a radial electric field, efficiently driving E × B rotation. However, existing theories ignore the nonresonant particles, which play a critical role in enforcing momentum conservation in quasilinear theory. Because cross field charge transport and momentum conservation are fundamentally linked, this non-consistency throws the rotation drive into question. This paper has two main goals. First, we provide a pedantic and cohesive introduction to the recently developed simple, general, self-consistent quasilinear theory for electrostatic waves that explains the torques which allow for current drive parallel to the magnetic field, and charge extraction across it; a theory that has largely resolved the question of rotation drive by alpha channeling. We show how the theory reveals a fundamental difference between the reaction of nonresonant particles to plane waves that grow in time vs steady-state waves that have a nonuniform spatial structure, allowing rotation drive in the latter case while precluding it in the former, and we review the local and global conservation laws that lead to this result. Second, we provide two new results in support of the theory. First, we provide a novel two-particle Hamiltonian model that rigorously establishes the relationship between charge transport and momentum conservation. Second, we compare the new quasilinear theory to the oscillation-center theories of ponderomotive forces, showing how the latter often obscure the time-dependent nonresonant recoil, but ultimately lead to similar results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗