Reversals and collisions optimize protein exchange in bacterial swarms
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Amiri, Aboutaleb↗
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Results for “Reversible computation”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Multi-point nonequilibrium umbrella sampling and associated fluctuation relations
We describe a simple method of umbrella trajectory sampling for Markov chains. The method allows the estimation of large-deviation rate functions, for path-extensive dynamic observables, for an arbitrary number of models within a certain family. The general relationship between probability distributions of dynamic observables of members of this family is an extended fluctuation relation. When the dynamic observable is chosen to be entropy production, members of this family include the forward Markov chain and its time reverse, whose probability distributions are related by the expected simple fluctuation relation.
97 MATHEMATICS AND COMPUTING↗
The apparent reversal of the Law of Mass Action in concentrated multicomponent aqueous solutions
Although it is well known that aqueous electrolyte solutions behave non-ideally, few are so non-ideal that adding an electrolyte to a saturated solution with a common ion enhances rather than depresses solubility. Nonetheless, this apparent reversal of the Law of Mass Action (LMA) has been observed in simple nitrate solutions at high concentrations. A leading hypothesis is that ion clusters are formed and stabilized by ions having different charge densities. We report the present study examines this concept, in part by reviewing relevant data from multicomponent aqueous solutions containing sodium nitrate (NaNO 3 ), sodium nitrite (NaNO 2 ), sodium hydroxide (NaOH), and sodium aluminate (NaAl(OH) 4 ) - the major constituents in alkaline nuclear waste. Here, NaOH and NaAl(OH) 4 did not enhance the solubility of NaNO 3 or NaNO 2 , whereas NaNO 2 and NaNO 3 enhanced rather than depressed the solubility of each other despite each having the sodium cation (Na + ) in common. Solutions evaluated in this study have more than 20 molal total Na + concentration, and most have less than one mole of water per mole of ion. Thus, this reversal of the LMA occurs in solutions where there is not enough water to fully hydrate the ions, pointing to the importance of ion cluster formation. Within the composition range of the solutions analyzed here, this reversal of the LMA occurs regardless of NaAl(OH) 4 and NaOH concentrations. Elevated temperatures also result in the reversal of the LMA in the subsystems NaNO 2 -NaNO 3 -H 2 O and NaOH-NaNO 3 -H 2 O, consistent with spectroscopic and computational studies showing enhanced interactions at higher temperatures. Although speciation in these highly concentrated electrolyte solutions is not well understood, the stabilization of ion clusters by: (i) optimizing charge density around the ions through different combinations of mixed cations and anions in solution; and (ii) high temperatures where ions experience prolonged contact, offers important clues for future research into how these species control solubility.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Transporter annotations are holding up progress in metabolic modeling
Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane transporters. These include general or non-specific substrate assignments, ambiguity in the localization, directionality and reversibility of a transporter, and the many-to-many mapping of substrates, transporters and genes. In this perspective, we summarize progress in both experimental and computational approaches used to determine the function of transporters and consider paths forward that integrate both. Investment in accurate, high-throughput functional characterization is needed to train the next-generation of predictive tools toward genome-scale metabolic network reconstructions that better predict phenotypes and interactions. More reliable predictions in this domain will benefit fields ranging from personalized medicine to metabolic engineering to microbial ecology.
Casey, John↗
Comparative efficiency of finite, boundary and hybrid element methods in elastostatics
The comparative computational efficiencies of the finite element (FEM), boundary element (BEM), and hybrid boundary element-finite element (HBFEM) analysis techniques are evaluated for representative bounded domain interior and unbounded domain exterior problems in elastostatics. Computational efficiency is carefully defined in this study as the computer time required to attain a specified level of solution accuracy. The study found the FEM superior to the BEM for the interior problem, while the reverse was true for the exterior problem. The hybrid analysis technique was found to be comparable or superior to both the FEM and BEM for both the interior and exterior problems.
Schwartz, C. W.↗
Research related to improved computer aided design software package
The comparative computational efficiencies of the finite element (FEM), boundary element (BEM), and hybrid boundary element-finite element (HVFEM) analysis techniques are evaluated for representative bounded domain interior and unbounded domain exterior problems in elastostatics. Computational efficiency is carefully defined in this study as the computer time required to attain a specified level of solution accuracy. The study found the FEM superior to the BEM for the interior problem, while the reverse was true for the exterior problem. The hybrid analysis technique was found to be comparable or superior to both the FEM and BEM for both the interior and exterior problems.
Walston, W. H., Jr.↗
Configurations of corotating shocks in the outer heliosphere
Configurations of corotating shocks in the outer heliosphere are computed on the assumption that the shocks move at constant speeds between collisions. The basic physical process is the interaction of a forward shock with a reverse shock. The points at which this interaction takes place are determined algebraically in terms of the initial shock positions and speeds. Between the points at which the shocks interact, the shocks have the form of Archimedian spirals. Shock configurations are determined for the case of two corotating shock pairs originating at 2.5 AU and for a single shock pair at 2.5 AU. In both cases the heliosphere is divided into several distinct regions distinguished by the number of times the particles have passed through a shock. Since the shock strengths decrease when a forward shock interacts with a reverse shock, corotating shocks are expected to be weaker at larger distances from the sun.
Burlaga, L. F.↗
Driven, steady-state RFP computations
The pseudospectral three-dimensional MHD code of Dahlburg et al. (1986 and 1987) is used to compute the dynamical behavior of a channel of magnetofluid carrying an axial current and magnetic flux. This situation contains the essential MHD behavior of the reversed-field pinch (RFP). An externally imposed electric field is applied to an initially current-free magnetofluid and drives currents that rise and eventually fluctuate about values corresponding to pinch ratios Theta of about 1.3, 2.2, and 4.5. A period of violent turbulence leads to an approximately force-free core, surrounded by an active MHD boundary layer that is not force-free. A steady state is reached that can apparently be sustained indefinitely (for several hundred Alfven transit times or longer). The turbulence level and time variability in the steady state increase with increasing Theta. The average toroidal magnetic field at the wall reverses for Theta = 2.2 and 4.5, but not for Theta = 1.3. Negative toroidal current filaments are observed. The Lundquist numbers are of the order of a few hundred.
Dahlburg, J. P.↗
Myths and realities: Defining re-engineering for a large organization
This paper describes the background and results of three studies concerning software reverse engineering, re-engineering, and reuse (R3) hosted by the Internal Revenue Service in 1991 and 1992. The situation at the Internal Revenue--aging, piecemeal computer systems and outdated technology maintained by a large staff--is familiar to many institutions, especially among management information systems. The IRS is distinctive for the sheer magnitude and diversity of its problems; the country's tax records are processed using assembly language and COBOL and spread across tape and network DBMS files. How do we proceed with replacing legacy systems? The three software re-engineering studies looked at methods, CASE tool support, and performed a prototype project using re-engineering methods and tools. During the course of these projects, we discovered critical issues broader than the mechanical definitions of methods and tool technology.
Yin, Sandra↗
Combustion Instabilities Modeled
NASA Lewis Research Center's Advanced Controls and Dynamics Technology Branch is investigating active control strategies to mitigate or eliminate the combustion instabilities prevalent in lean-burning, low-emission combustors. These instabilities result from coupling between the heat-release mechanisms of the burning process and the acoustic flow field of the combustor. Control design and implementation require a simulation capability that is both fast and accurate. It must capture the essential physics of the system, yet be as simple as possible. A quasi-one-dimensional, computational fluid dynamics (CFD) based simulation has been developed which may meet these requirements. The Euler equations of mass, momentum, and energy have been used, along with a single reactive species transport equation to simulate coupled thermoacoustic oscillations. A very simple numerical integration scheme was chosen to reduce computing time. Robust boundary condition procedures were incorporated to simulate various flow conditions (e.g., valves, open ends, and choked inflow) as well as to accommodate flow reversals that may arise during large flow-field oscillations. The accompanying figure shows a sample simulation result. A combustor with an open inlet, a choked outlet, and a large constriction approximately two thirds of the way down the length is shown. The middle plot shows normalized, time-averaged distributions of the relevant flow quantities, and the bottom plot illustrates the acoustic mode shape of the resulting thermoacoustic oscillation. For this simulation, the limit cycle peak-to-peak pressure fluctuations were 13 percent of the mean. The simulation used 100 numerical cells. The total normalized simulation time was 50 units (approximately 15 oscillations), which took 26 sec on a Sun Ultra2.
Paxson, Daniel E.↗
Conditional Pseudo-Reversible Normalizing Flow for Surrogate Modeling in Quantifying Uncertainty Propagation
We introduce a conditional pseudo-reversible normalizing flow (PR-NF) that directly learns conditional probability distributions from noisy physical models to efficiently quantify both forward and inverse uncertainty propagation. Traditional surrogate modeling approaches approximate only the deterministic component of physical models, requiring separate noise characterization and computationally expensive sampling methods for inverse problems. Here, in this work, we develop the conditional PR-NF model to directly learn and efficiently generate samples from the conditional probability density functions (PDFs). The training process utilizes dataset consisting of input-output pairs without requiring prior knowledge about the noise and the function. Once trained, our model efficiently generates samples from conditional PDFs for any input within the training domain. Moreover, the pseudo-reversibility feature allows for the use of fully connected neural network architectures, which simplifies the implementation and enables theoretical analysis. We provide a rigorous convergence analysis of the conditional PR-NF model, showing its ability to converge to the target conditional PDF using the Kullback−Leibler divergence. To demonstrate the effectiveness of our method, we apply it to several benchmark tests and a real-world geologic carbon storage problem.
97 MATHEMATICS AND COMPUTING↗
The Open High Throughput Computing Content Delivery Network
LHC experiments make extensive use of web proxy caches, especially for software distribution via the CernVM File System and for conditions data via the Frontier Distributed Database Caching system. Since many jobs read the same data, cache hit rates are high and hence most of the traffic flows efficiently over Local Area Networks. However, it is not always possible to have local web caches, particularly for opportunistic cases whereexperiments have little control over site services. The Open High Throughput Computing (HTC) Content Delivery Network (CDN), openhtc.io, aims to address this by using web proxy caches from a commercial CDN provider. Cloudflare provides a simple interface for registering DNS aliases of any web server and does reverse proxy web caching on those aliases. The openhtc.io domain is hosted on Cloudflare's free tier CDN which has no bandwidth limit and makes use of data centers throughout the world, so the average performance for clients is much improved compared to reading from CERN or a Tier 1. The load on WLCG servers is also significantly reduced. WLCG Web Proxy Auto Discovery is used to select local web caches when they are available and otherwise select openhtc.io caching. This paper describes the Open HTC CDN in detail and provides initial results from its use for LHC@Home and USCMS opportunistic computing.
97 MATHEMATICS AND COMPUTING↗
Atomistic Mechanisms of the Crystallographic Orientation‐Dependent Cu 1.8 S Conductive Channel Formation in Cu 2 S‐Based Memristors
Achieving multiple types of resistive switching in a single material with controlled ionic motion is a key challenge in neuromorphic computing, traditionally addressed by combining materials with distinct switching behaviors. Here, Cu 2-x S is identified as a promising candidate to overcome this limitation due to its hierarchical phase transitions. Using in situ biasing experiments, reversible and non-reversible phase transitions (and resistive switching) are demonstrated in γ-Cu 2 S by controlling the compliance current. The formation of parallel high-digenite Cu 1.8 S channels, orientated along the γ-Cu 2 S [201] crystallographic direction, drives the nonvolatile resistive switching. These channels emerge via an intermediate δ-Cu 2 S phase and are stabilized at room temperature by residual strains, alongside β-Cu 2 S phase. In conclusion, the work clarifies the complex, electrically triggered phase transformations in γ-Cu 2 S, and highlights the potential of Cu 2-x S as a versatile material for neuromorphic computing.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nickel–Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer
Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F 430 . The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C–S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni–thiol interaction between Ni(II)–MCR and inhibitor CoMSH, a Ni(I)–thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)–disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)–sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)–N/O complex, not Ni(I)–S. These studies rule out direct Ni(I)–sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)–sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Direct Observation of Alternating Octahedral and Prismatic Sodium Layers in O3-Type Transition Metal Oxides
The oxygen stacking of O3-type layered sodium transition metal oxides (O3-NaTMO 2 ) changes dynamically upon topotactic Na extraction and reinsertion. While the phase transition from octahedral to prismatic Na coordination that occurs at intermediate desodiation by transition metal slab gliding is well understood, the structural evolution at high desodiation, crucial to achieve high reversible capacity, remains mostly uncharted. In this work, the phase transitions of O3-type layered NaTMO 2 at high voltage are investigated by combining experimental and computational approaches. An OP2-type phase that consists of alternating octahedral and prismatic Na layers is directly observed by in situ X-ray diffraction and high-resolution scanning transmission electron microscopy. The origin of this peculiar phase is explained by atomic interactions involving Jahn–Teller active Fe 4+ and distortion tolerant Ti 4+ that stabilize the local Na environment. Finally, the path-dependent desodiation and resodiation pathways are also rationalized in this material through the different kinetics of the prismatic and octahedral layers, presenting a comprehensive picture about the structural stability of the layered materials upon Na intercalation.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
A combined experimental and machine learning exploration of Ti 2-x Zr x MnCrFeNi high entropy Laves hydrides
A series of high entropy AB 2 -type Ti 2-x Zr x MnCrFeNi alloys (x = 0.6, 0.7, 0.8, 0.9, 1.0, 1.1 and 1.2) were synthesized to investigate their potential for hydrogen storage and chemical compression. The influence of the Ti/Zr ratio was explored in terms of structural, microstructural and thermodynamic properties. The storage capacity together with the reaction enthalpy and entropy changes of the synthesized high entropy alloys were compared to predictions from Machine Learning (ML) to investigate changes in these properties across the explored composition space. The results revealed that a decreasing Zr content consistently lowered the hydride formation enthalpy and increased the plateau pressure from 8 to >90 bar H 2 at 25 °C, in good agreement with ML predictions. Selected compositions (x = 1.0 and 1.2) demonstrated reversible hydrogen storage capability over 150 cycles, with capacities of 1.34–1.40 wt % H 2 and remarkable reaction kinetics (<4 min) at ambient temperature. These experimental and computational findings highlight the potential of this Laves-HEA system as tuneable, stable, and cost-effective materials suitable for long-term operations in stationary hydrogen storage and compression applications.
36 MATERIALS SCIENCE↗
Stokesian dynamics with odd viscosity
Stokesian dynamics is a well-established computational method for simulating dynamics of many particles suspended in a conventional passive fluid medium. Active fluids composed of self-driving particles with broken time-reversal symmetry permit the emergence of a so-called odd viscosity. Here, in this work, we extended the conventional Stokesian dynamics formalism to incorporate the additional hydrodynamic effects due to odd viscosity, which enables simulating collective behavior of many particles suspended in an active fluid medium with both even viscosity and odd viscosity.
42 ENGINEERING↗
Multigas Adsorption with Single-Site Cooperativity in a Metal-Organic Framework
Cooperative gas adsorption in metal-organic frameworks (MOFs) is a rare phenomenon that generally involves long-range communication between multiple binding sites. We demonstrate a MOF containing cobalt(II)-methyl sites that selectively and reversibly capture two carbon monoxide (CO) molecules per site, leading to record-high adsorption capacities at ambient temperatures and pressures. Gas adsorption and structural, spectroscopic, and computational analyses support a mechanism in which binding of one CO molecule triggers a spin transition, followed by binding of a second CO molecule and migratory insertion of the first CO molecule into the cobalt-methyl bond to form an acetyl. The greater binding affinity associated with the second CO results in sigmoidal adsorption isotherms, a hallmark of cooperativity and phase-change materials, despite the absence of long-range interactions within the framework.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗