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DOE OSTI2024

Adaptive Laboratory Evolution for Enhanced Performance of Cupriavidus Necator on Formic Acid

The threat of global warming, driven by rising carbon emissions, highlights the need to decarbonize our economy. This requires innovative solutions for managing carbon waste and its effective utilization. One promising method for CO2 capture and sequestration is the electrochemical reduction of CO2 to formic acid, a soluble C1 molecule that can be used to store carbon and energy, and as a feedstock for biological conversion. Cupriavidus necator H16, a soil bacterium capable of consuming and growing on formic acid as its sole carbon and energy source, is well positioned to upgrade CO2-derived formic acid into platform chemicals and fuel precursors. To improve the performance of C. necator on formic acid, adaptive laboratory evolution (ALE), a proven tool for improving microbial fitness, has been conducted using continuous pH-stat bioreactors. The system works on the basis that consumption of formic acid raises the pH and triggers the addition of more formic acid to maintain the pH (in this case 6.7), such that formic acid is provided at the same rate as it is consumed. This system has been coupled with level control to achieve continuous fermentation where cells acquiring mutations that improve growth on formic acid become more abundant in the population, from which they can be isolated and characterized. During developmental experiments it was discovered that formic acid accumulated to inhibitory levels. It was determined that the nitrogen source, ammonium hydroxide, must be tailored to the carbon consumption to avoid formic acid accumulation. The ALE ran in three lineages for approximately 3000 hours and more than 500 generations. Evolved isolates obtained from each lineage demonstrated an increase in growth rate in conjunction with improve formate utilization compared to the parental strain when evaluated in pH-stat bioreactors. The isolates with improved performance were then subjected to whole genome sequencing to identify potentially causative mutations. Mutations in several key genes across different lineages have been found and will be evaluated individually and in combination to identify those that improve growth on formic acid. Incorporating these mutations into production strains has the potential to greatly improve formic acid conversion and further industrial decarbonization.

adaptive laboratory evolution↗

NASA NTRS1995

High-performance parallel analysis of coupled problems for aircraft propulsion

This research program deals with the application of high-performance computing methods to the numerical simulation of complete jet engines. The program was initiated in 1993 by applying two-dimensional parallel aeroelastic codes to the interior gas flow problem of a by-pass jet engine. The fluid mesh generation, domain decomposition and solution capabilities were successfully tested. Attention was then focused on methodology for the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion driven by these structural displacements. The latter is treated by an ALE technique that models the fluid mesh motion as that of a fictitious mechanical network laid along the edges of near-field fluid elements. New partitioned analysis procedures to treat this coupled 3-component problem were developed in 1994. These procedures involved delayed corrections and subcycling, and have been successfully tested on several massively parallel computers. For the global steady-state axisymmetric analysis of a complete engine we have decided to use the NASA-sponsored ENG10 program, which uses a regular FV-multiblock-grid discretization in conjunction with circumferential averaging to include effects of blade forces, loss, combustor heat addition, blockage, bleeds and convective mixing. A load-balancing preprocessor for parallel versions of ENG10 has been developed. It is planned to use the steady-state global solution provided by ENG10 as input to a localized three-dimensional FSI analysis for engine regions where aeroelastic effects may be important.

Felippa, C. A.↗

DOE OSTI2017

Bound-Preserving Reconstruction of Tensor Quantities for Remap in ALE Fluid Dynamics

We analyze several new and existing approaches for limiting tensor quantities in the context of deviatoric stress remapping in an ALE numerical simulation of elastic flow. Remapping and limiting of the tensor component-by-component is shown to violate radial symmetry of derived variables such as elastic energy or force. Therefore, we have extended the symmetry-preserving Vector Image Polygon algorithm, originally designed for limiting vector variables. This limiter constrains the vector (in our case a vector of independent tensor components) within the convex hull formed by the vectors from surrounding cells – an equivalent of the discrete maximum principle in scalar variables. We compare this method with a limiter designed specifically for deviatoric stress limiting which aims to constrain the J 2 invariant that is proportional to the specific elastic energy and scale the tensor accordingly. We also propose a method which involves remapping and limiting the J 2 invariant independently using known scalar techniques. The deviatoric stress tensor is then scaled to match this remapped invariant, which guarantees conservation in terms of elastic energy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1994

High-performance parallel analysis of coupled problems for aircraft propulsion

This research program deals with the application of high-performance computing methods for the analysis of complete jet engines. We have entitled this program by applying the two dimensional parallel aeroelastic codes to the interior gas flow problem of a bypass jet engine. The fluid mesh generation, domain decomposition, and solution capabilities were successfully tested. We then focused attention on methodology for the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion that results from these structural displacements. This is treated by a new arbitrary Lagrangian-Eulerian (ALE) technique that models the fluid mesh motion as that of a fictitious mass-spring network. New partitioned analysis procedures to treat this coupled three-component problem are developed. These procedures involved delayed corrections and subcycling. Preliminary results on the stability, accuracy, and MPP computational efficiency are reported.

Felippa, C. A.↗

NASA NTRS2003

Advanced Global Atmospheric Gases Experiment (AGAGE): MIT Contribution

We describe in detail the instrumentation and calibrations used in the ALE, GAGE and AGAGE experiments and present a history of the majority of the anthropogenic ozone- depleting and climate-forcing gases in air based on these experiments. Beginning in 1978, these three successive automated high frequency in-situ experiments have documented the long-term behavior of the measured concentrations of these gases over the past twenty years, and show both the evolution of latitudinal gradients and the high frequency variability due to sources and circulation. We provide estimates of the long-term trends in total chlorine contained in long- lived halocarbons involved in ozone depletion. We summarize interpretations of these measurements using inverse methods to determine trace gas lifetimes and emissions. Finally, we provide a combined observational and modeled reconstruction of the evolution of chlorocarbons by latitude in the atmosphere over the past sixty years which can be used as boundary conditions for interpreting trapped air in glaciers and oceanic measurements of chlorocarbon tracers of the deep oceanic circulation. Some specific conclusions are: (a) International compliance with the Montreal Protocol is so far resulting in chlorofluorocarbon and chlorocarbon mole fractions comparable to target levels, (b) Mole fractions of total chlorine contained in long-lived halocarbons (CCl2F2, CCl3F, CH3CCl3, CCl4, CHClF2, CCl2FCClF2, CH3Cl, CH2Cl2, CHCl3, CCl2=CCl2) in the lower troposphere reached maximum values of about 3.6 ppb in 1993 and are beginning to slowly decrease in the global lower atmosphere, (c) The chlorofluorocarbons have atmospheric lifetimes consistent with destruction in the stratosphere being their principal removal mechanism, (d) Multi-annual variations in chlorofluorocarbon and chlorocarbon emissions deduced from ALUGAGWAGAGE data are consistent approximately with variations estimated independently from industrial production and sales data where available (CCl2F2 (CFC-12) and CCl2FCClF2 (CFC-113) show the greatest discrepancies), (e) The mole fractions of the hydrochlorofluorocarbons and hydrofluorocarbons, which are replacing the regulated halocarbons, are rising very rapidly in the atmosphere but, with the exception of the much longer manufactured CHClF2 (HCFC-22), they are not yet at levels sufficient to contribute significantly to atmospheric chlorine loading. These replacement species could in the future provide independent estimates of the global weighted-average OH concentration provided their industrial emissions are accurately documented, (f) In the future, analysis of pollution events measured using high frequency in-situ measurements of chlorofluorocarbons and their replacements may enable emission estimates at the regional level which, together with industrial end-use data, are of sufficient accuracy to be capable of identifying regional non-compliance with the Montreal Protocol.

Kurylo, Michael↗

DOE OSTI2020

Numerical Considerations in the Modeling of a High Explosive Cylinder Experiment Using an ALE Continuum Mechanics Code

A series of experiments involving the detonation of PBX 9501 encased in a copper cylinder are modeled with the objective of evaluating a proposed set of phenomenological parameters for the Wescott–Stewart–Davis reactive burn model. The numerical analysis is conducted using the Los Alamos continuum mechanics code FLAG. Numerical considerations pertaining to various aspects of modeling the experiments using FLAG are discussed. It is shown that use of the proposed set of phenomenological parameters results in predictions of free-surface velocity that match empirically measured velocities reasonably well.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Investigation of the fragmentation of an explosively driven cylinder

Explosively driven fragmentation is highly complex. To better understand the field detonation, different methodologies (Lagrangian (with a failure threshold in VisIt and element erosion), ALE and embedded grid) were simulated to provide a comparison to the experimental data through the utilization of fragment distributions and gross deformation metrics. Provided with the geometrical parameters and the results from the experimental data, the computer simulations were conducted after the successful writing of each input file. Mesh refinement – a scalar multiplier applied to the mesh to refine the results – was then studied. The objective was to find a value that parallels the experimental results as the mesh can be refine indefinitely, theoretically. Various mesh resolution scales were simulated and the results graphically compared, using the damage and failure variables from a statistical Johnson Cook failure model, the number of fragments over time as well as time required for each simulation to run and number of processors utilized. The desired result is a calculated method to quantify the comparison being performed.

36 MATERIALS SCIENCE↗

DOE OSTI2019

A Finite-Volume method for compressible non-equilibrium two-phase flows in networks of elastic pipelines using the Baer–Nunziato model

A novel Finite-Volume scheme for the numerical computations of compressible two-phase flows in pipelines is proposed for the fully non-equilibrium Baer–Nunziato model. The present FV approach is the extension of the method proposed in Daude and Galon (2018) in the context of the Euler equations to the Baer–Nunziato model. In addition, proper approximations of the non-conservative terms are proposed to consider jumps of volume fraction as well as jumps of cross-section in order to respect uniform pressure and velocity profiles preservation. In particular, focus is given to the numerical treatment of abrupt changes in area and to networks wherein several pipelines are connected at junctions. The proposed method makes it possible to avoid the use of an iterative procedure for the solution of the junction problem. The present approach can also deal with general Equations Of State. In addition, the fluid–structure interaction of compressible fluid flowing in flexible pipes is also considered. Lastly, the proposed scheme is then assessed on a variety of shock-tubes and other transient flow problems and experiments demonstrating its capability to resolve such problems efficiently, accurately and robustly.

42 ENGINEERING↗

DOE OSTI2022

Multi-material swept face remapping on polyhedral meshes

Remapping is a conservative interpolation of a discretized intensive quantity between two meshes. In this article, we propose a novel multi-material flux remapping method that avoids the geometric computation of mesh-mesh intersections needed for an accurate intersection based remap. The flux remap is applicable to scalar quantities such as material density describing the multi-material flow between meshes with the same connectivity but small mesh displacements. Herein, the method is described for two- and three-dimensional polygonal/polyhedral meshes as it is implemented in Portage. Another open source library, Tangram, is used to calculate material interfaces in cells containing more than one material. Performance and accuracy of the flux remap are discussed with respect to Arbitrary Lagrangian-Eulerian simulations and compared to an accurate intersection based remap. In particular, cyclic remapping shows that the accuracy of the flux remap is limited to first order on material boundaries while maintaining second order accuracy in pure material regions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Ab Initio Studies of Discharge Mechanism of MnO 2 in Deep-Cycled Rechargeable Zn/MnO 2 Batteries

Rechargeable alkaline Zn/MnO 2 batteries are an attractive solution for large-scale energy storage applications. Recently, Bi and Cu additives have been used to increase the cycle life and capacity of rechargeable Zn/MnO 2 batteries, with an equivalent of the full two-electron capacity realized for many cycles, in the absence of zinc. However, the mechanism of the effect of Bi and Cu on the performance of rechargeable Zn/MnO 2 batteries has not been investigated in detail. We apply first-principles density functional computational methods to study the discharge mechanisms of the unmodified and Bi/Cu-modified γ -MnO 2 electrodes in rechargeable alkaline Zn/MnO 2 batteries. Using the results of our calculations, we analyze the possible redox reaction pathways in the γ -MnO 2 electrode and identify the electrochemical processes leading to the formation of irreversible discharge reaction products, such as hausmannite and hetaerolite. Our study demonstrates the possibility of formation of intermediate Bi-Mn and Cu-Mn oxides in deep-cycled Bi/Cu-modified MnO 2 electrodes. The formation of intermediate Bi-Mn and Cu-Mn oxides could reduce the rate of accumulation of irreversible reaction products in the MnO 2 electrode and improve the rechargeability and cyclability of Zn/MnO 2 batteries.

25 ENERGY STORAGE↗

NASA NTRS1999

Encapsulation system for the immunoisolation of living cells

The present invention is drawn to a composition of matter comprising high viscosity sodium alginate, cellulose sulfate and a multi-component polycation. Additionally, the present invention provides methods for making capsules, measuring capsule permeability to immunologically-relevant proteins and treating disease in an animal using encapsulated cells. Over one thousand combinations of polyanions and polycations were examined as polymer candidates suitable for encapsulation of living cells and thirty-three pairs were effective. The combination of sodium alginate, cellulose sulfate, poly(methylene-co-guanidine) hydrochloride, calcium chloride, and sodium chloride produced the most desirable results. Pancreatic islets encapsulated in this multicomponent capsule demonstrated glucose-stimulated insulin secretion in vitro and reversed diabetes without stimulating immune reaction in mice. The capsule formulation and system of the present invention allows independent adjustments of capsule size, wall thickness, mechanical strength and permeability, and offers distinct advantages for immunoisolating cells.

Wang, Taylor G.↗

DOE OSTI2017

The Power of Non-Hydrolytic Sol-Gel Chemistry: A Review

This review is devoted to non-hydrolytic sol-gel chemistry. During the last 25 years, non-hydrolytic sol-gel (NHSG) techniques were found to be attractive and versatile methods for the preparation of oxide materials. Compared to conventional hydrolytic approaches, the NHSG route allows reaction control at the atomic scale resulting in homogeneous and well defined products. Due to these features and the ability to design specific materials, the products of NHSG reactions have been used in many fields of application. The aim of this review therefore is to present an overview of NHSG research in recent years with an emphasis on the syntheses of mixed oxides, silicates and phosphates. The first part of the review highlights well known condensation reactions with some deeper insights into their mechanism and also presents novel condensation reactions established in NHSG chemistry in recent years. In the second section we discuss porosity control and novel compositions of selected materials. In the last part, the applications of NHSG derived materials as heterogeneous catalysts and supports, luminescent materials and electrode materials in Li-ion batteries are described.

25 ENERGY STORAGE↗

DOE OSTI2020

Benchmark Solutions for Radiation Transport in Stochastic Media with Inhomogeneous Material Statistics

Accurately solving implicit Monte Carlo (IMC) thermal photon transport problems with mixed material cells is important in realistic applications. The production IMC package at LLNL treats mixed material cells arising from ALE remap and hydrodynamics using the same approximate model. The new Imp IMC thermal photon transport package currently under development has both a material interface reconstruction (MIR) algorithm and a Levermore-Pomraning (LP) stochastic medium algorithm for treating mixed material cells. Existing stochastic medium algorithms for treating mixed material cells in IMC lack a complete theoretical basis. The IMC LP algorithm implementation has been demonstrated to reproduce published deterministic LP solutions for the particular case of spatially homogeneous material statistics. Realistic simulations will include spatially inhomogeneous material statistics (material mean chord lengths). In a previous investigation, the LP-model for transport in binary stochastic media in rod geometry was generalized to accommodate spatially varying material chord lengths, i.e., the mixing statistics were allowed to be nonhomogeneous. Analytical solutions were obtained and used to produce a verifi cation suite for the Imp IMC Levermore-Pomraning implementation for different spatial variations of the chord lengths. However, the accuracy of the LP model when the mixing statistics are nonhomogeneous has not been assessed and leaves open the question of whether local accuracy is improved or further degraded when chord lengths are not uniform. This shortcoming is rectifi ed here by developing benchmark analytic solutions for transport in binary Markovian stochastic mixtures in rod geometry with nonhomogeneous mixing statistics, using spatially varying chord lengths considered in the previous investigation based on the LP model. Methods for sampling a nonhomogeneous Poisson process (NHPP) are first described and used to construct individual realizations of the binary mixtures in rod geometry. Analytic solutions are then obtained for the forward and backward directed fluxes on a given realization, now viewed as a deterministic medium with alternating layers of the two materials with known interface locations. Finally, material averaged scalar fluxes are obtained using these sampling schemes with spatially linear and quadratic chord lengths and used to assess the accuracy of the previously obtained LP-model results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Multivariate moment closure techniques for stochastic kinetic models

Stochastic effects dominate many chemical and biochemical processes. Their analysis, however, can be computationally prohibitively expensive and a range of approximation schemes have been proposed to lighten the computational burden. These, notably the increasingly popular linear noise approximation and the more general moment expansion methods, perform well for many dynamical regimes, especially linear systems. At higher levels of nonlinearity, it comes to an interplay between the nonlinearities and the stochastic dynamics, which is much harder to capture correctly by such approximations to the true stochastic processes. Moment-closure approaches promise to address this problem by capturing higher-order terms of the temporally evolving probability distribution. Here, we develop a set of multivariate moment-closures that allows us to describe the stochastic dynamics of nonlinear systems. Multivariate closure captures the way that correlations between different molecular species, induced by the reaction dynamics, interact with stochastic effects. We use multivariate Gaussian, gamma, and lognormal closure and illustrate their use in the context of two models that have proved challenging to the previous attempts at approximating stochastic dynamics: oscillations in p53 and Hes1. In addition, we consider a larger system, Erk-mediated mitogen-activated protein kinases signalling, where conventional stochastic simulation approaches incur unacceptably high computational costs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

The seventh blind test of crystal structure prediction: structure generation methods

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Chemistry↗

DOE OSTI2024

The seventh blind test of crystal structure prediction: structure ranking methods

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

Chemistry↗