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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Redox regulation in chloroplast thylakoid lumen: The pmf changes everything, again

Abstract Photosynthesis is the foundation of life on Earth. However, if not well regulated, it can also generate excessive reactive oxygen species (ROS), which can cause photodamage. Regulation of photosynthesis is highly dynamic, responding to both environmental and metabolic cues, and occurs at many levels, from light capture to energy storage and metabolic processes. One general mechanism of regulation involves the reversible oxidation and reduction of protein thiol groups, which can affect the activity of enzymes and the stability of proteins. Such redox regulation has been well studied in stromal enzymes, but more recently, evidence has emerged of redox control of thylakoid lumenal enzymes. This review/hypothesis paper summarizes the latest research and discusses several open questions and challenges to achieving effective redox control in the lumen, focusing on the distinct environments and regulatory components of the thylakoid lumen, including the need to transport electrons across the thylakoid membrane, the effects of pH changes by the proton motive force (pmf) in the stromal and lumenal compartments, and the observed differences in redox states. These constraints suggest that activated oxygen species are likely to be major regulatory contributors to lumenal thiol redox regulation, with key components and processes yet to be discovered.

Plant Sciences↗
DOE OSTI2021

Distribution function of nuclei from $\mathcal{e}^±$ scattering in the presence of a strong primordial magnetic field

The amplitude of the primordial magnetic field (PMF) is constrained from observational limits on primordial nuclear abundances. Within this constraint, it is possible that nuclear motion is regulated by Coulomb scattering with electrons and positrons (e ± s), while e ± s are affected by a PMF rather than collisions. For example, at a temperature of 10 9 K, thermal nuclei typically experience ~ 10 21 scatterings per second that are dominated by very small angle scattering leading to minuscule changes in the nuclear kinetic energy of order $\mathcal{O}$(1) eV. In this paper the upper limit on the effects of a possible discretization of the e ± momenta by the PMF on the nuclear momentum distribution is estimated under the extreme assumptions that the momentum of the e ± is relaxed before and after Coulomb scattering to Landau levels, and that during Coulomb scattering the PMF is neglected. This assumption explicitly breaks the time reversal invariance of Coulomb scattering, and the Maxwell-Boltzmann distribution is not a trivial steady state solution of the Boltzmann equation under these assumptions. Here we numerically evaluate the collision terms in the Boltzmann equation, and show that the introduction of a special direction in the e ± distribution by the PMF generates no directional dependence of the collisional destruction term of nuclei. Large anisotropies in the nuclear distribution function are then constrained from big bang nucleosynthesis. Ultimately, we conclude that a PMF does not significantly affect the isotropy or big bang nucleosynthesis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Higher-Order VLP-Based Protein Macromolecular Framework Structures Assembled via Coiled-Coil Interactions

Hierarchical organization is one of the fundamental features observed in biological systems that allows for efficient and effective functioning. Virus-like particles (VLPs) are elegant examples of a hierarchically organized supramolecular structure, where many subunits are self-assembled to generate the functional cage-like architecture. Utilizing VLPs as building blocks to construct two- and three-dimensional (3D) higher-order structures is an emerging research area in developing functional biomimetic materials. VLPs derived from P22 bacteriophages can be repurposed as nanoreactors by encapsulating enzymes and modular units to build higher-order catalytic materials via several techniques. In this study, we have used coiled-coil peptide interactions to mediate the P22 interparticle assembly into a highly stable, amorphous protein macromolecular framework (PMF) material, where the assembly does not depend on the VLP morphology, a limitation observed in previously reported P22 PMF assemblies. Many encapsulated enzymes lose their optimum functionalities under the harsh conditions that are required for the P22 VLP morphology transitions. Therefore, the coiled-coil-based PMF provides a fitting and versatile platform for constructing functional higher-order catalytic materials compatible with sensitive enzymes. Finally, we have characterized the material properties of the PMF and utilized the disordered PMF to construct a biocatalytic 3D material performing single- and multistep catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2009

Propellant Mass Fraction Calculation Methodology for Launch Vehicles and Application to Ares Vehicles

Propellant Mass Fraction (pmf) calculation methods vary throughout the aerospace industry. While typically used as a means of comparison between candidate launch vehicle designs, the actual pmf calculation method varies slightly from one entity to another. It is the purpose of this paper to present various methods used to calculate the pmf of launch vehicles. This includes fundamental methods of pmf calculation that consider only the total propellant mass and the dry mass of the vehicle; more involved methods that consider the residuals, reserves and any other unusable propellant remaining in the vehicle; and calculations excluding large mass quantities such as the installed engine mass. Finally, a historical comparison is made between launch vehicles on the basis of the differing calculation methodologies, while the unique mission and design requirements of the Ares V Earth Departure Stage (EDS) are examined in terms of impact to pmf.

Holt, James B.↗
DOE OSTI2021

Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover

Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). Additionally, the highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Roles of Hydrogen Bonds and Alignment in Oriented Attachment of Gibbsite Nanoparticles: Insights from Molecular Dynamics

Oriented attachment (OA) of nanoparticles is an important crystal growth pathway in the synthesis of hierarchical structures. Although a significant understanding of OA has been made, the effect of atomistic misalignment and the roles of solvent/particle and particle/particle interactions on the structure–energy relationship during an OA remain elusive. In this study, we perform molecular dynamics simulations to calculate the potential of mean force (PMF) profile for gibbsite particle translation on a gibbsite slab with 1 or 2 intervening water layers (1W or 2W). The structures of the gibbsite surfaces and the confined water are analyzed to determine how the number and type of hydrogen bonds (H-bonds) influence the free energy profile during the translation. The PMF profile exhibits a periodicity of length 5.078 Å, consistent with the gibbsite unit cell size along the translation direction. The changes in the surface–water and water–water hydrogen bond network and water and surface OH groups’ orientations during the translation are strongly coupled with the changes in the PMF profile in the 1W case. However, when increasing the number of intervening water layers from 1W to 2W, the particle/slab misalignment becomes a dominant factor controlling the behavior of the PMF profile. We also establish a method to quantify misalignment between the particle and the slab, which exhibits a strong correlation with the free energy for the 2W case. These results shed more light into the roles of particle/slab misalignment and hydrogen bond network in the OA of mineral particles in aqueous solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Graph link prediction in computer networks using Poisson matrix factorisation

Graph link prediction is an important task in cybersecurity: relationships between entities within a computer network, such as users interacting with computers or system libraries and the corresponding processes that use them, can provide key insights into adversary behaviour. Poisson matrix factorisation (PMF) is a popular model for link prediction in large networks, particularly useful for its scalability. In this article PMF is extended to include scenarios that are commonly encountered in cybersecurity applications. Specifically, an extension is proposed to explicitly handle binary adjacency matrices and include known categorical covariates associated with the graph nodes. A seasonal PMF model is also presented to handle seasonal networks. To allow the methods to scale to large graphs, variational methods are discussed for performing fast inference. The results show an improved performance over the standard PMF model and other statistical network models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Chemical properties and single-particle mixing state of soot aerosol in Houston during the TRACER campaign

Abstract. A high-resolution soot particle aerosol mass spectrometer (SP-AMS) was used to selectively measure refractory black carbon (rBC) and its associated coating material using both the ensemble size-resolved mass spectral mode and the event trigger single particle (ETSP) mode in Houston, Texas, in summer 2022. This study was conducted as part of the Department of Energy Atmospheric Radiation Measurement (ARM) program's TRacking Aerosol Convection interactions ExpeRiment (TRACER) field campaign. The study revealed an average (±1σ) rBC concentration of 103 ± 176 ng m−3. Additionally, the coatings on the BC particles were primarily composed of organics (59 %; 219 ± 260 ng m−3) and sulfate (26 %; 94 ± 55 ng m−3). Positive matrix factorization (PMF) analysis of the ensemble mass spectra of BC-containing particles resolved four distinct types of soot aerosol, including an oxidized organic aerosol (OOABC,PMF) factor associated with processed primary organic aerosol, an inorganic sulfate factor (SO4,BC,PMF), an oxidized rBC factor (O-BCPMF), and a mixed mineral dust–biomass burning aerosol factor with significant contribution from potassium (K-BBBC,PMF). Additionally, K-means clustering analysis of the single-particle mass spectra identified eight different clusters, including soot particles enriched in hydrocarbon-like organic aerosol (HOABC,ETSP), sulfate (SO4,BC,ETSP), two types of rBC, OOA (OOABC,ETSP), chloride (ClBC,ETSP), and nitrate (NO3,BC,ETSP). The single-particle measurements demonstrate substantial variation in BC coating thickness with coating-to-rBC mass ratios ranging from 0.1 to 100. The mixing state index (χ), which denotes the degree of homogeneity of the soot aerosol, varied from 4 % to 94 % with a median of 40 %, indicating that the aerosol population lies in between internal and external mixing but has large temporal and source type variability. In addition, a significant fraction of BC-containing particles, a majority enriched with oxidized organics and sulfate, exhibit sufficiently high κ values and diameters conducive to activation as cloud nuclei under atmospherically relevant supersaturation conditions. This finding bears significance in comprehending the aging processes of rBC-containing particles and their activation into cloud droplets. Our analysis highlights the complex nature of soot aerosol and underscores the need to comprehend its variability across different environments for accurate assessment of climate change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2009

Propellant Mass Fraction Calculation Methodology for Launch Vehicles

Propellant Mass Fraction (pmf) calculation methods vary throughout the aerospace industry. While typically used as a means of comparison between competing launch vehicle designs, the actual pmf calculation method varies slightly from one entity to another. It is the purpose of this paper to present various methods used to calculate the pmf of a generic launch vehicle. This includes fundamental methods of pmf calculation which consider only the loaded propellant and the inert mass of the vehicle, more involved methods which consider the residuals and any other unusable propellant remaining in the vehicle, and other calculations which exclude large mass quantities such as the installed engine mass. Finally, a historic comparison is made between launch vehicles on the basis of the differing calculation methodologies.

Holt, James B.↗
DOE OSTI2020

2D Dam-Break Analysis of L Lake and PAR Pond Dams Using HEC-RAS

In 1991 a dam-break study was conducted for the high hazard dams located at L Lake and PAR Pond on the Savannah River Site. Two scenarios were considered, over topping from a Probable Maximum Flood (PMF), and a fair weather dam-break for either or both dams. Unfortunately, no inundation map was developed from the study. The purpose of this project was to redo the original dam-break study with improved data and methodology to generate Inundation maps to assist with emergency response and evacuation plans. The Hydrologic Engineering Center's River Analysis System (HEC-RAS) is a free to download river analysis modeling program developed by the US Army Corps of Engineers capable of 1D and 2D hydraulic calculations. Version 5.0.7 (released March 2019) was used for this project. Digital elevation models for the area were retrieved from the US Geological Survey database and converted to a .hdf file within the program. Then the 2D flood area was identified from the contours. Both L Lake and PAR Pond were inputted as 1D storage areas because DEM data does not contain elevation values under water bodies. An elevation vs volume curve was available for both storage areas. Initial elevations were set for both scenarios. Both dams are earthen dams. The Steel Creek dam at L Lake has 6 ft diameter conduit with an upper and lower sluice gate. PAR pond dam consist of a weir and sluice gate connected to an 8 x 8 ft channel. Both outlets were modeled with a pool elevation vs discharge curve. The steel creek dam sluice gates were assumed to be fully open in all cases. As in the previous study, the dams were set to breach when they were overtopped by 1.5 ft during PMF conditions (Figure 1). A fair weather breach was set to be due to a piping failure (Figure 1). In the dual dam break during fair weather conditions the PAR pond dam fails 3 hours after Steel Creek to achieve maximum flooding in the down stream reaches. Simulation was run 3 days for each case and with a 1 minute computational interval. Maximum flooding occurs under PMF conditions with the failure of both dams. PAR pond dam fails first 16 hours and 32 minutes after the start of the simulation with the Steel creek dam failing 6 minutes later. In all cases, the bridges and roads spanning Steel Creek and Lower Three Runs will be inundated and potentially washed away. The Burtons Ferry Highway south of the storage areas will be partially flooded during PMF failure, dual fair weather failure, and PAR pond failure under fair weather conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Potentials of mean force fail to describe chemical bond-breaking in solution

Many liquid phase studies assume that the potential energy surfaces of reacting molecules are the same as in the gas phase, neglecting complex solvent dynamics that can completely alter the nature of chemical reactivity. Even studies that include solvent effects typically only consider them in an average, equilibrium way as part of a potential of mean force (PMF). In this work, we use mixed quantum/classical simulations to compare how equilibrium and non-equilibrium solvent motions affect the photodissociation of a simple diatomic molecule, NaK + , in liquid tetrahydrofuran. A PMF analysis shows that as the excited-state molecule dissociates with the solvent at equilibrium, the bonding electron remains associated with K + at short bond distances but eventually localizes on Na + at the end of dissociation. When we examine non-equilibrium dynamical photodissociation trajectories, however, we find that they fall into three distinct categories: about a quarter of them have the bonding electron mainly associated with Na + , another quarter stay mainly associated with K + , and about half have the bonding electron shared roughly equally between the two ions. The results show that equilibrium PMFs cannot accurately describe the dynamics of bond-breaking chemical reactions in solution because there is insufficient time for the solvent to reach equilibrium on the time scale over which bond dissociation occurs. Furthermore, our analysis shows that the solvent coupling between the electronic energy surfaces is similar at and away from equilibrium, suggesting that other factors, such as solute velocity-driven solvent memory effects, play a more important role in explaining the failure of the equilibrium PMF to predict the non-equilibrium dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Deciphering the non-linear impact of Al on chemical durability of silicate glass

The role of Al in aluminosilicate glasses remains somewhat a mystery: at low concentrations, it increases the resistance to hydrolysis of the glass, whereas at high concentrations an opposite effect is observed. To understand the origin of the phenomenon on a fundamental atomistic scale, we performed 577 MD simulations and applied potential mean force (PMF) calculations to estimate the activation barriers for hydrolysis and to statistically correlate them with local structural features of the glass. Models of pure silicate and aluminosilicate glasses are constructed and investigated. PMF simulation results are further validated by the experimental measurements and revealed that Al is very easy to dissociate, but it also increases the glass chemical durability through significantly increasing both the strength of Si and network connectivity of the glass. In contrast, at high Al concentration, preferential dissolution of Al weakens the silicate network, which it supposes to strengthen, and so the glass resistance becomes poor. Through PMF calculations, we evaluated the activation barriers for dissociating bonds around Al as 0.49 eV, which is less than a half of the energy to dissociate bonds around Si in pure silicate (1.22 eV) and around Si in aluminosilicate glass (1.34 eV), all these energy differences being statistically significant. Molecular structural level investigation revealed that Si with Al as a second neighbor in the glass network has a significantly higher activation energy for dissociation than Si in pure silicate glass. Furthermore, the proposed approach opens the way to the development of quantitative predictive models of glass durability.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Impact of ion fluxes across thylakoid membranes on photosynthetic electron transport and photoprotection

In photosynthetic thylakoid membranes the proton motive force (pmf) not only drives ATP synthesis, in addition it is central to controlling and regulating energy conversion. As a consequence, dynamic fine-tuning of the two pmf components, electrical (Δψ) and chemical (ΔpH), is an essential element for adjusting photosynthetic light reactions to changing environmental conditions. Good evidence exists that the Δψ/ΔpH partitioning is controlled by thylakoid potassium and chloride ion transporters and channels. However, a detailed mechanistic understanding of how these thylakoid ion transporter/channels control pmf partitioning is lacking. In this work, we combined functional measurements on potassium and chloride ion transporter and channel loss-of-function mutants with extended mathematical simulations of photosynthetic light reactions in thylakoid membranes to obtain detailed kinetic insights into the complex interrelationship between membrane energization and ion fluxes across thylakoid membranes. The data reveal that potassium and chloride fluxes in the thylakoid lumen determined by the K + /H + antiporter KEA3 and the voltage-gated Cl – channel VCCN1/Best1 have distinct kinetic responses that lead to characteristic and light-intensity-dependent Δψ/ΔpH oscillations. These oscillations fine-tune photoprotective mechanisms and electron transport which are particularly important during the first minutes of illumination and under fluctuating light conditions. By employing the predictive power of the model, we unravelled the functional consequences of changes in KEA3 and VCCN1 abundance and regulatory/enzymatic parameters on membrane energization and photoprotection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Investigating PVC polymer–plasticizer interactions with atomistic MD simulations and potential of mean force calculations

For this work, atomistic molecular dynamics (MD) simulations coupled with potential of mean force (PMF) calculations were employed to investigate the interactions between PVC polymer chains containing 6–20 repeating units and various plasticizers, with the goal of identifying potential replacements for the toxic plasticizer di(2-ethylhexyl)phthalate (DEHP) used in blood bags. The selected plasticizers belong to various chemical families, such as orthophthalates, citrates, adipates, and the terephthalate DEHT. Both the polymer and the plasticizers lack ionizable groups, and their interactions are primarily governed by van der Waals and electrostatic forces. A model correlating PMF profiles with interaction forces was developed and validated across polyvinyl chloride (PVC) polymers of different lengths and all investigated plasticizers. This model provides insight into how structural variations in plasticizers influence their respective PMF values. The study ranks the investigated plasticizers based on binding affinity, identifying TOTM (tris(2-ethylhexyl) trimellitate, TEHTM), BTHC (butyryl trihexyl citrate, Citroflex B-6), ATHC (acetyl trihexyl citrate, Citroflex A-6, CA-6), and DEHT (bis(2-ethylhexyl)terephthalate, DOTP/DEHTP) as promising alternatives for further investigation. This comprehensive study encompasses PVC polymers of four different lengths and 14 plasticizers, with all data averaged over 30 independent simulations. The approach provides a deeper understanding of molecular interactions, enabling the tailoring of polymer–plasticizer systems for diverse applications, including extractables and leachables, with relevance spanning materials science to biomedical engineering, and also serves as a basis for developing coarse-grained simulation protocols. Overall, this study provides valuable insights for designing safer and more efficient plasticizer substitutes and is well supported by other studies.

Shet, Sai Athmeeya G. [Sri Sathya Sai Institute of↗
DOE OSTI2025

Cosmic recombination in the presence of primordial magnetic fields

Primordial magnetic fields (PMFs) may explain observations of magnetic fields on extragalactic scales. They are most cleanly constrained by measurements of cosmic microwave background radiation (CMB) anisotropies. Their effects on cosmic recombination may even be at the heart of the resolution of the Hubble tension. We present the most detailed analysis of the effects of PMFs on cosmic recombination to date. To this end we extend the public magneto-hydrodynamic code ENZO with a new cosmic recombination routine, Monte-Carlo simulations of Lyman-α photon transport, and a Compton drag term in the baryon momentum equation. The resulting code allows us, for the first time, to realistically predict the impact of PMFs on the cosmic ionization history and the clumping of baryons during cosmic recombination. Our results identify the importance of mixing of Lyman-α photons between overdense- and underdense- regions for small PMF strength. This mixing speeds up recombination beyond the speed-up due to clumping. We also investigate the effects of pecuilar flows on the recombination rate and find it to be small for small PMF strengths. For non-helical PMFs with a Batchelor spectrum we find a surprising dependency of results on ultra-violet magnetic modes. We further show that the increase in the ionization fraction at low redshift by hydrodynamic baryon heating due to PMF dissipation is completely compensated by the faster recombination from baryon clumping. In conclusion, the present study shall serve as a theoretical foundation for a future precise comparison of recombination with PMFs to CMB data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Generalized echo squeezing protocol with near-Heisenberg-limit sensitivity and strong robustness against detection noise and variation in squeezing parameter

We present a generalized echo squeezing protocol (GESP) as a generalization of the Schrödinger cat state protocol with the value of the squeezing parameter being an arbitrary number rather than π / 2 . We show analytically that over a very broad range of the squeezing parameter the sensitivity of the GESP reaches the Heisenberg limit within a factor of 2 . For a large number of atoms, N , this plateau interval is almost the whole range from zero to π / 2 , and the sensitivity is independent of the parity of N . Therefore, it is possible to operate a sensor over a wide interval of the squeezing parameter without changing the sensitivity. This is to be contrasted with the conventional echo squeezing protocol (CESP) which only works for a very small interval of the squeezing parameter. We also show that, in contrast to the CESP, the sensitivity of the GESP is close to the quantum Cramér-Rao bound over the whole range of the squeezing parameter, indicating that the phase-shift information contained in the quantum state is near-optimally extracted. We find that the enhancement in sensitivity in the case of the GESP is due to a combination of two parameters: the phase magnification factor (PMF) and the noise amplification factor (NAF). As the value of the squeezing parameter increases, both PMF and NAF increase, while keeping the ratio of the PMF to the NAF essentially constant, yielding a net enhancement of sensitivity at the Heisenberg limit within a factor of 2 over the whole plateau interval. An important consequence of this behavior is that the robustness of the GESP against detection noise easily exceeds that of the CESP for a broad range of values of the squeezing parameter. As such, in the context of an experimental study, it should be possible to achieve a net enhancement in sensitivity higher than that for the CESP, under typical conditions where detection noise exceeds the quantum projection noise of an unsqueezed state with the same number of atoms. Finally, we consider the fragility of the GESP against decoherence mechanisms, and show how a balance between the fragility against the decoherence mechanisms and the robustness against detection noise would in practice determine the optimal choice of parameters for the GESP.

Li, Jinyang↗
DOE OSTI2025

Source apportionment of aerosols at the White River IMPROVE site near the SAIL site

This data set contains source apportionment results at the White River IMPROVE site (39.1536, -106.8209), which is about 30 km north of the Surface Atmosphere Integrated Field Laboratory (SAIL) Campaign site. The IMPROVE network (Malm et al. 1994) collected 24-hour aerosol filter samples every three days over several decades at this site. Chemical concentrations in the PM2.5 fraction of 19 elements (Al, As, Br, Ca, Cl, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Se, Si, Ti, V, and Zn), along with nitrate, sulfate, elemental carbon (EC), organic carbon (OC), and calculated coarse mass concentrations (PM10−PM2.5 mass concentrations), from 2014 to 2023, were used as input for the PMF analysis. PMF was performed using EPA PMF 5.0 (Norris et al. 2014). A five-factor solution was chosen as the optimal solution. These factors were identified as coarse dust, fine dust, biomass burning, sulfate-dominated, and nitrate-dominated sources. This data set is useful for understanding aerosol sources and their long-term variability near this region.

biomass burning↗