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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"

Previously, we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step dt that is less than or equal to 0.5 fs to ensure equipartition between translational and rotational modes. We extended that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examined integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small time-step, dt, is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, is seen to be sensitive to dt. Using the mean volume estimated from the NpT simulation, we examined the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to dt. In going from a time-step of 2 fs to a time-step of 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein. The data-set contains the simulation metadata and log files that support the claims noted above.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ambient Ion Trapping and Separations for High Throughput Structurally Selective Material Deposition

While ion mobility coupled to mass spectrometry (IMS/MS) has been increasingly adapted to biological analysis, the structural and molecular specificity offered by IMS/MS has untapped potential for creating novel materials (for energy, catalysis, biomolecular switches etc.) with rationally tailored properties by precisely controlling the chemical structure and composition of these materials. While electrochemical and catalytic properties of the bulk material are understood by mass-selective ion-soft-landing, different structures of one molecule can exhibit distinct properties from the bulk. Many biological phenomenon occur at interfaces and are highly structurally specific. IMS/MS offers means to separate molecules in a sample (which is first ionized and released to gas phase from the condensed phase) based on mass and structure. Species thus separated can potentially be deposited onto surfaces with molecular and structural specificity, to perform fundamental investigations for understanding critical interfacial phenomenon. Key performance metrics for IMS/MS analysis are resolution of separations and sensitivity. Recently developed Structures for Lossless Ion Manipulations (SLIM)4 enabled unprecedented resolution in IMS separations. In addition, high sensitivity was enabled in SLIM due to lossless confinement of ions using radio frequency fields. Thus, SLIM enabled extremely long path length separations (up to 0.1 km thus far) providing efficient separation of molecular ions never before achieved (e.g. isotopologues, D&L amino acids). While SLIM has unprecedented analytical separations power/utility, the use of SLIM platform for depositing mobility and mass selected molecular ions has two specific technological challenges: (a) Pulsed nature of IMS separations and their low duty cycle and (b) the need for a low vacuum of ~4 torr for lossless ion confinement. These limitations lead to long deposition times due to loss of ions generated from the sample. Enabling ion confinement at atmospheric pressure will be path-breaking contribution to the fundamental understanding of ion manipulations and separations and will also enable novel science currently precluded due to the inability of the present technologies to confine ions under ambient conditions. Traditionally used radio frequency fields are ineffective in confining ions at high pressures due to ion/neutral collisions. To address these, we propose to (a) develop methods for confining and manipulating ions for lossless IMS separations at atmospheric pressure enabling high sensitivity and throughput and (b) use the high specificity of IMS/MS and high throughput from ambient ion confinement to perform mobility and mass selective ion deposition at atmospheric pressure. Our goal is to enable the study of the fundamental properties of energy/catalysis materials and biomolecules. This project paves the way for high-throughput, mass and structure selective material deposition for highly specific surface creation/functionalization (discussed in Section 2 of the report). Further, the developments reported continue to push the boundaries of this process to ambient conditions (discussed in Section 3 of the report). We conclude with a list of specific intellectual property and publications which have been the outcome of this funded project.

36 MATERIALS SCIENCE↗
DOE OSTI2023

NCSU RDMA data

NCSU RDMA Data Level b1: QC checks applied to measurements Data Format: CSV Description: See "instrument description Site: Houston, TX; Tracking Aerosol Convection interactions ExpeRiment (HOU) Location: Houston, TX; AMF1 (main site for TRACER) Facility Code: M1 Category: Aerosol Properties Data Type: PI Data Source Instrument/Data: Nano-Scanning Mobility Particle (SMPS); A Radial Differential Mobility Analyzer (RDMA) coupled with 1 Condensation Particle Counter Start Date: 2022-06-01 End Date: 2022-9-26 Contact PI: Markus Petters (mdpetter@ncsu.edu) Funding Source: DOE ASR award US Department of Energy, Office of Science, Biological and Environment Research (grant no. DE-SC 0021074) Instrument description The NCSU RDMA was operated at a sheath-to-sample flow ratio of 5:1.5 L min−1. The RDMA was configured to scan from 5 to 55 nm. It was located into the temperature-controlled trailer adjacent to the NCSU Flux Tower to observe size distributions of the aerosols.The sample line was dried with three silica-gel driers in series, and then neutralized with X-ray neutralizer. Please contact mdpetter@ncsu.edu for further information.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Future directions for active matter on ordered substrates

Active matter is a term encompassing particle-based assemblies with some form of self-propulsion, including certain biological systems as well as synthetic systems such as artificial colloidal swimmers, all of which can exhibit a remarkable variety of new kinds of nonequilibrium phenomena. A wealth of non-active condensed matter systems can be described in terms of a collection of particles coupled to periodic substrates, leading to the emergence of commensurate-incommensurate effects, Mott phases, tribology effects, and pattern formation. It is natural to ask how such phases are modified when the system is active. Here we provide an overview and future directions for studying individual and collectively interacting active matter particles coupled to periodic substrates, where new types of commensuration effects, directional locking, and active phases can occur. Importantly, further directions for exploration include directional locking effects, the realization of active solitons or active defects in incommensurate phases, active Mott phases, active artificial spin ice, active doping transitions, active floating phases, active surface physics, active matter time crystals, and active tribology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Editorial: Phenylpropanoid Systems Biology and Biotechnology

Phenylpropanoids are specialized metabolites involved in several aspects of plant growth and development and in the responses of plants to environmental stimuli. These compounds are synthesized from key intermediates of the shikimate pathway, which are structurally modified by the combined activities of lyases, transferases, ligases, reductases and oxygenases, resulting in the organ- and developmental-specific synthesis and accumulation of diverse metabolites (Vogt, 2010). The phenylpropanoid pathway provides the building blocks for lignin, suberin, and condensed tannins that play a role in structural support and mechanical strength. Lignin is a major contributor to feedstock recalcitrance and negatively affects the conversion of plant biomass into downstream products in biorefineries (Liu et al., 2021). Further, this pathway is key for the production of anthocyanins for organ pigmentation, flavonols and flavones for UV protection, various flavonoids and isoflavonoids for plant-microbe interactions, and antimicrobial phytoalexins for protection against pathogens (Deng and Lu, 2017). In addition to their biological functions in planta, phenylpropanoids are economically important metabolites. They constitute important components in the human diet, acting as nutraceutical compounds with antioxidant, chemopreventive, antimitotic, neuroprotective, cardioprotective, and anti-inflammatory activities. Several phenylpropanoids are considered high-value biochemicals employed in the production of fragrances, pharmaceuticals and biopolymers (Lin and Eudes, 2020).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigating Spatial Variability of Aerosol, Cloud Condensation Nuclei, and Ice Nucleating Particles in Mountainous Terrain Field Campaign Report

The U.S. Department of Energy Atmospheric System Research (ASR)-supported Surface Atmosphere Integrated Field Laboratory (SAIL) campaign in the East River Watershed (ERW) of the Upper Colorado River Basin in southwestern Colorado ran from fall 2021 to spring 2023. Two monitoring sites were deployed in the ERW as part of SAIL. The two sites were the Aerosol Observation System (AOS) located on Crested Butte Ski Mountain, and the second ARM Mobile Facility (AMF2), located at the Rocky Mountain Biological Laboratory in Gothic, Colorado. To gain a more comprehensive understanding of aerosols in complex, mountainous terrain, Handix Scientific deployed SAIL-Net, a distributed network of six measurement nodes spanning the domain of the SAIL research area from October 2021 to July 2023. Each node measured aerosol particles between 140 nm and 3.4 μm in diameter using a small portable optical particle spectrometer (POPS; Gao et al. 2016), cloud condensation nuclei (CNN) using a miniature CCN counter (CloudPuck), and ice nucleating particles (INP) using the time-resolved aerosol filter sampler (TRAPS; Creamean et al. 2018). Our approach was similar to other studies that aimed to better characterize and understand aerosols and gas-phase pollutants using networks of lower-cost sensors (Caubel et al. 2019, Kelly et al. 2021, Asher et al. 2022). Such studies have identified neighborhood-level variations in pollutant concentrations (Schneider et al. 2017, Popoola et al. 2018, Caubel et al. 2019). Small-scale variations such as this are poorly represented in models and poorly measured by a single monitoring system (Caubel et al. 2019). Previous work has shown the representation error (the ability of measurements to represent a larger area) increases with complex orography, leading to decreases in model accuracy (Schutgens et al. 2017). The overall goal of SAIL-Net was to improve our understanding of the variability of aerosol in the ERW, thus increasing our knowledge of aerosol-cloud interactions in this region and informing the usefulness of distributed networks of measurements for future studies. We met this goal by answering the following science questions: 1. What is the aerosol temporal variability, and how does aerosol inhomogeneity vary seasonally? Is there significant seasonal variability in sources, or are short-term meteorological conditions the most important determining factor in sources for cloud nuclei? 2. What is the aerosol spatial variability? What are the aerosol characteristics at cloud base, presumably the particles most representative of those acting as cloud nuclei? 3. How should measurement networks be designed to capture aerosol-cloud interactions, and what do they need to measure? Can a single measurement site accurately represent aerosol properties in regions of complex terrain? SAIL-Net consisted of six measurement nodes spread across the ERW near Crested Butte, Colorado. The primary objective in site placement was to select locations that captured the vertical variation in aerosol properties while also spanning the domain of the SAIL campaign. The elevation of the sites ranged from roughly 2750 m along the valley floor of the ERW to approximately 3500 m near the top of Crested Butte Mountain, which is one of the taller peaks in the ERW. The farthest distance between sites was 14 km, while the closest two sites were approximately 1 km apart. Two of the sites were collocated with the ARM SAIL sites; our instruments sat on top of one of the trailers at AOS and another one of our sites was located in a meadow just above AMF2.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

NCSU Flux Tower Data

NCSU Flux Tower Data Level b1: QC checks applied to measurements Data Format: CSV Description: See "instrument descripotion Site: Houston, TX; Tracking Aerosol Convection interactions ExpeRiment (HOU) Location: Houston, TX; AMF1 (main site for TRACER) Facility Code: M1 Category: Aerosol Properties Data Type: PI Data Source Instrument/Data: Sonic Anemometer, 3 Condensation Particle Counters, 1 SP2, 1 POPS Start Date: 2022-06-01 End Date: 2022-9-26 Contact PI: Markus Petters (mdpetter@ncsu.edu) Funding Source: DOE ASR award US Department of Energy, Office of Science, Biological and Environment Research (grant no. DE-SC 0021074) Instrument description The NCSU flux tower was located next to the AMF sampling pad. The flux tower consisted of a 10 m telescoping tower. Mounted at the top of the tower was a sonic anemometer (RM Young 8000) and a Krypton Hygrometer. A sample line (¼” conductive tubing) and communication line was laid to a trailer located underneath and slightly adjacent to the tower. The sample line brought aerosol inside the trailer at 4.5 L min-1, where it was distributed between 3 CPCs (TSI 3776c, Dc ~ 2.5 nm, TSI 3771, Dc ~10nm, and TSI 3772, Dc ~40 nm) with different size cuts. Also sampling was a printed particle optical spectrometer (POPS) and a single particle soot photometer (SP2). Please contact mdpetter@ncsu.edu for further information.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units

Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or posttranslational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to either the UBQLN2-binding surface of Ub or the spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model based on polyphasic linkage principles that accurately described the effects of different hubs on UBQLN2 phase separation, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. The extent to which polyubiquitin hubs promote UBQLN2 phase separation is encoded in the spacings between Ub units. This spacing is modulated by chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. The spacing in naturally occurring linear polyubiquitin chains is already optimized to promote phase separation with UBQLN2. We expect our findings to extend to other condensates, emphasizing the importance of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Optimizing biological carbon uptake by regulating carbonate-bicarbonate equilibrium

Balancing the global carbon budget is a grand challenge and a critical research mission for sustaining life on Earth. Oceans absorb ca. 30% of global anthropogenic CO 2 emissions and dissolved CO 2 in the oceans forms carbonic acid that dissociates to generate H + , bicarbonate, and carbonate. By regulating the carbonate-bicarbonate equilibrium, rates of marine photosynthesis can be substantially enhanced, thereby capturing and condensing CO 2 into a readily utilizable form. The specific goal of this project was to demonstrate enhanced marine biomass production at the bench-scale towards advancing sustainable marine CO 2 removal. Our proof-of-concept experimental results are highly promising and we have filed a PNNL invention disclosure. In consideration of which, no further details are included in this document.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Biological enhancement of cloud droplet concentrations observed off East Antarctica

Abstract The impact that biogenic emissions have on aerosol-cloud interactions across the Southern Ocean is poorly quantified. Here we use satellite and ship observations during austral summer to study these interactions. We present observational evidence that biogenic aerosols increase cloud condensation nuclei and cloud droplet number concentrations over the Southern Ocean off East Antarctica, coinciding with very low concentrations of ice-nucleating particles and higher occurrences of supercooled liquid-containing low-level clouds.

Mallet, Marc D.↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Data for Metabolic Engineering of β-Oxidation to Leverage Thioesterases for Production of 2-Heptanone, 2-Nonanone, and 2-Undecanone

Medium-chain length methyl ketones are potential blending fuels due to their cetane numbers and low melting temperatures. Biomanufacturing offers the potential to produce these molecules from renewable resources such as lignocellulosic biomass. In this work, we designed and tested metabolic pathways in Escherichia coli to specifically produce 2-heptanone, 2-nonanone and 2-undecanone. We achieved substantial production of each ketone by introducing chain-length specific acyl-ACP thioesterases, blocking the β-oxidation cycle at an advantageous reaction, and introducing active β-ketoacyl-CoA thioesterases. Using a bioprospecting approach, we identified 15 homologs of E. coli β-ketoacyl-CoA thioesterase (FadM) and evaluated the in vivo activity of each against various chain length substrates. The FadM variant from Providencia sneebia produced the most 2-heptanone, 2-nonanone, and 2-undecanone, suggesting it has the highest activity on the corresponding β-ketoacyl-CoA substrates. We tested enzyme variants, including acyl-CoA oxidases, thiolases, and bi-functional 3-hydroxyacyl-CoA dehydratases to maximize conversion of fatty acids to β-keto acyl-CoAs for 2-heptanone, 2-nonanone, and 2-undecanone production. In order to address the issue of product loss during fermentation, we applied a 20% (v/v) dodecane layer in the bioreactor and built an external water cooling condenser connecting to the bioreactor heat-transferring condenser coupling to the condenser. Using these modifications, we were able to generate up to 4.4 g/L total medium-chain length methyl ketones.

Metabolic Engineering↗
DOE OSTI2020

Basic Energy Sciences Program Update

This brochure describes updates to the BES program in FY 2019, including new awards, strategic planning activities, and recognition of BES Principal Investigators. It also describes select research highlights from the three divisions in BES.

14 SOLAR ENERGY↗
DOE OSTI2020

Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation

Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO 2 -concentrating mechanism by facilitating high CO 2 concentrations near the carboxylase Rubisco. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the α-carboxysome, there is little molecular insight into protein–protein interactions that drive the assembly process. In this work, studies on the α-carboxysome from Halothiobacillus neapolitanus demonstrate that Rubisco interacts with the N terminus of CsoS2, a multivalent, intrinsically disordered protein. X-ray structural analysis of the CsoS2 interaction motif bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate that this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate that CsoS2 acts as an interaction hub to condense Rubisco and enable efficient α-carboxysome formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Nonequilibrium statistical thermodynamics of multicomponent interfaces

Nonequilibrium interfacial thermodynamics has important implications for crucial biological, physical, and industrial-scale transport processes. Here, we discuss a theory of local equilibrium for multiphase multicomponent interfaces that builds upon the “sharp” interface concept first introduced by Gibbs, allowing for a description of nonequilibrium interfacial processes such as those arising in evaporation, condensation, adsorption, etc. By requiring that the thermodynamics be insensitive to the precise location of the dividing surface, one can identify conditions for local equilibrium and develop methods for measuring the values of intensive variables at the interface. We then use extensive, high-precision nonequilibrium molecular dynamics (NEMD) simulations to verify the theory and establish the validity of the local equilibrium hypothesis. In particular, we demonstrate that equilibrium equations of state are also valid out of equilibrium, and can be used to determine interfacial temperature and chemical potential(s) that are consistent with nonequilibrium generalizations of the Clapeyron and Gibbs adsorption equations. We also show, for example, that, far from equilibrium, temperature or chemical potential differences need not be uniform across an interface and may instead exhibit pronounced discontinuities. However, even in these circumstances, we demonstrate that the local equilibrium hypothesis and its implications remain valid. These results provide a thermodynamic foundation and computational tools for studying or revisiting a wide variety of interfacial transport phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Design of a bifunctional TEMPO-tertiary amine mesoporous silica catalyst for the three-step cascade synthesis of a chromene derivative

A key challenge is design of materials and processes whereby competing reagents or conditions do not harm the multi-step sequence, thus allowing for more efficient chemical synthesis with elimination of work-up and separation steps. In this work, a three-step reaction cascade is performed using a porous bifunctional dimethylpropylamine-TEMPO-MCM41 catalyst, converting the commodity chemicals benzyl alcohol, sodium hypochlorite, and malononitrile to a biologically active anti-cancer, and anti-malarial 2-amino-chromene derivative. The cascade first utilizes a TEMPO-catalyzed oxidation of benzyl alcohol to benzaldehyde with NaOCl as the terminal oxidant. This is followed by a two-step, dual base catalyzed Knoevenagel condensation with malononitrile followed by a Michael addition with lawsone. Optimal conditions converting benzyl alcohol to 2-amino-5,10-dioxo-4-phenyl-5,10-dihydro-4H-benzo[g]chromene-3-carbonitrile include the delayed addition of malononitrile and lawsone during the three-step reaction sequence, which results in a 2-amino-chromene yield of over 80%. The importance of stepwise reagent addition is rationalized due to the unfavorable adsorption of acidic lawsone on the surface-grafted base catalyst. Tertiary Brønsted base sites of dimethylpropylamine outperform the more Lewis basic primary propylamine functionalized catalyst. This work outlines a simple and effective method for generating mesoporous materials with two types of active sites via co-condensation and thiol-ene coupling procedures.

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

Superconducting disordered neural networks for neuromorphic processing with fluxons

In superconductors, magnetic fields are quantized into discrete fluxons (flux quanta Φ 0 ), made of microscopic circulating supercurrents. We introduce a multiterminal synapse network comprising a disordered array of superconducting loops with Josephson junctions. The loops can trap fluxons defining memory, while the junctions allow their movement between loops. Dynamics of fluxons through such a disordered system through a complex reconfigurable energy landscape represents brain-like spiking information flow. In this work, we experimentally demonstrate a three-loop network using YBa 2 Cu 3 O 7 –δ -based superconducting loops and Josephson junctions, which exhibit stable memory configurations of trapped flux in loops that determine the rate of flow of fluxons through synaptic connections. The memory states are, in turn, affected by the applied input signals but can also be externally configured electrically through control current/feedback terminals. These results establish a previously unexplored, biologically similar architectural approach to neuromorphic computing that is scalable while dissipating energy of atto Joules/spike.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗