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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations

We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.

chemical physics↗
DOE OSTI2024

Optimal spectral resolution for solids and liquids using FT and other infrared spectrometers: How much resolution do you really need?

In this study we investigate the possibility of using spectral resolutions for infrared measurements of solids and liquids that are not powers of two, e.g. are not at 1, 2, 4, 8, or 16 cm-1 resolution. In almost all reported literature of the last fifty years the resolution used to record for a Fourier transform infrared spectrum has been a power of two. This stems from the fact that 1) the Cooley-Tukey algorithm used to compute such a transform was constructed to use only powers of two and was also driven by 2) the fact that the computing horsepower required to compute the Fourier transform increases as N?log?_2 (N), where N is the number of points in the interferogram (spectrum). For typical spectra, however, the CPU time is no longer a consideration. Our study is based on both liquid and solid spectra, all of which were recorded at 2 cm-1 resolution. There were at total of 70 solids spectra representing 2,472 spectral peaks and 61 liquids spectra (1,765 spectral peaks), each peak being inspected for being singlet / multiplet in nature. Of the 1,765 liquid bands examined, only 27 had widths less than 5 cm-1. Of the 2,472 solid bands examined, only 39 peaks have widths less than 5 cm-1. For liquids, the mean peak width is 24.7 cm-1 but the median peak width is 13.7 cm-1, and, similarly, for solids, the mean peak width is 22.2 cm-1 but the median peak width is 11.2 cm-1. In both cases, solids and liquids, a skewed peak widths distribution was observed, the peak of the distribution representing narrower bands in the 7 to 9 cm-1 FWHM range but displaying a long tail to the very broad bands, with some displaying spectral widths of 100 cm-1 or more. Because one of the most important criteria for successful instrumental design in IR spectroscopy is the spectral resolution, the data were further analyzed showing that a value to resolve 95% of all bands is 5.7 cm-1 for liquids and 5.3 cm-1 for solids; such a resolution would capture the native linewidth (no instrumental broadening) of 95% of all the solids and liquid bands, respectively. Based on the present results we suggest that, when accounting only for intrinsic linewidths an optimized resolution of 6.0 cm-1 will capture 91% of all condensed-phase bands for IR detection of chemical, mineral, and biological materials.

Forland, Brenda M.↗
DOE OSTI2023

A state-of-the-art review of experimental and computational studies of granular materials: Properties, advances, challenges, and future directions

Modeling of heterogeneous materials and media is a problem of fundamental importance to a wide class of phenomena and systems, ranging from condensed matter physics, soft materials, and composite media to porous media, biological systems, geosystems, ceramic engineering, pharmaceutical science and even in space discoveries. Among the most important materials are granular systems, which have received intense interest from the engineering, physics, and mathematics communities. In this review paper, the recent developments and new advances in experimental, and computational methods on a variety of scales and physics that extend understanding to a wide range of materials and phenomena are reviewed. Experimental advances include computed neutron and nanometer-scale tomography, magnetic resonance imaging, refractive index matching, digital image correlation, acoustic emission analysis, and the most recent 4D techniques. Furthermore, a tremendous shift has occurred from the continuum scale to micro-scale and developing multiscale approaches. As such, various computational methods, including, constitutive modeling, discrete modeling, and multiscale approaches, have been developed. In conclusion, aside from all these evolutions, more complicated modeling called coupled, or multiphysics, systems representing a simultaneous presence of heat, fluid, chemical variation, and mechanical effect are also explored.

36 MATERIALS SCIENCE↗
DOE OSTI2021

BRAVE_EBC-TMT.1.0

Exhaled breath condensate (EBC) represents a low-cost and non-invasive means of examining respiratory health. EBC has been used to discover and validate exhaled volatile and non-volatile biomarkers of disease related to the respiratory system distress such as asthma, COPD, lung cancer, and secondary infections. One newly emerging utilization of EBC, is proteomics analysis, which can provide an unbiased snapshot into ongoing biological processes in the airway. Fully characterizing the biological landscape of EBC collections is challenging though, due to sample variability, and low detection sensitivity. EBC is primarily composed of condensed water, causing technical challenges with detecting key macromolecules from the dilute sample matrix; therefore, high sensitivity techniques are required to unlock the full capability of EBC as a method for non-invasive biomarker detection. To overcome some of these technical challenges for proteomic analyses, we applied our recently developed microscale proteomic techniques and developed a novel TMT based approach which enabled reliable, relative quantification with significantly improved detection of low abundance peptides/proteins across multiple healthy volunteer EBC samples. Our EBC collection design includes longitudinal EBC collections from five individual healthy volunteers on three separate days of the week with triplicate, back-to-back donations each day. Here, we report a total of 235 quantifiable proteins corresponding to 1,877 non-redundant peptides for evaluating sample collection reproducibility and establishing a healthy (human host) baseline EBC biomarker proteome studies. This work will pave the way for further investigations of EBC protein expression profiles and showcase the value of using non-invasive collection method techniques for clinically relevant biomarker discovery. This research was supported by the LDRD Biomedical Resilience And Readiness in AdVerse Operating Environments (BRAVE) Project (73748), and was conducted at Pacific Northwest National Laboratory (PNNL) in Richland, WA. PNNL is a multiprogram national laboratory operated by Battelle for the Department of Energy (DOE) under Contract DE-AC05-76RLO 1830.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Prediction of Self-Diffusion in Binary Fluid Mixtures Using Artificial Neural Networks

Artificial neural networks (ANNs) were developed to accurately predict the self-diffusion constants for individual components in binary fluid mixtures. The ANNs were tested on an experimental database of 4328 self-diffusion constants from 131 mixtures containing 75 unique compounds. The presence of strong hydrogen bonding molecules may lead to clustering or dimerization resulting in non-linear diffusive behavior. To address this, self- and binary association energies were calculated for each molecule and mixture to provide information on intermolecular interaction strength and were used as input features to the ANN. An accurate, generalized ANN model was developed with an overall average absolute deviation of 4.1%. Forward input feature selection reveals the importance of critical properties and self-association energies along with other fluid properties. Additional ANNs were developed with subsets of the full input feature set to further investigate the impact of various properties on model performance. The results from two specific mixtures are discussed in additional detail: one providing an example of strong hydrogen bonding and the other an example of extreme pressure changes, with the ANN models predicting self-diffusion well in both cases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

A multi-step nucleation process determines the kinetics of prion-like domain phase separation

Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Effects of Pollen on Hydrometeors and Precipitation in a Convective System

Anemophilous (wind-driven) pollen is one type of primary biological aerosol particle, which can rupture under high humidity conditions and form smaller sub-pollen particles (SPPs). Both pollen and SPPs can reach the upper troposphere under convective conditions, acting as cloud condensation nuclei (CCN) and ice nucleating particles (INPs), thus influencing cloud formation and precipitation. However, the impacts of these biological aerosols on cold cloud formation and local climate remain unclear as there are large uncertainties on their emission flux and ice nucleating abilities. Here, we incorporate pollen emission and rupture processes in the Weather Research and Forecasting Model with Chemistry (WRF-Chem) simulations and update the Morrison microphysics scheme within WRF-Chem using aerosol-aware INP parameterizations to account for pollen in addition to other anthropogenic and biogenic aerosol. INP parameterizations for pollen and SPP are derived from laboratory experiments. When including pollen rupture rates as observed in a series of chamber studies, SPP concentrations increase, leading to an increase of cloud ice and water by up to 50% and potentially extending the duration of the convective system. Among all simulated hydrometeors, graupel and raindrops exhibit the largest enhancements from the inclusion of SPPs, with intensifying precipitation at the backside of the convective system and a greater spatial extent. Sensitivity simulations indicate that SPPs have a greater effect on cloud microphysical processes than whole pollen grains, and further observational evidence is needed to constrain these processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Biological particles and aerosol-cloud interactions in the Southern Great Plains

The United States Southern Great Plains (SGP) is the genesis for much of the warm season precipitation in the central and eastern United States. While atmospheric thermodynamics and large-scale dynamics play an important role in formation of precipitation, precipitation mechanisms are also sensitive to aerosols. Aerosols can suppress precipitation as cloud condensation nuclei (CCN) or act as ice nucleating particles (INP) in deep convective clouds. This project focused on understanding the role of primary biological aerosol particles (PBAP) in the region and its influence on cloud formation. Specifically, we focused on biological aerosol in the form of pollen, one type of PBAP that is emitted in large yet variable quantities from vegetation in the mid latitudes. Field observations provide evidence of pollen in the planetary boundary layer and pollen components in cloud droplets and fine particulate matter. Further, pollen grains can easily rupture when wet, forming smaller, sub pollen particles with sizes less than one micron. We evaluated the potential for PBAP events at the Department of Energy (DoE) SGP Atmospheric Radiation Measurement (ARM) research facility due to the rich dataset available. We also developed model simulations that accounted for pollen emission and the generation of sub pollen particles, which have been shown to be both cloud condensation nuclei and ice nucleating particles. The proposed work was designed to address the following questions: 1. What are the physical and chemical signatures of biological aerosol such as pollen in SGP ARM measurements? 2. What is the role of pollen-derived particles on deep convection and precipitation in the Central US? Using measurements from the DoE SGP ARM site and recent airborne campaigns, we evaluated the signatures of pollen and pollen-derived aerosols on optical properties, cloud properties and precipitation (Subba et al., 2021). We identified pollen-driven events over the data record and used the Weather Research and Forecasting Model with fully coupled chemistry (WRF-Chem) to conduct chemically realistic simulations of aerosols during and summer mesoscale convective events in the Southern Great Plains (Subba et al., in review). This work improved our understanding of the role of biological aerosol on clouds and precipitation in the Central United States and placed these results in context with anthropogenically-driven processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane

We reconstitute a phosphotyrosine-mediated protein condensation phase transition of the ~200 residue cytoplasmic tail of the epidermal growth factor receptor (EGFR) and the adaptor protein, Grb2, on a membrane surface. The phase transition depends on phosphorylation of the EGFR tail, which recruits Grb2, and crosslinking through a Grb2-Grb2 binding interface. The Grb2 Y160 residue plays a structurally critical role in the Grb2-Grb2 interaction, and phosphorylation or mutation of Y160 prevents EGFR:Grb2 condensation. By extending the reconstitution experiment to include the guanine nucleotide exchange factor, SOS, and its substrate Ras, we further find that the condensation state of the EGFR tail controls the ability of SOS, recruited via Grb2, to activate Ras. These results identify an EGFR:Grb2 protein condensation phase transition as a regulator of signal propagation from EGFR to the MAPK pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biological particles and aerosol-cloud interactions in the Southern Great Plains (Final Report)

The United States Southern Great Plains (SGP) is the genesis for much of the warm season precipitation in the central and eastern United States. While atmospheric thermodynamics and large-scale dynamics play an important role in formation of precipitation, precipitation mechanisms are also sensitive to aerosols. Aerosols can suppress precipitation as cloud condensation nuclei (CCN) or act as ice nucleating particles (INP) in deep convective clouds. This project focused on understanding the role of primary biological aerosol particles (PBAP) in the region and its influence on cloud formation. Specifically, we focused on biological aerosol in the form of pollen, one type of PBAP that is emitted in large yet variable quantities from vegetation in the mid latitudes. Field observations provide evidence of pollen in the planetary boundary layer and pollen components in cloud droplets and fine particulate matter. Further, pollen grains can easily rupture when wet, forming smaller, sub pollen particles with sizes less than one micron. We evaluated the potential for PBAP events at the Department of Energy (DoE) SGP Atmospheric Radiation Measurement (ARM) research facility due to the rich dataset available. We also developed model simulations that accounted for pollen emission and the generation of sub pollen particles, which have been shown to be both cloud condensation nuclei and ice nucleating particles. The proposed work was designed to address the following questions: 1. What are the physical and chemical signatures of biological aerosol such as pollen in SGP ARM measurements? 2. What is the role of pollen-derived particles on deep convection and precipitation in the Central US? Using measurements from the DoE SGP ARM site and recent airborne campaigns, we evaluated the signatures of pollen and pollen-derived aerosols on optical properties, cloud properties and precipitation (Subba et al., 2021). We identified pollen-driven events over the data record and used the Weather Research and Forecasting Model with fully coupled chemistry (WRF-Chem) to conduct chemically realistic simulations of aerosols during and summer mesoscale convective events in the Southern Great Plains (Subba et al., in review). This work improved our understanding of the role of biological aerosol on clouds and precipitation in the Central United States and placed these results in context with anthropogenically-driven processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Aitken Mode Aerosols Buffer Decoupled Mid‐Latitude Boundary Layer Clouds Against Precipitation Depletion

Aerosol-cloud-precipitation interactions are a leading source of uncertainty in estimating climate sensitivity. Remote marine boundary layers where accumulation mode (~100–400 nm diameter) aerosol concentrations are relatively low are very susceptible to aerosol changes. These regions also experience heightened Aitken mode aerosol (~10–100 nm) concentrations associated with ocean biology. Aitken aerosols may significantly influence cloud properties and evolution by replenishing cloud condensation nuclei and droplet number lost through precipitation (i.e., Aitken buffering). We use a large-eddy simulation with an Aitken-mode enabled microphysics scheme to examine the role of Aitken buffering in a mid-latitude decoupled boundary layer cloud regime observed on 15 July 2017 during the Aerosol and Cloud Experiments in the Eastern North Atlantic flight campaign: cumulus rising into stratocumulus under elevated Aitken concentrations (~100–200 mg -1 ). In situ measurements are used to constrain and evaluate this case study. Our simulation accurately captures observed aerosol-cloud-precipitation interactions and reveals time-evolving processes driving regime development and evolution. Aitken activation into the accumulation mode in the cumulus layer provides a reservoir for turbulence and convection to carry accumulation aerosols into the drizzling stratocumulus layer above. Further Aitken activation occurs aloft in the stratocumulus layer. Together, these activation events buffer this cloud regime against precipitation removal, reducing cloud break-up and associated increases in heterogeneity. We examine cloud evolution sensitivity to initial aerosol conditions. With halved accumulation number, Aitken aerosols restore accumulation concentrations, maintain droplet number similar to original values, and prevent cloud break-up. Without Aitken aerosols, precipitation-driven cloud break-up occurs rapidly. In this regime, Aitken buffering sustains brighter, more homogeneous clouds for longer.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Designing a boron nitride polyethylene composite for shielding neutrons

Neutrons are encountered in many different fields, including condensed matter physics, space exploration, nuclear power, and healthcare. Neutrons interacting with a biological target produce secondary charged particles that are damaging to human health. The most effective way to shield neutrons is to slow them to thermal energies and then capture the thermalized neutrons. These factors lead us to consider potential materials solutions for neutron shields that maximize the protection of humans while minimizing the shield mass and adapt well to modern additive manufacturing techniques. Using hexagonal boron nitride (hBN) as a capture medium and high-density polyethylene (HDPE) as a thermalization medium, we aim to design the optimal internal structure of h 10 BN/HDPE composites by minimizing the effective dose, which is a measure of the estimated radiation damage exposure for a human. Through Monte Carlo simulations in Geant4, we find that the optimal structure reduces the effective dose up to a factor of 72 over aluminum (Al) and up to a factor of 4 over HDPE; this is a significant improvement in shielding effectiveness that could dramatically reduce the radiation exposure of occupational workers.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation

The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent Cα model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

APS Science 2020 (Vol. 1)

The U.S. Department of Energy's Advanced Photon Source (APS) is one of the world’s most productive x-ray light source facilities. Each year, the APS provides high-brightness x-ray beams to a diverse community of more than 5,000 researchers in materials science, chemistry, condensed matter physics, the life and environmental sciences, and applied research. Researchers using the APS produce over 2,000 publications each year detailing impactful discoveries, and solve more vital biological protein structures than users of any other x-ray light source research facility. APS x-rays are ideally suited for explorations of materials and biological structures; elemental distribution; chemical, magnetic, electronic states; and a wide range of technologically important engineering systems from batteries to fuel injector sprays, all of which are the foundations of our nation’s economic, technological, and physical well-being. The APS occupies an 80-acre site on the Argonne campus, about 25 miles from downtown Chicago, Illinois. It shares a site with the Center for Nanoscale Materials and the Advanced Protein Characterization Facility.

25 ENERGY STORAGE↗
DOE OSTI2023

Molecular Design of Functional Polymers for Silica Scale Inhibition

Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Finally, our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.

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

Equal abundance of summertime natural and wintertime anthropogenic Arctic organic aerosols

Aerosols play an important yet uncertain role in modulating the radiation balance of the sensitive Arctic atmosphere. Organic aerosol is one of the most abundant, yet least understood, fractions of the Arctic aerosol mass. Here we use data from eight observatories that represent the entire Arctic to reveal the annual cycles in anthropogenic and biogenic sources of organic aerosol. We show that during winter, the organic aerosol in the Arctic is dominated by anthropogenic emissions, mainly from Eurasia, which consist of both direct combustion emissions and long-range transported, aged pollution. In summer, the decreasing anthropogenic pollution is replaced by natural emissions. These include marine secondary, biogenic secondary and primary biological emissions, which have the potential to be important to Arctic climate by modifying the cloud condensation nuclei properties and acting as ice-nucleating particles. Their source strength or atmospheric processing is sensitive to nutrient availability, solar radiation, temperature and snow cover. Our results provide a comprehensive understanding of the current pan-Arctic organic aerosol, which can be used to support modelling efforts that aim to quantify the climate impacts of emissions in this sensitive region.

58 GEOSCIENCES↗
DOE OSTI2021

Electric fields and potentials in condensed phases

The electric fields and potentials inside and at the interface of matter are relevant to many branches of physics, chemistry, and biology. Accurate quantification of these fields and/or potentials is essential to control and exploit chemical and physical transformations. Before we understand the response of matter to external fields, it is first important to understand the intrinsic interior and interfacial fields and potentials, both classically and quantum mechanically, as well as how they are probed experimentally. Here we compare and contrast, beginning with the hydrogen atom in vacuum and ending with concentrated aqueous NaCl electrolyte, both classical and quantum mechanical electric potentials and fields. Here, we make contact with experimental vibrational Stark, electrochemical, X-ray, and electron spectroscopic probes of these potentials and fields, outline relevant conceptual difficulties, and underscore the advantage of electron holography as a basis to better understand electrostatics in matter.

Kathmann, Shawn M.↗