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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Functional anatomy of zinc finger antiviral protein complexes

Abstract ZAP is an antiviral protein that binds to and depletes viral RNA, which is often distinguished from vertebrate host RNA by its elevated CpG content. Two ZAP cofactors, TRIM25 and KHNYN, have activities that are poorly understood. Here, we show that functional interactions between ZAP, TRIM25 and KHNYN involve multiple domains of each protein, and that the ability of TRIM25 to multimerize via its RING domain augments ZAP activity and specificity. We show that KHNYN is an active nuclease that acts in a partly redundant manner with its homolog N4BP1. The ZAP N-terminal RNA binding domain constitutes a minimal core that is essential for antiviral complex activity, and we present a crystal structure of this domain that reveals contacts with the functionally required KHNYN C-terminal domain. These contacts are remote from the ZAP CpG binding site and would not interfere with RNA binding. Based on our dissection of ZAP, TRIM25 and KHNYN functional anatomy, we could design artificial chimeric antiviral proteins that reconstitute the antiviral function of the intact authentic proteins, but in the absence of protein domains that are otherwise required for activity. Together, these results suggest a model for the RNA recognition and action of ZAP-containing antiviral protein complexes.

Science & Technology - Other Topics↗
DOE OSTI2025

Functional protein mining with conformal guarantees

Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model. Our method (1) lets users select many biologically-relevant loss metrics (i.e. false discovery rate) and assigns reliable functional probabilities for annotating genes of unknown function; (2) achieves state-of-the-art performance in enzyme classification without training new models; and (3) robustly and rapidly pre-filters proteins for computationally intensive structural alignment algorithms. Our framework enhances the reliability of protein homology detection and enables the discovery of uncharacterized proteins with likely desirable functional properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗
DOE OSTI2022

The impact of bilateral injuries on the pathophysiology and functional outcomes of volumetric muscle loss

Volumetric muscle loss (VML)—defined as the irrecoverable loss of skeletal muscle tissue with associated persistent functional deficits—is among the most common and highly debilitating combat-related extremity injuries. This is particularly true in cases of severe polytrauma wherein multiple extremities may be involved as a result of high energy wounding mechanisms. As such, significant investment and effort has been made toward developing a clinically viable intervention capable of restoring the form and function of the affected musculature. While these investigations conducted to date have varied with respect to the species, breed, and sex of the chosen pre-clinical in-vivo model system, the majority of these studies have been performed in unilateral injury models, an aspect which may not fully exemplify the clinical representation of the multiply injured patient. Furthermore, while various components of the basal pathophysiology of VML (e.g., fibrosis and inflammation) have been investigated, relatively little effort has focused on how the pathophysiology and efficacy of pro-regenerative technologies is altered when there are multiple VML injuries. Thus, the purpose of this study was two-fold: (1) to investigate if/how the pathophysiology of unilateral VML injuries differs from bilateral VML injuries and (2) to interrogate the effect of bilateral VML injuries on the efficacy of a well-characterized regenerative therapy, minced muscle autograft (MMG). In contrast to our hypothesis, we show that bilateral VML injuries exhibit a similar systemic inflammatory response and improved muscle functional recovery, compared to unilateral injured animals. Furthermore, MMG treatment was found to only be effective at promoting an increase in functional outcomes in unilateral VML injuries. The findings presented herein add to the growing knowledge base of the pathophysiology of VML, and, importantly, reiterate the importance of comprehensively characterizing preclinical models which are utilized for early-stage screening of putative therapies as they can directly influence the translational research pipeline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Unraveling the functional dark matter through global metagenomics

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Characterizing quantum circuits with qubit functional configurations

Abstract We develop a systematic framework for characterizing all quantum circuits with qubit functional configurations. The qubit functional configuration is a mathematical structure that can classify the properties and behaviors of quantum circuits collectively. Major benefits of classifying quantum circuits in this way include: 1. All quantum circuits can be classified into corresponding types; 2. Each type characterizes important properties (such as circuit complexity) of the quantum circuits belonging to it; 3. Each type contains a huge collection of possible quantum circuits allowing systematic investigation of their common properties. We demonstrate the theory’s application to analyzing the hardware-efficient ansatzes of variational quantum algorithms. For potential applications, the functional configuration theory may allow systematic understanding and development of quantum algorithms based on their functional configuration types.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection

The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Aqueous solvation of the chloride ion revisited with density functional theory: impact of correlation and exchange approximations

The specificity of aqueous halide solvation is fundamental to a wide range of bulk and interfacial phenomena spanning from biology to materials science. Halide polarizability is thought to drive the ion specificity, and if so, it is essential to have an accurate description of the electronic properties of halide ions in water. To this end, the solvation of the chloride anion, Cl - has been reinvestigated with state-of-the-art density functional theory. Specifically, the PBE-D3, PBE0-D3, and SCAN functionals have been employed to probe the impact of correlation and exchange approximations. Anticipating the findings, adding exact exchange improves the electronic structure, but simultaneously significantly reduces the Cl - polarizability, resulting in an over-structured Cl–O radial distribution function (RDF) and longer water H-bond lifetimes to Cl - . SCAN does not yield as much improvement in the energetics of Cl - relative to bulk water, but does result in a smaller reduction of the polarizability and thus a less structured Cl–O RDF, which agrees better with experiment. Special consideration is therefore warranted in assessing the impact of exchange on the energy, charge density, and the charge density response when designing and testing hybrid functionals for aqueous halide solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Design and synthesis of aryl-functionalized carbazole-based porous coordination cages

A subset of coordination cages have garnered considerable recent attention for their potential permanent porosity in the solid state. Herein, we report a series of functionalized carbazole-based cages of the structure type M 12 (R-cdc) 12 (M = Cr, Cu, Mo) where the functional groups include a range of aromatic substituents. Single-crystal X-ray structure determinations reveal a variety of intercage interactions in these materials, largely governed by pi–pi stacking. Density functional theory for a subset of these cages was used to confirm that the nature of the increased stability of aryl-functionalized cages is a result of inter-cage ligand interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Electrochemical reduction of europium(iii) using tetra- n -octyl diglycolamide functionalized ordered mesoporous carbon microelectrodes

This work investigates the one-electron reduction of Eu(III) to Eu(II) with ordered mesoporous carbon (OMC) in cavity microelectrode (CME) systems. OMC materials with and without tetra-n-octyl diglycolamide (TODGA) functionalization were subjected to voltammetric measurements and compared with commercial carbon black Vulcan® XC-72. The electrochemical reduction of solution Eu(III) with unfunctionalized OMC, XC-72, and TODGA-functionalized OMC—both within the electrode matrix and on the electrode surface—is reported. The complexation of Eu(III) by TODGA-functionalized OMC prior to electrode preparation incorporates Eu(III) as part of the bulk electrode matrix. Under these conditions, the high capacitance obscures the Eu(III)/Eu(II) redox couple. A signal emerges above the background (capacitive) currents when 2-octanol is added to the TODGA-functionalized OMC as a wetting agent. In contrast, surface Eu(III)–TODGA complexation, when Eu(III) contacts the electrode surface exclusively after electrode preparation, provides a strong response. The addition of 2-octanol to TODGA reduces the capacitance of the electrode and narrows the Eu(III)/Eu(II) redox peak widths. In conclusion, the desorption by reductive stripping of Eu(II) was demonstrated using a 2-octanol modified TODGA OMC CME, opening the possibility for selective separation of Eu from adjacent trivalent lanthanides.

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

Asymmetric side-chain engineering in semiconducting polymers: a platform for greener processing and post-functionalization of organic electronics

Organic semiconducting polymers are a powerful platform for the design of next-generation technologies due to their excellent optoelectronic properties and solution processability, allowing access to low-cost and scalable manufacturing techniques such as spin-coating, slot-die coating and roll-to-roll printing. However, their extended π-conjugation results in low solubility, requiring the use of toxic halogenated solvents to generate thin films and devices. Furthermore, accessible post-functionalization of semiconductors toward the development of multifunctional devices and sensors remains a challenge due to limited solid-state chemistry for alkyl side chains. In this work, an asymmetric side-chain engineering approach was used to introduce terminal hydroxyl moieties alongside traditional solubilizing branched alkyl chains into an isoindigo-based polymer. The hydroxyl moieties led to significantly improved processability in alcohol-based solvents without sacrificing electronic performance in thin film organic field-effect transistors. Solid state morphologies of the thin films processed from both alcohol-based and traditional halogenated solvents were further characterized using atomic force microscopy and grazing incidence wide angle X-ray scattering. Additionally, Cryo-EM was utilized in order to characterize the role of asymmetric side-chain functionality in solution state aggregation. The versatility of this design was further probed using fluorescein isothiocyanate to directly functionalize the asymmetric polymer in thin film. Furthermore, this facile solid-state post-functionalization further demonstrates asymmetric side-chain engineering to be a viable approach toward the development of sustainably manufactured multifunctional electronics.

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

Rational design of stable functional metal–organic frameworks

Functional porous metal–organic frameworks (MOFs) have been explored for a number of potential applications in catalysis, chemical sensing, water capture, gas storage, and separation. MOFs are among the most promising candidates to address challenges facing our society related to energy and environment, but the successful implementation of functional porous MOF materials are contingent on their stability; therefore, the rational design of stable MOFs plays an important role towards the development of functional porous MOFs. In this Focus article, we summarize progress in the rational design and synthesis of stable MOFs with controllable pores and functionalities. The implementation of reticular chemistry allows for the rational top-down design of stable porous MOFs with targeted topological networks and pore structures from the pre-selected building blocks. We highlight the reticular synthesis and applications of stable MOFs: (1) MOFs based on high valent metal ions (e.g., Al 3+ , Cr 3+ , Fe 3+ , Ti 4+ and Zr 4+ ) and carboxylate ligands; (2) MOFs based on low valent metal ions (e.g., Ni 2+ , Cu 2+ , and Zn 2+ ) and azolate linkers. We envision that the synthetic strategies, including modulated synthesis and post-synthetic modification, can potentially be extended to other more complex systems like metal-phosphonate framework materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Microstructure of amide-functionalized polyethylenes determined by NMR relaxometry

Amidation of polyethylenes creates a range of amide-containing materials with enhanced properties, but the effect of these functional groups on the microstructure of these new materials is not known. Here we employ solid-state nuclear magnetic resonance (NMR) techniques to analyze the microstructure of amide-modified polyethylenes. While a decrease in crystallinity was observed with increasing amounts of functionalization, we found by measuring the chain mobility of the crystalline, amorphous, and interphasial regions of the polyethylenes with NMR relaxation techniques that the grafted amidyl groups partition into the rigid amorphous fraction (RAF) between the crystalline and amorphous regions. The chemical specificity of these NMR experiments creates precise assessments of the location of functional groups within the materials. Together, these insights into the microstructure and morphology of amide-containing polyethylenes lay a foundation for a deeper understanding of the structure and properties of functional polyolefins.

Haber, Shira [Lawrence Berkeley National Laborator↗
DOE OSTI2020

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green’s functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Investigating the minimum post-burst energy required to function an exploding bridgewire detonator

The minimum energy required after bridge-burst to function a commercially available RP-1 exploding bridgewire detonator with a gold bridgewire was investigated using two capacitor discharge units (CDUs) making use of state-of-the-art on/off high-voltage high-current switches. Both switches are capable of shutting off the current flow in ≈100ns and the conduction time was varied systematically to limit the duration of electrical energy delivered from the CDU until a detonation go/no-go threshold was reached. It was found that the minimal extra electrical energy required for a soft-fire (a statistically marginal go) was approximately half that required for a hard-fire (a definite go). Furthermore, the measured energy required to function the RP-1 detonator from the 11.5 kV CDU was approximately 20 mJ greater than for the 600 V CDU, and it is postulated that this was due to arcing across the detonator terminals and an associated current shunt that was not efficient at depositing energy conducive to detonator functioning. Measurements of the bridgewire temperatures bursting in air showed that the maximum temperature reached was consistent (≈18kK) when sufficient energy was delivered that the detonator functioned (either soft- or hard-fire), but that the temperature for a sub-threshold bridgewire burst was significantly cooler at approximately 8 kK. Furthermore, it was demonstrated that the intensity of the light emitted at burst scaled with deposited energy. A related finding is that the light emission from the bridgewire peaks some tens of nanoseconds after both peak voltage and peak electrical power.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2020

Two-temperature warm dense hydrogen as a test of quantum protons driven by orbital-free density functional theory electronic forces

We consider a steady-state (but transient) situation in which a warm dense aggregate is a two-temperature system with equilibrium electrons at temperature Te, ions at Ti, and Te ≠ Ti. Such states are achievable by pump–probe experiments. For warm dense hydrogen in such a two-temperature situation, we investigate nuclear quantum effects (NQEs) on structure and thermodynamic properties, thereby delineating the limitations of ordinary ab initio molecular dynamics. We use path integral molecular dynamics (PIMD) simulations driven by orbital-free density functional theory (OFDFT) calculations with state-of-the-art noninteracting free-energy and exchange-correlation functionals for the explicit temperature dependence. We calibrate the OFDFT calculations against conventional (explicit orbitals) Kohn–Sham DFT. We find that when the ratio of the ionic thermal de Broglie wavelength to the mean interionic distance is larger than about 0.30, the ionic radial distribution function is meaningfully affected by the inclusion of NQEs. Moreover, NQEs induce a substantial increase in both the ionic and electronic pressures. This confirms the importance of NQEs for highly accurate equation-of-state data on highly driven hydrogen. For Te > 20 kK, increasing Te in the warm dense hydrogen has slight effects on the ionic radial distribution function and equation of state in the range of densities considered. In addition, we confirm that compared with thermostatted ring-polymer molecular dynamics, the primitive PIMD algorithm overestimates electronic pressures, a consequence of the overly localized ionic description from the primitive scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Static dipole polarizabilities of polyacenes using self-interaction-corrected density functional approximations

Density functional approximations are known to significantly overestimate the polarizabilities of long chain-like molecules. We study the static electric dipole polarizabilities and the vertical ionization potentials of polyacenes from benzene to pentacene using the Fermi-L\"owdin orbital based self-interaction corrected (FLOSIC) density functional method. The orbital-by-orbital self-interaction correction corrects for the overestimation tendency of density functional approximations. The polarizabilities calculated with FLOSIC-DFA are however overly corrected. We also tested the recently developed locally-scaled self-interaction correction (LSIC) method on the polyacenes. The local-scaling method applies full SIC in the one-electron regions and restores the proper behavior of the SIC exchange-correlation functionals in the uniform density limit. The results show that LSIC removes the overcorrection tendency of the FLOSIC-DFA and produces results that are in excellent agreement with reference CCSD values. The vertical ionization potentials with LSIC also show good agreement with available experimental values.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Real-time equation-of-motion CC cumulant and CC Green’s function simulations of photoemission spectra of water and water dimer

Newly developed coupled-cluster (CC) methods enable simulations of ionization potentials and spectral functions of molecular systems in a wide range of energy scales ranging from core-binding to valence. This paper discusses the results obtained with the real-time equation-of-motion CC cumulant (RT-EOM-CC) approach and CC Green’s function (CCGF) approaches in applications to the water and water dimer molecules. Here, we compare the ionization potentials obtained with these methods for the valence region with the results obtained with the coupled-cluster with singles, doubles, and perturbative triples formulation as a difference of energies for N and N – 1 electron systems. All methods show good agreement with each other. They also agree well with the experiment with errors usually below 0.1 eV for the ionization potentials. We also analyze unique features of the spectral functions, associated with the position of satellite peaks, obtained with the RT-EOM-CC and CCGF methods employing single and double excitations, as a function of the monomer OH bond length and the proton transfer coordinate in the dimer. Finally, we analyze the impact of the basis set effects on the quality of calculated ionization potentials and find that the basis set effects are less pronounced for the augmented-type sets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗