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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

CTT: Tools for Fine Alignment of Flash X-ray Systems

The CTT code is a compilation of the python code that was prototyped in the interest of making a method for fine alignment of Flash X-ray Systems at the lab. It contains python code for interacting with LTT and running optimization loops using LTT simulations or ray tracing with RaySpace. It Includes classes for creating phantom objects and modular geometry objects in the simulations. It allows one to generate a random phantom that has been optimized to stay with a certain cubic volume and maximize the minimum distance between any two ball phantom centers in all projections. It was primarily made to work on ball phantoms which were simulated as Teflon spheres. It allows the alignment from some nominal position to some displaced position to simulate recovery of a real geometry from the nominal geometry of the system. Fine alignment can be done with the projections in LTT while a rough alignment is faster using rayspace. If rayspace works well for the use case it should be preferred since it is considerably faster and less resource intensive in general. Some Notes about using this code is that one will have to edit the imports for the files to get to the correct LTT path, LTT GUI path and to the CTT path when importing. This was made by using anaconda with python 3 on windows 10. The LTT code was stored in a anaconda environment which seemed to help the python find the LTT although it shouldn’t be necessary if you append the path in your code using sys.path.append(r'add the path you want here’). The sys.path.append method is a quick way to give your python code access to a given folder when running it (such as LTT or CTT). Note that since the code was originally made with paths for a specific machine that a new user will have to edit those paths to make it work in all the files that use the old paths. This is somewhat tedious but will be required to run the code on a new machine. The methodology used to run and make these notebooks starts with opening a command prompt as administrator in windows 10. After this one would activate the anaconda environment in the appropriate directory using “conda activate myenv” in the command prompt. After this open a jupyter-notebook using the keyword “jupyter-notebook". After that a notebook should open in a browser. Note that some libraries used may not come with anaconda so those may have to be installed. There shouldn’t be much though since the main things used are scipy, numpy, matplotlib, and LTT. LTTQuicksetup also requires some paths that will be specific to the computer so that should be changed as well.

42 ENGINEERING↗
DOE OSTI2019

Mediation of plant–mycorrhizal interaction by a lectin receptor-like kinase

The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant–microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and the ectomycorrhizal fungus Laccaria bicolor . Furthermore, this finding uncovers an important molecular step in the establishment of symbiotic plant–fungal associations and provides a molecular target for engineering beneficial mycorrhizal relationships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Urban morphology and urban water demand evolution in the Los Angeles region

Detailed description of the dataset sources used in this study, the experimental workflow, and plotting for the paper figures provided at the associated GitHub Meta Repo: https://github.com/IMMM-SFA/Ferencz_et_al_2024_ERL The future water demand projections from this study are hypothetical future water demands that reflect the population and urban land cover changes represented by the scenarios considered. The intent and emphasis of this work is investigating the interactions between population change, evolution of urban morphology, and water demand. These projections are not meant to be likely future demands for specific water providers or the LA region and should not be interpreted as such. The folders contain input and output data for each step of the "Recreate my Experiment" workflow described in the associated GitHub meta-repository as well as data used for plotting Figures for the paper that this dataset supports. Description of each folder's contents and use: Step_1a: Inputs to the associated python script provided on the GitHub repo. Step_1b: Inputs (downscaled population rasters) used by the associated python script provided on the GitHub repo. Original 1-km squared rasters that were downscaled also provided. Step_1c: Urban growth projection rasters corresponding to SSP3 and SSP5 population scenarios are provided in separate subfolders as well as the water provider boundaries used for analysis. Outputs of data processing also provided. Associated python script provided on GitHub. Step_1d: Description of Inputs used by the QGIS Model Builder GUI that automates geospatial processing and clipping the of the high-resolution 60 cm land cover data for each urban land class footprint within a defined polygon boundary. The Model Builder is provided on the GitHub repo and can be used by QGIS. The outputs of this step are in "Clipped Provider Hi Res Landcover". If the user wants to use The Model Builder for different regions of LA or to test our outputs, they will need to download the hi resolution landcover raster listed in the Readme and in Ref [2] of the GitHub Page. Step_1e: All necessary inputs to generate average monthly demand over the 2017-2021 period and the minimum and maximum demands over the 2014-2021 for each water provider. Associated python scripts are on GitHub. Step 2: Output data about land cover metrics (areas and fractions) for each urban land class for each water provider. Associated python script on GitHub. Uses outputs from Step 1d "Clipped Provider Hi Res Landcover" Step 3: Both the Inputs for and Outputs from the urban projection raster analysis Python script on GitHub. The inputs are urban land class rasters for specific SSP and zoning scenarios (low, medium, high) from Step 1c. The outputs are rasters of urban pixels that were converted to a higher land class and the number of land class units that changed (Values of 1, 2, or 3). For example, a value of 2 could be LC 21 -> 23 or LC 22 -> 24. These maps are label "intensification." The other outputs are "urban growth" rasters showing the conversion of non urban to urban land, which are indicated by pixel values of 1. These are used for the urban growth change maps in Figure 3. Step 4: Output projections of indoor and outdoor annual and monthly demands for each water provider for the average, minimum, and maximum monthly demand scenarios for each of the four urban growth scenarios (SSP3 med, SSP5 low, SSP5 med, and SSP5 high). The outputs also include metrics on each water provider used for the demand sensitivity analysis presented in Figure 8. Outputs from Step 4 are used for Figures 4 - 8 of the paper. Figures: This folder has data used for plotting Figures 1 through 5, and 8. Data for Figures 6 and 7 are sourced directly from folders associated with the Processing and Analysis Steps 1 - 4. The GitHub meta repository provides descriptions of how each figure was made and the associated plotting scripts used.

Los Angeles↗
DOE OSTI2023

Implanting Transition Metal into Li 2 O-Based Cathode Prelithiation Agent for High-Energy-Density and Long-Life Li-Ion Batteries

Compensating the irreversible loss of limited active lithium (Li) is essentially important for improving the energy-density and cycle-life of practical Li-ion battery full-cell, especially after employing high-capacity but low initial coulombic efficiency anode candidates. Introducing prelithiation agent can provide additional Li source for such compensation. Herein, we precisely implant trace Co (extracted from transition metal oxide) into the Li site of Li 2 O, obtaining (Li 0.66 Co 0.11$\square$0.23 ) 2 O (CLO) cathode prelithiation agent. Further, the synergistic formation of Li vacancies and Co-derived catalysis efficiently enhance the inherent conductivity and weaken the Li-O interaction of Li 2 O, which facilitates its anionic oxidation to peroxo/superoxo species and gaseous O 2 , achieving 1642.7 mAh/g ~Li2O prelithiation capacity (≈980 mAh/g for prelithiation agent). Coupled 6.5 wt % CLO-based prelithiation agent with LiCoO 2 cathode, substantial additional Li source stored within CLO is efficiently released to compensate the Li consumption on the SiO/C anode, achieving 270 Wh/kg pouch-type full-cell with 92 % capacity retention after 1000 cycles.

25 ENERGY STORAGE↗
DOE OSTI2016

Refined hyperentanglement purification of two-photon systems for high-capacity quantum communication with cavity-assisted interaction

Hyperentanglement, defined as the entanglement in multiple degrees of freedom (DOFs) of a photonic quantum system, has attracted much attention recently as it can improve the channel capacity of quantum communication largely. Here we present a refined hyperentanglement purification protocol (hyper-EPP) for two-photon systems in mixed hyperentangled states in both the spatial-mode and polarization DOFs, assisted by cavity quantum electrodynamics. By means of the spatial (polarization) quantum state transfer process, the quantum states that are discarded in the previous hyper-EPPs can be preserved. That is, the spatial (polarization) state of a four-photon system with high fidelity can be transformed into another four-photon system with low fidelity, not disturbing its polarization (spatial) state, which makes this hyper-EPP take the advantage of possessing a higher efficiency.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Urban morphology and urban water demand evolution in the Los Angeles region

Detailed description of the dataset sources used in this study, the experimental workflow, and plotting for the paper figures provided at the associated GitHub Meta Repo: https://github.com/IMMM-SFA/Ferencz_et_al_2024_ERL The future water demand projections from this study are hypothetical future water demands that reflect the population and urban land cover changes represented by the scenarios considered. The intent and emphasis of this work is investigating the interactions between population change, evolution of urban morphology, and water demand. These projections are not meant to be likely future demands for specific water providers or the LA region and should not be interpreted as such. The folders contain input and output data for each step of the "Recreate my Experiment" workflow described in the associated GitHub meta-repository as well as data used for plotting Figures for the paper that this dataset supports. Description of each folder's contents and use: Step_1a: All necessary inputs to the associated python script provided on the GitHub repo. Step_1b: All necessary inputs (downscaled population rasters) used by the associated python script provided on the GitHub repo. Original 1-km squared rasters that were downscaled also provided. Step_1c: Urban growth projection rasters corresponding to SSP3 and SSP5 population scenarios are provided in separate subfolders as well as the water provider boundaries used for analysis. Outputs of data processing also provided. Associated python script provided on GitHub. Step_1d: Description of Inputs used by the QGIS Model Builder GUI that automates geospatial processing and clipping the of the high resolution land cover data for each urban land class footprint within a defined polygon boundary. The Model Builder is provided on the GitHub repo and can be used by QGIS. The outputs of this step are in "Clipped Provider Hi Res Landcover". If the user wants to use The Model Builder for different regions of LA or two test our outputs, they will need to download the hi resolution landcover raster listed in the Readme and in Ref [2] of the GitHub Page. Step_1e: All necessary inputs to generate average monthly demand for each water provider. Associated python script on GitHub. Step 2: Output data about land cover metrics (areas and fractions) for each urban land class for each water provider. Associated python script on GitHub. Uses outputs from Step 1d "Clipped Provider Hi Res Landcover" Step 3: Inputs for and Outputs from the urban projection raster analysis Python script on GitHub. The outputs are rasters of urban pixels that were converted to a higher land class and the number of land class units that changed (Values of 1, 2, or 3). For example, a value of 2 could be LC 21 -> 23 or LC 22 -> 24. These maps are label "intensification." The other outputs are "urban growth" rasters showing the conversion of non urban to urban land, which are indicated by pixel values of 1. Step 4: Output projections of indoor and outdoor annual and monthly demands for each water provider. These are used for Figures 4 - 7 of the paper. Figures: This folder has data used for plotting Figures 1 through 5. Data for Figures 6 and 7 are sourced directly from folders associated with the Processing and Analysis Steps 1 - 4 and the plotting scripts for Figures 6 and 7 are commented with what folder paths are needed to generate the figures. The GitHub page provides descriptions of how each figure was made and the associated plotting scripts used.

Los Angeles↗
DOE OSTI2020

Electrical detection of magnon-photon interactions via an auxiliary spin-wave mode

We report on the electrical detection of a hybrid magnon-photon system which comprises a magnetic sample coupled to a planar cavity. While the uniform Kittel mode has the largest coupling strength among all the magnon modes, it generates only a modest voltage signal by means of the inverse spin-Hall effect. We have found that the generated voltage can be significantly enhanced by introducing a higher-order magnon mode, which possesses a much higher spin pumping efficiency, and furthermore, it is nearly degenerated with the Kittel mode. In this work, the experimental results can be explained by our theoretical model and suggest that the use of an auxiliary magnon mode can realize the configuration of a magnon-photon system with both strong coupling and large spin current.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Predicted polymorph manipulation in an exotic double perovskite oxide

Predicted polymorph manipulation offers a cutting-edge route to design function-oriented materials in an exotic double perovskite-related oxide A 2 BB'O 6 with small A-site cations. Herein, first-principles density functional theory calculations in light of the equation of state for solid, for the first time, was used to predict the Mg 3 TeO 6 (R$\bar{3}$) with combining macron])-to-perovskite (P2 1 /n) type phase transition in Mn 3 TeO 6 at around 5 GPa, regardless of the deployment of magnetic interactions. The high-pressure synthesis and synchrotron diffraction crystal structure analysis corroborated experimentally the polymorph variation in Mn 2 2+ Mn 2+ Te 6+ O 6 , which was accompanied by a 13 K increase in the antiferromagnetic ordering temperature (37 K) in the high-pressure perovskite polymorph compared to that of the ambient-pressure R$\bar{3}$ phase (24 K). The magnetodielectric coupling remains up to 50 K with the maximum being around the magnetic ordering temperature in the perovskite Mn 3 TeO 6 . Thus, the predicted polymorph manipulation here offers the possibility of discovering accelerated materials by inverse design in exotic perovskite oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus

Summary Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans ‐eQTL were genes involved in plant hormone responses and root development. Overexpression of PtrXB38 in Populus led to significant increases in callusing and formation of both stem‐born roots and base‐born adventitious roots. Omics studies revealed that genes and proteins controlling auxin transport and signaling were involved in PtrXB38‐mediated adventitious root formation. Protein–protein interaction assays indicated that PtrXB38 interacts with components of endosomal sorting complexes required for transport machinery, implying that PtrXB38‐regulated root development may be mediated by regulating endocytosis pathway. Taken together, this work identified a crucial root development regulator and sheds light on the discovery of other plant developmental regulators through combining eQTL mapping and omics approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To reflect how this process can be accelerated, we employed a genome-wide association mapping of ca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among crucial associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Long noncoding RNA Nespas inhibits apoptosis of epileptiform hippocampal neurons by inhibiting the PI3K/Akt/mTOR pathway

Highlights: • Nespas is downregulated and inhibits hippocampal neuron apoptosis in epileptic mouse models. • Nespas binds with miR-615–3p in epileptiform hippocampal neurons. • MiR-615–3p targets Psmd11 in epileptiform hippocampal neurons. • Nespas inhibits hippocampal neuron apoptosis in epilepsy by upregulating Psmd11 and inhibiting the PI3K/Akt/mTOR pathway. Epilepsy is one of the most common neurological diseases with spontaneous recurrent seizures. Long noncoding RNAs (lncRNAs) are crucial modulators in numerous diseases, including epilepsy. However, the functional role and potential mechanism of lncRNA Nespas in epilepsy remain unknown. Our study clarified that Nespas was underexpressed in epileptiform hippocampal tissues and neurons. Furthermore, Nespas promoted hippocampal neuron viability and proliferation, and inhibited hippocampal neuron apoptosis. Mechanistically, Nespas interacted with microRNA 615–3p (miR-615–3p) in epileptiform hippocampal neurons. 26S proteasome non-ATPase regulatory subunit 11 (Psmd11) was a downstream target of miR-615–3p, and Nespas elevated Psmd11 expression via competitively binding to miR-615–3p in epileptiform hippocampal neurons. In addition, rescue assays suggested that Nespas promoted hippocampal neuron viability and proliferation, and suppressed hippocampal neuron apoptosis by upregulation of Psmd11. Furthermore, Nespas suppressed the PI3K/Akt/mTOR pathway via upregulating Psmd11 in epileptiform hippocampal neurons. This report explored the function and regulatory mechanism of Nespas in epileptiform hippocampal neurons for the first time. Our findings revealed that Nespas suppressed the apoptosis of epileptiform hippocampal neurons by inhibiting the PI3K/Akt/mTOR pathway via upregulation of Psmd11 at a miR-615–3p dependent way, indicating that Nespas may offer a new direction for the treatment of epilepsy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Metabolic patterns in Septoria canker resistant and susceptible Populus trichocarpa genotypes 24 hours post-inoculation

Sphaerulina musiva is an economically and ecologically important fungal pathogen that causes Septoria stem canker and leaf spot disease of Populus species. Here, to bridge the gap between genetic markers and structural barriers previously found to be linked to Septoria (Sphaerulina musiva) canker disease resistance in poplar, we employed hydrophilic interaction liquid chromatography (HILIC) and tandem mass spectrometry (MS/MS) to identify and quantify metabolites involved with signaling and cell wall re-modelling. Fluctuations in signaling molecules, organic acids, amino acids, sterols, phenolics, and saccharides in resistant and susceptible Populus trichocarpa inoculated with Sphaerulina musiva, were observed. The patterns of 222 metabolites in the resistant host implicates systemic acquired resistance (SAR), cell wall apposition, and lignin deposition as modes of resistance to this hemibiotrophic pathogen. This pattern is consistent with the expected response to the biotrophic phase of S. musiva colonization during the first 24 hours post-inoculation. The fungal pathogen metabolized key regulatory signals of SAR, other phenolics, and precursors of lignin biosynthesis which were depleted in the susceptible host. This is the first study to characterize metabolites associated with the response to initial colonization by S. musiva between resistant and susceptible hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant–microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Moiré excitons: From programmable quantum emitter arrays to spin-orbit–coupled artificial lattices

Highly uniform and ordered nanodot arrays are crucial for high-performance quantum optoelectronics, including new semiconductor lasers and single-photon emitters, and for synthesizing artificial lattices of interacting quasiparticles toward quantum information processing and simulation of many-body physics. Van der Waals heterostructures of two-dimensional semiconductors are naturally endowed with an ordered nanoscale landscape, that is, the moiré pattern that laterally modulates electronic and topographic structures. We find that these moiré effects realize superstructures of nanodot confinements for long-lived interlayer excitons, which can be either electrically or strain tuned from perfect arrays of quantum emitters to excitonic superlattices with giant spin-orbit coupling (SOC). Besides the wide-range tuning of emission wavelength, the electric field can also invert the spin optical selection rule of the emitter arrays. This unprecedented control arises from the gauge structure imprinted on exciton wave functions by the moiré, which underlies the SOC when hopping couples nanodots into superlattices. We show that the moiré hosts complex hopping honeycomb superlattices, where exciton bands feature a Dirac node and two Weyl nodes, connected by spin-momentum–locked topological edge modes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis

In plants, the pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, in this study, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance. We discovered that Arabidopsis AtDGCR14L is required for maintaining plant salt stress tolerance and the constitutively spliced and active isoforms of important stress- and/or abscisic acid (ABA)-responsive genes. We also identified the interaction between AtDGCR14L and splicing factor U1-70k, which needs a highly conserved three amino acid (TWG) motif in DGCR14. Different from wild-type AtDGCR14L, the overexpression of TWG-substituted AtDGCR14L mutant did not change salt stress tolerance or pre-mRNA splicing of stress/ABA-responsive genes. Additionally, SWITCH3A (SWI3A) is a core subunit of the SWI/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes. We found that SWI3A, whose splicing depends on AtDGCR14L, actively enhances salt stress tolerance. These results revealed that AtDGCR14L may play an essential role in crosstalk between plant salt-stress response and pre-mRNA splicing mechanisms. We also unveiled the potential role of SWI3A in controlling salt stress tolerance. The TWG motif in the intrinsically disordered region of AtDGCR14L is highly conserved and crucial for DGCR14 functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The ETROC Project: Precision Timing ASIC Development for LGAD-based CMS Endcap Timing Layer (ETL) Upgrade

The ETROC (Endcap Timing Readout Chip) is being developed for the LGAD-based CMS Endcap Timing Layer (ETL) at HL-LHC. The ETL on each side of the interaction region will be instrumented with a two-disk system of MIP-sensitive LGAD silicon devices to be read out by ETROCs for precision timing measurement with down to 30 ps timing resolution. The ETROC is designed to handle a 16 x 16 pixel cell matrix, with each pixel cell being 1.3 mm x 1.3 mm to match the LGAD sensor pixel size. Approximately 15% of the sensors near the highest eta region will experience hadron fluence above 1e15 neq/cm² towards end of operation of HL-LHC, resulting in small signal amplitude with LGAD gain reduced to around 10. For this reason, the front-end design for preamplifier and discriminator has been specifically optimized for the reduced LGAD signals, with enough flexibilities to meet the ETL specific needs for time resolution, power budget and radiation profile.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. In this work, we present a computational tool, Glycan Modeler for in silico N–/O –glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader , a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-μs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler . Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.

59 BASIC BIOLOGICAL SCIENCES↗