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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

High Residual Collagen-Induced Platelet Reactivity Predicts Development of Restenosis in the Superficial Femoral Artery After Percutaneous Transluminal Angioplasty in Claudicant Patients

PurposeAlthough platelet reactivity is routinely inhibited with aspirin after percutaneous angioplasty (PTA) in peripheral arteries, the restenosis rate in the superficial femoral artery (SFA) is high. Interaction of activated platelets and the endothelium in the region of intervention could be one reason for this as collagen in the subendothelium activates platelets.Materials and MethodsA prospective study evaluating on-site platelet reactivity during PTA and its influence on the development of restenosis with a total of 30 patients scheduled for PTA of the SFA. Arterial blood was taken from the PTA site after SFA; platelet function was evaluated with light transmission aggregometry. After 3, 6, 12, and 24 months, duplex sonography was performed and the restenosis rate evaluated.ResultsEight out of 30 patients developed a hemodynamically relevant restenosis (>50 % lumen narrowing) in the PTA region during the 24-month follow-up period. High residual collagen-induced platelet reactivity defined as AUC >30 was a significant predictor for the development of restenosis [adjusted odds ratio 11.8 (9.4, 14.2); P = .04].ConclusionsHigh residual collagen-induced platelet reactivity at the interventional site predicts development of restenosis after PTA of the SFA. Platelet function testing may be useful for identifying patients at risk.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue

Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the –EKHVP– motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic crenarchaeon Ignicoccus hospitalis . We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (₋E₂₃T₂₄HVP₋), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2018

Detection of Carbendazim Residues in Aqueous Samples by Fluorescent Quenching of Plant Esterase

A method based on the inhibition of plant esterase from pesticides has been proposed and validated for the determination of carbendazim residues in aqueous samples. After optimization in pH, temperature, and detection time, a lower detection limit of 0.105 μM was obtained in the linear range from 0.105 to 41.84 μM. Upon analysis of the detection mechanism, carbendazim was found to be binding to plant esterase via the van der Waals force and the hydrogen bond with a single binding site through an exothermic reaction. Moreover, the proposed method was satisfactorily applied to the analysis of carbendazim residues in different aqueous samples, obtaining a remarkably good agreement with the standardized reference method.

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

Residually Stressed Bimaterial Beam Specimen for Measuring Environmentally Assisted Crack Growth

Background: Subcritical crack growth can occur in a brittle material when the stress intensity factor is smaller than the fracture toughness if an oxidizing agent (such as water) is present at the crack tip. Objective: Here we present a novel bi-material beam specimen which can measure environmentally assisted crack growth rates. The specimen is “self-loaded” by residual stress and requires no external loading. Methods: Two materials with different coefficient of thermal expansion are diffusion bonded at high temperature. After cooling to room temperature a subcritical crack is driven by thermal residual stresses. A finite element model is used to design the specimen geometry in terms of material properties in order to achieve the desired crack tip driving force. Results: The specimen is designed so that the crack driving force decreases as the crack extends, thus enabling the measurement of the crack velocity versus driving force relationship with a single test. The method is demonstrated by measuring slow crack growth data in soda lime silicate glass and validated by comparison to previously published data. Conclusions: The self-loaded nature of the specimen makes it ideal for measuring the very low crack velocities needed to predict brittle failure at long lifetimes.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization

BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND3{sub 56–58}, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. - Highlights: • BEND3 localizes to the nucleus. • The N-terminal 60 amino acids region of BEND3 contains NLS. • Amino acids located between 56 and 58 of BEND3 (KRK) are part of NLS. • KRK motif is highly conserved among BEND3 homologs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Characterization of amino acid residues within the N-terminal region of Ubc9 that play a role in Ubc9 nuclear localization

As the sole E2 enzyme for SUMOylation, Ubc9 is predominantly nuclear. However, the underlying mechanisms of Ubc9 nuclear localization are still not well understood. Here we show that RNAi-depletion of Imp13, an importin known to mediate Ubc9 nuclear import, reduces both Ubc9 nuclear accumulation and global SUMOylation. Furthermore, Ubc9-R13A or Ubc9-H20D mutation previously shown to interrupt the interaction of Ubc9 with nucleus-enriched SUMOs reduces the nuclear enrichment of Ubc9, suggesting that the interaction of Ubc9 with the nuclear SUMOs may enhance Ubc9 nuclear retention. Moreover, Ubc9-R17E mutation, which is known to disrupt the interaction of Ubc9 with both SUMOs and Imp13, causes a greater decrease in Ubc9 nuclear accumulation than Ubc9-R13A or Ubc9-H20D mutation. Lastly, Ubc9-K74A/S89D mutations that perturb the interaction of Ubc9 with nucleus-enriched SUMOylation-consensus motifs has no effect on Ubc9 nuclear localization. Altogether, our results have elucidated that the amino acid residues within the N-terminal region of Ubc9 play a pivotal role in regulation of Ubc9 nuclear localization. - Highlights: • Imp13-mediated nuclear import of Ubc9 is critical for global SUMOylation. • Ubc9 mutations disrupting Ubc9-SUMO interaction decrease Ubc9 nuclear accumulation. • N-terminal amino acid residues of Ubc9 are critical for Ubc9 nuclear enrichment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Effects of lysine residues on structural characteristics and stability of tau proteins

Pathological amyloid proteins have been implicated in neuro-degenerative diseases, specifically Alzheimer's, Parkinson's, Lewy-body diseases and prion related diseases. In prion related diseases, functional tau proteins can be transformed into pathological agents by environmental factors, including oxidative stress, inflammation, Aβ-mediated toxicity and covalent modification. These pathological agents are stable under physiological conditions and are not easily degraded. This un-degradable characteristic of tau proteins enables their utilization as functional materials to capturing the carbon dioxides. For the proper utilization of amyloid proteins as functional materials efficiently, a basic study regarding their structural characteristic is necessary. Here, we investigated the basic tau protein structure of wild-type (WT) and tau proteins with lysine residues mutation at glutamic residue (Q2K) on tau protein at atomistic scale. We also reported the size effect of both the WT and Q2K structures, which allowed us to identify the stability of those amyloid structures. - Highlights: • Lysine mutation effect alters the structure conformation and characteristic of tau. • Over the 15 layers both WT and Q2K models, both tau proteins undergo fractions. • Lysine mutation causes the increment of non-bonded energy and solvent accessible surface area. • Structural instability of Q2K model was proved by the number of hydrogen bonds analysis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Loop engineering reveals the importance of active-site-decorating loops and gating residue in substrate affinity modulation of arginine deiminase (an anti-tumor enzyme)

Highlights: • Loop engineering on the active-site-decorating loops yielded several PpADI variants with low S{sub 0.5} values. • Several amino acid positions in active-site-decorating loops essential for the substrate affinity of PpADI were identified. • High loop flexibility (especially the gating residue Arg400) is beneficial for the substrate affinity of PpADI. Protein engineering of enzyme loop regions is an effective strategy to improve enzymatic properties. Previous studies that aimed to boost the activity of PpADI (an arginine deiminase from Pseudomonas plecoglossicida) under physiological conditions yielded several significantly improved variants that harbor substitutions predominantly located in active-site-decorating loops. A multi-site saturation mutagenesis at four positions in loop 1 (37, 38, 42, and 43) and three positions in loop 4 (402, 403, and 404) was performed to elucidate the importance of these loops in modulating the substrate affinity of PpADI. The identified “best” variant (M6-L1-4) showed a decreased S{sub 0.5} (‘K{sub M}’) of 0.48 mM compared with the parent M6 (0.81 mM). Subsequently, a rational design to recombine beneficial substitutions within loops 1 and 4 yielded variant L6 with a substantially decreased S{sub 0.5} value (0.17 mM). A comprehensive simulation analysis resulted in a conclusion that high loop flexibility (especially the gating residue Arg400) is beneficial for substrate affinity due to less efficient blocking of the active site.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Computational investigation on CO 2 adsorption in titanium carbide-derived carbons with residual titanium

We develop a new approach for modeling titanium carbide derived-carbon (TiC-CDC) systems with residual titanium by the generation of modified atomistic structures based on a silicon carbide derived-carbon (SiC-CDC) model and the application of weighted combinations of these structures. In our approach, the original SiC-CDC structure is modified by (i) removing carbon, (ii) adding carbon and (iii) adding titanium. The new atomic scale carbide-derived carbon (CDC) structures are investigated using classical molecular dynamics simulations, and their pure CO 2 adsorption isotherms are calculated using grand canonical Monte Carlo simulations. The system of TiC-CDC with residual titanium is modeled as weighted combinations of pure carbon CDC structures, CDC structures with titanium and a TiC crystalline structure. Our modeling is able to produce both structural properties and adsorption isotherms in accordance with experimental data. The fraction of different models in the systems successfully reflects the structural differences in various experimental TiC-CDC samples. The modeling also suggests that in partially etched TiC-CDC systems, the titanium that may be accessible to CO 2 gas at the transitional interface may provide significant interaction sites for CO 2 and may lead to more efficient overall gas adsorption.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Boosting the use of bauxite residue (red mud) in cement - Production of an Fe-rich calciumsulfoaluminate-ferrite clinker and characterisation of the hydration

Highlights: • Incorporation of 35 wt% of bauxite residue for production of CSAF clinker • Thermochemical calculations as suitable tool for predicting phase assemblage • Hydration of the cement was found to be accelerated in contrast to other CSA cements. • High early compressive strengths of 40 MPa In the present work, calciumsulfoaluminate-ferrite clinker was produced using 35 wt% of bauxite residue in combination with alumina, clay, limestone and gypsum. At a temperature of 1300 °C, the hydraulic phases ye'elimite, ferrite and C{sub 2}S were formed. Computed thermochemical predictions were a significantly better match for the real mineralogy than modified Bogue equations. Hydration of the clinker led to the formation of ettringite and monosulfate, resulting in compressive strengths of 17 MPa after 28d. Compressive strengths of 40 MPa after 2d, and 28d-strengths exceeding 50 MPa, were reached in blends with 10 wt% of anhydrite. The strength development was due to the rapid formation of ettringite, mainly originating from ye'elimite, which did not convert to AFm phases and led to a compact microstructure. Only when the ye'elimite dissolution decreased, did the ferrite phase react. In pastes with additional sulfates, ferrite hydration led to the formation of ettringite and to hydrogarnet. Cement nomenclature is used in this work.{sup 1}.

36 MATERIALS SCIENCE↗
DOE OSTI2023

HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues

Protease inhibitors are the most potent antivirals against HIV-1, but they still lose efficacy against resistant variants. Improving the resistance profile is key to developing more robust inhibitors, which may be promising candidates for simplified next-generation antiretroviral therapies. Here, in this study, we explored analogs of darunavir with a P1 phosphonate modification in combination with increasing size of the P1′ hydrophobic group and various P2′ moieties to improve potency against resistant variants. The phosphonate moiety substantially improved potency against highly mutated and resistant HIV-1 protease variants, but only when combined with more hydrophobic moieties at the P1′ and P2′ positions. Phosphonate analogs with a larger hydrophobic P1′ moiety maintained excellent antiviral potency against a panel of highly resistant HIV-1 variants, with significantly improved resistance profiles. The cocrystal structures indicate that the phosphonate moiety makes extensive hydrophobic interactions with the protease, especially with the flap residues. Many residues involved in these protease-inhibitor interactions are conserved, enabling the inhibitors to maintain potency against highly resistant variants. These results highlight the need to balance inhibitor physicochemical properties by simultaneous modification of chemical groups to further improve resistance profiles.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Metal residues, histopathology and presence of parasites in the liver and gills of fourhorn sculpin (Myoxocephalus quadricornis) and shorthorn sculpin (Myoxocephalus scorpius) near a former lead-zinc mine in East Greenland

Fourhorn sculpins (Myoxocephalus quadricornis) and shorthorn sculpins (Myoxocephalus scorpius) have been considered suitable local bioindicators for environmental monitoring studies in the Arctic. Because these species share many characteristics, data from the two species have previously been pooled when assessing marine metal contamination. A chemical and histological study was conducted on fourhorn and shorthorn sculpins collected around a contaminated lead-zinc mine at East Greenland to investigate whether there were any differences in the residues of metals, histopathology and parasites in liver and gills between the two sculpin species. The results demonstrated that concentrations of copper (Cu), zinc (Zn), mercury (Hg) and lead (Pb) were significantly higher in the fourhorn sculpins (p<0.001) while there were no significant differences for arsenic (As) or cadmium (Cd). Furthermore, density of blood vessel fibrosis (p=0.028), prevalence and density of chondroplasia (p=0.002 and p=0.005, respectively), number of mucin-containing mucous cells (p<0.001) and chloride cells (p<0.001) and mean intensity of colonial Peritricha (p<0.001) were significantly higher in fourhorn sculpin. Based on these results we suggest that pooling the two species when conducting environmental assessments is not recommended as it can lead to incorrect conclusions. We propose that a larger study investigating the biological effects of zinc-lead mining in Greenland is needed. - Highlights: • Fourhorn sculpins (Myoxocephalus quadricornis) more sensitive to pollution than shorthorn sculpins (Myoxocephalus scorpius). • Metal residues, histological changes and presence of parasites were species-specific. • Different sculpin species should not be pooled together as pollution biomarkers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Positron Emission Tomography/Computed Tomography Imaging of Residual Skull Base Chordoma Before Radiotherapy Using Fluoromisonidazole and Fluorodeoxyglucose: Potential Consequences for Dose Painting

Purpose: To detect the presence of hypoxic tissue, which is known to increase the radioresistant phenotype, by its uptake of fluoromisonidazole (18F) (FMISO) using hybrid positron emission tomography/computed tomography (PET/CT) imaging, and to compare it with the glucose-avid tumor tissue imaged with fluorodeoxyglucose (18F) (FDG), in residual postsurgical skull base chordoma scheduled for radiotherapy. Patients and Methods: Seven patients with incompletely resected skull base chordomas were planned for high-dose radiotherapy (dose {>=}70 Gy). All 7 patients underwent FDG and FMISO PET/CT. Images were analyzed qualitatively by visual examination and semiquantitatively by computing the ratio of the maximal standardized uptake value (SUVmax) of the tumor and cerebellum (T/C R), with delineation of lesions on conventional imaging. Results: Of the eight lesion sites imaged with FDG PET/CT, only one was visible, whereas seven of nine lesions were visible on FMISO PET/CT. The median SUVmax in the tumor area was 2.8 g/mL (minimum 2.1; maximum 3.5) for FDG and 0.83 g/mL (minimum 0.3; maximum 1.2) for FMISO. The T/C R values ranged between 0.30 and 0.63 for FDG (median, 0.41) and between 0.75 and 2.20 for FMISO (median,1.59). FMISO T/C R >1 in six lesions suggested the presence of hypoxic tissue. There was no correlation between FMISO and FDG uptake in individual chordomas (r = 0.18, p = 0.7). Conclusion: FMISO PET/CT enables imaging of the hypoxic component in residual chordomas. In the future, it could help to better define boosted volumes for irradiation and to overcome the radioresistance of these lesions. No relationship was founded between hypoxia and glucose metabolism in these tumors after initial surgery.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Residual Tumor After Neoadjuvant Chemoradiation Outside the Radiation Therapy Target Volume: A New Prognostic Factor for Survival in Esophageal Cancer

Purpose/Objective(s): The aim of this study was to analyze the accuracy of gross tumor volume (GTV) delineation and clinical target volume (CTV) margins for neoadjuvant chemoradiation therapy (neo-CRT) in esophageal carcinoma at pathologic examination and to determine the impact on survival. Methods and Materials: The study population consisted of 63 esophageal cancer patients treated with neo-CRT. GTV and CTV borders were demarcated in situ during surgery on the esophagus, using anatomical reference points to provide accurate information regarding tumor location at pathologic evaluation. To identify prognostic factors for disease-free survival (DFS) and overall survival (OS), a Cox regression analysis was performed. Results: After resection, macroscopic residual tumor was found outside the GTV in 7 patients (11%). Microscopic residual tumor was located outside the CTV in 9 patients (14%). The median follow-up was 15.6 months. With multivariate analysis, only microscopic tumor outside the CTV (hazard ratio [HR], 4.96; 95% confidence interval [CI], 1.03-15.36), and perineural growth (HR, 5.77; 95% CI, 1.27-26.13) were identified as independent prognostic factors for OS. The 1-year OS was 20% for patients with tumor outside the CTV and 86% for those without (P<.01). For DFS, microscopic tumor outside the CTV (HR, 5.92; 95% CI, 1.89-18.54) and ypN+ (HR, 3.36; 95% CI, 1.33-8.48) were identified as independent adverse prognostic factors. The 1-year DFS was 23% versus 77% for patients with or without tumor outside the CTV (P<.01). Conclusions: Microscopic tumor outside the CTV is associated with markedly worse OS after neo-CRT. This may either stress the importance of accurate tumor delineation or reflect aggressive tumor behavior requiring new adjuvant treatment modalities.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Influence of Residual Tumor Volume and Radiation Dose Coverage in Outcomes for Clival Chordoma

Purpose: The purpose of this study was to evaluate factors associated with tumor control in clival chordomas. Methods and Materials: A retrospective review of 39 patients treated with surgery and proton therapy for clival chordomas between 2004 and 2014 was performed. The median prescribed dose was 77.4 Gy (relative biological effectiveness [RBE]); range was 70.2-79.2 Gy (RBE). Minimum and median doses to gross tumor volume (GTV), radiation dose received by 1 cm{sup 3} of GTV (D1cm{sup 3}), and the equivalent uniform dose were calculated. Receiver operating characteristics curves evaluated the predictive sensitivity and specificity for local failure of potential cutpoint values for GTV and D1cm{sup 3}. Results: After a median follow-up of 51 months, the 5-year estimate of local control (LC) was 69.6% (95% confidence interval [CI] 50.0%-89.2%), and overall survival (OS) was 81.4% (95% CI: 65.3%-97.5%). Tumor histology, GTV at the time of radiation, and prescribed radiation dose were significantly associated with local control on multivariate analysis, whereas D1cm{sup 3} was associated with overall survival. Compared to those patients whose conditions remained controlled, patients experiencing tumor failure had statistically significant larger GTVs and lower D1cm{sup 3}, and prescribed and median doses to GTV. A subset of 21 patients with GTV of ≤20 cm{sup 3} and D1cm{sup 3} of >67 Gy (RBE) had a median follow-up of 47 months. The 5-year estimate of local control in this subset was 81.1% (95% CI: 61.7%-100%; P=.004, overall comparison by GTV ≤20 cm{sup 3} stratified by D1cm{sup 3}). A D1cm{sup 3} of 74.5 Gy (RBE) had 80% sensitivity for local control and 60% specificity, whereas a GTV of 9.3 cm{sup 3} had 80% sensitivity for local control and 66.7% specificity. Conclusions: Local control of clival chordomas was associated with both smaller size of residual tumor and more complete high-dose coverage of residual tumor. Multidisciplinary care should seek maximal safe surgical resection, particularly to facilitate delivery of high-dose radiation therapy in proximity to critical structures. A D1cm{sup 3} ≥74.5 Gy (RBE) represents a proposed treatment planning objective.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Climate change impact on residual contaminants under sustainable remediation

This study investigates the potential impact of climate change on residual contaminants in vadose zones and groundwater. We assume that the effect of climate changes can be represented by perturbations in the natural recharge through the aquifer system. We perform numerical modeling of unsaturated/saturated flow and transport and consider different performance metrics: contaminant concentrations at observation wells and contaminant export at the site's boundary. We evaluate the effect of increasing and decreasing recharge as well as the impact of potential failure of surface capping structures employed to immobilize vadose zone contaminants. Our approach is demonstrated in a real case study by simulating transport of non-reactive radioactive tritium at the U.S. Department of Energy's Savannah River Site. Results show that recharge changes significantly affect well concentrations: after an initial slight dilution we identify a significant concentration increase at different observation wells some years after the recharge increase and/or the cap failure, as a consequence of contaminants' mobilization. This effect is generally emphasized and occurs earlier as the recharge increases. Under decreased aquifers' recharge the concentration could slightly increase for some years, due to a decrease of dilution, depending on the magnitude of the negative recharge shift. We identify trigger levels of recharge above which the concentration/export breakthrough curves and the time of exceedance of the Maximum Contaminant Level for tritium are remarkably affected. Moreover, we observe that the contaminant export at the control plane, identified as the risk pathway to the downgradient population, may only be minimally affected by shifts in the natural recharge regime, except for some extreme cases. We conclude that more frequent sampling and in-situ monitoring near the source zone should be adopted to better explain concentrations' anomalies under changing climatic conditions. Moreover, the maintenance of the cap is critical not only to sequester residual contaminants in the vadose zone, but also to reduce the uncertainty associated with future precipitation changes. Finally, realistic flow and transport simulations achieved through proper calibration processes, rather than conservative modeling, should be adopted to identify non-trivial trade-offs which enable better allocation of resources towards reducing uncertainty in decision making.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Adaptive enriched Galerkin methods for miscible displacement problems with entropy residual stabilization

Here we present a novel approach to the simulation of miscible displacement by employing adaptive enriched Galerkin finite element methods (EG) coupled with entropy residual stabilization for transport. In particular, numerical simulations of viscous fingering instabilities in heterogeneous porous media and Hele–Shaw cells are illustrated. EG is formulated by enriching the conforming continuous Galerkin finite element method (CG) with piecewise constant functions. The method provides locally and globally conservative fluxes, which are crucial for coupled flow and transport problems. Moreover, EG has fewer degrees of freedom in comparison with discontinuous Galerkin (DG) and an efficient flow solver has been derived which allows for higher order schemes. Dynamic adaptive mesh refinement is applied in order to reduce computational costs for large-scale three dimensional applications. In addition, entropy residual based stabilization for high order EG transport systems prevents spurious oscillations. Numerical tests are presented to show the capabilities of EG applied to flow and transport.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. Here, we used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a “key in a keyhole” pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.

59 BASIC BIOLOGICAL SCIENCES↗