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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Lysine Possesses the Optimal Chain Length for Histone Lysine Methyltransferase Catalysis

Histone lysine methyltransferases (KMTs) represent an important class of epigenetic enzymes that play essential roles in regulation of gene expression in humans. Members of the KMT family catalyze the transfer of the methyl group from S-adenosylmethionine (SAM) to lysine residues in histone tails and core histones. Here we report combined MALDI-TOF MS experiments, NMR analyses and quantum mechanical/molecular dynamics studies on human KMT-catalyzed methylation of the most related shorter and longer lysine analogues, namely ornithine and homolysine, in model histone peptides. Our experimental work demonstrates that while lysine is an excellent natural substrate for KMTs, ornithine and homolysine are not. This study reveals that ornithine does not undergo KMT-catalyzed methylation reactions, whereas homolysine can be methylated by representative examples of human KMTs. The results demonstrate that the specificity of KMTs is highly sensitive to the side chain length of the residue to be methylated. The origin for the degree of the observed activities of KMTs on ornithine and homolysine is discussed.

Science & Technology - Other Topics↗
DOE OSTI2019

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chain-length-controllable upcycling of polyolefins to sulfate detergents

Escalating global plastic pollution and the depletion of fossil-based resources underscore the urgent need for innovative end-of-life plastic management strategies in the context of a circular economy. Thermolysis is capable of upcycling end-of-life plastics to intermediate molecules suitable for downstream conversion to eventually high-value chemicals, but tuning the molar mass distribution of the products is challenging. Here, in this study, we report a temperature-gradient thermolysis strategy for the conversion of polyethylene and polypropylene into hydrocarbons with tunable molar mass distributions. The whole thermolysis process is catalyst- and hydrogen-free. The thermolysis of polyethylene and polyethylene/polypropylene mixtures with tailored temperature gradients generated oil with an average chain length of ~C 14 . The oil featured a high concentration of synthetically useful α-olefins. Computational fluid dynamics simulations revealed that regulating the reactor wall temperature was the key to tuning the hydrocarbon distributions. Subsequent oxidation of the obtained α-olefins by sulfuric acid and neutralization by potassium hydroxide afforded sulfate detergents with excellent foaming behaviour and emulsifying capacity and low critical micelle concentration. Overall, this work provides a viable approach to producing value-added chemicals from end-of-life plastics, improving the circularity of the anthropogenic carbon cycle.

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

Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production

Abstract Despite advances in understanding the metabolism of Pseudomonas putida KT2440, a promising bacterial host for producing valuable chemicals from plant-derived feedstocks, a strain capable of producing free fatty acid-derived chemicals has not been developed. Guided by functional genomics, we engineered P. putida to produce medium- and long-chain free fatty acids (FFAs) to titers of up to 670 mg/L. Additionally, by taking advantage of the varying substrate preferences of paralogous native fatty acyl-CoA ligases, we employed a strategy to control FFA chain length that resulted in a P. putida strain specialized in producing medium-chain FFAs. Finally, we demonstrate the production of oleochemicals in these strains by synthesizing medium-chain fatty acid methyl esters, compounds useful as biodiesel blending agents, in various media including sorghum hydrolysate at titers greater than 300 mg/L. This work paves the road to produce high-value oleochemicals and biofuels from cheap feedstocks, such as plant biomass, using this host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Sub-10 nm Gate Length Graphene Transistors: Operating at Terahertz Frequencies with Current Saturation

Radio-frequency application of graphene transistors is attracting much recent attention due to the high carrier mobility of graphene. The measured intrinsic cut-off frequency (fT) of graphene transistor generally increases with the reduced gate length (Lgate) till Lgate 5 40 nm, and the maximum measured fT has reached 300 GHz. Using ab initio quantum transport simulation, we reveal for the first time that fT of a graphene transistor still increases with the reduced Lgate when Lgate scales down to a few nm and reaches astonishing a few tens of THz. We observe a clear drain current saturation when a band gap is opened in graphene, with the maximum intrinsic voltage gain increased by a factor of 20. Our simulation strongly suggests it is possible to design a graphene transistor with an extraordinary high fT and drain current saturation by continuously shortening Lgate and opening a band gap.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Load partitioning between the bcc-iron matrix and NiAl-type precipitates in a ferritic alloy on multiple length scales

An understanding of load sharing among constituent phases aids in designing mechanical properties of multiphase materials. Here we investigate load partitioning between the body-centered-cubic iron matrix and NiAl-type precipitates in a ferritic alloy during uniaxial tensile tests at 364 and 506 C on multiple length scales by in situ neutron diffraction and crystal plasticity finite element modeling. Our findings show that the macroscopic load-transfer efficiency is not as high as that predicted by the Eshelby model; moreover, it depends on the matrix strain-hardening behavior. We explain the grain-level anisotropic load-partitioning behavior by considering the plastic anisotropy of the matrix and elastic anisotropy of precipitates. We further demonstrate that the partitioned load on NiAl-type precipitates relaxes at 506 C, most likely through thermally-activated dislocation rearrangement on the microscopic scale. Furthermore, the study contributes to further understanding of load-partitioning characteristics in multiphase materials.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication

Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer

The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral tree of life . However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. Lastly, the resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Molecular dynamics study of the effect of alkyl chain length on melting points of [CnMIM][PF6] ionic liquids

Based on molecular dynamics simulations, the melting points T-m of a series of 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids [CnMIM][PF6] with n = 2, 4, 10, 12, and 14 were studied using the free energy-based pseudosupercritical path (PSCP) method. The experimental trend that the Tm decreases with increasing alkyl chain length for ILs with short alkyl chains and increases for the ones with long alkyl chains was correctly captured. Further analysis revealed that the different trends are the results of the balance between fusion enthalpy and fusion entropy. For the ILs with short alkyl chains (ethyl and butyl groups), fusion entropy plays the dominant role so that [C4MIM][PF6], which has a larger fusion entropy due to its higher liquid phase entropy has the lower melting temperature. As for the ILs with long alkyl chains, due to the enhanced van der Waals interactions brought about by the long non-polar alkyl chains, enthalpy becomes the deciding factor and the melting points increase when the alkyl chain goes from C10 to C14. While the melting points for [C2MIM][PF6] and [C4MIM][PF6] were quantitatively predicted and the trends for the long chain ILs were captured correctly, the absolute melting points for [C10MIM][PF6], [C12MIM][PF6] and [C14MIM][PF6] were systematically overestimated in the simulations. Three possible reasons for the overestimation were studied but all ruled out. Further simulation or experimental studies are needed to explain the difference.

Zhang, Y↗
DOE OSTI2014

Length Scale of Leidenfrost Ratchet Switches Droplet Directionality

Arrays of tilted pillars with characteristic heights spanning from hundreds of nanometers to tens of micrometers were created using wafer level processing and used as Leidenfrost ratchets to control droplet directionality. Dynamic Leidenfrost droplets on the ratchets with nanoscale features were found to move in the direction of the pillar tilt while the opposite directionality was observed on the microscale ratchets. This remarkable switch in the droplet directionality can be explained by varying contributions from the two distinct mechanisms controlling droplet motion on Leidenfrost ratchets with nanoscale and microscale features. In particular, asymmetric wettability of dynamic Leidenfrost droplets upon initial impact appears to be the dominant mechanism determining their directionality on tilted nanoscale pillar arrays. By contrast, asymmetric wetting does not provide a strong enough driving force compared to the forces induced by asymmetric vapour flow on arrays of much taller tilted microscale pillars. Furthermore, asymmetric wetting plays a role only in the dynamic Leidenfrost regime, for instance when droplets repeatedly jump after their initial impact. The point of crossover between the two mechanisms coincides with the pillar heights comparable to the values of the thinnest vapor layers still capable of cushioning Leidenfrost droplets upon their initial impact. The proposed model of the length scale dependent interplay between the two mechanisms points to the previously unexplored ability to bias movement of dynamic Leidenfrost droplets and even switch their directionality.

Agapov, Rebecca L↗
DOE OSTI2016

Patterning at the 10 nanometer length scale using a strongly segregating block copolymer thin film and vapor phase infiltration of inorganic precursors

Here in this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order–disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. Lastly, we conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes.

36 MATERIALS SCIENCE↗
DOE OSTI2016

A multiple length scale description of the mechanism of elastomer stretching

Conventionally, the stretching of rubber is modeled exclusively by rotations of segments of the embedded polymer chains; i.e. changes in entropy. However models have not been tested on all relevant length scales due to a lack of appropriate probes. Here we present a universal X-ray based method for providing data on the structure of rubbers in the 2–50 Å range. First results relate to the elongation of a silicone rubber. We identify several non-entropic contributions to the free energy and describe the associated structural changes. By far the largest contribution comes from structural changes within the individual monomers, but among the contributions is also an elastic strain, acting between chains, which is 3–4 orders of magnitude smaller than the macroscopic strain, and of the opposite sign, i.e. extension of polymer chains in the direction perpendicular to the stretch. We find this may be due to trapped entanglements relaxing to positions close to the covalent crosslinks.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Low energy electron attenuation lengths in core–shell nanoparticles

Here, a velocity map imaging spectrometer is used to measure photoemission from free core–shell nanoparticles, where a salt core is coated with a liquid hydrocarbon shell (i.e. squalane). By varying the radial thickness of the hydrocarbon shell, electron attenuation lengths (EALs) are determined by measuring the decay in photoemission intensity from the salt core. In squalane, electrons with kinetic energy (KE) above 2 eV are found to have EALs of 3–5 nm, whereas electrons with smaller KE (<2 eV) have significantly larger EALs of >15 nm. These results (in the context of other energy-resolved EAL measurements) suggest that the energy dependent behavior of low energy electrons is similar in dielectrics when KE > 2 eV. At this energy the EALs do not appear to exhibit strong energy dependence. However, at very low KE (<2 eV), the EALs diverge and appear to be extremely material dependent.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Effect of processing and end groups on the crystal structure of polypeptoids studied by cryogenic electron microscopy at atomic length scales

Cryogenic electron microscopy at atomic length scales was used to study the structure of self-assembled crystalline nanosheets obtained from a series of polypeptoids with the same chain architecture but with different end groups. While long-range order is enhanced by slowing down the self-assembly process, the dominant crystalline motif was found to be a sensitive function of both processing details and end group chemistry. In some cases, adjacent rows of polypeptoid molecules adopt anti-parallel V-shaped side chain conformations. In other cases, adjacent rows of polypeptoid molecules adopt parallel V-shaped side chain conformations. Interestingly, the unit cell is rectangular in both cases with dimensions a = 4.5 Å and c = 50 Å. In all cases, long-range order, quantified by the average number of concatenated unit cells of the same type, is more prevalent along the a direction.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Dispersing nano- and micro-sized portlandite particulates via electrosteric exclusion at short screening lengths

In spite of their high surface charge (zeta potential ζ = +34 mV), aqueous suspensions of portlandite (calcium hydroxide: Ca(OH) 2 ) exhibit a strong tendency to aggregate, and thereby present unstable suspensions. While a variety of commercial dispersants seek to modify the suspension stability and rheology (e.g., yield stress, viscosity), it remains unclear how the performance of electrostatically and/or electrosterically based additives is affected in aqueous environments having either a high ionic strength and/or a pH close to the particle's isoelectric point (IEP). We show that the high native ionic strength (pH ≈ 12.6, IEP: pH ≈ 13) of saturated portlandite suspensions strongly screens electrostatic forces (Debye length: κ -1 = 1.2 nm). As a result, coulombic repulsion alone is insufficient to mitigate particle aggregation and affect rheology. However, a longer-range geometrical particle–particle exclusion that arises from electrosteric hindrance caused by the introduction of comb polyelectrolyte dispersants is very effective at altering the rheological properties and fractal structuring of suspensions. As a result, comb-like dispersants that stretch into the solvent reduce the suspension's yield stress by 5× at similar levels of adsorption as compared to linear dispersants, thus enhancing the critical solid loading (i.e., at which jamming occurs) by 1.4×. Significantly, the behavior of diverse dispersants is found to be inherently related to the thickness of the adsorbed polymer layer on particle surfaces. These outcomes inform the design of dispersants for concentrated suspensions that present strong charge screening behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Ion diffusion coefficients in poly(3-alkylthiophenes) for energy conversion and biosensing: role of side-chain length and microstructure

Conductive polymers are promising materials as active elements for energy storage and conversion devices due to mixed ion–electron conduction. The ion diffusion coefficient is a relative measure of the efficacy of ion transport, allowing for comparison between materials and electrochemical conditions. In this work, diffusion coefficients of hexafluorophosphate (PF6–) counterions in poly(3-alkylthiophene) (P3AT) materials are measured as a function of both side-chain length and microstructure using electrochemical impedance spectroscopy (EIS). For semi-crystalline films, the diffusion coefficient is found to be anomalous and nearly independent of applied electrochemical potential. Here, the anomalous behavior of diffusion indicates that spin casting yields compact films with an enthalpic barrier to ion transport, attributed to ionic trapping. Diffusion coefficient values ~10 –11 cm 2 s –1 were measured for all films, indicating interchain spacing, in the absence of strong intermolecular interactions with the electrolyte, is not a viable design strategy to control ion transport. For the prototypical system of poly(3-hexylthiophene), we observe almost no potential dependence in ion transport for regioregular and regiorandom films of comparable molecular weight, with both exhibiting anomalous diffusion. Alternatively, changing the microstructure of poly(3-hexylthiophene) to a mostly amorphous, ion-imprinted structure yields ~500× increase in the diffusion coefficient to ~2 × 10 –8 cm 2 s –1 at 0.8 V vs. Ag/Ag + with behavior closer to ordinary diffusion. Collectively, these results indicate new insight into ion transport in conductive polymers, where ionic trapping effects can be mitigated through electrodeposition protocols over post-synthesis processing (i.e. spin coating).

14 SOLAR ENERGY↗
DOE OSTI2021

Enhanced medium chain length-polyhydroxyalkanoate production by co-fermentation of lignin and holocellulose hydrolysates

Biological lignin conversion to medium chain length-polyhydroxyalkanoates (mcl-PHA) has recently emerged as an attractive alternative to petroleum-based plastics due to the renewable nature of lignin and the value-added applications of mcl-PHA. Previous reports suggested that addition of limited glucose can improve mcl-PHA accumulation in Pseudomonas putida KT2440 grown in lignin substrates. Herein, we propose a biorefinery process to systematically release lignin and sugars from lignocellulosic biomass and evaluate the potential of co-utilization of all biomass components for conversion to mcl-PHA. Our results indicate that a sequential treatment composed of acid pretreatment, enzymatic hydrolysis and alkaline treatment produces a suitable lignin stream for mcl-PHA production in engineered P. putida. In addition, the PHA titer could be increased by 71% when the lignin stream (AH) was combined with the enzymatic hydrolysate (EH) at a ratio of 75 : 25. Higher ratios of EH : AH negatively affect mcl-PHA accumulation as well as mixtures with sugars from the acid hydrolysate. The optimization of the fermentation conditions, including the inoculum (OD 600 ) and substrate (soluble solid content (SSC)), was carried out by a central composite design. The optimal conditions were achieved at OD 600 = 2.17 and SSC = 68.28 g L –1 . Under these conditions, the titer increased 4.3 fold, achieving a mcl-PHA production of 1.38 g L –1 . Lignin characterization before and after fermentation by nuclear magnetic resonance and gas chromatography showed that p-coumarates were mainly consumed during the fermentation for mcl-PHA production. Overall, this biorefinery strategy allowed us to increase mcl-PHA production by utilizing the different lignocellulosic fractions. Unlike previous studies, no model substrates were utilized at any stage of the fermentation process, representing a step forward towards process feasibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗