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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict intra-chain residue-residue distances of monomers accurately, but few methods can accurately predict inter-chain residue-residue distances of complexes. We develop a deep learning method CDPred (i.e., Complex Distance Prediction) based on the 2D attention-powered residual network to address the gap. Tested on two homodimer datasets, CDPred achieves the precision of 60.94% and 42.93% for top L/5 inter-chain contact predictions (L: length of the monomer in homodimer), respectively, substantially higher than DeepHomo’s 37.40% and 23.08% and GLINTER’s 48.09% and 36.74%. Tested on the two heterodimer datasets, the top Ls/5 inter-chain contact prediction precision (Ls: length of the shorter monomer in heterodimer) of CDPred is 47.59% and 22.87% respectively, surpassing GLINTER’s 23.24% and 13.49%. Moreover, the prediction of CDPred is complementary with that of AlphaFold2-multimer.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2022

A framework to quantify mass flow and assess food loss and waste in the US food supply chain

Abstract Reducing food loss and waste can improve the efficiency of food supply chains and provide food security. Here we estimate mass flow as well as food loss and waste along the US food supply chain for 10 commodity groups and nine management pathways to provide a baseline for designing efficient strategies to reduce, recycle, and recover food loss and waste. We estimate a total food loss and waste of 335.4 million metric tonnes from the U.S. food supply chain in 2016. Water evaporation (19%), recycling (55%), and landfill, incineration, or wastewater treatment (23%) accounted for most of the loss and waste. The consumption stage accounted for 57% of the food loss and waste disposed of through landfill, incineration, or wastewater treatment. Manufacturing was the largest contributor to food loss and waste (61%) but had a high recycling rate. High demand, perishable products accounted for 67% of food waste. We suggest that funding for infrastructure and incentives for earlier food donation can promote efficiency and sustainability of the supply chain, promote FLW collection and recycling along the U.S. FSC, and improve consumer education in order to move towards a circular economy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Rouse mode analysis of chain relaxation in polymer nanocomposites

Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, as in the case of a polymer–solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Furthermore, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Effect of chiral 2-ethylhexyl side chains on chiroptical properties of the narrow bandgap conjugated polymers PCPDTBT and PCDTPT

Two narrow bandgap conjugated polymers containing chiral 2-ethylhexyl side chains were synthesized: poly[(4,4-bis(2-ethylhexyl)cyclopenta-[2,1-b:3,4-b']dithiophene)-2,6-diyl-alt-(2,1,3-benzothiadiazole)-4,7-diyl] (PCPDTBT*) and poly[(4,4-bis(2-ethylhexyl)cyclopenta[2,1-b:3,4-b0]dithiophene)-2,6-diyl-alt-[1,2,5]-thiadiazolo[3,4-c]pyridine] (PCDTPT*). The presence of a chiral substituent provides a handle to study the geometry of interchain aggregates and/or the secondary structure of these conjugated polymers in solution and in thin films via circular dichroism (CD) spectroscopy, provided that the asymmetry in the side-chain is translated to the optically active conjugated backbone. CD signals are observed for PCPDTBT* and PCDTPT* in poor solvent systems, which indicate the presence of chiral ordering in the aggregates. PCPDTBT* shows greater chiral order than PCDTPT* based on their relative anisotropy factors. Additionally, GIWAXS analysis reveals that PCPDTBT* films are more ordered than what is observed for the same polymer containing racemic 2-ethylhexyl chains. Upon solution deposition, the chiral ordering is found to translate to the solid-state microstructure for PCPDTBT* but not PCDTPT*. The presence of a pyridyl nitrogen on the thiadiazolo[3,4-c]pyridine ring of PCDTPT* favors a planar conformation for the backbone such that it has a higher rotational barrier compared to PCPDTBT*. This larger rotational barrier appears to limit the ability of PCDTPT* to adopt a helical structure or relevant chain distortions for achieving chiral aggregates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Chain dynamics and nanoparticle motion in attractive polymer nanocomposites subjected to large deformations

The effect of large deformation on the chain dynamics in attractive polymer nanocomposites was investigated using neutron scattering techniques. Quasielastic neutron backscattering measurements reveal a substantial reduction of polymer mobility in the presence of attractive, well-dispersed nanoparticles. Additionally, large deformations are observed to cause a further slowing down of the Rouse rates at high particle loadings, where the interparticle spacings are slightly smaller than the chain dimensions, i.e. in the strongly confined state. No noticeable change, however, was observed for a lightly confined system. The reptation tube diameter, measured by neutron spin echo, remained unchanged after shear, suggesting that the level of chain-chain entanglements is not significantly affected. The shearinduced changes in the interparticle bridging reflects on the slow nanoparticle motion measured by X-ray photon correlation spectroscopy. These results provide a first step for understanding how large shear can significantly affect the segmental motion in nanocomposites and open up new opportunities for designing mechanically responsive soft materials.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Altering surface fluctuations by blending tethered and untethered chains

"Partially tethering" a thin film of a polymer melt by covalently attaching to the substrate a fraction of the chains in an unentangled melt dramatically increases the relaxation time of the surface height fluctuations. This phenomenon is observed even when the film thickness, h, is 20 times the unperturbed chain radius, R g,tethered , of the tethered chains, indicating that partial tethering is more influential than any physical attraction with the substrate. Furthermore, a partially tethered layer of a low average molecular weight of 5k showed much slower surface fluctuations than did a reference layer of pure untethered chains of much greater molecular weight (48k), so the partial tethering effect is stronger than the effects of entanglement and increase in glass transition temperature, Tg, with molecular weight. Partial tethering offers a means of tailoring these fluctuations which influence wetting, adhesion, and tribology of the surface.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Role of solvation site segmental dynamics on ion transport in ethylene-oxide based side-chain polymer electrolytes

Ion conducting capability is often imparted to polymeric materials through short polyether side-chains, and yet the impact of this graft polymer architecture on ion solvation and conduction has not been fully explored. Here, we use a combination of impedance spectroscopy, vibrational spectroscopy, and atomistic molecular dynamics (MD) to compare the conductivity, ionic interactions, and polymer dynamics in a series of graft polyether electrolytes. We find that in poly[(oligo ethylene oxide)methyl ether methacrylate] (POEM), a widely used graft polymer electrolyte, the ionic conductivity drops more than an order of magnitude as the side-chain length is decreased from nine ethylene oxide (EO) units to three. This difference in conductivity is unexplained by differences in the calorimetric glass transition temperature (T g ), which varies only slightly with side-chain length. Furthermore, through vibrational spectroscopy and MD simulations we demonstrate that both linear and graft polyethers solvate Li⁺ ions effectively and dissociate them from large counterions, irrespective of side-chain length. Li⁺ ions do, however, show preferential solvation by EO units far from the methacrylate backbone. Similarly, EO units far from the backbone show enhanced segmental dynamics, while those near the immobile methacrylate group move substantially more slowly, as quantified by bond vector autocorrelation relaxation times. This heterogeneity in both ion solvation and local segmental relaxation explains variation in ion conductivity where material-averaged properties such as T g and number of free ions fail to do so. Importantly, the ionic conductivity is dictated primarily by the segmental mobility of the EO units which form effective solvation sites, rather than system-wide dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Three-chain B{sub 6n+14} cages as possible precursors for the syntheses of boron fullerenes

Using the first principle methods, we proposed a series of three-chain boron cages B{sub 6n+14} (n = 1–12) which are mainly built by fusing three boron semi-double-rings. Their simple geometric structures (approximate D{sub 3} or C{sub 3} symmetry) facilitate their bottom-up syntheses from the hexagonal B{sub 7} and the double-chain boron clusters, such as B{sub 2}, B{sub 4}, B{sub 6}, B{sub 8}H{sub 2}, B{sub 10}H{sub 2}, B{sub 12}H{sub 2}, and the double ring B{sub 20}. The spherical shapes of these three-chain boron cages show that they could be taken as the possible precursors to further synthesize the boron fullerenes, such as B{sub 80}. Therefore, these three-chain boron cages provide a possible synthesis pathway of the boron fullerenes from the experimentally synthesized small planar boron clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Conductance and spin-filter effects of oxygen-incorporated Au, Cu, and Fe single-atom chains

We studied the spin-polarized electron transport in oxygen-incorporated Au, Cu, and Fe single-atom chains (SACs) by first-principles calculations. We first investigated the mechanism responsible for the low conductance (<1G{sub 0}) of the Au and Cu SACs in an oxygen environment reported in recent experiments. We found that for the Au SACs, the low conductance plateau around 0.6G{sub 0} can be attributed to a distorted chain doped with a single oxygen atom, while the 0.1G{sub 0} conductance comes from a linear chain incorporated with an oxygen molecule and is caused by an antibonding state formed by oxygen's occupied frontier orbital with d{sub z} orbitals of adjacent Au atoms. For the Cu SACs, the conductance about 0.3G{sub 0} is ascribed to a special configuration that contains Cu and O atoms in an alternating sequence. This exhibits an even-odd conductance oscillation with an amplitude of ∼0.1G{sub 0}. In contrast, for the alternating Fe-O SACs, conductance overall decreases with an increase in O atoms and it approaches nearly zero for the chain with more than four O atoms. While the Cu-O SACs behave as perfect spin filters for one spin channel due to the half metallic nature, the Fe-O SACs can serve as perfect spin filters for two spin channels depending on the polarity of the applied gate voltage.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Lattice model of linear telechelic polymer melts. I. Inclusion of chain semiflexibility in the lattice cluster theory

The lattice cluster theory (LCT) for the thermodynamics of polymer systems has recently been reformulated to treat strongly interacting self-assembling polymers composed of fully flexible linear telechelic chains [J. Dudowicz and K. F. Freed, J. Chem. Phys. 136, 064902 (2012)]. Here, we further extend the LCT for linear telechelic polymer melts to include a description of chain semiflexibility, which is treated by introducing a bending energy penalty whenever a pair of consecutive bonds from a single chain lies along orthogonal directions. An analytical expression for the Helmholtz free energy is derived for the model of semiflexible linear telechelic polymer melts. The extension provides a theoretical tool for investigating the influence of chain stiffness on the thermodynamics of self-assembling telechelic polymers, and for further exploring the influence of self-assembly on glass formation in such systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Plasmon-induced dynamics of H{sub 2} splitting on a silver atomic chain

Localized surface plasmon resonances (LSPR) supported in metal nanostructures can be efficiently harnessed to drive photocatalytic reactions, whose atomic scale mechanism remains a challenge. Here, real-time dynamics of H{sub 2} photosplitting on a linear silver atomic chain, upon exposure to femtosecond laser pulses, has been investigated using time-dependent density functional theory. The wavelength dependent H{sub 2} splitting process is strongly coupled to LSPR excitation in silver chain. We identify that hot electrons produced in the silver chain by plasmon excitation are transferred to the antibonding state of the adsorbed H{sub 2} and trigger H{sub 2} dissociation, consistent with experimental observations. Increasing illumination intensity and the length of atomic chain promote H{sub 2} splitting, thanks to stronger LSPR. Dynamic electronic response can be quantitatively described within the present approach, providing insights towards a complete fundamental understanding on plasmon-induced chemical reactions at the microscopic scale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Perturbation theory for multicomponent fluids based on structural properties of hard-sphere chain mixtures

An analytical expression for the Laplace transform of the radial distribution function of a mixture of hard-sphere chains of arbitrary segment size and chain length is used to rigorously formulate the first-order Barker-Henderson perturbation theory for the contribution of the segment-segment dispersive interactions into thermodynamics of the Lennard-Jones chain mixtures. Based on this approximation, a simple variant of the statistical associating fluid theory is proposed and used to predict properties of several mixtures of chains of different lengths and segment sizes. The theory treats the dispersive interactions more rigorously than the conventional theories and provides means for more accurate description of dispersive interactions in the mixtures of highly asymmetric components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains

The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M{sup β}, is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from −1.8 to −2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature T{sub g} where dynamic heterogeneity does not complicate the description of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔH{sub a} and entropy ΔS{sub a} of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a “critical” chain length, n ≈ 17. A close examination of this phenomenon indicates that a “buckling transition” from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔS{sub a} ∝ ΔH{sub a}, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔH{sub a} and ΔS{sub a} with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell. We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

A non-additive repulsive contribution in an equation of state: The development for homonuclear square well chains equation of state validated against Monte Carlo simulation

This work consists of the adaptation of a non-additive hard sphere theory inspired by Malakhov and Volkov [Polym. Sci., Ser. A 49(6), 745–756 (2007)] to a square-well chain. Using the thermodynamic perturbation theory, an additional term is proposed that describes the effect of perturbing the chain of square well spheres by a non-additive parameter. In order to validate this development, NPT Monte Carlo simulations of thermodynamic and structural properties of the non-additive square well for a pure chain and a binary mixture of chains are performed. Good agreements are observed between the compressibility factors originating from the theory and those from molecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Fast equilibration protocol for million atom systems of highly entangled linear polyethylene chains

Equilibrated systems of entangled polymer melts cannot be produced using direct brute force equilibration due to the slow reptation dynamics exhibited by high molecular weight chains. Instead, these dense systems are produced using computational techniques such as Monte Carlo-Molecular Dynamics hybrid algorithms, though the use of soft potentials has also shown promise mainly for coarse-grained polymeric systems. Through the use of soft-potentials, the melt can be equilibrated via molecular dynamics at intermediate and long length scales prior to switching to a Lennard-Jones potential. We will outline two different equilibration protocols, which use various degrees of information to produce the starting configurations. In one protocol, we use only the equilibrium bond angle, bond length, and target density during the construction of the simulation cell, where the information is obtained from available experimental data and extracted from the force field without performing any prior simulation. In the second protocol, we moreover utilize the equilibrium radial distribution function and dihedral angle distribution. This information can be obtained from experimental data or from a simulation of short unentangled chains. Both methods can be used to prepare equilibrated and highly entangled systems, but the second protocol is much more computationally efficient. These systems can be strictly monodisperse or optionally polydisperse depending on the starting chain distribution. Our protocols, which utilize a soft-core harmonic potential, will be applied for the first time to equilibrate a million particle system of polyethylene chains consisting of 1000 united atoms at various temperatures. Calculations of structural and entanglement properties demonstrate that this method can be used as an alternative towards the generation of entangled equilibrium structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗