Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular assembly”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Releasing chemical energy in spatiallyprogrammed ferroelectrics

Chemical energy ferroelectrics are generally solid macromolecules showing spontaneous polarization and chemical bonding energy. These materials still suffer drawbacks, including the limited control of energy release rate, and thermal decomposition energy well below total chemical energy. To overcome these drawbacks, we report the integrated molecular ferroelectric and energetic material from machine learning-directed additive manufacturing coupled with the ice-templating assembly. The resultant aligned porous architecture shows a low density of 0.35 g cm -3 , polarization-controlled energy release, and an anisotropic thermal conductivity ratio of 15. Thermal analysis suggests that the chlorine radicals react with macromolecules enabling a large exothermic enthalpy of reaction (6180 kJ kg -1 ). In addition, the estimated detonation velocity of molecular ferroelectrics can be tuned from 6.69 ± 0.21 to 7.79 ± 0.25 km s -1 by switching the polarization state. These results provide a pathway toward spatially programmed energetic ferroelectrics for controlled energy release rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A Structural Perspective on the Alphavirus Life Cycle

Alphaviruses are mosquito-borne, enveloped viruses with a positive-sense, single-stranded RNA genome. Alphaviruses enter host cells via receptor-mediated endocytosis, using various cellular surface receptors such as matrix remodeling-associated protein 8 (MXRA8), low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3), and very low-density lipoprotein receptor (VLDLR), which facilitate binding to the viral glycoproteins. Following entry, viral proteins are expressed and nonstructural proteins assemble into replication complexes in host cells, driving RNA synthesis and genome replication. Viral assembly occurs at the plasma membrane, where nascent virions bud from the host cell in a process driven by capsid and spike proteins. Recent combinatorial structural studies have provided detailed molecular insights into various steps of the alphavirus life cycle. These structural insights into the alphavirus life cycle enhance our understanding of viral replication and assembly, with significant implications for antiviral strategies and the development of alphavirus-based vaccine vectors.

RNA virus↗
DOE OSTI2024

Interfacial Electrochemistry of Catalyst-Coordinated Graphene Nanoribbons

The immobilization of molecular electrocatalysts on conductive electrodes is an appealing strategy for enhancing their overall activity relative to those of analogous molecular compounds. Here, in this study, we report on the interfacial electrochemistry of self-assembled two-dimensional nanosheets of graphene nanoribbons (GNR-2DNS) and analogs containing a Rh-based hydrogen evolution reaction (HER) catalyst (RhGNR-2DNS) immobilized on conductive electrodes. Proton-coupled electron transfer (PCET) taking place at N-centers of the nanoribbons was utilized as an indirect reporter of the interfacial electric fields experienced by the monolayer nanosheet located within the electric double layer. The experimental Pourbaix diagrams were compared with a theoretical model, which derives the experimental Pourbaix slopes as a function of parameter f, a fraction of the interfacial potential drop experienced by the redox-active group. Interestingly, our study revealed that GNR-2DNS was strongly coupled to glassy carbon electrodes (f = 1), while RhGNR-2DNS was not (f = 0.15). We further investigated the HER mechanism by RhGNR-2DNS using electrochemical and X-ray absorption spectroelectrochemical methods and compared it to homogeneous molecular model compounds. RhGNR-2DNS was found to be an active HER electrocatalyst over a broader set of aqueous pH conditions than its molecular analogs. We find that the improved HER performance in the immobilized catalyst arises due to two factors. First, redox-active bipyrimidine-based ligands were shown to dramatically alter the activity of Rh sites by increasing the electron density at the active Rh center and providing RhGNR-2DNS with improved catalysis. Second, catalyst immobilization was found to prevent catalyst aggregation that was found to occur for the molecular analog in the basic pH. Overall, this study provides valuable insights into the mechanism by which catalyst immobilization can affect the overall electrocatalytic performance.

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

FiXR : a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Ab initio reconstruction methods have revolutionized the capabilities of small-angle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. In this work, it is proposed to use SAXS measurements, together with diffraction theory, to infer the electron distribution of the average cross-section of a fiber. This cross-section is modeled as a discrete electron density with continuous support, allowing representations beyond binary distributions. Additional constraints, such as non-negativity or smoothness/connectedness, can also be added to the framework. The proposed approach is tested using simulated SAXS data from amyloid β fibril models and using measured data of Tobacco mosaic virus from SAXS experiments, recovering the geometry and density of the cross-sections in all cases. The approach is further tested by analyzing SAXS data from different amyloid β fibril assemblies, with results that are in agreement with previously proposed models from cryo-EM measurements. The limitations of the proposed method, together with an analysis of the robustness of the method and the combination with different experimental sources, are also discussed.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Sampling Rare Events in Aqueous Systems Using Molecular Simulations

Birth of a new distinct phase is a phenomenon encountered in a myriad of processes, and has wide ranging consequences in material processing, biological self-assembly, separations and several other processes. Several phase transitions are nucleation driven. The nucleation events occur over nanosecond timescales and involve hundreds to thousands of molecules. These length and timescales are difficult to access in experiments, thereby making experimental studies of nucleation challenging. On the other hand, molecular simulations sample the nanosecond and nanometer scales making them ideal to study nucleation. However, nucleation is a rare event, meaning that the waiting time to observe one nucleation event is significant. This makes simulation studies of rare events challenging. The project focused on a multi-pronged approach to address such challenges to develop the next generation rare event sampling methods for molecular simulations. The key outcomes of our work include developing more effective methods for sampling rare events, utilizing machine learning to better elucidate nucleation mechanisms, development of software for easy implementation of the methodologies, and applications of the methods to realistic systems to push the method applicability beyond model systems. Overall, this work has enabled pushing the frontiers of molecular simulations to study rare events with a focus on nucleation in aqueous solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Symmetry-breaking in double gyroid block copolymer films by non-affine distortion

Soft-matter bicontinuous networks find a double gyroid structure from block copolymer (BCP) self-assembly. A gyroid structure composed of dissimilar blocks has proven its potential as a soft crystal capable of tuning structural periodicity and symmetry, of which the lattice dimension is variable with molecular weight of the polymer. Using an asymmetric polystyrene- b -poly(methyl methacrylate) (PS- b -PMMA), in this study we show that the self-assembled gyroid films formed via a solvent vapor annealing (SVA) process undergo unique structural distortion due to directional deformation immediately upon deswelling. During the SVA process with PS- b -PMMA films, transient cylinders developed from the as-cast morphology transform into a cubic gyroid structure in a swollen state. Rapid and spontaneous deswelling processes -the manners in which the films contract along the z-direction while retaining an enlarged lateral dimension of the cubic form -lead to triclinic gyroid structures with z-directional contraction ratios ( C z ) of 2.5 and 2.0, respectively. Our X-ray analysis reveals that the deswelling process of the swollen gyroid films produces a notable symmetry-breaking in non-affine gyroid structure that elicits several forbidden reflections such as {110} and {200} reflections. For further characterization of the symmetry-breaking, we delineate the structural features of noncubic gyroid films by computing electron-density difference maps assisted with X-ray measurements. Level-set approach is accordingly developed to quantitate the structural characteristics of the maps in terms of inversion symmetry-breaking, suggesting its possible application to optical Weyl photonic crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A Fluorinated Lewis Acidic Organoboron Tunes Polysulfide Complex Structure for High–Performance Lithium–Sulfur Batteries

Many challenges in lithium-sulfur (Li–S) batteries are associated with the radical change in lithium polysulfide (LPS) solubility during cycling, but chemical approaches to address such inconsistency are still lacking. Here, the use of a strong Lewis acidic fluorinated organoboron, tri(2,2,2-trifluoroethyl) borate (TFEB), is reported as a multi-functional mediator to simultaneously overcome multiple technical barriers in practical Li–S batteries. TFEB acts as an anion acceptor and forms strong molecular complexes with Lewis basic LPS. The TFEB-LPS complexes have consistent solubility across the full polysulfide spectrum and deliver several times improved better redox kinetics, unlocking a true redox catalytic mechanism that covers the majority of redox events in thick sulfur cathodes. As a result, Li–S batteries evaluated under practical conditions exhibit significantly improved discharge capacity, rate capability, and cycling stability with the addition of the TFEB additive. More importantly, TFEB also contributes to the stabilization of lithium anode in the presence of polysulfides by generating strong interfacial film. These attributes significantly improve the cycling stability of practical Li–S pouch cells, which are assembled with a unit energy density of 219 Wh kg –1 . Finally, the results provide new molecular insights on the design of unlocking solvation networks of practical Li–S systems.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Peeling back the layers: Investigating the effects of polyelectrolyte layering on surface structure and stability of oil-in-water nanoemulsions

Layer-by-layer deposition of polyelectrolytes is a useful technique for modifying surface functionalities. For drug delivery systems, alternating layers of biopolymers coat nanoemulsions, which house and protect the cargo until the time and destination of delivery. In this report we investigate molecular factors contributing to the stability and interfacial properties of nanoemulsions prepared by a co-adsorption of polymers poly(styrene sulfonate) and polyethylenimine (PEI), and surfactant dodecyltrimethylammonium bromide. We hypothesize the interplay between electrosteric and hydrophobic effects upon multi-polymer co-adsorption contributes to both macroscopic and molecular-level interfacial properties of nanoemulsions. To probe interfacial layering properties, we use vibrational sum frequency scattering spectroscopy with ζ -potential measurements to determine the adsorptive behavior and molecular conformational arrangement of the polymer layers. Complementing these interfacial studies are dynamic light scattering experiments measuring the nanoemulsion size distribution and polydispersity index over a 30-day period. Our light scattering, ζ -potential, and spectroscopic results of the nanoemulsion surface show that the duration of droplet stability and the degree of molecular orientation of adsorbed polymers can be tuned by surfactant concentration, PEI concentration, and pH. These results illustrate how molecular surface properties of multi-polymer coated nanoemulsions contribute to synergistic effects and droplet stability, enabling advancements in applications surrounding biopharmaceuticals, cosmetics, and food sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Photoinduced Carrier Generation and Distribution in Solution-Deposited Titanyl Phthalocyanine Monolayers

We prepared titanyl phthalocyanine (TiOPc) monolayers on sapphire-prism supported Au{111} substrates through solution deposition and characterized their photoresponses using a custom-built laser-assisted scanning tunneling microscope under ambient conditions. Two types of lattice structures (hexagonal and rectangular) were observed, and the distributions of photoinduced charges were measured under evanescently introduced 633 and 780 nm laser illumination. The distributions of photoexcited electrons in molecules in hexagonal lattices match theoretically calculated charge density changes in TiOPc molecules upon excitation. However, the photoresponses of TiOPc molecules in rectangular lattices are different than those predicted and TiOPc molecules in these arrangements may have lower excitation probabilities at 633 and 780 nm. Our results suggest that the photocarrier generation efficiency of TiOPc molecules is related to their packing arrangements in monolayers and local environments. The growth mechanisms of the monolayers and their connections to different polymorphs of TiOPc are worth to be further explored so that the photogenerated electronic property changes that we observed at the molecular level can provide more accurate guidance to the application of TiOPc crystals and assemblies.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Characterizing Absolute Orientations in DNA Self-Assembly of Single Molecules

DNA self-assembly of single molecules (i.e., dyes) with deterministic orientations is a powerful approach for engineering mo-lecular excitons. However, current determination methods of the dye orientation relative to DNA do not account for the orien-tation of the dye plane, which is a missing degree of freedom needed to define absolute three-dimensional orientations. In this work, we combine fluorescence-detected linear dichroism, defocused dipole imaging, and DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy to determine the absolute three-dimensional orientations of single Cy5 dyes relative to host DNA duplexes which includes the dye plane orientation. The data revealed that the absorption and emission dipoles are perpendicular to the DNA duplex, and the mean dye plane is parallel to the DNA bases, which supports the notion that Cy5 dyes intercalate between DNA base pairs. The presented methodology will inspire the investigation of the dye plane orientation for controlling dye arrangement configurations beyond spontaneous π-stacking between dyes as well as achieving novel dye-DNA arrangements.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Nickel(ii) complexes based on dithiolate–polyamine binary ligand systems: crystal structures, hirshfeld surface analysis, theoretical study, and catalytic activity study on photocatalytic hydrogen generation

To ascertain the influence of binary ligand systems [1,1-dicyanoethylene-2,2-dithiolate (i-mnt -2 ) and polyamine {tetraen = tris(2-aminoethyl)amine, tren = diethylene triamine and opda = o-phenylenediamine}] on the coordination modes of the Ni(II) metal center and resulting supramolecular architectures, a series of nickel(II) thiolate complexes [Ni(tetraen)(i-mnt)](DMSO) (1), [Ni 2 (tren) 2 (i-mnt) 2 ] (2), and [Ni 2 (i-mnt) 2 (opda) 2 ] n (3) have been synthesized in high yield in one step in water and structurally characterized by single crystal X-ray crystallography and spectroscopic techniques. X-ray diffraction studies disclose the diverse i-mnt -2 coordination to the Ni +2 center in the presence of active polyamine ligands, forming a slightly distorted octahedral geometry (NiN 4 S 2 ) in 1, square planar (NiS 4 ) and distorted octahedral geometries (NiN 6 ) in the bimetallic co-crystallized aggregate of cationic [Ni(tren) 2 ] +2 and anionic [Ni(i-mnt) 2 ] -2 in 2, and a one dimensional (1D) polymeric chain along the [100] axis in 3, having consecutive square planar (NiS 4 ) and octahedral (NiN 6 ) coordination kernels. The N–H···O, N–H···S, N–H···N, N–H···S, N–H···N, and N–H···O type hydrogen bonds stabilize the supramolecular assemblies in 1, 2, and 3 respectively imparting interesting graph-set-motifs. The molecular Hirshfeld surface analyses (HS) and 2D fingerprint plots were utilized for decoding all types of non-covalent contacts in the crystal networks. Atomic HS analysis of the Ni +2 centers reveals significant Ni–N metal–ligand interactions compared to Ni–S interactions. We have also studied the unorthodox interactions observed in the solid state structures of 1–3 by QTAIM and NBO analyses. Moreover, all the complexes proved to be highly active water reduction co-catalysts (WRC) in a photo-catalytic hydrogen evolution process involving iridium photosensitizers, wherein 2 and 3 having a square planar arrangement around the nickel center(s) – were found to be the most active ones, achieving 1000 and 1119 turnover numbers (TON), respectively.

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

Structural elucidation of polydopamine facilitated by ionic liquid solvation

Minimal understanding of the formation mechanism and structure of polydopamine (pDA) and its natural analogue, eumelanin, impedes the practical application of these versatile polymers and limits our knowledge of the origin of melanoma. The lack of conclusive structural evidence stems from the insolubility of these materials, which has spawned significantly diverse suggestions of pDA's structure in the literature. We discovered that pDA is soluble in certain ionic liquids. Using these ionic liquids (ILs) as solvents, we present an experimental methodology to solvate pDA, enabling us to identify pDA's chemical structure. The resolved pDA structure consists of self-assembled supramolecular aggregates that contribute to the increasing complexity of the polymer. The underlying molecular energetics of pDA solvation and a macroscopic picture of the disruption of the aggregates using IL solvents have been investigated, along with studies of the aggregation mechanism in water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Stable White Organic Light-emitting Diodes Enabled by New Materials with Reduced Excited State Lifetime (Final Report)

The Georgia Institute of Technology assembled a multidisciplinary team with complementary expertise in the areas of multi-level molecular simulations (Brédas), chemical synthesis and material characterization (Marder), and device physics and engineering (Kippelen). The team engaged in a two-year integrated theoretical and experimental program to develop blue-emissive layers that can yield simultaneously near 100% internal quantum efficiency (IQE) and short excited-state lifetimes to overcome the existing efficiency vs. stability tradeoff displayed by blue-emitting OLEDs and by WOLEDs, and to demonstrate stable WOLEDs that fulfill or exceed the 2020 target metrics (RDP 2016 section C.1.2) ahead of schedule. In this program, we investigated two general approaches involving the development of wide-bandgap ambipolar hosts with a low ΔEST. Ambipolar host achieved by intermolecular through-space D:A interactions and by intramolecular through-bond interactions between covalently linked D and A segments. Novel hosts were incorporated in to blue-emissive layers (EML) by combining them with suitable fluorescent guest emitters having high quantum yields of emission (Φem) to demonstrate blue-emitting OLEDs with high EQE and low roll-off. This final report describes the most important results achieved during this program

36 MATERIALS SCIENCE↗
DOE OSTI2022

Hierarchical, Self-Assembled Metasurfaces via Exposure-Controlled Reflow of Block Copolymer-Derived Nanopatterns

Here, nanopatterning for the fabrication of optical metasurfaces entails a need for high-resolution approaches like electron beam lithography that cannot be readily scaled beyond prototyping demonstrations. Block copolymer thin film self-assembly offers an attractive alternative for producing periodic nanopatterns across large areas, yet the pattern feature sizes are fixed by the polymer molecular weight and composition. Here, a general strategy is reported that overcomes the limitation of fixed feature size by treating the copolymer thin film as a hierarchical resist, in which the nanoscale pattern motif is defined by self-assembly. Feature sizes can then be tuned by thermal reflow controlled locally by irradiative crosslinking or chemical alteration using lithographic ultraviolet light or electron beam exposure. Using blends of polystyrene-block-poly(methylmethacrylate) (PS-b-PMMA) with PS and PMMA homopolymer, we demonstrate both self-assembled PS grating and hexagonal hole patterns; exposure-controlled reflow is then used to reduce hole diameter by as much as 50% or increase PS grating linewidth by more than 180%. Transferring these nanopatterns, or their inverse obtained by a lift-off approach, into silicon yields structural colors that may be prescriptively controlled based on nanoscale feature size. Furthermore, patterned exposure enables area-selective feature size control, yielding uniform structural color patterns across centimeter square areas. Electron beam lithography is also used to show that the lithographic resolution of this selective-area control can be extended to the nanoscale dimensions of the self-assembled features. The exposure-controlled reflow approach demonstrated here takes a pivotal step towards fabricating complex, hierarchical optical metasurfaces using scalable self-assembly methods.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Auxetic Two-Dimensional Nanostructures from DNA

Architectured materials exhibit negative Poisson's ratios and enhanced mechanical properties compared with regular materials. Their auxetic behaviors emerge from periodic cellular structures regardless of the materials used. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. There are also molecular auxetics including natural crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by biomolecular self-assembly. In this work, we demonstrate two-dimensional auxetic nanostructures using DNA origami. Structural reconfigurations are performed by two-step DNA reactions and complemented by mechanical deformation studies using molecular dynamics simulations. We find that the auxetic behaviors are mostly defined by geometrical designs, yet the properties of the materials also play an important role. From elasticity theory, we introduce design principles for auxetic DNA metamaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Using metacommunity ecology to understand environmental metabolomes

Abstract Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.

54 ENVIRONMENTAL SCIENCES↗