Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “chain conformation”

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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Cholesterol modulates membrane elasticity via unified biophysical laws

Cholesterol and lipid unsaturation underlie a balance of opposing forces that features prominently in adaptive cell responses to diet and environmental cues. These competing factors have resulted in contradictory observations of membrane elasticity across different measurement scales, requiring chemical specificity to explain incompatible structural and elastic effects. Here, we demonstrate that – unlike macroscopic observations – lipid membranes exhibit a unified elastic behavior in the mesoscopic regime between molecular and macroscopic dimensions. Using nuclear spin techniques and computational analysis, we find that mesoscopic bending moduli follow a universal dependence on the lipid packing density regardless of cholesterol content, lipid unsaturation, or temperature. Our observations reveal that compositional complexity can be explained by simple biophysical laws that directly map membrane elasticity to molecular packing associated with biological function, curvature transformations, and protein interactions. The obtained scaling laws closely align with theoretical predictions based on conformational chain entropy and elastic stress fields. These findings provide unique insights into the membrane design rules optimized by nature and unlock predictive capabilities for guiding the functional performance of lipid-based materials in synthetic biology and real-world applications.

Kumarage, Teshani [Virginia Polytechnic Inst. and ↗
DOE OSTI2023

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

Abstract Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these predictions vary, however, and they do not take into account ligands, covalent modifications or other environmental factors. Here, we evaluate how well AlphaFold predictions can be expected to describe the structure of a protein by comparing predictions directly with experimental crystallographic maps. In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses. We further suggest that it is important to consider the confidence in prediction when interpreting AlphaFold predictions and to carry out experimental structure determination to verify structural details, particularly those that involve interactions not included in the prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Non-covalent planarizing interactions yield highly ordered and thermotropic liquid crystalline conjugated polymers

Controlling the multi-level assembly and morphological properties of conjugated polymers through structural manipulation has contributed significantly to the advancement of organic electronics. In this work, a redox active conjugated polymer, TPT–TT, composed of alternating 1,4-(2-thienyl)-2,5-dialkoxyphenylene (TPT) and thienothiophene (TT) units is reported with non-covalent intramolecular S⋯O and S⋯H–C interactions that induce controlled main-chain planarity and solid-state order. As confirmed by density functional theory (DFT) calculations, these intramolecular interactions influence the main chain conformation, promoting backbone planarization, while still allowing dihedral rotations at higher kinetic energies (higher temperature), and give rise to temperature-dependent aggregation properties. Thermotropic liquid crystalline (LC) behavior is confirmed by cross-polarized optical microscopy (CPOM) and closely correlated with multiple thermal transitions observed by differential scanning calorimetry (DSC). This LC behavior allows us to develop and utilize a thermal annealing treatment that results in thin films with notable long-range order, as shown by grazing-incidence X-ray diffraction (GIXD). Specifically, we identified a first LC phase, ranging from 218 °C to 107 °C, as a nematic phase featuring preferential face-on π–π stacking and edge-on lamellar stacking exhibiting a large extent of disorder and broad orientation distribution. A second LC phase is observed from 107 °C to 48 °C, as a smectic A phase featuring sharp, highly ordered out-of-plane lamellar stacking features and sharp tilted backbone stacking peaks, while the structure of a third LC phase with a transition at 48 °C remains unclear, but resembles that of the solid state at ambient temperature. Furthermore, the significance of thermal annealing is evident in the ∼3-fold enhancement of the electrical conductivity of ferric tosylate-doped annealed films reaching 55 S cm −1 . More importantly, thermally annealed TPT–TT films exhibit both a narrow distribution of charge-carrier mobilities (1.4 ± 0.1) × 10 −2 cm 2 V −1 s −1 along with a remarkable device yield of 100% in an organic field-effect transistor (OFET) configuration. This molecular design approach to obtain highly ordered conjugated polymers in the solid state affords a deeper understanding of how intramolecular interactions and repeat-unit symmetry impact liquid crystallinity, solution aggregation, solution to solid-state transformation, solid-state morphology, and ultimately device applications.

Chemistry↗
DOE OSTI2024

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL . Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

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

High-temperature low-humidity proton exchange membrane with “stream-reservoir” ionic channels for high-power-density fuel cells

The perfluorosulfonic acid (PFSA) proton exchange membrane (PEM) is the key component for hydrogen fuel cells (FCs). We used in situ synchrotron scattering to investigate the PEM morphology evolution and found a “stream-reservoir” morphology, which enables efficient proton transport. The short-side-chain (SSC) PFSA PEM is fabricated under the guidance of morphology optimization, which delivered a proton conductivity of 193 milliSiemens per centimeter [95% relativity humidity (RH)] and 40 milliSiemens per centimeter (40% RH) at 80°C. The improved glass transition temperature, water permeability, and mechanical strength enable high-temperature low-humidity FC applications. Performance improvement by 82.3% at 110°C and 25% RH is obtained for SSC-PFSA PEM FCs compared to Nafion polymer PEM devices. The insights in chain conformation, packing mechanism, crystallization, and phase separation of PFSAs build up the structure-property relationship. In addition, SSC-PFSA PEM is ideal for high-temperature low-humidity FCs that are needed urgently for high-power-density and heavy-duty applications.

25 ENERGY STORAGE↗
DOE OSTI2023

Understanding the Structure and Dynamics of Conjugated Polymers by Advancing Deuteration Chemistry and Neutron Scattering (Final Report)

The overarching goal of the proposed work was to set up a partnership between the University of Southern Mississippi (USM) and Oak Ridge National Laboratory (ORNL) to develop novel approaches to measure the backbone rigidity of conjugated polymers (CPs) and understand the critical role of sidechains on the backbone conformation and the materials macroscopic property. The backbone rigidity greatly influences the electronic properties of CPs, which ultimately determines the functionality and performance of these materials. Improvements in the electronic properties of CPs would allow for enhanced charge transport in semiconductor devices, improved photovoltaic performance, recycling of waste heat in thermoelectrics, and discovery of new phenomena that will enable the next generation of energy technologies. Although significant progress has been made to optimize the optical and electronic properties of CPs, largely through Edisonian methodologies, it remains a challenge to experimentally characterize conjugated backbone conformation (chain rigidity, torsion, planarity, and short-range order) and relate these to the fundamental optical and electronic properties (electronic coupling, charge transport, etc.). This has left fundamental gaps in our knowledge of the most basic structure/property relationships within these systems, precluded the study of fundamental physical phenomena, and constrained the design and realization of new electronic and device functionalities. Thus, the major goal of this work is to use novel deuteration methodologies via systematic synthetic approaches, and neutron scattering techniques to comprehensively characterize the structural and dynamic properties of CPs in contrast-matching solvents. Our work would, for the first time, elucidate the relationship between backbone rigidity and macroscopic properties. They will also allow a rational formulation of design principles for next-generation CPs that are resilient to disorder through precise control of the delocalized electrons along the polymer backbone. Overall, this project will advance our understanding of the structure, dynamics, and fundamental physics of these materials, which is crucial for enabling the prediction, design, control, and manipulation of current and emerging material electronic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Data Mining of Polymer Phase Transitions upon Temperature Changes by Small and Wide-Angle X-ray Scattering Combined with Raman Spectroscopy

The complex physical transformations of polymers upon external thermodynamic changes are related to the molecular length of the polymer and its associated multifaceted energetic balance. The understanding of subtle transitions or multistep phase transformation requires real-time phenomenological studies using a multi-technique approach that covers several length-scales and chemical states. A combination of X-ray scattering techniques with Raman spectroscopy and Differential Scanning Calorimetry was conducted to correlate the structural changes from the conformational chain to the polymer crystal and mesoscale organization. Current research applications and the experimental combination of Raman spectroscopy with simultaneous SAXS/WAXS measurements coupled to a DSC is discussed. In particular, we show that in order to obtain the maximum benefit from simultaneously obtained high-quality data sets from different techniques, one should look beyond traditional analysis techniques and instead apply multivariate analysis. Data mining strategies can be applied to develop methods to control polymer processing in an industrial context. Crystallization studies of a PVDF blend with a fluoroelastomer, known to feature complex phase transitions, were used to validate the combined approach and further analyzed by MVA.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

TPSAS-NF1676L-34417-DND

A boron nitride nanotube (BNNT), an electrically-insulating counterpart of a carbon nanotube (CNT), is a great nanofiller candidate for ferroelectric polymeric nanocomposites due to BNNT?s exceptional properties in piezoelectricity, thermal stability, mechanical strength, and radiation shielding capability. Fast and high-yield polar crystallization of polyvinylidene fluoride (PVDF) was accomplished by incorporating BNNTs as a nucleating agent. As-fabricated BNNT-PVDF nanocomposites were characterized by Fourier-transform infrared spectroscopy (FTIR), wide-angle X-ray diffraction (XRD), and differential scanning calorimetry (DSC) to identify and quantify chain conformations. Besides, piezoelectric constants, d33 of BNNT-PVDF nanocomposites were measured and compared with that of a mechanically drawn beta phase polar PVDF. The polar transformation due to BNNT incorporation has a great advantage over conventional beta or gamma transformation methods that require (1) mechanical drawing often resulting in defects or (2) high-temperature annealing for an extended time. In addition to the fast polar crystallization, BNNTs had a role of reinforcement of the polymer matrix. The improved Young?s modulus and electromechanical coupling coefficient of BNNT-PVDF nanocomposites indicated potential applications in energy harvesting under harsh environments such as large deformation, wide temperature cycles, and high radiation.

Dongwon Lee↗
DOE OSTI2023

Anti-polyelectrolyte and polyelectrolyte effects on conformations of polyzwitterionic chains in dilute aqueous solutions

Abstract Polyzwitterions (PZs) are considered as model synthetic analogs of intrinsically disordered proteins. Based on this analogy, PZs in dilute aqueous solutions are expected to attain either globular (i.e. molten, compact) or random coil conformations. Addition of salt is expected to open these conformations. To the best of our knowledge, these hypotheses about conformations of PZs have never been verified. In this study, we test these hypotheses by studying effects of added salt [potassium bromide (KBr)] on gyration and hydrodynamic radii of poly(sulfobetaine methacrylate) in dilute aqueous solutions using dynamic light scattering and small-angle X-ray scattering, respectively. Effects of zwitteration are revealed by direct comparisons of the PZs with the polymers of the same backbone but containing (1) no explicit charges on side groups such as poly(2-dimethylaminoethyl methacrylate)s and (2) explicit cationic side groups with tertiary amino bromide pendants. Zeta-potential measurements, transmission electron microscopy, and ab initio molecular dynamics simulations reveal that the PZs acquire net positive charge in near salt-free conditions due to protonation but retain coiled conformations. Added KBr leads to nonmonotonic changes exhibiting an increase followed by a decrease in radius of gyration (and hydrodynamic radius), which are called antipolyelectrolyte and polyelectrolyte effects, respectively. Charge regulation and screening of charge–charge interactions are discussed in relation to the antipolyelectrolyte and polyelectrolyte effects, respectively, which highlight the importance of salt in affecting net charge and conformations of PZs.

36 MATERIALS SCIENCE↗
DOE OSTI2022

High-Performance Non-fullerene organic solar cells enabled by noncovalent Conformational locks and Side-Chain engineering

Three novel small molecular acceptors (SMAs) BO-2F, BO-C8-2F and BO-C2C6-C8-2F were designed and synthesized. These acceptors all possess planar molecular backbone because of the introduction of intramolecular noncovalent interaction. Among them, BO-C2C6-C8-2F with four side chains, which has the highest solubility, can form more appropriate nanomorphology when blending with PBDB-T. Hence, organic solar cells (OSCs) based on PBDB-T:BO-C2C6-C8-2F displayed an outstanding power convesion efficiency (PCE) of 14.25%, which is higher than BO-2F and BO-C8-2F based ones. To the best of our knowledge, the PCE of 14.25% is one of the highest for the OSCs based on A-π-D-π-A type SMAs. Finally, our results have demonstrated that the combination of side-chain engineering and intramolecular conformation lock has a great prospect in the design of high performance SMAs for OSCs.

14 SOLAR ENERGY↗
DOE OSTI2025

Directing Polymorphism of Colloid Crystals Using Conformational Entropy of Polymer Chains

Controlling the polytypes of close-packed structures of spherical colloids is still a challenging problem despite their wide occurrence. Here, in this work, we show that systematic engineering of the polytype structures of close-packed colloids is possible by using the conformational entropy of polymer chains confined in the interstitial space of colloid crystals. Our interstitial space analysis shows that the hexagonal close-packed (HCP) structures offer larger local interstitial space domains, and the structure director chains in favor of HCP counteract the entropic advantages of the face-centered cubic (FCC) lattices. Using model block copolymer colloids and the known lattice entropy of FCC, a proportionality parameter, β CP = 1.91 × 10 –3 ± 3.67 × 10 –4 , for quantifying the conformational entropy contribution toward HCP structures is extracted. This work demonstrates that the interstitial space of colloid crystals serves as a new structure engineering tool for the self-assembly of colloids.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Microscopic characterization of Ising conformal field theory in Rydberg chains

Rydberg chains provide an appealing platform for probing conformal field theories (CFTs) that capture universal behavior in a myriad of physical settings. Focusing on a Rydberg chain at the Ising transition separating charge density wave and disordered phases, we establish a detailed link between microscopics and low-energy physics emerging at criticality. Here, we first construct lattice incarnations of primary fields in the underlying Ising CFT including chiral fermions, a nontrivial task given that the Rydberg chain Hamiltonian does not admit an exact fermionization. With this dictionary in hand, we compute correlations of microscopic Rydberg operators, paying special attention to finite, open chains of immediate experimental relevance. We further develop a method to quantify how second-neighbor Rydberg interactions tune the sign and strength of four-fermion couplings in the Ising CFT. Finally, we determine how the Ising fields evolve when four-fermion couplings drive an instability to Ising tricriticality. Our results pave the way to a thorough experimental characterization of Ising criticality in Rydberg arrays and can inform the design of novel higher-dimensional phases based on coupled critical chains.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

The effect of polymer grafting on the mechanical properties of PEG-grafted cellulose nanocrystals in poly(lactic acid)

Poly(lactic acid) (PLA) is a commercially available bio-based polymer that is a potential alternative to many commodity petrochemical-based polymers. However, PLA's thermomechanical properties limit its use in many applications. Incorporating polymer-grafted cellulose nanocrystals (CNCs) is one potential route to improving these mechanical properties. One key challenge in using these polymer-grafted nanoparticles is to understand which variables associated with polymer grafting are most important for improving composite properties. In this work, poly(ethylene glycol)-grafted CNCs are used to study the effects of polymer grafting density and molecular weight on the properties of PLA composites. All CNC nanofillers are found to reinforce PLA above the glass transition temperature, but non-grafted CNCs and CNCs grafted with short PEG chains (<2 kg mol –1 ) are found to cause significant embrittlement, generally resulting in less than 3% elongation-at-break. By grafting higher molecular weight PEG (10 kg mol –1 ) onto the CNCs at a grafting density where the polymer chains are predicted to be in the semi-dilute polymer brush conformation (~0.1 chains nm –2 ), embrittlement can be avoided.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers

Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike image generation or even the closely related problem of protein structure prediction, there are currently no data sources with sufficient breadth to parametrize generative models for conformational ensembles. To enable discovery, a fundamentally different approach to building generative models is required: models should be able to propose rare, albeit physical, conformations that may not arise in even the largest data sets. Here, in this work, we introduce a modular strategy to generate conformations based on “backmapping” from a fixed protein backbone that (1) maintains conformational diversity of the side chains and (2) couples the side-chain fluctuations using global information about the protein conformation. Our model combines simple statistical models of side-chain conformations based on rotamer libraries with the now ubiquitous transformer architecture to sample with atomistic accuracy. Together, these ingredients provide a strategy for rapid data acquisition and hence a crucial ingredient for scalable physical simulation with generative neural networks.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Composite entanglement topology and extensional rheology of symmetric ring-linear polymer blends

Extensive molecular simulations are applied to characterize the equilibrium dynamics, entanglement topology, and nonlinear extensional rheology of symmetric ring-linear polymer blends with systematically varied ring fraction ϕR. Chains with degree of entanglement Z≈14 are mixed to produce 10 well-entangled systems with ϕR varying from neat linear to neat ring melts. Z is large enough that except for very large ϕR, the rings are threaded by multiple linear chains in equilibrium. Primitive path analysis is used to visualize and quantify the structure of the composite ring-linear entanglement network. We measure the quantity of ring-linear threading and linear-linear entanglement as a function of ϕR and identify with simple arguments a ring fraction ϕR≈0.4 where the topological constraints of the composite entanglement network are maximized. These topological analyses are used to rationalize the ϕR-dependence of ring and linear chain dynamics, conformations, and rheology. Simulations of startup uniaxial elongation flows demonstrate the extensional stress overshoot observed in recent filament stretching experiments and characterize how it depends on the blend composition and entanglement topology. The overshoot is driven by an overstretching and recoil of ring polymers due to the convective unthreading of rings from linear chains.

O’Connor, Thomas C.↗
DOE OSTI2021

Local orientation of chains at crystal/amorphous interfaces buried in isotactic polypropylene thin films

A better understanding of the aggregation states of polymer chains in thin films is of pivotal importance for developing thin film polymer devices in addition to its inherent scientific interest. Here we report the preferential orientation of the crystalline lamellae for isotactic polypropylene (iPP) in spin-coated films by grazing incidence of wide-angle X-ray diffraction in conjunction with sum frequency generation vibrational spectroscopy, which provides information on the local conformation of chains at crystal/amorphous interfaces buried in a thin film. The crystalline orientation of iPP, which formed cross-hatched lamellae induced by lamellar branching, altered from a mixture of edge-on and face-on mother lamellae to preferential face-on mother lamellae with decreasing thickness. Here, the orientation of methyl groups at the crystal/amorphous interfaces in the interior region of the iPP films changed, accompanied by a change in the lamellar orientation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1994

Conformational Characteristics of Poly(tetrafluoroethylene) (PTFE) Based Upon Ab Initio Electronic Structure Calculations on Model Molecules

Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.

Smith, Grant D.↗
DOE OSTI2020

Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

36 MATERIALS SCIENCE↗