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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗
NASA NTRS1988

Convection effects in protein crystal growth

Protein crystals for X-ray diffraction study are usually grown resting on the bottom of a hanging drop of a saturated protein solution, with slow evaporation to the air in a small enclosed cell. The evaporation rate is controlled by hanging the drop above a reservoir of water, with its saturation vapor pressure decreased by a low concentration of a passive solute. The drop has a lower solute concentration, and its volume shrinks by evaporation until the molecular concentrations match. Protein crystals can also be grown from a seed crystal suspended or supported in the interior of a supersaturated solution. The main analysis of this report concerns this case because it is less complicated than hanging-drop growth. Convection effects have been suggested as the reason for the apparent cessation of growth at a certain rather small crystal size. It seeems that as the crystal grows, the number of dislocations increases to a point where further growth is hindered. Growth in the microgravity environment of an orbiting space vehicle has been proposed as a method for obtaining larger crystals. Experimental observations of convection effects during the growth of protein crystals have been reported.

Roberts, Glyn O.↗
DOE OSTI2024

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

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

Scale and rate in CdS pressure-induced phase transition

Here, we describe recent efforts to improve our predictive modeling of rate-dependent behavior at, or near, a phase transition using molecular dynamics simulations. Cadmium sulfide (CdS) is a well-studied material that undergoes a solid-solid phase transition from wurtzite to rock salt structures between 3 and 9 GPa. Atomistic simulations are used to investigate the dominant transition mechanisms as a function of orientation, size and rate. We found that the final rock salt orientations were determined relative to the initial wurtzite orientation, and that these orientations were different for the two orientations and two pressure regimes studied. The CdS solid-solid phase transition is studied, for both a bulk single crystal and for polymer-encapsulated spherical nanoparticles of various sizes.

42 ENGINEERING↗
DOE OSTI2020

A pathway to synthesizing single-crystal Fe and FeCr films

Nuclear reactor environments provide a unique scientific and engineering challenge wherein materials must tolerate prolonged exposure to concurrent irradiation, elevated temperatures, and corrosive media. However, uncontrolled variability in material composition and structure often prohibits truly single-variable experiments that can reveal basic aspects of environmental damage. Here, Magnetron sputtering is used to provide a more controlled model system for these fundamental studies, yielding reproducible single-crystal Fe and FeCr thin films containing 8 and 18 at.% Cr. Electron microscopy is used to determine the systematic correlations between growth conditions and the resulting film microstructure and surface morphology. It is found that the substrate temperature and applied radio frequency (RF) bias can be tuned to obtain consistent homogeneous and single crystal films with a minimal amount of Ar impurities from the RF bias process. Epitaxial, single-crystal Fe films are obtained on MgO substrates at 500 °C with 10 Watt (W) RF bias deposition. However, when Cr is alloyed with Fe, higher substrate temperatures (600 °C) and applied RF biases (15 W) are required to achieve a similar epitaxial single-crystal FeCr film. Accelerated molecular dynamics simulations reveal that Cr impedes surface transport, explaining the need for higher temperature and bias during the growth of the Cr-bearing films.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Barrierless nucleation in glassy precursors drives zeolite formation

Zeolites are crystalline, microporous silicates widely used in catalysis and separations, yet the molecular mechanisms of their formation remain unresolved. Experiments indicate that hydrothermal synthesis of silica zeolites from clear solution proceeds through amorphous nanoaggregates that gradually develop zeolite order in an apparently continuous amorphous to crystal transformation. Here, we combine molecular simulations with advanced algorithms that identify zeolite order and computer vision to elucidate the pathway from clear solution to zeolite nanocrystal. We show that at conditions of hydrothermal synthesis of silica zeolites, the transformation of precursor aggregate into zeolite is not limited by nucleation barriers but by the slow dynamics of reorganization in the glassy precursor matrix. The negligible nucleation barriers result in spinodal-like crystallization that leads to a gradual formation of a mosaic of small crystallites that explain the seemingly continuous character of zeolite crystallization and the catalytic activity of X-ray amorphous, protozeolites and embryonic zeolites. We find that zeolite-like porosity and short-range order emerge early within glassy precursors, well before crystallinity is detected in transmission electron microscopy (TEM) images or X-ray diffraction. The nanoaggregate’s temperature-size phase diagram reveals a convergence of the zeolite–amorphous equilibrium and maximum crystallization rate at ~3 nm diameter nanoparticle diameters and ~200 °C. This convergence signals the termination of the first-order amorphous-to-zeolite transition. Our results provide a unifying framework for understanding nucleation of silica zeolites from solution and suggest that barrierless nucleation may govern the formation of other nanoparticle systems, including minerals and oxides synthesized far below their bulk melting points.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Employing a Narrow-Band-Gap Mediator in Ternary Solar Cells for Enhanced Photovoltaic Performance

Ternary organic solar cells (OSCs) provide a convenient and effective means to further improve the power conversion efficiency (PCE) of binary ones via composition control. However, the role of the third component remains to be explored in specific binary systems. Herein, we report ternary blend solar cells by adding the narrow-band-gap donor PCE10 as the mediator into the PBDB-T:IDTT-T binary blend system. The extended absorption, efficient fluorescence resonance energy transfer, enhanced charge dissociation, and induced tighter molecular packing of the ternary blend films enhance the photovoltaic properties of devices and deliver a champion PCE of 10.73% with an impressively high open-circuit voltage (VOC) of 1.03 V. Good miscibility and similar molecular packing behavior of the components guarantee the desired morphology in the ternary blend films, leading to solar cell devices with over 10% PCEs at a range of compositions. Our results suggest that ternary systems with properly aligned energy levels and overlapping absorption among the components hold great promises to further enhance the performance of corresponding binary ones.

14 SOLAR ENERGY↗
DOE OSTI2025

Applications of Nickelate perovskites for neuromorphic computing from electronic structure and Machine Learning

While the limit of Moore's law is presently being reached with current microelectronic technologies, we need to develop new paradigms that overcome this limitation. In that respect, neuromorphic computing is a concept that emulates the neural behavior and response of the human brain, and it has been recognized as a promising alternative approach. In this research project, we will perform multi-fidelity scale bridging to explore the potential use of materials with metal to insulator transition for neuromorphic applications. In particular, rare earth nickelates are promising for such purposes, as the transition in these materials is quite sensitive to a broad set of different external stimuli. Our multi-fidelity approach will bridge the high-fidelity electronic structure calculations with classical potentials. We will bridge dynamical mean field theory with a classical atomistic representation via a deep learning force field. The neural network is trained with energies, charges, and forces obtained by accurate electronic structure theories based on Dynamical Mean Field Theory. The configurational space is generated from known crystal phases, ab initio molecular dynamics with exchange-correlation functionals corrected with the Hubbard model, disordered phases with different concentrations of oxygen vacancies, and nonsymmetrical positions and induced strain by grain interfaces or contact with a substrate. Strategies to train the model with a reduced number of training examples are obtained from active learning methods, and new structures for improving the learning process are generated by using machine learning autoencoders. This classical potential will be validated through a diversity of electronic structure methods and represents an important step to combine the flexibility and accuracy of first-principles with the speed of classical potentials. The generated multi-fidelity surrogate model will be used to understand the role of strain, oxygen vacancies, proton doping, the variation of the crystal phase, substrate effects, vibrational effects as the octahedral rotation, grain boundaries and defect effects on the response of a Metal to Insulator Transition (MIT) in correlated materials. Long time and large-scale simulations will help understand the role of different stimuli to control the hysteresis of the MIT, as it has been experimentally suggested. Selected configurations will be analyzed with higher-level theories to provide an accurate electronic description and to study how the orbitals and charges are rearranged under different conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dynamic Structural Change of Plant Epidermal Cell Walls under Strain

Abstract The molecular foundations of epidermal cell wall mechanics are critical for understanding structure–function relationships of primary cell walls in plants and facilitating the design of bioinspired materials. To uncover the molecular mechanisms regulating the high extensibility and strength of the cell wall, the onion epidermal wall is stretched uniaxially to various strains and cell wall structures from mesoscale to atomic scale are characterized. Upon longitudinal stretching to high strain, epidermal walls contract in the transverse direction, resulting in a reduced area. Atomic force microscopy shows that cellulose microfibrils exhibit orientation‐dependent rearrangements at high strains: longitudinal microfibrils are straightened out and become highly ordered, while transverse microfibrils curve and kink. Small‐angle X‐ray scattering detects a 7.4 nm spacing aligned along the stretch direction at high strain, which is attributed to distances between individual cellulose microfibrils. Furthermore, wide‐angle X‐ray scattering reveals a widening of (004) lattice spacing and contraction of (200) lattice spacing in longitudinally aligned cellulose microfibrils at high strain, which implies longitudinal stretching of the cellulose crystal. These findings provide molecular insights into the ability of the wall to bear additional load after yielding: the aggregation of longitudinal microfibrils impedes sliding and enables further stretching of the cellulose to bear increased loads.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Role of Static Displacements in Stabilizing Body Centered Cubic High Entropy Alloys

The configurational entropy of high entropy alloys (HEAs) plays little role in the stabilization of one particular crystal structure over another. We show that disorder-induced atomic displacements help stabilize body centered cubic (bcc) structure HEAs with average valences <4.7. These disorder-induced atomic displacements mimic the temperature-induced vibrations that stabilize the bcc structure of group IV elemental metals at high temperatures. The static displacements are significantly larger than for face centered cubic HEAs, approaching values associated with the Lindemann criterion for melting. Chemical disorder in high entropy alloys have a previously unidentified, nonentropic energy contribution that stabilizes a particular crystalline ground state.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Tuning the melting point of selected ionic liquids through adjustment of the cation’s dipole moment.

In prior research with thermally robust salts [Cassity et al., PCCP, 2017, 19, 31560] it was noted that an increase in the dipole moment of the cation generally led to a decrease in the melting point. Molecular dynamics simulations of the liquid state revealed that an increased dipole moment reduces cation-cation repulsions through dipole-dipole alignment. This was believed to reduce the liquid phase enthalpy, which would tend to lower the melting point of the IL. Here, we also test this principle by replacing hydrogen atoms with fluorine atoms at selected positions within the cation. This allows us to alter the electrostatics of the cation without substantially affecting the sterics. Furthermore, the strength of the dipole moment can be controlled by choosing different positions within the cation for replacement. We studied variants of four different parent cations paired with bistriflimide and determined their melting points, and enthalpies and entropies of fusion through DSC experiments. The decreases in the melting point were determined to be enthalpically driven. We found that the dipole moment of the cation, as determined by quantum chemical calculations, is inversely correlated with the melting point of the given compound. Molecular dynamics simulations of the crystalline and solid states of two isomers showed differences in their enthalpies of fusion that closely matched those seen experimentally. Moreover, this reduction in the enthalpy of fusion was determined to be caused by an increase in the enthalpy of the crystalline state. We provide evidence that dipole-dipole interactions between cations leads to the formation of cationic domains in the crystalline state. These cationic associations partially block favourable cation–anion interactions, which are recovered upon melting. If, however, the dipole- dipole interactions between cations is too strong they have a tendency to form glasses. This study provides a design rule for lowering the melting point of structurally similar ILs by altering their dipole moment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
NASA NTRS1991

Protein crystal growth in space

Studies of protein crystal growth in the microgravity environment in space are described with special attention given to the crystal growth facilities and the techniques used in Space Shuttle experiments. The properties of large space-grown crystals of gamma interferon, elastase, lathyros ochrus lectin I, and few other proteins grown on various STS flights are described. A comparison of the microgravity-grown crystals with the bast earth-grown crystals demonstrated that the space-grown crystals are more highly ordered at the molecular level than their earth-grown counterparts. When crystallization conditions were optimized, the microgravity-grown protein crystals were larger, displayed more uniform morphologies, and yielded diffraction data to significantly higher resolution than their earth-grown counterparts.

Delucas, Lawrence J.↗
DOE OSTI2022

Vibrational modes and crystallographic structure of Cd 3 As 2 and (Cd 1-x Zn x ) 3 As 2 epilayers

Low-temperature Raman scattering is used to study the crystal structure of molecular-beam epitaxially grown layers of the Dirac semimetal Cd 3 As 2 and its related alloy (Cd 1-x Zn x ) 3 As 2 . The combination of narrow-linewidth spectra, multiple growth directions and full polarization analysis allows improved accuracy in identifying the irreducible representation of over 57 Raman-active vibrations. Several disagreements with previous identifications are found. Structurally, the results agree with the centrosymmetric I41/acd space group of bulk-grown Cd 3 As 2 and are clearly distinct from the Raman spectra of nanoscale platelets and wires. Three-fold twinning is seen in (112) Cd 3 As 2 grown on (111) zincblende substrates corresponding to the three possible tetragonal orientations. In dilute (Cd 1-x Zn x ) 3 As 2 , phonons have a frequency and scattering amplitude dependence on Zn concentration that is continuous with Cd 3 As 2 but at least one frequency is absent at the alloy endpoint, preventing a simple one-mode description of the alloy phonon.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Water Structure and Dynamics Near the Surfaces of Silicalite-1

Zeolites are crystalline microporous aluminosilicates that are commonly used as industrial sorbents and membranes. Solvent structuring and dynamics near zeolite crystal surfaces are thought to influence interfacial transport and molecular recognition processes, as well as fundamental aspects of their crystallization from solution. Here, in this work, we use molecular dynamics (MD) simulations to investigate the behavior of interfacial water near the exposed (010), (100), and (101) crystal faces of silicalite-1, one of the most widely studied zeolites. The MD simulations reveal that water’s translational and orientational order is strongly influenced by the distinct corrugations, pore apertures, and functional group distributions presented on each surface. Specifically, we observe two distinct hydration layers near each surface. Water molecules in the contact layer are hydrogen bonded to two or three exposed surface silanol groups. The relative populations of water molecules that are doubly and triply hydrogen bonded to the surface strongly depend on the distribution of the exposed silanols. The interactions with exposed surface silanols also influence water’s local orientational order and distribution across each surface. We also show that the structuring of the solvent near the different faces of silicalite-1 strongly impacts the interfacial dynamics. The translational and orientational relaxation dynamics of water are slowest in the contact layers and correlate with structural ordering near each face.

42 ENGINEERING↗
DOE OSTI2025

Effects of crystallization on micro-mechanical behavior of polyethylene nanocomposites using Raman spectroscopy

Recent work has shown that nanoparticles can be ordered in semicrystalline polymers by controlling the crystallization rate, specifically by forcing them to migrate to the amorphous regions of the lamellar morphology. Here, we study the micromechanical behavior of neat polyethylene and silica/polyethylene nanocomposites filled with 15 nm brush-modified silica in the quenched and slow-crystallized organized state. The molecular response to loading in tension was monitored with Raman spectroscopy using the peaks associated with crystalline and amorphous regions. The addition of nanofillers dramatically reduced the shift in the amorphous peaks, indicating that in addition to carrying some load, the brush-modified nanoparticles may be acting as tie molecules that restrict amorphous deformation. The higher degree of lamellar organization and the organization of the nanoparticles also impacted the crystalline peak shifts, but more subtly.

Polyethylene↗
DOE OSTI2020

Local Structure of Glassy Lithium Phosphorus Oxynitride Thin Films: A Combined Experimental and Ab Initio Approach

Abstract Lithium phosphorus oxynitride (LiPON) is an amorphous solid‐state lithium ion conductor displaying exemplary cyclability against lithium metal anodes. There is no definitive explanation for this stability due to the limited understanding of the structure of LiPON. Herein, we provide a structural model of RF‐sputtered LiPON. Information about the short‐range structure results from 1D and 2D solid‐state NMR experiments. These results are compared with first principles chemical shielding calculations of Li‐P‐O/N crystals and ab initio molecular dynamics‐generated amorphous LiPON models to unequivocally identify the glassy structure as primarily isolated phosphate monomers with N incorporated in both apical and as bridging sites in phosphate dimers. Structural results suggest LiPON′s stability is a result of its glassy character. Free‐standing LiPON films are produced that exhibit a high degree of flexibility, highlighting the unique mechanical properties of glassy materials.

Marple, Maxwell A. T.↗
DOE OSTI2020

Local Structure of Glassy Lithium Phosphorus Oxynitride Thin Films: A Combined Experimental and Ab Initio Approach

Lithium phosphorus oxynitride (LiPON) is an amorphous solid–state lithium ion conductor displaying exemplary cyclability against lithium metal anodes. There is no definitive explanation for this stability due to the limited understanding of the structure of LiPON. Herein, we provide a structural model of RF–sputtered LiPON. Information about the short–range structure results from 1D and 2D solid–state NMR experiments. These results are compared with first principles chemical shielding calculations of Li–P–O/N crystals and ab initio molecular dynamics–generated amorphous LiPON models to unequivocally identify the glassy structure as primarily isolated phosphate monomers with N incorporated in both apical and as bridging sites in phosphate dimers. Structural results suggest LiPON's stability is a result of its glassy character. In conclusion, free–standing LiPON films are produced that exhibit a high degree of flexibility, highlighting the unique mechanical properties of glassy materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Hierarchical assemblies of polypeptoids for rational design of advanced functional nanomaterials

Polypeptoids (poly-N-substituent glycines) are a class of highly tailorable peptidomimetic polymers. Polypeptoids have identical backbones as polypeptides (poly-C-substituent glycines), but sidechains of polypeptoids are appended to backbone nitrogen rather than α-carbon of polypeptides. As a result, peptoid backbone lacks of chirality and hydrogen bond donors. This unique structure gives polypeptoids a combined merit of both high stability as synthetic polymers and biocompatibility as biopolymers. In addition, peptoid sequences can be engineered precisely to assemble specific crystalline patterns such as spheres, fibers, ribbons, tubes, and sheets, which shows promising potentials of polypeptoids for different applications such as antimicrobials, catalysts, drug delivery, and templating inorganic materials. In this review, we summarize recent investigations into hierarchical self-assembly pathways and molecular structures of peptoid crystals that are of interest as templates for fabricating functional materials for potential biomedical, biochemical, and bioengineering applications. Furthermore, this review provides a summary of recent experimental and computational studies of polypeptoid assembly in solution and solid-liquid interfaces, current achievements in the field, and discusses future challenges and opportunities for the rational design of self-assembled polypeptoid nanomaterials.

36 MATERIALS SCIENCE↗