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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

Background The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use. Results We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes. Conclusions AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.

Allopolyploids↗
DOE OSTI2023

The crystal structure of feitknechtite (β-MnOOH) and a new MnOOH polymorph

Studies suggest that feitknechtite (β-MnOOH) is a prevalent, and perhaps necessary, intermediate phase during the synthesis of birnessite-like phases, the abiotic oxidation of Mn2+, and the transformation of biogenic hexagonal phyllomanganates to more complex Mn oxides in laboratory and natural systems. Researchers have generally described feitknechtite as consisting of pyrochroite-like (or cadmium iodide-like) Mn-O octahedral layers, but a detailed crystal structure has not been reported. For this work, we used TEM/SAED and powder XRD and Rietveld refinements to derive the unit cell and, for the first time, report a complete structure description for feitknechtite (β-MnOOH). Rietveld refinements were also completed for three natural feitknechtite/hausmannite samples, and time-resolved synchrotron XRD experiments were used to follow the thermal transformation of feitknechtite to hausmannite. Additionally, we identified and report the structure for a second, and perhaps novel, MnOOH polymorph (proposed designation ε-MnOOH), mixed with the synthetic feitknechtite, that is similar to β-MnOOH but with a different layer stacking.

58 GEOSCIENCES↗
DOE OSTI2023

The Polymorphic Membrane Protein G Has a Neutral Effect and the Plasmid Glycoprotein 3 an Antagonistic Effect on the Ability of the Major Outer Membrane Protein to Elicit Protective Immune Responses against a Chlamydia muridarum Respiratory Challenge

Chlamydia trachomatis is the most common bacterial sexually transmitted pathogen. The number of chlamydial infections continuous to increase and there is an urgent need for a safe and efficacious vaccine. To assess the ability of the Chlamydia muridarum polymorphic membrane protein G (PmpG) and the plasmid glycoprotein 3 (Pgp3) as single antigens, and in combination with the major outer-membrane protein (MOMP) to induce protection, BALB/c mice were immunized utilizing CpG-1826 and Montanide ISA 720 VG as adjuvants. Following vaccination with MOMP, significant humoral and cell-mediated immune responses were observed, while immunization with PmpG, or Pgp3, elicited weaker immune responses. Weaker immune responses were induced with MOMP+Pgp3 compared with MOMP alone. Following the intranasal challenge with C. muridarum, mice vaccinated with MOMP showed robust protection against body-weight loss, inflammatory responses in the lungs and number of Chlamydia recovered from the lungs. PmpG and Pgp3 elicited weaker protective responses. Mice immunized with MOMP+PmpG, were no better protected than animals vaccinated with MOMP only, while Pgp3 antagonized the protection elicited by MOMP. In conclusion, PmpG and Pgp3 elicited limited protective immune responses in mice against a respiratory challenge with C. muridarum and failed to enhance the protection induced by MOMP alone. The virulence of Pgp3 may result from its antagonistic effect on the immune protection induced by MOMP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled‐Coil Patches and Patterns

Abstract DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence‐specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well‐defined micron‐scale structures through hierarchical self‐assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled‐coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher‐order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled‐coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA‐based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5‐10‐fold increase in bending stiffness. The results provide a foundation for stimulus‐responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Observation of Thermally Induced Piezomagnetic Switching in Cu 2 OSeO 3 Polymorph Synthesized under High-Pressure

A polymorph of Cu 2 OSeO 3 with the distorted kagome lattice is successfully obtained using the high-pressure synthesis technique (Cu 2 OSeO 3 -HP). The structural analysis using X-ray and neutron powder diffraction suggests that the tetrahedral Cu 2+ clusters [similar to those in Cu 2 OSeO 3 ambient-pressure phase (Cu 2 OSeO 3 -AP)] exist in Cu 2 OSeO 3 -HP but with three symmetry inequivalent sites. No structural change is observed between 1.5 K and the room temperature. The complex magnetic H-T phase diagram is established based on the temperature- and field-dependent magnetization data, indicating two distinct antiferromagnetic phases at low and intermediate temperatures, in addition to the higher-temperature spin-glass-like phase. The low temperature phase is identified by neutron powder diffraction refinements as a canted noncollinear antiferromagnetic order with a weak ferromagnetic component along the b-axis. Size of the refined ordered moment is ≈1.00(4) µ B in Cu 2 OSeO 3 -HP, indicating a large enhancement compared to that of Cu 2 OSeO 3 -AP (≈0.61 µ B ). By applying a uniaxial stress, finite enhancement of weak ferromagnetic component in the noncollinear antiferromagnetic phase in Cu 2 OSeO 3 -HP is observed, which is the clear evidence of the piezomagnetic effect. Interestingly, the sign of the induced magnetization changes on heating from the low-temperature to the intermediate-temperature phases, indicating a novel piezomagnetic switching effect in this compound.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Resolving Lonsdaleite's decade-long controversy: Atomistic insights into a metastable diamond polymorph

Lonsdaleite, a theoretically proposed hexagonal diamond polymorph, has remained at the center of a five-decade scientific controversy since its 1967 identification. While some studies claim it exhibits superior hardness through compression-induced structural changes, others contend it is merely a stacking-faulted cubic diamond. Meteoritic samples and synthetic preparations have yielded conflicting evidence, with even advanced characterisation techniques like XRD and TEM failing to provide definitive proof. In this work, we employ first-principles density functional theory (DFT) and molecular dynamics (MD) simulations to generate unambiguous theoretical fingerprints through XRD, Raman, and SAED patterns that distinguish true Lonsdaleite from cubic diamond and its defective variants. Our atomistic approach quantifies the thermodynamic metastability of Lonsdaleite under realistic pressure-temperature conditions, reveals distinct spectral signatures through simulated Raman and resolves the structural ambiguity through generalised stacking fault energy analysis. By establishing clear criteria for definitive identification, this study provides long-awaited clarity to the Lonsdaleite debate while offering a robust computational framework for characterising metastable carbon phases in meteoritic, synthetic and industrial materials.

DFT↗
DOE OSTI2021

The Plasma Levels and Polymorphisms of Vitronectin Predict Radiation Pneumonitis in Patients With Lung Cancer Receiving Thoracic Radiation Therapy

Our previous findings have identified vitronectin (VTN) as a potential biomarker for radiation pneumonitis (RP) through proteomics and molecular mechanism studies. In a recent study, we further explored associations of plasma level and single nucleotide polymorphisms of VTN with the risk of RP in patients with lung cancer receiving radiation therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Contrasting magnetic properties of polymorphic TbPt 3

Here, in this work, we report the contrasting magnetic behaviour of a bimorphic intermetallic compound TbPt 3 that undergoes a structural phase transformation from cubic AuBe 5 -type structure to the cubic AuCu 3 -type structure on annealing at high temperature for a very short time. The magnetic ground state configuration of TbPt 3 changes from ferromagnetic (FM) in AuBe 5 -type crystalline phase to antiferromagnetic (AFM) in AuCu 3 -type phase. However, the AFM ground state of the AuCu 3 -type compound is unstable, as a moderate magnetic field can induce the FM character through metamagnetic transformation. To understand the said crystallographic as well as magnetic transformations, structural and magnetic ab-initio calculations have been carried out for both phases. From theoretical calculations we have proposed that although the AuBe 5 -type structure of TbPt 3 irreversibly transforms to the AuCu 3 -type TbPt 3 by a very short heat treatment, the application of moderate magnetic field on AuCu 3 -type structure may result in recovering the magnetic properties of AuBe 5 -type structure of TbPt 3 . As the two different polymorphs exist simultaneously at ambient condition, TbPt 3 thus provides us a great opportunity to study directly the effect of crystal structure on its physical properties and vice versa.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Enhancing Properties with Distortion: A Comparative Study of Two Iron Phosphide Fe 2 P Polymorphs

Iron phosphide (Fe 2 P) crystallizes in its own hexagonal crystal structure type (h-Fe 2 P). As found in meteorites, orthorhombic polymorph (o-Fe 2 P) was originally reported as a high-temperature and high-pressure phase. Recently, o-Fe 2 P was described as being stable at ambient pressure, yet no synthetic methods were developed for single-crystal growth or single-phase bulk powder synthesis. Here, we report a successful method for growing o-Fe 2 P single crystals and synthesizing phase-pure polycrystalline samples using tin-flux. In situ powder X-ray diffraction studies showed that the phase transition from o-Fe 2 P to h-Fe 2 P occurs at about 873 K, and below that temperature, the formation of the o-Fe 2 P phase is favored thermodynamically rather than kinetically. Systematic comparison of transport, magnetic, and electrocatalytic properties of both h-Fe 2 P and o-Fe 2 P phases showed a substantial impact of the crystal structure on properties. The orthorhombic structural distortion resulted in considerable changes in magnetic properties, with the o-Fe 2 P phase exhibiting a 60% lower Fe magnetic moment and a substantially higher ferromagnetic Curie temperature than h-Fe 2 P. Further, electrochemical measurements toward the hydrogen evolution reaction in acidic media showed that the o-Fe 2 P phase requires an 80 mV lower overpotential than the h-Fe 2 P phase to generate a current density of -10 mA/cm 2 , and their electronic structures suggest that the higher density of states at the Fermi energy is the origin of superior catalytic activity in o-Fe 2 P.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Leveraging Polymorphism in YbCuBi to Map Transport and Elastic Properties

AMX Zintl compounds with the hexagonal ZrBeSi structure have gained significant attention for their remarkable vacancy tolerance and low thermal conductivity. Their 2D honeycomb sublattice, composed of M–X covalent bonds, is believed to contribute to high anharmonicity and unusual thermal transport properties. In this study, we explore the temperature-dependent polymorphism of YbCuBi as a model system to investigate the relationship between the structure and elastic and thermal transport properties in AMX Zintls. YbCuBi undergoes a structural transition from the “flat” Cu–Bi layers in the ZrBeSi structure to corrugated layers in the LiGaGe structure below 410 K, resulting in a distortion of its centrosymmetric structure. To probe the effects of this crystallographic transition, we employ inelastic neutron scattering and temperature-dependent resonant ultrasound spectroscopy. These experimental findings, coupled with first-principles calculations and thermal conductivity measurements, allow us to elucidate a direct relationship between corrugation of the honeycomb lattice and the observed changes in elastic and thermal transport properties. These insights can be extended to other Zintl phases with similar structure types, providing a platform for the rational design of functional materials with tailored thermal properties.

Chemical structure↗
DOE OSTI2020

Discovery of Rhombohedral NaIrO 3 Polymorph by In Situ High-Pressure Synthesis of High-Oxidation-State Materials Using Laser Heating in Diamond Anvil Cells

Here, we report a new in-situ synthesis method effective for discovery of high oxidation state materials using laser heated diamond anvil cells. The issue of chemical reduction during thermally induced phase transitions that occur spontaneously in a noble gas pressure transmitting media (PTM) can be overcome by thermal decomposition of an oxygen-rich solid PTM (NaCl + NaClO 3 ). To illustrate the technical challenges the method overcomes, we applied this new method for two known phase transitions from pentavalent A (I) B (V) O 3 perovskites to the post-perovskite structure. We successfully synthesized and quenched the two post-perovskites, NaOsO 3 and NaIrO 3 , to ambient conditions and furthermore, we report the discovery of a new low-pressure polymorph of NaIrO 3 , illustrating the high potential for new materials discovery. This new method will enable realization of new high oxidation state post-perovskites and can be applied for many other structure families in a P, T parameter space which is not easily accessible using conventional high-pressure synthesis methods.

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

Fe 0.6 Pd 0.4 Te 2 : A New Polymorph of FeTe 2 and PdTe 2 Stable at Ambient Pressure

Whereas pyrite space group is a high pressure polymorph of FeTe 2 , here we report pyrite-type single crystal Fe 0.6 Pd 0.4 Te 2 prepared using Pd substitution on Fe atomic site with ambient pressure crystal growth methods. Here, Fe 0.6(1) Pd 0.4(1) Te 2 single crystals show metal behavior above 15 K abided by Bloch-Grüneisen relation, and display resistivity upturn below 15 K due to disorder-related scattering of correlated electronic states.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

LeaPP: Learning Pathways to Polymorphs through Machine Learning Analysis of Atomic Trajectories

Understanding the mechanisms underlying crystal nucleation and growth is crucial for many technological applications. Due to the short length and time scales involved, crystal nucleation is often studied using molecular simulations. Most existing approaches to extract the nucleation mechanism from simulations focus on the analysis of static snapshots of the configurations, potentially overlooking subtle local fluctuations and the history of the particles involved in the formation of solid nuclei. Here, in this work, we propose a novel methodology called LeaPP that categorizes nucleation trajectories based on the temporal information of their constituent particles. We leverage the time evolution of the local environment of the crystallizing particles to encapsulate the relationship between the structure and dynamics and distinguish between different evolving particle paths. Identification of the distinct particle paths further enables characterizing the nucleation trajectories into different pathways. Collectively, LeaPP provides a more nuanced understanding of nucleation through an unsupervised approach with lesser dependence on traditional order parameters. Furthermore, the pathways identified by LeaPP are predictive of the resulting polymorph. We demonstrate LeaPP on three different systems─Lennard-Jones-like particles, Ni 3 Al, and water on surfaces. The general methodology underlying LeaPP─considering the time evolution of the building blocks─applies to a wide range of self-assembly problems.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Achieving Phase Control of Polymorphic Tungsten Carbide Catalysts

The polymorphism of tungsten carbide (W x C) and the challenge of selectively synthesizing pure phases have impeded a precise understanding of catalytic structure−property relationships. This study establishes a framework for phase-selective synthesis of W x C through controlling carburization kinetics. By maintaining particle sizes below 10 nm, β-W 2 C is selectively synthesized using gaseous carbon precursors (CH 4 /H 2 ) via temperature-programmed carburization (TPC). Our findings reveal that W 2 C stabilization is predominantly dictated by particle size and carburization kinetics rather than support interactions, providing a tunable approach to synthesize tungsten carbide catalysts. We elucidate the mechanistic pathway of WO x carburization, demonstrating that CH 4 activation occurs at mild temperatures via lattice oxygen. Our reactor studies establish ex situ synthesized β- W 2 C as an active and stable catalyst for the reverse water-gas shift (RWGS) reaction. However, the need for passivation and reduction pretreatment leads to a complex surface structure with diminished intrinsic activity. In contrast, our in situ synthesis protocol for β-W 2 C eliminates the need for passivation and exhibits increased CO STY during RWGS, illustrating the intrinsically higher activity compared to metallic W, WC 1−x (0.5 < x < 1), and stoichiometric WC.

CO2 conversion↗
DOE OSTI2023

Understanding the Polymorphism of Cobalt Nanoparticles Formed in Electrodeposition–An In Situ XRD Study

An advanced synchrotron-based in situ X-ray diffraction (XRD) technique is successfully developed and employed to track and monitor the formation and phase selection of cobalt (Co) in electrodeposition in real time and verify DFT computational results. The impacts of a number of controlling factors including the pH of the electrolyte and deposition overpotential are systematically studied. The results show that the yielded phase of the electrodeposited Co is controlled by both thermodynamics and kinetics. The low pH low overpotential condition favors the formation of the thermodynamically stable fcc phase. While the high pH high overpotential condition promotes the formation of the metastable hcp phase. The experimental results agree well with the nanometric phase diagram computed with DFT. Layer-by-layer alternative stacking of fcc-hcp polymorphic phases can be facilely fabricated by just varying the overpotential. This work not only offers an effective means to control the phase of electroplating of Co but also presents a new approach to reveal the fundamental insights of the formation of metals under electrochemical reduction driving force.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Polymorphism of feldspars above 10 GPa

Feldspars are rock-forming minerals that make up most of the Earth’s crust. Along the mantle geotherm, feldspars are stable at pressures up to 3 GPa and may persist metastably at higher pressures under cold conditions. Previous structural studies of feldspars are limited to ~10 GPa, and have shown that the dominant mechanism of pressure-induced deformation is the tilting of AlO 4 and SiO 4 tetrahedra in a tetrahedral framework. Herein, based on results of in situ single-crystal X-ray diffraction studies up to 27 GPa, we report the discovery of new high-pressure polymorphs of the feldspars anorthite (CaSi 2 Al 2 O 8 ), albite (NaAlSi 3 O 8 ) , and microcline (KAlSi 3 O 8 ). The phase transitions are induced by severe tetrahedral distortions, resulting in an increase in the Al and/or Si coordination number. High-pressure phases derived from feldspars could persist at depths corresponding to the Earth upper mantle and could possibly influence the dynamics and fate of cold subducting slabs.

58 GEOSCIENCES↗
DOE OSTI2023

Unraveling two distinct polymorph transition mechanisms in one n-type single crystal for dynamic electronics

Cooperativity is used by living systems to circumvent energetic and entropic barriers to yield highly efficient molecular processes. Cooperative structural transitions involve the concerted displacement of molecules in a crystalline material, as opposed to typical molecule-by-molecule nucleation and growth mechanisms which often break single crystallinity. Cooperative transitions have acquired much attention for low transition barriers, ultrafast kinetics, and structural reversibility. However, cooperative transitions are rare in molecular crystals and their origin is poorly understood. Crystals of 2-dimensional quinoidal terthiophene (2DQTT-o-B), a high-performance n-type organic semiconductor, demonstrate two distinct thermally activated phase transitions following these mechanisms. Here we show reorientation of the alkyl side chains triggers cooperative behavior, tilting the molecules like dominos. Whereas, nucleation and growth transition is coincident with increasing alkyl chain disorder and driven by forming a biradical state. We establish alkyl chain engineering as integral to rationally controlling these polymorphic behaviors for novel electronic applications.

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

Directing polymorph specific calcium carbonate formation with de novo protein templates

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-C a2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗