Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Coexistence of vitreous and crystalline phases of H₂O at ambient temperature.

ABSTRACT: Formation of vitreous ice during rapid compression of water at room temperature is important for biology and the study of biological systems. Here, we show that Raman spectra of rapidly compressed water at greater than 1 GPa at room temperature exhibits the signature of high-density amorphous ice, whereas the X-ray diffraction (XRD) pattern is dominated by crystalline ice VI. To resolve this apparent contradiction, we used molecular dynamics simulations to calculate full vibrational spectra and diffraction patterns of mixtures of vitreous ice and ice VI, including embedded interfaces between the two phases. We show quantitatively that Raman spectra, which probe the local polarizability with respect to atomic displacements, are dominated by the vitreous phase, whereas a small amount of the crystalline component is readily apparent by XRD. The results of our combined experimental and theoretical studies have implications for detecting vitreous phases of water, survival of biological systems under extreme conditions, and biological imaging. The results provide additional insight into the stable and metastable phases of H₂O as a function of pressure and temperature, as well as of other materials undergoing pressure-induced amorphization and other metastable transitions.

SUBMITTER: Shargh AK

PROVIDER: S-EPMC9271169 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Coexistence of fluid and crystalline phases of proteins in photosynthetic membranes.

Project description:Photosystem II (PSII) and its associated light-harvesting complex II (LHCII) are highly concentrated in the stacked grana regions of photosynthetic thylakoid membranes. PSII-LHCII supercomplexes can be arranged in disordered packings, ordered arrays, or mixtures thereof. The physical driving forces underlying array formation are unknown, complicating attempts to determine a possible functional role for arrays in regulating light harvesting or energy conversion efficiency. Here, we introduce a coarse-grained model of protein interactions in coupled photosynthetic membranes, focusing on just two particle types that feature simple shapes and potential energies motivated by structural studies. Reporting on computer simulations of the model's equilibrium fluctuations, we demonstrate its success in reproducing diverse structural features observed in experiments, including extended PSII-LHCII arrays. Free energy calculations reveal that the appearance of arrays marks a phase transition from the disordered fluid state to a system-spanning crystal. The predicted region of fluid-crystal coexistence is broad, encompassing much of the physiologically relevant parameter regime; we propose experiments that could test this prediction. Our results suggest that grana membranes lie at or near phase coexistence, conferring significant structural and functional flexibility to this densely packed membrane protein system.

| S-EPMC3762348 | biostudies-other

Coexistence of structural and magnetic phases in van der Waals magnet CrI3.

Project description:CrI3 has raised as an important system to the emergent field of two-dimensional van der Waals magnetic materials. However, it is still unclear why CrI3 which has a ferromagnetic rhombohedral structure in bulk, changed to anti-ferromagnetic monoclinic at thin layers. Here we show that this behaviour is due to the coexistence of both monoclinic and rhombohedral crystal phases followed by three magnetic transitions at TC1 = 61 K, TC2 = 50 K and TC3 = 25 K. Each transition corresponds to a certain fraction of the magnetically ordered volume as well as monoclinic and rhombohedral proportion. The different phases are continuously accessed as a function of the temperature over a broad range of magnitudes. Our findings suggest that the challenge of understanding the magnetic properties of thin layers CrI3 is in general a coexisting structural-phase problem mediated by the volume-wise competition between magnetic phases already present in bulk.

| S-EPMC8560937 | biostudies-literature

Coexistence of phases in a protein heterodimer.

Project description:A heterodimer consisting of two or more different kinds of proteins can display an enormous number of distinct molecular architectures. The conformational entropy is an essential ingredient in the Helmholtz free energy and, consequently, these heterodimers can have a very complex phase structure. Here, it is proposed that there is a state of proteins, in which the different components of a heterodimer exist in different phases. For this purpose, the structures in the protein data bank (PDB) have been analyzed, with radius of gyration as the order parameter. Two major classes of heterodimers with their protein components coexisting in different phases have been identified. An example is the PDB structure 3DXC. This is a transcriptionally active dimer. One of the components is an isoform of the intra-cellular domain of the Alzheimer-disease related amyloid precursor protein (AICD), and the other is a nuclear multidomain adaptor protein in the Fe65 family. It is concluded from the radius of gyration that neither of the two components in this dimer is in its own collapsed phase, corresponding to a biologically active protein. The UNRES energy function has been utilized to confirm that, if the two components are separated from each other, each of them collapses. The results presented in this work show that heterodimers whose protein components coexist in different phases, can have intriguing physical properties with potentially important biological consequences.

| S-EPMC3411598 | biostudies-literature

EARLY FLOWERING3 sub-nuclear localization responds to changes in ambient temperature.

Project description: Not available

| S-EPMC8644450 | biostudies-literature

Post-natal development of brown adipocytes in white fat: Phases independent and dependent of the ambient temperature

Project description:Decreased ambient temperature, from birth to weaning, significantly reduced fat mass (FM) and adiposity in developing mice. Changes in FM content in 10 day-old mice raised at 17°C were not accompanied by precocious induction of brown adipocytes in inguinal white adipose tissue (WAT). Brown phenotype was induced in 21 day-old mice independently of ambient temperature (17°C or 29°C) however the expression of Ucp1 and other brown fat biomarker genes was greater in animals raised at 17°C suggesting increased adaptive thermogenesis. Accordingly, we predict that the induction of brown adipocytes in WAT follows a strict developmental program and the number of potential brown adipocytes in WAT is determined genetically.

2015-05-03 | GSE62350 | GEO

Ta2 +-mediated ammonia synthesis from N2 and H2 at ambient temperature.

Project description:In a full catalytic cycle, bare Ta2 + in the highly diluted gas phase is able to mediate the formation of ammonia in a Haber-Bosch-like process starting from N2 and H2 at ambient temperature. This finding is the result of extensive quantum chemical calculations supported by experiments using Fourier transform ion cyclotron resonance MS. The planar Ta2N2 +, consisting of a four-membered ring of alternating Ta and N atoms, proved to be a key intermediate. It is formed in a highly exothermic process either by the reaction of Ta2 + with N2 from the educt side or with two molecules of NH3 from the product side. In the thermal reaction of Ta2 + with N2, the N?N triple bond of dinitrogen is entirely broken. A detailed analysis of the frontier orbitals involved in the rate-determining step shows that this unexpected reaction is accomplished by the interplay of vacant and doubly occupied d-orbitals, which serve as both electron acceptors and electron donors during the cleavage of the triple bond of N?N by the ditantalum center. The ability of Ta2 + to serve as a multipurpose tool is further shown by splitting the single bond of H2 in a less exothermic reaction as well. The insight into the microscopic mechanisms obtained may provide guidance for the rational design of polymetallic catalysts to bring about ammonia formation by the activation of molecular nitrogen and hydrogen at ambient conditions.

| S-EPMC6243240 | biostudies-literature

Coexistence of strongly buckled germanene phases on Al(111).

Project description:We report a study of structural and electronic properties of a germanium layer on Al(111) using scanning tunneling microscopy (STM), low energy electron diffraction and core-level photoelectron spectroscopy. Experimental results show that a germanium layer can be formed at a relatively high substrate temperature showing either (3×3) or (?7×?7)R±19.1° reconstructions. First-principles calculations based on density functional theory suggest an atomic model consisting of a strongly buckled (2×2) germanene layer, which is stable in two different orientations on Al(111). Simulated STM of both orientations fit nicely with experimental STM images and the Ge 3d core-level data decomposed into four components is consistent with the suggested model.

| S-EPMC5629377 | biostudies-literature

Perhydroazulene-based liquid-crystalline materials with smectic phases.

Project description:New liquid-crystalline materials with a perhydroazulene core were synthesized and the stereochemistry of these compounds was investigated. The mesomorphic properties of the new LC compounds were investigated by differential scanning colorimetry, polarizing optical microscopy and X-ray diffraction. We report here on the LC properties of nonchiral materials, which predominantly exhibit smectic phases and display nematic phases only within narrow temperature ranges. The dependence of the mesogenic behavior of the new materials on the stereochemistry of the core system was also investigated. All newly synthesized compounds were fully characterized by the usual spectroscopic and analytical methods.

| S-EPMC3326617 | biostudies-literature

Coexistence of three liquid phases in individual atmospheric aerosol particles.

Project description:Individual atmospheric particles can contain mixtures of primary organic aerosol (POA), secondary organic aerosol (SOA), and secondary inorganic aerosol (SIA). To predict the role of such complex multicomponent particles in air quality and climate, information on the number and types of phases present in the particles is needed. However, the phase behavior of such particles has not been studied in the laboratory, and as a result, remains poorly constrained. Here, we show that POA+SOA+SIA particles can contain three distinct liquid phases: a low-polarity organic-rich phase, a higher-polarity organic-rich phase, and an aqueous inorganic-rich phase. Based on our results, when the elemental oxygen-to-carbon (O:C) ratio of the SOA is less than 0.8, three liquid phases can coexist within the same particle over a wide relative humidity range. In contrast, when the O:C ratio of the SOA is greater than 0.8, three phases will not form. We also demonstrate, using thermodynamic and kinetic modeling, that the presence of three liquid phases in such particles impacts their equilibration timescale with the surrounding gas phase. Three phases will likely also impact their ability to act as nuclei for liquid cloud droplets, the reactivity of these particles, and the mechanism of SOA formation and growth in the atmosphere. These observations provide fundamental information necessary for improved predictions of air quality and aerosol indirect effects on climate.

| S-EPMC8072205 | biostudies-literature

The Magic-Size Nanocluster (CdSe)34 as a Low-Temperature Nucleant for Cadmium Selenide Nanocrystals; Room-Temperature Growth of Crystalline Quantum Platelets.

Project description:Reaction of Cd(OAc)2·2H2O and selenourea in primary-amine/secondary-amine cosolvent mixtures affords crystalline CdSe quantum platelets at room temperature. Their crystallinity is established by X-ray diffraction analysis (XRD), high-resolution transmission electron microscopy (TEM), and their sharp extinction and photoluminescence spectra. Reaction monitoring establishes the magic-size nanocluster (CdSe)34 to be a key intermediate in the growth process, which converts to CdSe quantum platelets by first-order kinetics with no induction period. The results are interpreted to indicate that the critical crystal-nucleus size for CdSe under these conditions is in the range of (CdSe)34 to (CdSe)68. The nanocluster is obtained in isolated form as [(CdSe)34(n-octylamine)16(di-n-pentylamine)2], which is proposed to function as crystal nuclei that may be stored in a bottle.

| S-EPMC3985485 | biostudies-literature