ResearchPad - condensed-matter-physics https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Crystal structure of <i>Thermus thermophilus</i> methylenetetrahydrofolate dehydrogenase and determinants of thermostability]]> https://www.researchpad.co/article/elastic_article_13865 The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for the thermostability of this enzyme. The description of rotamer distributions by Gini coefficients and Kullback–Leibler (KL) divergence both revealed significant correlations with temperature. The emerging view seems to indicate that a static salt bridge/charged residue network plays a fundamental role in the temperature resistance of Thermus thermophilus MTHFD by enhancing both electrostatic interactions and entropic energy dispersion. Furthermore, this analysis uncovered a relationship between residue mutations and evolutionary pressure acting on thermophilic organisms and thus could be of use for the design of future thermostable enzymes.

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<![CDATA[The Rho-associated kinase inhibitor fasudil can replace Y-27632 for use in human pluripotent stem cell research]]> https://www.researchpad.co/article/elastic_article_7829 Poor survival of human pluripotent stem cells (hPSCs) following freezing, thawing, or passaging hinders the maintenance and differentiation of stem cells. Rho-associated kinases (ROCKs) play a crucial role in hPSC survival. To date, a typical ROCK inhibitor, Y-27632, has been the primary agent used in hPSC research. Here, we report that another ROCK inhibitor, fasudil, can be used as an alternative and is cheaper than Y-27632. It increased hPSC growth following thawing and passaging, like Y-27632, and did not affect pluripotency, differentiation ability, and chromosome integrity. Furthermore, fasudil promoted retinal pigment epithelium (RPE) differentiation and the survival of neural crest cells (NCCs) during differentiation. It was also useful for single-cell passaging of hPSCs and during aggregation. These findings suggest that fasudil can replace Y-27632 for use in stem research.

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<![CDATA[ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient <i>hsdRMS</i> restriction system broadening conjugation host range]]> https://www.researchpad.co/article/elastic_article_7739 Horizontal gene transfer is the main mechanism by which bacteria acquire and disseminate new traits, such as antibiotic resistance genes, that allow adaptation and evolution. Here we identified a gene, ardC, that enables a plasmid to increase its conjugative host range, and thus positively contributes to plasmid fitness. The crystal structure of the antirestriction protein ArdC revealed a fold different from other antirestriction proteins. Our results have wide implications for understanding how a gene enlarges the environments a plasmid can colonize and point to new targets to harness the bacterial DNA uptake control.

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<![CDATA[Nutritional and physicochemical characteristics of purple sweet corn juice before and after boiling]]> https://www.researchpad.co/article/elastic_article_7720 Sweet corn juice is becoming increasingly popular in China. In order to provide valuable health-related information to consumers, the nutritional and physicochemical characteristics of raw and boiled purple sweet corn juices were herein investigated. Sugars, antinutrients, total free phenols, anthocyanins, and antioxidant activity were analyzed by conventional chemical methods. The viscosity and stability of juices were determined by Ubbelohde viscosity meter and centrifugation, respectively. Boiling process could elevate viscosity, stability and sugar content, and reduce antinutrients, total free phenols, anthocyanins, and antioxidant activity in corn juice. In addition, short time boiling efficiently reduced the degradation of anthocyanins during subsequent refrigeration. The content of amino acids, vitamin B1/B2 and E were detected by High Performance Liquid Chromatography. Gas Chromatography Mass Spectrometry was used for the analysis of fatty acids and aroma compounds. Several aroma compounds not previously reported in corn were identified, including 1-heptanol, 2-methyl-2-butenal, (Z)-3-nonen-1-ol, 3-ethyl-2-methyl-1,3-hexadiene, and 2,4-bis(1,1-dimethylethyl)phenol. Interestingly, the boiling process had no apparent effect on the amino acids profile, but it caused a 45.8% loss of fatty acids in the juice by promoting the retention of fatty acids in the corn residue. These results provide detailed information that could be used for increasing consumers’ knowledge of sweet corn juice, further development of sweet corn juice by food producers, and maize breeding programs.

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<![CDATA[Microbeam X-ray diffraction study of lipid structure in stratum corneum of human skin]]> https://www.researchpad.co/article/elastic_article_7631 Human skin, not previously frozen, was studied by small-angle X-ray diffraction. The samples were folded so that a 6μm X-ray beam passed through the top layer of skin, stratum corneum. Diffraction patterns recorded with this method consisted of peaks at about q = 0.5, 1.0 and 1.4 nm-1 in the direction perpendicular to the skin surface more clearly than in previous studies. These peaks are interpreted to arise from lipids between corneocytes. A simple unit of a linear electron density profile with three minima was used to account for the observed intensity profiles. Combinations of calculated diffraction from models with one, two and three units accounted for the major part of the observed diffraction pattern, showing the diversity in the structure of the intercellular lipids.

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<![CDATA[Three-dimensional magnetism and the Dzyaloshinskii-Moriya interaction in <i>S</i> = 3/2 kagome staircase Co<sub>3</sub>V<sub>2</sub>O<sub>8</sub>]]> https://www.researchpad.co/article/elastic_article_7719 Time-of-flight neutron data reveal spin waves in the ferromagnetic ground state of the kagome staircase material Co3V2O8. While previous work has treated this material as quasi–two-dimensional, we find that an inherently three-dimensional description is needed to describe the spin wave spectrum throughout reciprocal space. Moreover, spin wave branches show gaps that point to an unexpectedly large Dzyaloshinskii-Moriya interaction on the nearest-neighbor bond, with D1J1/2. A better understanding of the Dzyaloshinskii-Moriya interaction in this material should shed light on the multiferroicity of the related Ni3V2O8. At a higher temperature where Co3V2O8 displays an antiferromagnetic spin density wave structure, there are no well-defined spin wave excitations, with most of the spectral weight observed in broad diffuse scattering centered at the (0, 0.5, 0) antiferromagnetic Bragg peak.

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<![CDATA[Refined symmetry indicators for topological superconductors in all space groups]]> https://www.researchpad.co/article/elastic_article_7716 Topological superconductors are exotic phases of matter featuring robust surface states that could be leveraged for topological quantum computation. A useful guiding principle for the search of topological superconductors is to relate the topological invariants with the behavior of the pairing order parameter on the normal-state Fermi surfaces. The existing formulas, however, become inadequate for the prediction of the recently proposed classes of topological crystalline superconductors. In this work, we advance the theory of symmetry indicators for topological (crystalline) superconductors to cover all space groups. Our main result is the exhaustive computation of the indicator groups for superconductors under a variety of symmetry settings. We further illustrate the power of this approach by analyzing fourfold symmetric superconductors with or without inversion symmetry and show that the indicators can diagnose topological superconductors with surface states of different dimensionalities or dictate gaplessness in the bulk excitation spectrum.

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<![CDATA[Surface-state Coulomb repulsion accelerates a metal-insulator transition in topological semimetal nanofilms]]> https://www.researchpad.co/article/N0a4ade9e-7b60-44fc-88b4-e5bfe548c8eb

Increased Coulomb repulsion from surface states substantially modulates quantum confinement in topological semimetal nanofilms.

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<![CDATA[Microscopic pathways for stress relaxation in repulsive colloidal glasses]]> https://www.researchpad.co/article/Na082c33b-f870-4886-b656-a338eb2fabeb

How residual stresses in colloids generate directional and heterogeneous motions down to fundamental length scales.

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<![CDATA[The effect of Mn2Sb2 and Mn2Sb secondary phases on magnetism in (GaMn)Sb thin films]]> https://www.researchpad.co/article/N94466bcc-ad77-4d3b-8f3f-3aceb39bbed5

In this work, a detailed study of structural, electrical and magnetic characterization of (GaMn)Sb diluted magnetic semiconductors (DMS) is presented. (GaMn)Sb thin films were grown by DC magnetron co-sputtering method as an innovative procedure to fabricate III-V DMS. The presence of unusual Mn2Sb2 and Mn2Sb secondary phases, induced by substrate temperature and deposition time, were revealed through XRD measurements. Magnetization measurements allow determining crossover between a paramagnetic-like to a ferromagnetic-like behavior controlled by secondary phases. It was found that both, the magnetic remanence and magnetic coercivity, increases with substrate temperature. Interestingly, the magnetic response is paramagnetic at lower deposition times and substrate temperatures, and XRD measurements suggest the absence of Mn2Sb and Mn2Sb2 in secondary phases. For longer deposition times or higher substrate temperature, XRD shows the presence of Mn2Sb2 and Mn2Sb phases and ferromagnetic-like behavior. The DC resistivity of our samples was characterized and the carrier density was determined by Hall measurements and, in contrast with the reported in other studies, found them to be a p-type semiconductor with carrier densities as big as one order of magnitude larger than reported values. From the ferromagnetic-like samples, evidence of an anomalous Hall-effect in the sample was found, with higher magnetic saturation and a anomalous Hall conductivity of 2380 S/cm. All the results point to a contribution of the secondary phases to the overall magnetic response of the samples used, and suggest the importance of studying the formation of secondary phases in the growth of DMS, especially, for the case of (GaMn)Sb where Mn ion can have multiple oxidation states.

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<![CDATA[Four-wave mixing of topological edge plasmons in graphene metasurfaces]]> https://www.researchpad.co/article/N3e5b3352-8705-493d-9b5e-bb322490e321

It is demonstrated that net optical gain can be achieved via topologically protected four-wave mixing in a graphene metasurface.

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<![CDATA[High-frequency rectification via chiral Bloch electrons]]> https://www.researchpad.co/article/Ne2b629de-c87a-465c-9632-724022c3d4df

Engineering quantum crystals realizes high-frequency rectifiers by rational material design.

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<![CDATA[Scaling, rotation, and channeling behavior of helical and skyrmion spin textures in thin films of Te-doped Cu2OSeO3]]> https://www.researchpad.co/article/N0ecd204c-15d0-4098-ad5b-56fd27cdab92

We report on scaling, rotation, and channeling behavior of helical and skyrmion spin textures in thin films of Te-doped Cu2OSeO3.

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<![CDATA[Chiral superconductivity in the alternate stacking compound 4Hb-TaS2]]> https://www.researchpad.co/article/N734210af-0ecf-4171-948b-fc8335194069

Chiral superconductivity in 4Hb-TaS2 was discovered using muon spin rotation.

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<![CDATA[Nonreciprocal transport in gate-induced polar superconductor SrTiO3]]> https://www.researchpad.co/article/N13bebcd3-3e09-488b-9c02-4611e11cf398

Characteristics of gate-induced 2D superconductor SrTiO3, a possible Rashba superconductor, are studied via nonlinear transport.

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<![CDATA[The electronic thickness of graphene]]> https://www.researchpad.co/article/N34d390e3-f4c7-426b-8396-a65465411992

The electronic thickness of graphene is measured by two capacitively coupled, atomically close graphene layers.

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<![CDATA[Local Berry curvature signatures in dichroic angle-resolved photoelectron spectroscopy from two-dimensional materials]]> https://www.researchpad.co/article/Nccbefd34-f6f7-490a-bc40-1902bd0fa9c1

Orbital polarization and Berry curvature signatures are mapped out by circular dichroism in angle-resolved photoemission.

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<![CDATA[Scalable Majorana vortex modes in iron-based superconductors]]> https://www.researchpad.co/article/Nbc0fabdd-ba1e-4042-ad64-e47058f382f2

A simulation study with experimental data analysis shows the presence of multiple Majorana modes in iron-based superconductors.

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<![CDATA[Generalized Anderson’s theorem for superconductors derived from topological insulators]]> https://www.researchpad.co/article/N1c88d9d5-a670-4596-9732-cfd177ee2307

Cooper pairs in unconventional superconductors having extra internal degrees of freedom are protected in an unexpected way.

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<![CDATA[Automated structure discovery in atomic force microscopy]]> https://www.researchpad.co/article/Nbac1a396-0a61-42e9-8558-9c2080e4396f

We develop a deep learning method that predicts atomic structure directly from experimental atomic force microscopy images.

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