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https://www.readbyqxmd.com/read/28805849/topology-of-polymer-chains-under-nanoscale-confinement
#1
Vahid Satarifard, Maziar Heidari, Samaneh Mashaghi, Sander J Tans, Mohammad Reza Ejtehadi, Alireza Mashaghi
Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of lp under a spherical confinement of radius Rc...
August 14, 2017: Nanoscale
https://www.readbyqxmd.com/read/28805826/violation-of-ohm-s-law-in-a-weyl-metal
#2
Dongwoo Shin, Yongwoo Lee, M Sasaki, Yoon Hee Jeong, Franziska Weickert, Jon B Betts, Heon-Jung Kim, Ki-Seok Kim, Jeehoon Kim
Ohm's law is a fundamental paradigm in the electrical transport of metals. Any transport signatures violating Ohm's law would give an indisputable fingerprint for a novel metallic state. Here, we uncover the breakdown of Ohm's law owing to a topological structure of the chiral anomaly in the Weyl metal phase. We observe nonlinear I-V characteristics in Bi0.96Sb0.04 single crystals in the diffusive limit, which occurs only for a magnetic-field-aligned electric field (E∥B). The Boltzmann transport theory with the charge pumping effect reveals the topological-in-origin nonlinear conductivity, and it leads to a universal scaling function of the longitudinal magnetoconductivity, which completely describes our experimental results...
August 14, 2017: Nature Materials
https://www.readbyqxmd.com/read/28805825/the-processing-and-heterostructuring-of-silk-with%C3%A2-light
#3
Mehra S Sidhu, Bhupesh Kumar, Kamal P Singh
Spider silk is a tough, elastic and lightweight biomaterial, although there is a lack of tools available for non-invasive processing of silk structures. Here we show that nonlinear multiphoton interactions of silk with few-cycle femtosecond pulses allow the processing and heterostructuring of the material in ambient air. Two qualitatively different responses, bulging by multiphoton absorption and plasma-assisted ablation, are observed for low- and high-peak intensities, respectively. Plasma ablation allows us to make localized nanocuts, microrods, nanotips and periodic patterns with minimal damage while preserving molecular structure...
August 14, 2017: Nature Materials
https://www.readbyqxmd.com/read/28805653/magneto-optical-properties-of-topological-insulator-thin-films-with-broken-inversion-symmetry
#4
Kulsoom Rahim, Ahsan Ullah, Muhammad Tahir, Kashif Sabeeh
We determine the optical response of ultrathin film topological insulators in the presence of a quantizing external magnetic field taking into account both hybridization between surface states, broken inversion symmetry and explicit time reversal symmetry breaking by the magnetic field. We find that breaking of inversion symmetry in the system, which can be due to interaction with a substrate or electrical gating, results in Landau level crossings and opening of additional optical transition channels that were previously forbidden...
August 14, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28805230/the-influence-of-topological-phase-transition-on-the-superfluid-density-of-overdoped-copper-oxides
#5
V R Shaginyan, V A Stephanovich, A Z Msezane, G S Japaridze, K G Popov
We show that a quantum phase transition, generating flat bands and altering Fermi surface topology, is a primary reason for the exotic behavior of the overdoped high-temperature superconductors represented by La2-xSrxCuO4, whose superconductivity features differ from what is predicted by the classical Bardeen-Cooper-Schrieffer theory. This observation can open avenues for chemical preparation of high-Tc materials. We demonstrate that (1) at temperature T = 0, the superfluid density ns turns out to be considerably smaller than the total electron density; (2) the critical temperature Tc is controlled by ns rather than by doping, and is a linear function of the ns; (3) at T > Tc the resistivity ρ(T) varies linearly with temperature, ρ(T) ∝ αT, where α diminishes with Tc → 0, whereas in the normal (non superconducting) region induced by overdoping, Tc = 0, and ρ(T) ∝ T(2)...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28805214/the-low-populated-folding-intermediate-of-a-mutant-of-the-fyn-sh3-domain-identified-by-a-simple-model
#6
Jing Wu, Guojun Chen, Zhuqing Zhang, Ping Zhang, Tao Chen
Experimental studies indicate that the A39V/N53P/V55L Fyn SH3 domain folds from the unfolded state to the native state via a low-populated on-pathway intermediate, whereas the folding of the wildtype is two-state-like. To get insights into the biophysical basis of their different folding mechanisms, we used native-centric models with and without additional transferrable, sequence-dependent nonnative hydrophobic interactions to study the folding behaviors of the Fyn SH3 domain and its mutant. The pure native-centric model predicts that both the wildtype and the mutant fold in a two-state manner, without any detectable intermediate...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28804969/on-chip-andreev-devices-hard-superconducting-gap-and-quantum-transport-in-ballistic-nb-in0-75-ga0-25-as-quantum-well-nb-josephson-junctions
#7
Kaveh Delfanazari, Reuben K Puddy, Pengcheng Ma, Teng Yi, Moda Cao, Yilmaz Gul, Ian Farrer, David A Ritchie, Hannah J Joyce, Michael J Kelly, Charles G Smith
A superconducting hard gap in hybrid superconductor-semiconductor devices has been found to be necessary to access topological superconductivity that hosts Majorana modes (non-Abelian excitation). This requires the formation of homogeneous and barrier-free interfaces between the superconductor and semiconductor. Here, a new platform is reported for topological superconductivity based on hybrid Nb-In0.75 Ga0.25 As-quantum-well-Nb that results in hard superconducting gap detection in symmetric, planar, and ballistic Josephson junctions...
August 14, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28804927/hedgehog-like-upconversion-crystals-controlled-growth-and-molecular-sensing-at-single-particle-level
#8
Xiaowang Liu, Xiyan Li, Xian Qin, Xiaoji Xie, Ling Huang, Xiaogang Liu
Topological control of nanostructures plays a crucial role in understanding the crystal growth process at the nanometer length scale. Here, the scalable synthesis of upconversion materials with distinct hedgehog-like morphologies by a seed-mediated synthetic procedure is reported. It is demonstrated that a close match in the crystal lattice between the core and shell components is essential for synthesizing such hierarchical nanostructures. These optical nanomaterials also enable the development of a single-particle-based platform for high-sensitivity molecular sensing...
August 14, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28804744/reduced-rich-club-connectivity-is-related-to-disability-in-primary-progressive-ms
#9
Jan-Patrick Stellmann, Sibylle Hodecker, Bastian Cheng, Nadine Wanke, Kim Lea Young, Claus Hilgetag, Christian Gerloff, Christoph Heesen, Götz Thomalla, Susanne Siemonsen
OBJECTIVE: To investigate whether the structural connectivity of the brain's rich-club organization is altered in patients with primary progressive MS and whether such changes to this fundamental network feature are associated with disability measures. METHODS: We recruited 37 patients with primary progressive MS and 21 healthy controls for an observational cohort study. Structural connectomes were reconstructed based on diffusion-weighted imaging data using probabilistic tractography and analyzed with graph theory...
September 2017: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/28804492/population-genetic-differentiation-and-taxonomy-of-three-closely-related-species-of-saxifraga-saxifragaceae-from-southern-tibet-and-the-hengduan-mountains
#10
Qing-Bo Gao, Yan Li, Zhuo-Ma Gengji, Richard J Gornall, Jiu-Li Wang, Hai-Rui Liu, Liu-Kun Jia, Shi-Long Chen
The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28803781/myc-regulates-chromatin-decompaction-and-nuclear-architecture-during-b-cell-activation
#11
Kyong-Rim Kieffer-Kwon, Keisuke Nimura, Suhas S P Rao, Jianliang Xu, Seolkyoung Jung, Aleksandra Pekowska, Marei Dose, Evan Stevens, Ewy Mathe, Peng Dong, Su-Chen Huang, Maria Aurelia Ricci, Laura Baranello, Ying Zheng, Francesco Tomassoni Ardori, Wolfgang Resch, Diana Stavreva, Steevenson Nelson, Michael McAndrew, Adriel Casellas, Elizabeth Finn, Charles Gregory, Brian Glenn St Hilaire, Steven M Johnson, Wendy Dubois, Maria Pia Cosma, Eric Batchelor, David Levens, Robert D Phair, Tom Misteli, Lino Tessarollo, Gordon Hager, Melike Lakadamyali, Zhe Liu, Monique Floer, Hari Shroff, Erez Lieberman Aiden, Rafael Casellas
50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input...
July 28, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28802479/emulsion-templated-vesicles-with-symmetric-or-asymmetric-membranes
#12
REVIEW
Yuting Huang, Shin-Hyun Kim, Laura R Arriaga
Emulsion droplets with well-controlled topologies are used as templates for forming vesicles with either symmetric or asymmetric membranes. This review summarizes the available technology to produce these templates, the strategies and critical parameters involved in the transformation of emulsion droplets into vesicles, and the properties of the generated vesicles, with a special focus on the composition and material distribution of the vesicle membrane. Here, we also address limitations in the field and point to future fundamental and applied research in the area...
July 17, 2017: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#13
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28802020/investigating-the-diversity-of-effector-genes-in-the-banana-pathogen-fusarium-oxysporum-f-sp-cubense-reveals-evidence-of-horizontal-gene-transfer
#14
Elizabeth Czislowski, Sam Fraser-Smith, Manuel Zander, Wayne T O'Neill, Rachel A Meldrum, Lucy T T Tran-Nguyen, Jacqueline Batley, Elizabeth A B Aitken
It is hypothesised that the virulence of phytopathogenic fungi is mediated through the secretion of small effector proteins that interfere with the defence responses of the host plant. In Fusarium oxysporum, one family of effectors, the secreted in xylem (SIX) genes, have been identified. We sought to characterise the diversity and evolution of the SIX genes in the banana-infecting lineages of F. oxysporum f.sp. cubense (Foc). Whole-genome sequencing data was generated for the 23 genetic lineages of Foc, which were subsequently queried for the 14 known SIX genes (SIX1-SIX14)...
August 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28801928/cyclic-oligomer-design-with-de-novo-%C3%AE-%C3%AE-proteins
#15
Yu-Ru Lin, Nobuyasu Koga, Sergey M Vorobiev, David Baker
We have previously shown that monomeric globular αβ- proteins can be designed de novo with considerable control over topology, size and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone...
August 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28801603/identifying-the-tilt-angle-and-correcting-the-orbital-angular-momentum-spectrum-dispersion-of-misaligned-light-beam
#16
Peng Zhao, Shikang Li, Yu Wang, Xue Feng, Cui Kaiyu, Liu Fang, Wei Zhang, Yidong Huang
The axis tilt of light beam in optical system would introduce the dispersion of orbital angular momentum (OAM) spectrum. To deal with it, a two-step method is proposed and demonstrated. First, the tilt angle of optical axis is identified with a deduced relation between the tilt angle and the variation of OAM topological charges with different reference axes, which is obtained with the help of a charge coupled device (CCD) camera. In our experiments, the precision of measured tilt angle is about 10(-4) rad with topological charges of -3~3...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801508/intricate-and-cell-type-specific-populations-of-endogenous-circular-dna-eccdna-in-caenorhabditis-elegans-and-homo-sapiens
#17
Massa J Shoura, Idan Gabdank, Loren Hansen, Jason Merker, Jason Gotlib, Stephen D Levene, Andrew Z Fire
Investigations aimed at defining the 3-D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in C. elegans and in three human cell types, utilizing a set of DNA-topology dependent approaches for enrichment and characterization...
August 11, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28800534/molecular-understanding-of-the-interaction-of-methyl-hydrogen-sulfate-with-ammonia-dimethylamine-water
#18
Xia Sheng, Hailiang Zhao, Lin Du
Theoretical calculations at the B3LYP-D3/aug-cc-pVTZ (aug-cc-pV(T+d)Z for sulfur) level were used to investigate the contribution of methyl hydrogen sulfate (MHS) to new particle formation with the common atmospheric aerosol nucleation precursors including water (H2O), ammonia (NH3), and dimethylamine (DMA). A typical characteristic feature of the MHS-containing complexes is the formation of six- or eight-membered ring structures via SOH⋯O (MHS donor), OH⋯O/N (H2O donor) and NH⋯O/N (NH3/DMA donor). The stability of the complexes was evaluated based on the calculated binding energies...
August 4, 2017: Chemosphere
https://www.readbyqxmd.com/read/28800102/a-grid-connected-photovoltaic-inverter-with-battery-supercapacitor-hybrid-energy-storage
#19
Víctor Manuel Miñambres-Marcos, Miguel Ángel Guerrero-Martínez, Fermín Barrero-González, María Isabel Milanés-Montero
The power generation from renewable power sources is variable in nature, and may contain unacceptable fluctuations, which can be alleviated by using energy storage systems. However, the cost of batteries and their limited lifetime are serious disadvantages. To solve these problems, an improvement consisting in the collaborative association of batteries and supercapacitors has been studied. Nevertheless, these studies don't address in detail the case of residential and large-scale photovoltaic systems. In this paper, a selected combined topology and a new control scheme are proposed to control the power sharing between batteries and supercapacitors...
August 11, 2017: Sensors
https://www.readbyqxmd.com/read/28799862/disrupted-topologic-efficiency-of-white-matter-structural-connectome-in-individuals-with-subjective-cognitive-decline
#20
Ni Shu, Xiaoni Wang, Qiuhui Bi, Tengda Zhao, Ying Han
Purpose To determine whether individuals with subjective cognitive decline (SCD), which is defined by memory complaints with normal performance at objective neuropsychologic examinations, exhibit disruptions of white matter (WM) connectivity and topologic alterations of the brain structural connectome. Materials and Methods Diffusion-tensor magnetic resonance imaging and graph theory approaches were used to investigate the topologic organization of the brain structural connectome in 36 participants with SCD (21 women: mean age, 62...
August 11, 2017: Radiology
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