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Ivan Yu Chernyshov, Philip V Toukach
Motivation: Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. Results: The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule...
March 14, 2018: Bioinformatics
Deepak Reddy Gade, Amareswararao Makkapati, Rajesh Babu Yarlagadda, Godefridus J Peters, B S Sastry, V V S Rajendra Prasad
Overexpression of P-glycoprotein (P-gp) leads to the emergence of multidrug resistance (MDR) in cancer treatment. Acridones have the potential to reverse MDR and sensitize cells. In the present study, we aimed to elucidate the chemosensitization potential of acridones by employing various molecular modelling techniques. Pharmacophore modeling was performed for the dataset of chemosensitizing acridones earlier proved for cytotoxic activity against MCF7 breast cancer cell line. Gaussian-based QSAR studies also performed to predict the favored and disfavored region of the acridone molecules...
February 24, 2018: Computational Biology and Chemistry
M Kulik, D Kołodyńska, A Bayramov, A Drozdziel, A Olejniczak, J Żuk
The surfaces of (100) GaAs were irradiated with In+ ions. The implanted samples were isobaric annealed at 800°C and then of dielectric function, the surface atomic concentrations of atoms and also the chemical composition of the near surface layers in these implanted semiconductor samples were obtained. The following investigation methods were used: spectroscopic ellipsometry (SE), Rutherford backscattering spectrometry analyses (RBSA) and X-ray photoelectron spectroscopy (XPS) in the study of the above mentioned quantities, respectively...
February 12, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
A Garbout, M Férid
Considering the features in changing the structure and properties of rare earth titanates pyrochlores, the substituted Dy2 Ti2 O7 may be very attractive for various applications. Effect of Sm and Y substitution on the structural properties of Dy2 Ti2 O7 ceramic was established. These ceramics were prepared by solid-state reaction and characterized by X-ray diffraction and Raman spectroscopy. Both analysis show that YDyTi2 O7 with the pyrochlore structure is obtained after heating at 1400°C, but SmDyTi2 O7 has already formed after sintering at 1200°C...
March 10, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
David M Thal, Ziva Vuckovic, Christopher J Draper-Joyce, Yi-Lynn Liang, Alisa Glukhova, Arthur Christopoulos, Patrick M Sexton
G protein-coupled receptors (GPCRs) are the largest superfamily of cell surface receptor proteins and are important drug targets for many human diseases. In the last decade, remarkable progress has been made in the determination of atomic structures of GPCRs with over 200 structures from 53 unique receptors having been solved. Technological advances in protein engineering and X-ray crystallography have driven much of the progress to date. However, recent advances in cryo-electron microscopy have facilitated the structural determination of three new structures of active-state GPCRs in complex with heterotrimeric G protein...
March 13, 2018: Current Opinion in Structural Biology
Hendrik Göddeke, M Hadi Timachi, Cedric A Hutter, Laura Galazzo, Markus A Seeger, Mikko Karttunen, Enrica Bordignon, Lars V Schäfer
ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemo-mechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological membranes. The precise nature of the structural dynamics behind the large-scale conformational transition as well as the coupling of NBD and TMD motions is still unresolved...
March 16, 2018: Journal of the American Chemical Society
Marcin Maździarz, Adam Mrozek, Wacław Kuś, Tadeusz Burczyński
A potentially new, single-atom thick semiconducting 2D- graphene -like material, called Anisotropic-cyclicgraphene , has been generated by the two stage searching strategy linking molecular and ab initio approach. The candidate was derived from the evolutionary-based algorithm and molecular simulations was then profoundly analysed using first-principles density functional theory from the structural, mechanical, phonon, and electronic properties point of view. The proposed polymorph of graphene ( rP16 -P1m1) is mechanically, dynamically, and thermally stable and can achieve semiconducting with a direct band gap of 0...
March 16, 2018: Materials
Francesca Malvano, Luigi Maritato, Giovanni Carapella, Pasquale Orgiani, Roberto Pilloton, Marisa Di Matteo, Donatella Albanese
Due to their interesting ferroelectric, conductive and dielectric properties, in recent years, perovskite-structured materials have begun to attract increasing interest in the biosensing field. In this study, a strontium titanate perovskite layer (SrTiO₃) has been synthesized on a platinum electrode and exploited for the development of an impedimetric label-free immunosensor for Escherichia coli O157:H7 detection. The electrochemical characterization of the perovskite-modified electrode during the construction of the immunosensor, as well as after the interaction with different E...
March 16, 2018: Biosensors
Qiang Zhang, Tianyuan Xin, Xiaoke Lu, Yuexia Wang
We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method...
March 16, 2018: Materials
N G Fischer, A Tsujimoto, A G Baruth
OBJECTIVE: Limited information is available on how to polish and finish zirconia surfaces following computer-aided design/computer-aided manufacturing (CAD/CAM), specifically, how differing application forces and reuse of zirconia polishing systems affect zirconia topography. PURPOSE: To determine the effect of differing, clinically relevant, polishing application forces and multiple usages of polishing burs on the surface topography of CAD/CAM zirconia. METHODS: One hundred twenty 220-grit carbide finished zirconia disks were sintered according to manufacturer's directions and divided into two groups for the study of two coarse polishing bur types...
March 16, 2018: Operative Dentistry
Julian C Berengut, Dmitry Budker, Cédric Delaunay, Victor V Flambaum, Claudia Frugiuele, Elina Fuchs, Christophe Grojean, Roni Harnik, Roee Ozeri, Gilad Perez, Yotam Soreq
We explore a method to probe new long- and intermediate-range interactions using precision atomic isotope shift spectroscopy. We develop a formalism to interpret linear King plots as bounds on new physics with minimal theory inputs. We focus only on bounding the new physics contributions that can be calculated independently of the standard model nuclear effects. We apply our method to existing Ca^{+} data and project its sensitivity to conjectured new bosons with spin-independent couplings to the electron and the neutron using narrow transitions in other atoms and ions, specifically, Sr and Yb...
March 2, 2018: Physical Review Letters
Jingshan Han, Thibault Vogt, Christian Gross, Dieter Jaksch, Martin Kiffner, Wenhui Li
We present an experimental demonstration of converting a microwave field to an optical field via frequency mixing in a cloud of cold ^{87}Rb atoms, where the microwave field strongly couples to an electric dipole transition between Rydberg states. We show that the conversion allows the phase information of the microwave field to be coherently transferred to the optical field. With the current energy level scheme and experimental geometry, we achieve a photon-conversion efficiency of ∼0.3% at low microwave intensities and a broad conversion bandwidth of more than 4 MHz...
March 2, 2018: Physical Review Letters
Wei Qin, Adam Miranowicz, Peng-Bo Li, Xin-You Lü, J Q You, Franco Nori
We propose an experimentally feasible method for enhancing the atom-field coupling as well as the ratio between this coupling and dissipation (i.e., cooperativity) in an optical cavity. It exploits optical parametric amplification to exponentially enhance the atom-cavity interaction and, hence, the cooperativity of the system, with the squeezing-induced noise being completely eliminated. Consequently, the atom-cavity system can be driven from the weak-coupling regime to the strong-coupling regime for modest squeezing parameters, and even can achieve an effective cooperativity much larger than 100...
March 2, 2018: Physical Review Letters
Rui Liu, Huimin Chen, Liping Fang, Cuihong Xu, Zuoliang He, Yujian Lai, Huachao Zhao, Deribachew Bekana Hirpa, Jing-Fu Liu
AuPd bimetallic nanocatalysts exhibit superior catalytic performance in the cleavage of carbon-halogen bonds (C-X) in the hazardous halogenated pollutants. A better understanding of how Au atoms promote the reactivity of Pd sites rather than vaguely interpreting as bimetallic effect, and determining which type of Pd sites are necessary for these reactions are crucial factors for the design of atomically precise nanocatalysts that make full use of both the Pd and Au atoms. Herein, we systematically manipulated the coordination number of Pd-Pd, d-orbital occupation state and Au-Pd interface of the Pd reactive centers, and studied the structure-activity relationship of Au-Pd in the catalyzed cleavage of C-X bonds...
March 16, 2018: Environmental Science & Technology
Joyce Pham, Gordon J Miller
Using density functional theory, the crystal structure variation of AAuAl (A = Ca, Sc, and Ti) from orthorhombic Co2 Si-type to distorted hexagonal Fe2 P-type and then Ni2 In-type structures is shown to correlate with their electronic structures and valence electron counts, sizes of the active metals A, and site preferences for Au and Al atoms, which are arranged to maximize Au-Al nearest neighbor contacts. An evaluation of chemical pressure imposed by the varying A metals using total energy vs volume calculations indicates that larger unit cell volumes favor the orthorhombic structure, whereas smaller volumes favor the hexagonal structures...
March 16, 2018: Inorganic Chemistry
Qin Xiang, Yuping Liu, Xuefeng Zou, Bingbing Hu, Yujie Qiang, Danmei Yu, Wei Yin, Changguo Chen
In this work, g-C3N4@GO gel-like hybrid is obtained by assembling intentionally exfoliated g-C3N4 sheets on graphene oxide (GO) sheets under a hydrothermal condition. A specific N-doping process is firstly designed by heating the g-C3N4@GO interlaced hybrid in vacuum to form nitrogen-doped graphene nanosheets (NGS) with high level of pyridinic-N (56.0%) and edge-rich defect structure. The prepared NGS exhibited a great electrocatalysis for oxygen reduction reaction (ORR) in terms of the activity, durability, methanol tolerance, and the reaction kinetics...
March 16, 2018: ACS Applied Materials & Interfaces
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Iain M Aldous, Laurence J Hardwick
The deposition and dissolution of sodium superoxide (NaO2 ) was investigated by atomic force microscopy. Rectangular prisms consisting of 8 smaller sub-structures grew from NaO2 platelets, when discharged in 0.5 M NaClO4 , diethylene glycol dimethyl ether on highly ordered pyrolytic graphite. During oxidation the 8 sub-structures are conserved. Ring-like structures of Na2 CO3 of 200 nm diameter remain at the end of oxidation.
March 16, 2018: Chemical Communications: Chem Comm
Ze Yang, Xiangyan Shen, Ning Wang, Jianjiang He, Xiaodong Li, Xin Wang, Zhufeng Hou, Kun Wang, Juan Gao, Tonggang Jiu, Changshui Huang
The qualitative and quantitative nitrogen-doping strategy for carbon materials is reported here. Novel porous nanocarbon networks pyrimidine-graphdiyne (PM-GDY) and pyridine-graphdiyne (PY-GDY) films with large areas were successfully prepared. These films are self-supported, uniform, continuous, flexible, transparent, and quantitively doped with merely pyridine-like nitrogen (N) atoms through the facile chemical synthesis route. Theoretical predictions imply these N doped carbonaceous materials are much favorable for storing lithium (Li)-ions since the pyridinic N can enhance the interrelated binding energy...
March 16, 2018: ACS Applied Materials & Interfaces
Julia Tesch, Fabian Paschke, Mikhail Fonin, Marko Wietstruk, Stefan Böttcher, Roland J Koch, Aaron Bostwick, Chris Jozwiak, Eli Rotenberg, Anna Makarova, Beate Paulus, Elena Voloshina, Yuriy Dedkov
The implementation of graphene in semiconducting technology requires precise knowledge about the graphene-semiconductor interface. In our work the structure and electronic properties of the graphene/n-Ge(110) interface are investigated on the local (nm) and macro (from μm to mm) scales via a combination of different microscopic and spectroscopic surface science techniques accompanied by density functional theory calculations. The electronic structure of freestanding graphene remains almost completely intact in this system, with only a moderate n-doping indicating weak interaction between graphene and the Ge substrate...
March 16, 2018: Nanoscale
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