jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Venkata S. Mandala | Shu-Yu Liao | Martin D. Gelenter | Mei Hong
Source: Scientific Reports (article, 2019-03-06)
Field: Chemistry — Spectroscopy

The Transmembrane Conformation of the Influenza B Virus M2 Protein in Lipid Bilayers Influenza A and B viruses cause seasonal flu epidemics. The M2 protein of influenza B (BM2) is a membrane-embedded tetrameric proton channel that is essential for the viral lifecycle. BM2 is a functional analog of AM2 but shares only 24% sequence identity for the transmembrane (TM) domain. The structure and function of AM2, which is targeted by two antiviral drugs, have been well characterized. In comparison, much less is known about the structure of BM2 and no drug is so far available to inhibit this protein. Here we use solid-state NMR spectroscopy to investigate the conformation of BM2(1-51) in phospholipid bilayers at high pH, which corresponds to the closed state of the channel. Using 2D and 3D correlation NMR experiments, we resolved and assigned the <sup>13</sup>C and <sup>15</sup>N chemical shifts of 29 residues of the TM domain, which yielded backbone (φ, ψ) torsion angles. Residues 6-28 form a well-ordered α-helix, whereas residues 1-5 and 29-35 display chemical shifts that are indicative of random coil or β-sheet conformations. The length of the BM2-TM helix resembles that of AM2-TM, despite their markedly different amino acid sequences. In comparison, large <sup>15</sup>N chemical shift differences are observed between bilayer-bound BM2 and micelle-bound BM2, indicating that the TM helix conformation and the backbone hydrogen bonding in lipid bilayers differ from the micelle-bound conformation. Moreover, H<sup>N</sup> chemical shifts of micelle-bound BM2 lack the periodic trend expected for coiled coil helices, which disagree with the presence of a coiled coil structure in micelles. These results establish the basis for determining the full three-dimensional structure of the tetrameric BM2 to elucidate its proton-conduction mechanism. Lipid bilayer ; Transmembrane domain ; Chemical shift ; Random coil ; Helix (gastropod) ; Chemistry ; Micelle ; Crystallography ; Nuclear magnetic resonance spectroscopy ; Transmembrane protein ; Hydrogen bond ; Protein structure ; Stereochemistry ; Biophysics ; Circular dichroism ; Membrane ; Molecule ; Biochemistry ; Biology ; Receptor ; Organic chemistry Advanced NMR Techniques and Applications ; Lipid Membrane Structure and Behavior ; Protein Structure and Dynamics
Authors: Janko Kos | Ana Mitrović
Source: Acta Biochimica Polonica (review, 2019-12-13)
Field: Chemistry — Organic Chemistry

Nitroxoline: repurposing its antimicrobial to antitumor application Cancer is a disease receiving an outstanding input of funds for basic and clinical research but is, nevertheless, still the second leading cause of death in the developed world and a great burden for health systems. New drugs are therefore needed to improve therapy, prolong survival of cancer patients and improve their quality of life. The high cost of development and clinical evaluation of new drugs limits the number that actually enter clinical use. To overcome this problem, repurposing of established drugs for new indications has gained a lot of interest, especially in the field of oncology. The well-established antimicrobial agent nitroxoline has been identified as a promising candidate to be repurposed for cancer treatment in several independent studies. Here we have reviewed a wide range of molecular mechanisms and tumor models involving nitroxoline in impairment of tumor progression. Furthermore, nitroxoline was used as a lead compound for structure-based chemical synthesis of new derivatives in order to improve its potency as well as selectivity for various targets. The potent antitumor activity of nitroxoline points strongly in the direction of its repurposing for cancer treatment and to the benefits of this strategy for patients and healthcare system. Repurposing ; Drug repositioning ; Medicine ; Antimicrobial ; Cancer ; Disease ; Cancer therapy ; Pharmacology ; Drug ; Internal medicine ; Biology Synthesis and Catalytic Reactions ; Nitric Oxide and Endothelin Effects ; Synthesis and biological activity
Authors: Ashesh Ghosh | Kenneth S. Schweizer
Source: The Journal of Chemical Physics (article, 2019-12-26)
Field: Materials Science — Materials Chemistry

Microscopic theory of the influence of strong attractive forces on the activated dynamics of dense glass and gel forming fluids We theoretically study the nonmonotonic (re-entrant) activated dynamics associated with a finite time scale kinetically defined repulsive glass to fluid to attractive glass transition in high volume fraction particle suspensions interacting via strong short range attractive forces. The classic theoretical "projection" approximation that replaces all microscopic forces by a single effective force determined solely by equilibrium pair correlations is revisited based on the "projectionless dynamic theory" (PDT). A hybrid-PDT approximation is formulated that explicitly quantifies how attractive forces induce dynamical constraints, while singular hard core interactions are treated based on the projection approach. Both the effects of interference between repulsive and attractive forces, and structural changes due to attraction-induced bond formation that competes with caging, are included. Combined with the microscopic Elastically Collective Nonlinear Langevin Equation (ECNLE) theory of activated relaxation, the resultant approach appears to properly capture both the re-entrant dynamic crossover behavior and the strong nonmonotonic variation of the activated structural relaxation time with attraction strength and range at very high volume fractions as observed experimentally and in simulations. Testable predictions are made. Major differences compared to both ideal mode coupling theory and ECNLE theory based on the full force projection approximation are identified. Calculations are also performed for smaller time and length scale intracage dynamics relevant to the non-Gaussian parameter based on analyzing the dynamic free energy that controls particle trajectories. Implications of the new theory for thermal glass forming liquids with relatively long range attractive forces are briefly analyzed. Langevin dynamics ; Microscopic theory ; Relaxation (psychology) ; Particle (ecology) ; Range (aeronautics) ; Crossover ; Coupling (piping) ; Thermal fluctuations ; Volume fraction ; Glass transition Material Dynamics and Properties ; Advanced Physical and Chemical Molecular Interactions ; Electrostatics and Colloid Interactions
Authors: Muhammad Mohsin | Naiwen Li | Sohail Muhammad | KASHIF MAJEED MUHAMMAD
Source: Industria Textila (article, 2019-01-01)
Field: Materials Science — Polymers and Plastics

Investigation of various factors affecting the coefficient of friction of yarnby using Taguchi method This research aims to analyze certain effects of yarn characteristics such as: cotton type, yarn quality, yarn spinning technique, yarn twist and linear density and yarn finish on coefficient of friction of yarn by using Taguchi approach. For evaluation of levels and response factors, 72 experiments are performed by using L36 orthogonal design twice for Taguchi approach. The results show that yarns comprising of finer fibers, combed, waxed, Rotor spun, optimum twist and low linear density have lowest coefficient of friction of yarn, which ultimately improves subsequent textile processes and improve product qualities. Yarn ; Taguchi methods ; Spinning ; Linear density ; Materials science ; Composite material ; Rotor (electric) ; Friction coefficient ; Orthogonal array ; Coefficient of friction ; Engineering drawing ; Mechanical engineering ; Engineering Textile materials and evaluations
Authors: Y Yunus | Devianti Devianti | Purwana Satriyo | Agus Arip Munawar
Source: IOP Conference Series Earth and Environmental Science (article, 2019-10-01)
Field: Chemistry — Analytical Chemistry

Rapid Prediction of Soil Quality Indices Using Near Infrared Spectroscopy Abstract To determine soil macro nutrients and other quality indices, conventional and laborious procedures were employed. However, this method is time consuming, involve chemical materials and laborious. Thus, alternative fast and environmental friendly method is required to determine several quality indices in agricultural soil. This present study is aimed to apply near infrared spectroscopy (NIRS) in determining soil macro nutrients namely N, P and K. Diffuse reflectance spectrum of soil samples were acquired and recorded in wavelength range from 1000 to 2500 nm. Near infrared spectrum were enhanced using de-trending (DT) method. Prediction models, used to predict N, P and K, were established using principal component regression (PCR) algorithm followed by leverage validation. The results showed that NIRS method can determine all three quality indices with good accuracy and robustness. Maximum correlation coefficient (r) for N, P, K prediction were achieved using DT correction method with r = 0.86 for N prediction, r = 0.90 for both P and K prediction. Based on obtained results, it may conclude that NIRS can applied as an alternative rapid and simultaneous method in predicting soil quality indices. Principal component analysis ; Leverage (statistics) ; Correlation coefficient ; Principal component regression ; Macro ; Linear regression ; Soil quality ; Environmental science ; Near-infrared spectroscopy ; Soil test ; Mathematics ; Soil science ; Statistics ; Computer science ; Soil water ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Soil Geostatistics and Mapping ; Smart Agriculture and AI
Authors: Benjamin A. Frandsen | Yoav Kalcheim | Ilya Valmianski | Alexander McLeod | Zurab Guguchia | Sky C. Cheung | Alannah M. Hallas | M. N. Wilson | Yipeng Cai | G. M. Luke | Z. Salman | Andreas Suter | T. Prokscha | Taito Murakami | Hiroshi Kageyama | D. N. Basov | Iván K. Schuller | Y. J. Uemura
Source: Physical review. B./Physical review. B (article, 2019-12-23)
Field: Materials Science — Polymers and Plastics

Intertwined magnetic, structural, and electronic transitions in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi mathvariant="normal">V</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:mrow></mml:math> We present a coordinated study of the paramagnetic-to-antiferromagnetic, rhombohedral-to-monoclinic, and metal-to-insulator transitions in thin-film specimens of the classic Mott insulator ${\mathrm{V}}_{2}{\mathrm{O}}_{3}$ using low-energy muon spin relaxation, x-ray diffraction, and nanoscale-resolved near-field infrared spectroscopic techniques. The measurements provide a detailed characterization of the thermal evolution of the magnetic, structural, and electronic phase transitions occurring in a wide temperature range, including quantitative measurements of the high- and low-temperature phase fractions for each transition. The results reveal a stable coexistence of the high- and low-temperature phases over a broad temperature range throughout the transition. Careful comparison of temperature dependence of the different measurements, calibrated by the resistance of the sample, demonstrates that the electronic, magnetic, and structural degrees of freedom remain tightly coupled to each other during the transition process. We also find evidence for antiferromagnetic fluctuations in the vicinity of the phase transition, highlighting the important role of the magnetic degree of freedom in the metal-insulator transition. Antiferromagnetism ; Monoclinic crystal system ; Condensed matter physics ; Paramagnetism ; Phase transition ; Materials science ; Physics ; Crystal structure ; Crystallography ; Chemistry Transition Metal Oxide Nanomaterials ; Advanced Condensed Matter Physics ; Ga2O3 and related materials
Authors: Martin Meere | Giuseppe Pontrelli | Sean McGinty
Source: Acta Biomaterialia (article, 2019-06-22)
Field: Materials Science — Materials Chemistry

Modelling phase separation in amorphous solid dispersions Materials science ; Phase diagram ; Ostwald ripening ; Amorphous solid ; Dispersion (optics) ; Thermodynamics ; Solid solution ; Recrystallization (geology) ; Phase (matter) ; Nanotechnology ; Chemistry ; Physics ; Crystallography ; Organic chemistry ; Optics Crystallization and Solubility Studies ; Drug Solubulity and Delivery Systems ; Analytical Chemistry and Chromatography
Authors: Yue Zhu | Yujin Ji | Zhengyu Ju | Yu Kang | Paulo J. Ferreira | Yuanyue Liu | Guihua Yu
Source: Angewandte Chemie International Edition (article, 2019-09-24)
Field: Materials Science — Materials Chemistry

Ultrafast Intercalation Enabled by Strong Solvent–Host Interactions: Understanding Solvent Effect at the Atomic Level Solvents play an essential role in many areas of chemistry and is the cornerstone of understanding reactivity in solution-phase reactions. Solvent effects have been widely observed in intercalation reactions; however, understanding of the influence of solvents on the thermodynamics and kinetics remains largely elusive in intercalation chemistry. Now, the solvent-dependent kinetics of ferrocene intercalation into a layered vanadyl phosphate (VOPO<sub>4</sub> ⋅2 H<sub>2</sub> O) host is presented, with a special focus on primary alcohols. From methanol to 1-hexnaol, the intercalation rate peaks in 1-propanol (80 times faster than the slowest case in methanol). Similar kinetics of exfoliation are also found in these solvents without ferrocene. The correlation between intercalation and exfoliation is understood at atomic level by DFT calculations, which reveal the role of pre-intercalated solvent molecules play in intralayer interactions, interlayer expansion, and layer sliding. Intercalation (chemistry) ; Exfoliation joint ; Solvent ; Chemistry ; Ferrocene ; Kinetics ; Methanol ; Solvent effects ; Inorganic chemistry ; Reactivity (psychology) ; Graphene ; Physical chemistry ; Materials science ; Organic chemistry ; Nanotechnology Polyoxometalates: Synthesis and Applications ; Transition Metal Oxide Nanomaterials ; Ionic liquids properties and applications
Authors: Maria Gombotz | Sarah Lunghammer | Stefan Breuer | Ilie Hanzu | Florian Preishuber‐Pflügl | Martin Wilkening
Source: Physical Chemistry Chemical Physics (article, 2019-01-01)
Field: Materials Science — Materials Chemistry

Spatial confinement – rapid 2D F<sup>−</sup>diffusion in micro- and nanocrystalline RbSn<sub>2</sub>F<sub>5</sub> Diffusion of small ions in materials with confined space for translational dynamics can be quite different to isotropic (3D) diffusion, which is found in the majority of solids. Finding credible indications for 2D diffusion is not as easy as it looks at first glance, especially if only powder samples are available. Here we chose the ternary fluoride RbSn2F5 as a new model system to seek out low-dimensional anion diffusion in a nanocrystalline material. We prepared RbSn2F5via mechanochemically-assisted solid state synthesis and used both ac conductivity spectroscopy and spin-lock NMR relaxation measurements to find evidence that the fluorine ions preferably diffuse between the Rb-rich layers. In both cases the diffusion induced spin-lock NMR rates are only consistent with conductivity data if they are analyzed with the semi-empirical spectral density function for 2D jump diffusion as introduced by P. M. Richards [Solid State Commun., 1978, 25, 1019]. Nanocrystalline material ; Materials science ; Diffusion ; Nanocrystal ; Nanoparticle ; Nanotechnology ; Physics ; Thermodynamics Solid-state spectroscopy and crystallography ; Advancements in Battery Materials ; Advanced Battery Materials and Technologies
Authors: Ramamurthy Katikireddy | Ramu Kakkerla | M. P. S. Murali Krishna | Durgaiah Gandamalla | Y. N. Reddy | Mavurapu Satyanarayana
Source: Heterocyclic Communications (article, 2019-01-01)
Field: Chemistry — Organic Chemistry

Synthesis and Biological Evaluation of ( <i>E</i> )- <i>N</i> ’-Benzylidene-7-methyl-2-propyl-1 <i>H</i> -benzo[ <i>d</i> ] imidazole-5-carbohydrazides as Antioxidant, Anti-inflammatory and Analgesic agents Abstract ( E )- N ’-Benzylidene-7-methyl-2-propyl-1 H -benzo [ d ]imidazole-5-carbohydrazides (5a-r) have been synthesized from 7-methyl-2-propyl-1 H -benzo[ d ]imidazole-5-carbohydrazide ( 3 ) by condensing with different aromatic aldehydes ( 4a-r ). Title compounds ( 5a-r ) were evaluated for in vitro antioxidant activity and based on their potential for antioxidant property, selected compounds 5d and 5m-p were screened for in vivo anti-inflammatory and analgesic activity. The results indicate that the compound 5o and 5p are effective against anti-inflammatory and analgesic activity. The biological data was further supported by molecular docking studies, which revealed the binding pattern and the affinity of the molecules in the active site of COX-2. Imidazole ; Chemistry ; Antioxidant ; Docking (animal) ; In vivo ; Stereochemistry ; Anti-inflammatory ; In vitro ; Molecule ; Analgesic agents ; Analgesic ; Pharmacology ; Biochemistry ; Organic chemistry ; Medicine ; Biology Synthesis and biological activity ; Synthesis and Reactions of Organic Compounds ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Hailong Che | Jianzhi Zhu | Shidong Song | Alexander F. Mason | Shoupeng Cao | Imke A. B. Pijpers | Loai K. E. A. Abdelmohsen | Jan C. M. van Hest
Source: Angewandte Chemie (article, 2019-07-03)
Field: Materials Science — Biomaterials

ATP‐Mediated Transient Behavior of Stomatocyte Nanosystems Abstract In nature, dynamic processes are ubiquitous and often characterized by adaptive, transient behavior. Herein, we present the development of a transient bowl‐shaped nanoreactor system, or stomatocyte, the properties of which are mediated by molecular interactions. In a stepwise fashion, we couple motility to a dynamic process, which is maintained by transient events; namely, binding and unbinding of adenosine triphosphate (ATP). The surface of the nanosystem is decorated with polylysine (PLL), and regulation is achieved by addition of ATP. The dynamic interaction between PLL and ATP leads to an increase in the hydrophobicity of the PLL–ATP complex and subsequently to a collapse of the polymer; this causes a narrowing of the opening of the stomatocytes. The presence of the apyrase, which hydrolyzes ATP, leads to a decrease of the ATP concentration, decomplexation of PLL, and reopening of the stomatocyte. The competition between ATP input and consumption gives rise to a transient state that is controlled by the out‐of‐equilibrium process. Apyrase ; Nanoreactor ; Adenosine triphosphate ; Biophysics ; Transient (computer programming) ; ATP hydrolysis ; Polylysine ; Chemistry ; Motility ; Biochemistry ; Cell biology ; Enzyme ; Biology ; Computer science ; ATPase Supramolecular Self-Assembly in Materials ; RNA Interference and Gene Delivery ; Dendrimers and Hyperbranched Polymers
Authors: Pin-Wen Guan | Gregory Houchins | Venkatasubramanian Viswanathan
Source: The Journal of Chemical Physics (article, 2019-12-23)
Field: Materials Science — Materials Chemistry

Uncertainty quantification of DFT-predicted finite temperature thermodynamic properties within the Debye model Density functional theory (DFT) calculations are routinely used to screen for functional materials for a variety of applications. This screening is often carried out with a few descriptors, which use ground-state properties that typically ignore finite temperature effects. Finite-temperature effects can be included by calculating the vibration properties, and this can greatly improve the fidelity of computational screening. An important challenge for DFT-based screening is the sensitivity of the predictions to the choice of the exchange correlation function. In this work, we rigorously explore the sensitivity of finite temperature thermodynamic properties to the choice of the exchange correlation functional using the built-in error estimation capabilities within the Bayesian Error Estimation Functional-van der Waals (BEEF-vdW). The vibrational properties are estimated using the Debye model, and we quantify the uncertainty associated with finite-temperature properties for a diverse collection of materials. We find good agreement with experiment and small spread in predictions over different exchange correlation functionals for Mg, Al<sub>2</sub>O<sub>3</sub>, Al, Ca, and GaAs. In the case of Li, Li<sub>2</sub>O, and NiO, however, we find a large spread in predictions as well as disagreement between experiment and functionals due to complex bonding environments. While the energetics generated by the BEEF-vdW ensemble is typically normal, the complex mapping through the Debye model leads to the derived finite temperature properties having non-Gaussian behavior. We test a wide variety of probability distributions that best represent the finite temperature distribution and find that properties such as specific heat, Gibbs free energy, entropy, and thermal expansion coefficient are well described by normal or transformed normal distributions, while the prediction spread of volume at a given temperature does not appear to be drawn from a single distribution. Given the computational efficiency of the approach, we believe that uncertainty quantification should be routinely incorporated into finite-temperature predictions. In order to facilitate this, we have open-sourced the code base under the name dePye. Sensitivity (control systems) ; Uncertainty quantification ; van der Waals force ; Bayesian probability ; Debye ; Material properties ; Debye model ; Canonical ensemble Machine Learning in Materials Science ; Thermal Expansion and Ionic Conductivity ; Advanced Chemical Physics Studies
Authors: Armand van Deursen | P.A.A.F. Wouters | Fred Steennis
Source: IEEE Transactions on Power Delivery (article, 2019-03-07)
Field: Materials Science — Materials Chemistry

Corrosion in Low-Voltage Distribution Networks and Perspectives for Online Condition Monitoring The low-voltage distribution grid is an essential link for the integration of distributed renewable sources. It is expected to experience stronger loading and load variation in the near future. At the same time, part of the low-voltage network is an aging infrastructure. Distribution system operators are therefore becoming increasingly interested in being able to diagnose their low-voltage assets. This paper describes corrosion phenomena that are observed in aluminum conductors after a damage is inflicted to a cable section. Such a damage is suspected to initiate long-term degradation. Short-duration intermittent current peaks are observed in laboratory experiments and similar peaks are now also recorded in the field. The perspectives for online monitoring, by registering these events, are investigated by having a large number of measurement devices installed on connections in service. The research is directed to gain a better understanding of the relation between the current peaks and cable circuit failures as well as the underlying degradation mechanisms. Low voltage ; Electrical engineering ; Voltage ; Degradation (telecommunications) ; Electrical conductor ; Corrosion ; Grid ; Reliability engineering ; Smart grid ; Computer science ; Engineering ; Materials science ; Geology High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Electrical Fault Detection and Protection