jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Qiang Zhu | Yongxian Wu | Ray Luo
Source: ChemRxiv (preprint, 2023-11-24)
Field: Chemistry — Physical and Theoretical Chemistry

Understanding and Fine Tuning the Propensity of ATP-Driven Liquid-Liquid Phase Separation with Oligolysine Liquid-Liquid Phase Separation (LLPS) plays pivotal roles in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The primary driving force behind this phenomenon is the electrostatic interaction between oligolysine and ATP. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of $\alpha$-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases. Ionic liquid ; Chemical physics ; Chemistry ; Biophysics ; Physics ; Biology ; Biochemistry Electrostatics and Colloid Interactions ; Block Copolymer Self-Assembly
Authors: Sarah Trimpin | Ellen D. Inutan | Hope Coffinberger | Khoa Hoang | Frank S. Yenchick | James Wager‐Miller | M. Pophristić | Ken Mackie | Charles N. McEwen
Source: European Journal of Mass Spectrometry (article, 2023-11-24)
Field: Chemistry — Spectroscopy

Instrumentation development, improvement, simplification, and miniaturization: The multifunctional plate source for use in mass spectrometry In remembrance of Prof. Dr Przybylski, we are presenting a vision towards his beloved mass spectrometry (MS) and its far-reaching promises outside of the academic laboratory. Sub-atmospheric pressure (AP) ionization MS is well positioned to make a step-change in direct ionization, a concept that allows <i>sublimation/evaporation</i> ionization and mass analyses of volatile and nonvolatile molecules from clean or dirty samples, directly, accurately, sensitively, and in a straightforward manner that has the potential to expand the field of MS into unchartered application areas. Contrary to ambient ionization MS, ionization commences in the sub-AP region of the mass spectrometer, important for practical and safety reasons, and offers <i>inter alia</i>, simplicity, speed, sensitivity, and robustness directly from real-world samples without cleanup. The plate source concept, presented here, provides an easy to use, rapid, and direct sample introduction from AP into the sub-AP of a mass spectrometer. Utilizing sub-AP ionization MS based on the plate source concept, small to large molecules from various environments that would be deemed too dirty for some direct MS methods are demonstrated. The new source concept can be expanded to include multiple ionization methods using the same plate source "front end" without the need to vent the mass spectrometer between the different methods, thus allowing ionization of more compounds on the same mass spectrometer for which any one ionization method may be insufficient. Examples such as fentanyl, gamma-hydroxybutyric acid, clozapine, 1-propionyllysergic acid, hydrocodone angiotensin I and II, myoglobin, and carbonic anhydrase are included. Mass spectrometry ; Ion source ; DART ion source ; Ionization ; Chemistry ; Ambient ionization ; Chemical ionization ; Analytical Chemistry (journal) ; Direct electron ionization liquid chromatography–mass spectrometry interface ; Electron ionization ; Chromatography ; Ion Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Pesticide Residue Analysis and Safety
Authors: Marco Moors | Kirill Yu. Monakhov
Source: ChemRxiv (preprint, 2023-12-13)
Field: Materials Science — Materials Chemistry

Capacitor or Memristor – Janus Behavior of Polyoxometalates Polyoxometalates (POMs) have attracted much attention in the development of data storage devices with new nanophysics. Numerous studies can be found on their integration into charge-based and resistive types of memory. However, the question of whether the POM behaves as a molecular capacitor or as a molecular memristor remains largely unexplored. In this Article, we clarify this fundamental question by placing the individual electronic properties of POMs in the context of their chemical and technical environment. By controlling the charge stabilization of reduced POMs through chemical functionalization, choice of countercations, surface properties, and intermolecular interactions, various physical switching mechanisms can be realized, demonstrating the remarkable uniqueness of these molecular oxides. Memristor ; Context (archaeology) ; Nanotechnology ; Janus ; Capacitor ; Charge (physics) ; Resistive random-access memory ; Materials science ; Electrical engineering ; Physics ; Engineering ; Voltage ; Quantum mechanics Polyoxometalates: Synthesis and Applications ; Conducting polymers and applications ; Advanced Memory and Neural Computing
Authors: Krishna Kishor H G | S A Hitesh | Navneet Karanth P | U G Shreya | N V Navneet
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2023-02-06)
Field: Chemistry — Analytical Chemistry

Admet, Biological Activity Prediction and Docking Studies of Main Phytoconstituents Present in Eucalyptus Using Computational Tools In-silico studies and computational tools are widely used in the field of drug discovery and drug design because of the advantages that they offer over traditional methods, such as reduced timeand cost. Eucalyptus, scientific name Eucalyptus globulus, family Myrtaceae, has long been known to possess medicinal properties, evidenced by its inclusion in many herbal formulations by traditional systems of medicine. Its activity is mainly due to mixture of volatile oils, terprnoids esters ketones etc. In this study, the most active of the phytoconstituents were screened using multiple sources to analyze their suitability as new drug molecules. First, the SMILES of the constituents were obtained using PubChem, an online chemical database. These SMILES were then used to predict the various parameters of the compounds using ADMETLab 2.0, which gave results about the constituents’ physicochemical properties, medicinal chemistry, absorption, distribution, metabolism, excretion, and toxicity parameters. Then the molecules were screened in PASS Online, an online activity predictor, which indicated that 5 of the constituents were mainly antieczemic in their activity, with the remaining constituents showing mainly carminative activity and also some antineoplasticactivity. To test the antieczemic activity of the compounds, they were imported into the docking software Maestro by Schrodinger, where they were prepared using LigPrep, and were docked against the human histamine receptor in complex with doxepin obtained from PDB (Protein ID:3RZE), using the compound flucloxacillin (- 7.708) as a synthetic standard. Among the phytoconstituents assessed spathulenol showed highest antieczemic activity (-6.368) compared to the standard flucloxacillin Docking (animal) ; Eucalyptus ; Computational biology ; Chemistry ; Biology ; Computer science ; Botany ; Medicine ; Veterinary medicine Spectroscopy and Chemometric Analyses
Authors: Thomas Sayer | Yusef Farah | Rachelle Austin | Justin B. Sambur | Amber T. Krummel | Andrés Montoya−Castillo
Source: arXiv (Cornell University) (preprint, 2023-03-22)
Field: Materials Science — Materials Chemistry

Trion formation resolves observed peak shifts in the optical spectra of transition metal dichalcogenides Monolayer transition metal dichalcogenides (TMDs) have the potential to unlock novel photonic and chemical technologies if their optoelectronic properties can be understood and controlled. Yet, recent work has offered contradictory explanations for how TMD absorption spectra change with carrier concentration, fluence, and time. Here, we test our hypothesis that the large broadening and shifting of the strong band-edge features observed in optical spectra arise from the formation of negative trions. We do this by fitting an ab initio based, many-body model to our experimental electrochemical data. Our approach provides an excellent, global description of the potential-dependent linear absorption data. We further leverage our model to demonstrate that trion formation explains the non-monotonic potential dependence of the transient absorption spectra, including through photoinduced derivative lineshapes for the trion peak. Our results motivate the continued development of theoretical methods to describe cutting-edge experiments in a physically transparent way. Trion ; Spectral line ; Monolayer ; Materials science ; Photonics ; Molecular physics ; Absorption spectroscopy ; Absorption (acoustics) ; Transition metal ; Condensed matter physics ; Chemistry ; Optoelectronics ; Physics ; Nanotechnology ; Optics ; Quantum mechanics 2D Materials and Applications ; Quantum Dots Synthesis And Properties ; Luminescence and Fluorescent Materials
Authors: Eng Tuan Poh | Yung Zhen Tan | Justin Boon Shuan Neo | Chee How Ong | Azianty Saroni | Zheng Zhang | Jianhui Li | Boon Tong Goh | Chorng Haur Sow
Source: Journal of Materials Chemistry C (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Multi-dimensional dynamic fluorescence readout from laser engineered In<sub>2</sub>O<sub>3</sub> nanowire micropatterns A laser-irradiated array of In 2 O 3 nanowires presents yellow and blue fluorescence states that can be dynamically altered under UV light for anti-counterfeiting features based upon microscale patterning, color evolution and time-domain encoding. Microscale chemistry ; Materials science ; Fluorescence ; Nanowire ; Laser ; Nanotechnology ; Optoelectronics ; Irradiation ; Domain (mathematical analysis) ; Optics ; Physics ZnO doping and properties ; Thin-Film Transistor Technologies ; Gas Sensing Nanomaterials and Sensors
Authors: A.G. Borisov | A. Nuradynov | V. U. Sheigam
Source: Journal of Metallic Material Research (article, 2023-06-26)
Field: Materials Science — General Materials Science

Impact of Cooling Rate on the Results of Vibration Treatment of the Aluminum Casting The effect of vibration (50 Hz) on the formation of aluminum castings of 99.5% purity at various cooling rates was studied. It was found that the presence of vibration leads to an increase in the cooling rate of the castings. It was found that the higher the speed without vibration, the stronger the effect of increasing the speed when vibration was applied. Apparently, this effect is associated with additional mixing of the melt by free-floating crystals. Vibration ; Aluminium ; Materials science ; Casting ; Water cooling ; Mixing (physics) ; Metallurgy ; Mechanical vibration ; Composite material ; Mechanical engineering ; Acoustics ; Engineering ; Physics Material Properties and Applications ; Industrial Engineering and Technologies ; Diverse Industrial Engineering Technologies
Authors: Farha Naaz | M.S. Chauhan | Kedar Yadav | Surender Singh | Ashok Kumar | Dasari L. V. K. Prasad
Source: arXiv (Cornell University) (preprint, 2023-01-13)
Field: Materials Science — Materials Chemistry

Structural phase transitions in perovskite BaCeO3 with data mining and first-principles theoretical calculations Several experiments conducted over decades have revealed that the perovskite-structured BaCeO3 goes through a series of temperature-induced structural phase transitions. However, it has been frequently observed that the number of phases and the sequence in which they appear as a function of temperature differ between experiments. Insofar as neutron diffraction and Raman spectroscopy experiments are concern, four structures are well characterized with three transitions: Pnma to Imma [563 K] to R-3c [673 K] to Pm-3m [1173 K]. In contrast, thermoanalytical methods showed multiple singularities corresponding to at-least three more structural transitions at around 830 K, 900 K, and 1030 K. In account of these conflicting experimental findings, we computed free energy phase diagram for BaCeO3 employing crystal structure data mining in conjunction with first principles electronic structure and phonon lattice dynamics. A total of 34 polymorphs have been predicted, the most stable of which follows the Glazer classification of the perovskite tilt system. It has been predicted that the Cmcm and P4/mbm phases surpass Pnma at 666 K and 1210 K, respectively. At any temperature, two alternate tetragonal phases (P42/nmc and I4/mcm) are also found to be 20 to 30 meV less favored than the Pnma. While the calculated stability order of the predicted polymorphs is in acceptable agreement with the results of neutron diffraction, the transitions observed in thermoanalytical studies could be ascribed to the development of four novel phases (Cmcm, P4/mbm, P42/nmc, and I4/mcm) at intermediate temperatures. However, we analyze that the R-3c phase predominantly stabilized over a broad temperature field, masking all subsequent phases up until the cubic Pm-3m. Consequently, the novel phases predicted to occur in thermoanalytical studies are only fleetingly metastable. Tetragonal crystal system ; Neutron diffraction ; Perovskite (structure) ; Phase diagram ; Crystallography ; Raman spectroscopy ; Materials science ; Phonon ; Crystal structure ; Phase transition ; Diffraction ; Phase (matter) ; Structural stability ; Condensed matter physics ; Chemistry ; Physics Advanced Thermoelectric Materials and Devices ; Machine Learning in Materials Science ; Magnetic and transport properties of perovskites and related materials
Authors: Robert J. Meier
Source: Molecules (article, 2023-08-24)
Field: Chemistry — Organic Chemistry

Comment on Naef, R.; Acree, W.E., Jr. Revision and Extension of a Generally Applicable Group-Additivity Method for the Calculation of the Standard Heat of Combustion and Formation of Organic Molecules. Molecules 2021, 26, 6101 Next to the paper referred to in the title [...]. Additive function ; Extension (predicate logic) ; Combustion ; Standard enthalpy of formation ; Molecule ; Group (periodic table) ; Thermodynamics ; Mathematics ; Chemistry ; Materials science ; Computational chemistry ; Applied mathematics ; Physical chemistry ; Physics ; Computer science ; Organic chemistry ; Mathematical analysis Chemical Thermodynamics and Molecular Structure ; Phase Equilibria and Thermodynamics ; Thermal and Kinetic Analysis
Authors: Yannick Anguy | Margaux Haurat | Michel Dumon
Source: Macromolecules (article, 2023-12-01)
Field: Materials Science — Polymers and Plastics

The Quest for Contrast in Digital Images of Micro-/Nanostructured Polymer Blends before and after CO<sub>2</sub>Foaming: General Interest of Directional Diffusive Filtering for Edge Enhancement Multiphase materials composed of several phases with smooth interphases or sharp interfaces are ubiquitous in polymer science. This study addresses the challenge to identify and segment automatically the right interfaces and interphases in electronic digital images for a sound analysis of the structuration of materials at the micro-/nanoscale. The selected strategy is to primarily enhance the contrast between phases in digital transmission electron microscopy/scanning electron microscopy images for a straightforward subsequent segmentation of phases, i.e., by a simple threshold of the gray-level intensity histogram. To do so, a nonlinear transient (time-dependent) diffusion process is used. In the diffusive process, the gray-level intensity spreads nonuniformly across the image pixels, i.e., adaptively to local properties of the image. When computed at a large enough time of the diffusive process, the reconstructed image tends to a piecewise constant solution representing a simplified image at a lower resolution with sharper boundaries, bringing about the sought local contrast enhancement. The solution image is shown to facilitate the automatic segmentation step and the calculation of representative size distributions. This approach is, in particular, very suited to the characterization of multimodal samples including different scales of porosity. While this (first of two parts) methodological article is useful to multiphase polymeric materials in general, the methodology was here developed for an in-depth study of acrylic block copolymer nanostructures, enabling the monitoring of micro-/nanosized foams produced by one-step batch scCO2 green foaming. Pixel ; Materials science ; Piecewise ; Digital image ; Histogram ; Porous medium ; Segmentation ; Computer science ; Image processing ; Biological system ; Porosity ; Artificial intelligence ; Image (mathematics) ; Mathematics ; Composite material Polymer Foaming and Composites ; Phase Equilibria and Thermodynamics ; Enhanced Oil Recovery Techniques
Authors: Daniel Hedlund | Simon R. Larsen | Martin Sahlberg | Peter Svedlindh | Vitalii Shtender
Source: Scripta Materialia (article, 2023-05-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Influence of Mn content on the magnetic properties of the hexagonal Mn(Co,Ge)2 phase Herein, we report on the effect of Mn content on the magnetic properties of the hexagonal Mn(Co,Ge)2 with composition Mn36+xCo49-xGe15.This compound was previously described as Mn2Co3Ge (MgZn2-type structure), but later as Mn(Co,Ge)2 with its own structure type, all samples in this work follow the same superstructure model. Samples were synthesized by induction melting, the crystal structures were evaluated using a combination of X-ray diffraction together with scanning electron microscopy equipped and an energy dispersive X-ray spectroscopy detector. The Curie temperature (TC) is shifted towards lower temperature as the Mn content is increased. On the other hand, the spin reorientation temperature (TSRT) increases and the magnetic moment decreases as the Mn content is increased. The magnetocaloric properties were investigated for the x=1 alloy, Mn37Co48Ge15. It was found that the isothermal entropy change is 2 J kg−1 K−1 at room temperature for an applied field of 5 T. Materials science ; Magnetic refrigeration ; Curie temperature ; Alloy ; Superstructure ; Isothermal process ; Analytical Chemistry (journal) ; Crystallography ; Crystal structure ; Content (measure theory) ; Scanning electron microscope ; Energy-dispersive X-ray spectroscopy ; Magnetic moment ; Ferromagnetism ; Condensed matter physics ; Magnetization ; Magnetic field ; Metallurgy ; Thermodynamics ; Chemistry Magnetic and transport properties of perovskites and related materials ; Shape Memory Alloy Transformations ; Inorganic Chemistry and Materials
Authors: Juraj Lipscher
Source: CHIMIA International Journal for Chemistry (article, 2023-10-25)
Field: Chemistry — Physical and Theoretical Chemistry

Reflections on Challenges and Rewards in Teaching Chemistry The author gives his personal and subjective view of the manifold challenges in teaching chemistry and argues that, in most cases, the challenges lie in the difficulty of balancing two opposing concerns and thus can be formulated as dilemmas. He discusses, among others, the role of general education, language skills, finding the correct level of simplification, and specific problems of teaching the language of chemistry. Furthermore, he points out possibilities to overcome the pitfalls inherent in teaching chemistry and describes examples of the challenges and their solutions. Awareness of individual challenges is the prerequisite to finding solutions and improving one's teaching. Chemistry ; Nanotechnology ; Biochemical engineering ; Data science ; Computer science ; Engineering ; Materials science Various Chemistry Research Topics
Authors: O. Turkot | Fabio Dall’Antonia | Richard Bean | E Juncheng | Hans Fangohr | Danilo E. Ferreira de Lima | Sravya Kantamneni | Henry Kirkwood | F. Koua | Adrian P. Mancuso⋈ | Diogo V. M. Melo | Adam Round | Michael J. Schuh | E. V. Sobolev | Raphaël de Wijn | James Wrigley | Luca Gelisio
Source: Preprints.org (preprint, 2023-09-21)
Field: Materials Science — Materials Chemistry

EXtra-Xwiz: A Tool to Streamline Serial Femtosecond Crystallography Workflows at European XFEL X-ray free electron lasers deliver photon pulses that are bright enough to observe diffraction from extremely small crystals, at a time scale outrunning their destruction. As crystals are continuously replaced, this technique is termed serial femtosecond crystallography (SFX). Due to its high pulse repetition rate, the European XFEL enables the collection of rich and extensive data sets, suited to study various scientific problems including ultrafast processes. The enormous data rate, data complexity, and the nature of the pixelized multi-modular area detectors at European XFEL pose severe challenges to users. To streamline the analysis of SFX data, we developed the semi-automated pipeline EXtra-Xwiz around the established CrystFEL program suite, processing diffraction patterns on detector frames into structure factors. Here we present EXtra-Xwiz, and introduce its architecture and use by means of a tutorial. Future plans for its development and expansion are also discussed. Femtosecond ; Pipeline (software) ; Suite ; Ultrashort pulse ; Detector ; Laser ; Computer science ; Workflow ; Modular design ; Optics ; Diffraction ; Computer hardware ; Physics ; Database ; Geography Enzyme Structure and Function ; Advanced X-ray Imaging Techniques ; Advanced Electron Microscopy Techniques and Applications