jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Wenjun Chen | Bo Jiang | Zourong Ruan | Dandan Yang | Yin Hu | Honggang Lou
Source: BMC Pharmacology and Toxicology (article, 2024-08-26)
Field: Chemistry — Organic Chemistry

Population pharmacokinetic analysis of febuxostat with high focus on absorption kinetics and food effect Febuxostat is commonly used in clinic for the treatment of hyperuricemia. Multiple-peak phenomenon has been observed in human plasma concentration-time profiles of febuxostat, but has not been paid enough attention in previous research. This study takes a pivotal step forward by conducting a comprehensive population pharmacokinetic (PopPK) analysis of febuxostat in a healthy Chinese cohort, with a central focus on delineating its absorption profile under contrasting fasting and fed conditions, while concurrently assessing the influence of food alongside other potential covariates on febuxostat's PK profile. The plasma concentration data used for modeling was obtained from two bioequivalence (BE) studies. Subjects were administered febuxostat 20 mg or 80 mg under fasting or fed condition. Goodness-of-fit plots, visual predict check (VPC), and normalized prediction distribution error (NPDE) were used for model evaluation. Based on the established model, PK profiles in healthy Caucasian subjects were simulated with parameter adjustment for race difference on clearance and bioavailability. Data from 128 subjects were used in the PopPK analysis. Febuxostat concentration-time curves were described by a two-compartment model with two deposit absorption compartments and lag times (Tlag). Prandial states (Food) showed significant impact on absorption rate ka1 and ka2, as well as Tlag1, and body weight was identified as a significant covariate on the apparent distribution volume. The PopPK analysis of febuxostat in healthy Chinese volunteers, under both fasted and fed conditions, successfully characterized its PK profile and underscored the significant influence of food on absorption. The potential difference of absorption between Chinese population and Caucasian population indicated from the simulations needs further investigation. Febuxostat ; Kinetics ; Pharmacokinetics ; Focus (optics) ; Population ; Population pharmacokinetics ; Absorption (acoustics) ; Pharmacology ; Chemistry ; Medicine ; Materials science ; Biochemistry ; Environmental health ; Physics ; Optics Carbohydrate Chemistry and Synthesis ; Biochemical Analysis and Sensing Techniques ; Alcohol Consumption and Health Effects
Authors: Jiao Huang | Qianli Xing | Jinglong Ji | Bo Yang
Source: Neural Networks (article, 2024-10-31)
Field: Materials Science — Materials Chemistry

PerCNet: Periodic complete representation for crystal graphs Representation (politics) ; Mathematics ; Computer science ; Artificial intelligence ; Combinatorics ; Discrete mathematics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; X-ray Diffraction in Crystallography
Authors: Kirti Sharma | Atul Sharma | Mohit Sanduja | Vikas Jogpal | Asim Kumar Mishra | Girish Kumar | Tarun Virmani | Omar M. Noman | Abdulsalam Alhalmi
Source: Open Chemistry (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Exploring novel antitubercular agents: Innovative design of 2,3-diaryl-quinoxalines targeting DprE1 for effective tuberculosis treatment Abstract The rising instances of drug resistance in Mycobacterium tuberculosis strains pose a significant global health challenge. Conventional tuberculosis (TB) treatments, which typically involve multiple antibiotics, face hurdles like drug resistance, reduced effectiveness, and heightened toxicity. Consequently, there is a pressing need for innovative anti-TB agents with new modes of action. Decaprenyl-phosphoryl-β- d -ribose 2′-epimerase 1(DprE1), a crucial enzyme in Mycobacterium tuberculosis , plays a vital role in cell wall biosynthesis – a critical aspect for the bacterium’s survival. Building on the success of diarylquinolines like bedaquiline, targeting DprE1 presents a promising avenue for developing anti-TB drugs, especially against drug-resistant strains. Our research focused on discovering novel DprE1 inhibitors using a ligand-based drug design strategy, starting with the established non-covalent inhibitor Ty38c. We assembled a library of 16 molecules, modifying them based on factors like drug-like properties, chemical accessibility, and synthetic feasibility. Molecular docking analyses of this library identified three molecules with binding affinities comparable to Ty38c. Among these, KS_QD_05 and KS_QD_04 are promising candidates, which were further validated through molecular dynamics simulation studies where root-mean-square deviation (RMSD) values of all three complexes reached a plateau, measuring around 0.3 nm, indicating that the apoprotein and all complexes stabilized during the simulation. The ligands KS_QD_04 and KS_QD_05 displayed significantly stable deviation. KS_QD_05 reached about 0.1 nm equilibrium value. However, the ligand KS_QD_04 reached an RMSD value of 0.17 nm and showed distress at 70 nm. KS_QD_04 and KS_QD_05 showed an average value of 1-3 H-bond interaction and regarding the RMSF values, both the compounds showed fluctuations less than 0.5 nm in the case of Mtb. DprE1 enzyme. This indicates the potential of both compounds to become lead compounds in the pursuit of DprE1 inhibitors for TB treatment. Tuberculosis ; Medicine ; Mycobacterium tuberculosis ; Pharmacology ; Pathology Synthesis and Biological Evaluation ; Synthesis and biological activity ; Multicomponent Synthesis of Heterocycles
Authors: Jordan Hobbs | Calum J. Gibb | Ewan Cruickshank | Rebecca Walker | Richard J. Mandle
Source: Liquid Crystals (preprint, 2024-04-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Rapid conformational analysis of semi-flexible liquid crystals We present an approach for rapid conformational analysis of semi-flexible liquid crystals. We use a simple graphical user interface (GUI) tool that leverages rules-based methods for efficient generation of bend-angle distributions, offering a significant improvement over traditional single-conformer analysis. Our methods demonstrated proficiency in approximating molecular shapes comparable to those obtained from molecular&#13;\ndynamics (MD) simulations, albeit with notable deviations in the under sampling of hairpin conformations and oversampling of extended configurations.&#13;\nRe-evaluation of existing data revealed an apparent weak correlation between NTB transition temperatures and bend angles, underscoring the complexity of molecular shapes beyond mere geometry. Furthermore, we integrated this conformational analysis into a pipeline of algorithmic molecular design, utilizing a fragment-based genetic algorithm to generate novel cyanobiphenyl-containing materials. This integration opens new avenues for the&#13;\nexploration of liquid crystalline materials, particularly in systems where systematic conformer searches are impractical, such as large oligomeric systems. Our findings highlight the potential and growing importance of computational approaches in accelerating the design and synthesis of next-generation liquid crystalline materials. Conformational isomerism ; Molecular dynamics ; Pipeline (software) ; Graphical user interface ; Oversampling ; Fragment (logic) ; Computer science ; Interface (matter) ; Materials science ; Chemistry ; Chemical physics ; Biological system ; Molecule ; Algorithm ; Computational chemistry Liquid Crystal Research Advancements ; Molecular spectroscopy and chirality ; Neurobiology and Insect Physiology Research
Authors: Jolanta Nieszporek | Tomasz Pańczyk | Krzysztof Nieszporek
Source: Molecules (article, 2024-07-23)
Field: Chemistry — Electrochemistry

The Comparison of Catalytic Activity of Carbimazole and Methimazole on Electroreduction of Zinc (II) in Chlorates (VII): Experimental and Molecular Modelling Study With the help of electrochemical methods, including CV and EIS, the influence of methimazole, carbimazole, and the concentration of the supporting electrolyte on the kinetics and mechanism of zinc electroreduction on a mercury electrode was compared and analyzed. Moreover, molecular dynamics simulations of zinc/carbimazole and zinc/methimazole solutions were carried out to determine the effect of drugs on the hydration sphere of Zn<sup>2+</sup> ions. It was shown that the electroreduction of Zn<sup>2+</sup> in the presence of methimazole and carbimazole occurs in two steps and the first one determines the kinetics of the entire process. The presence of both drugs in the solution and the increase in the concentration of the supporting electrolyte reduce the degree of hydration of the depolarizer ions and the hydration of the electrode surface, what is a factor favoring the rate of electroreduction. Based on theoretical studies, the formation of stable complexes between Zn<sup>2+</sup> and the molecules of both drugs in a solution was considered unlikely. However, active complexes can be formed between depolarizer ions and molecules adsorbed at the electrode surface. They constitute a bridge facilitating charge exchange during the electrode reaction, revealing the catalytic abilities of methimazole and carbimazole. In the range of c<sub>drug</sub> ≤ 1 × 10<sup>-3</sup> mol dm<sup>-3</sup>, carbimazole is a better catalyst, whereas in the range of c<sub>drug</sub> ≥ 5 × 10<sup>-3</sup> mol dm<sup>-3</sup>, it is methimazole. The effectiveness of both compounds in catalyzing the first stage of the electrode reaction increases with the increase in the NaClO<sub>4</sub> concentration. Carbimazole ; Methimazole ; Zinc ; Chemistry ; Catalysis ; Nuclear chemistry ; Inorganic chemistry ; Biochemistry ; Organic chemistry ; Medicine ; Endocrinology ; Graves' disease Electrochemical Analysis and Applications ; Trace Elements in Health
Authors: Guoping Gao | Lin‐Wang Wang
Source: STAR Protocols (article, 2024-04-16)
Field: Chemistry — Electrochemistry

Protocol for evaluating the effect of potential on electrochemical reactions via the grand canonical fixed-potential technique The grand canonical constant potential approach is a cornerstone for modeling the electrochemical reactions under work conditions. Here, we present a protocol for evaluating the effect of potential on electrochemical reactions using the grand canonical fixed-potential technique. We describe steps for installing PWmat software, preparing input files for the fixed-potential calculation, and simulating different electrochemical states under the same potential. We then detail procedures for analyzing the free energy evolution under the same potential. For complete details on the use and execution of this protocol, please refer to Gao et al.<sup>1</sup><sup>,</sup><sup>2</sup><sup>,</sup><sup>3</sup>. Protocol (science) ; Electrochemistry ; Mathematics ; Computer science ; Chemistry ; Physical chemistry ; Medicine Electrochemical Analysis and Applications ; Machine Learning in Materials Science ; Electrocatalysts for Energy Conversion
Authors: Yanchen Wu | Fei Wang | Sai Zheng | Britta Nestler
Source: Soft Matter (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Evolution dynamics of thin liquid structures investigated using a phase-field model Liquid structures of thin-films and torus droplets are omnipresent in daily lives. The morphological evolution of liquid structures suspending in another immiscible fluid and sitting on a solid substrate is investigated by using three-dimensional (3D) phase-field (PF) simulations. Here, we address the evolution dynamics by scrutinizing the interplay of surface energy, kinetic energy, and viscous dissipation, which is characterized by Reynolds number Re and Weber number We. We observe special droplet breakup phenomena by varying Re and We. In addition, we gain the essential physical insights into controlling the droplet formation resulting from the morphological evolution of the liquid structures by characterizing the top and side profiles under different circumstances. We find that the shape evolution of the liquid structures is intimately related to the initial shape, Re, We as well as the intrinsic wettability of the substrate. Furthermore, it is revealed that the evolution dynamics are determined by the competition between the coalescence phenomenology and the hydrodynamic instability of the liquid structures. For the coalescence phenomenology, the liquid structure merges onto itself, while the hydrodynamic instability leads to the breakup of the liquid structure. Last but not least, we investigate the influence of wall relaxation on the breakup outcome of torus droplets on substrates with different contact angles. We shed light on how the key parameters including the initial shape, Re, We, wettability, and wall relaxation influence the droplet dynamics and droplet formation. These findings are anticipated to contribute insights into droplet-based systems, potentially impacting areas like ink-jet printing, drug delivery systems, and microfluidic devices, where the interplay of surface energy, kinetic energy, and viscous dissipation plays a crucial role. Breakup ; Wetting ; Dynamics (music) ; Relaxation (psychology) ; Chemical physics ; Field (mathematics) ; Materials science ; Phase (matter) ; Liquid phase ; Mechanics ; Nanotechnology ; Statistical physics ; Physics ; Thermodynamics ; Composite material ; Mathematics ; Psychology ; Social psychology Solidification and crystal growth phenomena ; Fluid Dynamics and Thin Films ; Fluid Dynamics and Heat Transfer
Authors: Xiong Yi | Shengfang Li | Pin Wen | Shilin Yan
Source: Polymers (article, 2024-03-22)
Field: Chemistry — Organic Chemistry

Numerical Simulation of Polyacrylamide Hydrogel Prepared via Thermally Initiated Frontal Polymerization Traditional polymer curing techniques present challenges such as a slow processing speed, high energy consumption, and considerable initial investment. Frontal polymerization (FP), a novel approach, transforms monomers into fully cured polymers through a self-sustaining exothermic reaction, which enhances speed, efficiency, and safety. This study focuses on acrylamide hydrogels, synthesized via FP, which hold significant potential for biomedical applications and 3D printing. Heat conduction is critical in FP, particularly due to its influence on the temperature distribution and reaction rate mechanisms, which affect the final properties of polymers. Therefore, a comprehensive analysis of heat conduction and chemical reactions during FP is presented through the establishment of mathematical models and numerical methods. Existing research on FP hydrogel synthesis primarily explores chemical modifications, with limited studies on numerical modeling. By utilizing Differential Scanning Calorimetry (DSC) data on the curing kinetics of polymerizable deep eutectic solvents (DES), this paper employs Malek's model selection method to establish an autocatalytic reaction model for FP synthesis. In addition, the finite element method is used to solve the reaction-diffusion model, examining the temperature evolution and curing degree during synthesis. The results affirm the nth-order autocatalytic model's accuracy in studying acrylamide monomer curing kinetics. Additionally, factors such as trigger temperature and solution initial temperature were found to influence the FP reaction's frontal propagation speed. The model's predictions on acrylamide hydrogel synthesis align with experimental data, filling the gap in numerical modeling for hydrogel FP synthesis and offering insights for future research on numerical models and temperature control in the FP synthesis of high-performance hydrogels. Curing (chemistry) ; Materials science ; Exothermic reaction ; Monomer ; Polymerization ; Differential scanning calorimetry ; Self-healing hydrogels ; Autocatalysis ; Polymer ; Chemical engineering ; Thermodynamics ; Polymer chemistry ; Composite material ; Chemistry ; Organic chemistry ; Catalysis Photopolymerization techniques and applications ; Additive Manufacturing and 3D Printing Technologies ; Pigment Synthesis and Properties
Authors: Aeneas Jerron Velu | Pathmathas Thirunavukkarasu | Talal Rahman | Kamal Mustafa | Dhayalan Velauthapillai
Source: ACS Omega (article, 2024-04-17)
Field: Materials Science — Biomaterials

Computational Analysis of Biodegradable Polyester Materials for Biomedical Applications: Investigating Molecular Weight Change due to Hydrolysis Biopolymers have gained significant importance in the field of biomedicine, particularly in addressing organ and tissue loss in living organisms. These polymers exhibit temporary functionality during treatment and undergo biodegradation once their intended purpose is fulfilled. The diverse characteristics of these biopolymers expand their range of applications, albeit necessitating extensive experimentation and a time commitment for thorough investigation. Computational models have emerged as a promising avenue for predictive analysis, complementing traditional experimental methods. In this study, we delve into the degradation dynamics of polyester materials with a specific emphasis on the hydrolysis process. We employed an appropriate reaction diffusion model to unveil the underlying mechanisms governing material weight loss and erosion within a two-dimensional framework for a rectangular slice of the implant. By bridging computational modeling with empirical research, this study provides valuable insights into the behavior of biopolymers, contributing to a deeper understanding of these materials and their potential for advanced biomedical applications. To illustrate this framework's effectiveness, we conducted a case study using experimental data from the literature, focusing on poly(d,l-lactic acid) material. Polyester ; Biochemical engineering ; Hydrolytic degradation ; Nanotechnology ; Computer science ; Biodegradation ; Materials science ; Biomedicine ; Polymer ; Chemistry ; Engineering ; Bioinformatics ; Organic chemistry biodegradable polymer synthesis and properties ; Bone Tissue Engineering Materials ; Additive Manufacturing and 3D Printing Technologies
Authors: Thilo Bissbort | Harry Becker | Sumit Chakraborty
Source: Geochimica et Cosmochimica Acta (article, 2024-01-26)
Field: Materials Science — Ceramics and Composites

Diffusion of H-bearing species in anorthite-diopside glass below and across the glass transition Diffusion of hydrogen (H) in silicate glasses plays a critical role in many applications because already at small concentrations the presence of H and its mobility have significant effects on the physical and chemical properties of materials. Although many of these applications such as weathering and alteration occur at low temperatures (e.g., < 600 °C), a quantification of diffusion rates at associated conditions have been hindered due to analytical and experimental difficulties in the past. This is especially problematic because it is not clear whether an extrapolation of high-temperature data across the glass transition to low temperatures based on an Arrhenius law is valid. A recently developed experimental technique has now made it possible to report here diffusion rates of H in anorthite-diopside (50/50 mol%) glass between 150 – 600 °C and pressures of 1 atm and 2 kbar. Numerical modelling was used to extract diffusion rates from nanoscale diffusion profiles measured by Nuclear Resonance Reaction Analysis in our thin-film diffusion couples that were produced by pulsed laser deposition. We considered different boundary conditions that are related to the experimental techniques applied and tested two models (i) a single-diffusant species model with different dependencies on total water concentration (H2Ot), (ii) a speciation-diffusion model that considers the coexistence of molecular H2O and OH as species withing the glass. An exponential dependency on H2Ot in model (i) describes the measured profiles adequately. Diffusion coefficients for H2Ot that we obtained from the single-diffusant, and the speciation-diffusion model show minor differences (∼ 0.2 log units). Our results include three major findings: (i) The diffusivity-temperature relationship between 150 and 600 °C does not follow an Arrhenius law. Instead, the trend exhibits a marked change in slope between 350 and 450 °C. A change in activation energy of diffusion is likely related to a change from a glass to a supercooled melt, which can be fit by a modified Vogel-Fulcher-Tammann (VFT) equation. (ii) All experiments at higher temperatures (≥ 450 °C) are better fitted within the scope of a two-species model considering OH to be mobile. (iii) A comparison with published diffusion data reveals that a change in activation energy is much more pronounced in depolymerized melts (e.g., basalt) than in polymerized melts (e.g., rhyolite). Anorthite ; Diopside ; Diffusion ; Bearing (navigation) ; Mineralogy ; Glass transition ; Geology ; Thermodynamics ; Materials science ; Composite material ; Physics Glass properties and applications ; Material Dynamics and Properties ; Geological and Geochemical Analysis
Authors: Weiheng Huang | Pei-Hua Chen | Chin‐Wen Chen | Chie‐Shaan Su | Muoi Tang | Jung-Chin Tsai | Yan-Ping Chen | Feng‐Huei Lin
Source: Molecules (article, 2024-09-06)
Field: Materials Science — Polymers and Plastics

Experimental Study for the Sorption and Diffusion of Supercritical Carbon Dioxide into Polyetherimide Supercritical carbon dioxide (SCCO<sub>2</sub>) is a non-toxic and environmentally friendly fluid and has been used in polymerization reactions, processing, foaming, and plasticizing of polymers. Exploring the behavior and data of SCCO<sub>2</sub> sorption and dissolution in polymers provides essential information for polymer applications. This study investigated the sorption and diffusion of SCCO<sub>2</sub> into polyetherimide (PEI). The sorption and desorption processes of SCCO<sub>2</sub> in PEI samples were measured in the temperature range from 40 to 60 °C, the pressure range from 20 to 40 MPa, and the sorption time from 0.25 to 52 h. This study used the ex situ gravimetric method under different operating conditions and applied the Fickian diffusion model to determine the mass diffusivity of SCCO<sub>2</sub> during sorption and desorption processes into and out of PEI. The equilibrium mass gain fraction of SCCO<sub>2</sub> into PEI was reported from 9.0 wt% (at 60 °C and 20 MPa) to 12.8 wt% (at 40 °C and 40 MPa). The sorption amount increased with the increasing SCCO<sub>2</sub> pressure and decreased with the increasing SCCO<sub>2</sub> temperature. This study showed the crossover phenomenon of equilibrium mass gain fraction isotherms with respect to SCCO<sub>2</sub> density. Changes in the sorption mechanism in PEI were observed when the SCCO<sub>2</sub> density was at approximately 840 kg/m<sup>3</sup>. This study qualitatively performed FTIR analysis during the SCCO<sub>2</sub> desorption process. A CO<sub>2</sub> antisymmetric stretching mode was observed near a wavenumber of 2340 cm<sup>-1</sup>. A comparison of loss modulus measurements of pure and SCCO<sub>2</sub>-treated PEI specimens showed the shifting of loss maxima. This result showed that the plasticization of PEI was achieved through the sorption process of SCCO<sub>2</sub>. Sorption ; Desorption ; Polyetherimide ; Supercritical fluid ; Gravimetric analysis ; Supercritical carbon dioxide ; Polymer ; Diffusion ; Chemical engineering ; Materials science ; Mass fraction ; Analytical Chemistry (journal) ; Chemistry ; Polymer chemistry ; Chromatography ; Organic chemistry ; Adsorption ; Thermodynamics Polymer Foaming and Composites ; Phase Equilibria and Thermodynamics ; Polymer crystallization and properties
Authors: Xinyi Jiang | Yi-Ming Hu | Ruizhe Gao | Baihui Xing | Chao Yang | Zhengli Hua
Source: International Journal of Hydrogen Energy (article, 2024-12-21)
Field: Materials Science — Metals and Alloys

Combined effects of internal gaseous hydrogen and external stray currents on hydrogen concentration in X80 buried pipelines Hydrogen ; Pipeline transport ; Environmental science ; Materials science ; Geology ; Chemistry Hydrogen embrittlement and corrosion behaviors in metals ; Material Properties and Failure Mechanisms ; Offshore Engineering and Technologies