jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Roman M. Dickey | Michaela A. Jones | Neil D. Butler | Ishika Govil | Aditya M. Kunjapur
Source: AIChE Journal (article, 2023-08-28)
Field: Materials Science — Biomaterials

Genome engineering allows selective conversions of terephthalaldehyde to multiple valorized products in bacterial cells Abstract Deconstruction of polyethylene terephthalate (PET) plastic waste generates opportunities for valorization to alternative products. We recently designed an enzymatic cascade that could produce terephthalaldehyde (TPAL) from terephthalic acid. Here, we showed that the addition of TPAL to growing cultures of Escherichia coli wild‐type strain MG1655 and an engineered strain for r educed aromatic a ldehyde re duction (RARE) strain resulted in substantial reduction. We then investigated if we could mitigate this reduction using multiplex automatable genome engineering (MAGE) to create an E. coli strain with 10 additional knockouts in RARE. Encouragingly, we found this newly engineered strain enabled a 2.5‐fold higher retention of TPAL over RARE after 24 h. We applied this new strain for the production of para ‐xylylenediamine (pXYL) and observed a 6.8‐fold increase in pXYL titer compared with RARE. Overall, our study demonstrates the potential of TPAL as a versatile intermediate in microbial biosynthesis of chemicals that derived from waste PET. Strain (injury) ; Polyethylene terephthalate ; Escherichia coli ; Terephthalic acid ; Metabolic engineering ; Materials science ; Chemistry ; Enzyme ; Biology ; Biochemistry ; Polyester ; Composite material ; Gene biodegradable polymer synthesis and properties ; Microplastics and Plastic Pollution ; Microbial Metabolic Engineering and Bioproduction
Authors: Pierre-Antoine Geslin
Source: Computational Materials Science (article, 2023-11-08)
Field: Materials Science — Materials Chemistry

Modeling of solid solution strengthening in FCC alloys: Atomistic simulations, statistical models and elastic continuous approaches Materials science ; Statistical physics ; Dislocation ; Range (aeronautics) ; Physics ; Composite material Microstructure and mechanical properties ; Advanced materials and composites ; Advanced Materials Characterization Techniques
Authors: Alistair Speidel | Ivan Bisterov | Shamraze Ahmed | Adam T. Clare
Source: Acta Materialia (article, 2023-12-13)
Field: Materials Science — Surfaces, Coatings and Films

Ambient grain orientation imaging on complex surfaces Crystal orientation imaging is generally confined to the laboratory, typically following destructive sectioning, with most current techniques reliant on electron-material interactions that require a vacuum. This information is gathered in a manner that requires careful planning, however a more desirable approach would allow the manufacturer to acquire this data non-destructively at the point of manufacture, with little or no time penalty. We show that coupling a numerically controlled etching method to topographical data processing can be used to spatially map grain orientations over planar and non-planar surfaces. Our method allows the construction of large area orientation maps (≈400 mm2) in agreement with electron backscatter diffraction datasets. We have characterised spatial and angular resolution limits for the technique, which are correlated to length scales of microscale etch surfaces and our ability to measure their geometries. This approach has the potential to augment materials processing technologies, where resultant microstructures require strict control in order to guarantee through-life integrity. Microscale chemistry ; Materials science ; Electron backscatter diffraction ; Orientation (vector space) ; Planar ; Angular resolution (graph drawing) ; Image resolution ; Microstructure ; Optics ; Computer science ; Computer vision ; Composite material ; Geometry ; Computer graphics (images) Electron and X-Ray Spectroscopy Techniques ; Non-Destructive Testing Techniques ; Force Microscopy Techniques and Applications
Authors: Michela Romanini | Roberto Macovez | Sofia Valenti | Wahi Noor | J. Ll. Tamarit
Source: International Journal of Molecular Sciences (review, 2023-12-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Dielectric Spectroscopy Studies of Conformational Relaxation Dynamics in Molecular Glass-Forming Liquids We review experimental results obtained with broadband dielectric spectroscopy concerning the relaxation times and activation energies of intramolecular conformational relaxation processes in small-molecule glass-formers. Such processes are due to the interconversion between different conformers of relatively flexible molecules, and generally involve conformational changes of flexible chain or ring moieties, or else the rigid rotation of planar groups, such as conjugated phenyl rings. Comparative analysis of molecules possessing the same (type of) functional group is carried out in order to test the possibility of assigning the dynamic conformational isomerism of given families of organic compounds to the motion of specific molecular subunits. These range from terminal halomethyl and acetyl/acetoxy groups to both rigid and flexible ring structures, such as the planar halobenzene cycles or the buckled saccharide and diazepine rings. A short section on polyesters provides a generalisation of these findings to synthetic macromolecules. Conformational isomerism ; Intramolecular force ; Relaxation (psychology) ; Macromolecule ; Chemistry ; Molecule ; Conjugated system ; Spectroscopy ; Ring (chemistry) ; Dielectric ; Molecular dynamics ; Computational chemistry ; Nuclear magnetic resonance spectroscopy ; Chemical physics ; Crystallography ; Materials science ; Stereochemistry ; Polymer ; Organic chemistry Liquid Crystal Research Advancements ; Material Dynamics and Properties ; Photochemistry and Electron Transfer Studies
Authors: Jieying Liang | Qianfan Chen | Joel Yong | Hiroki Suyama | Joanna Biazik | Bosiljka Njegic | Aditya Rawal | Kang Liang
Source: Chemical Science (article, 2023-12-13)
Field: Materials Science — Materials Chemistry

Covalent-organic framework nanobionics for robust cytoprotection We present a novel study introducing a durable and robust covalent-organic framework (COF) nanocoating, developed <i>in situ</i> on living cells. This COF nanocoating demonstrates remarkable resistance against a diverse range of lethal stressors, including high temperature, extreme pH, ultraviolet radiation, toxic metal ions, organic pollutants, and strong oxidative stress. Notably, the nanocoating exhibits exceptional cell survival enhancement under high temperature and strongly acidic conditions, an aspect yet unexplored in the case of metal-organic framework nanocoatings and other nanomaterials. Moreover, functionalization of the nanocoating with an exogenous enzyme catalase enables yeast fermentation and ethanol production even under strong oxidative stress. Our findings establish the durable and robust COF nanocoating as a reliable platform for safeguarding vulnerable microorganisms to allow their utilisation in a wide range of adverse environments. Cytoprotection ; Covalent bond ; Chemistry ; Combinatorial chemistry ; Nanotechnology ; Computer science ; Biochemistry ; Materials science ; Organic chemistry ; Oxidative stress Advanced Nanomaterials in Catalysis ; Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications
Authors: Chengyuan Wen | Roy Odle | Shengfeng Cheng
Source: Polymers (article, 2023-04-04)
Field: Materials Science — Polymers and Plastics

Molecular Weight Distribution of Branched Polymers: Comparison between Monte Carlo Simulation and Flory-Stockmayer Theory It is challenging to predict the molecular weight distribution (MWD) for a polymer with a branched architecture, though such information will significantly benefit the design and development of branched polymers with desired properties and functions. A Monte Carlo (MC) simulation method based on the Gillespie algorithm is developed to quickly compute the MWD of branched polymers formed through step-growth polymerization, with a branched polyetherimide from two backbone monomers (4,4'-bisphenol A dianhydride and m-phenylenediamine), a chain terminator (phthalic anhydride), and a branching agent (tris[4-(4-aminophenoxy)phenyl] ethane) as an example. This polymerization involves four reactions that can be all reduced to a condensation reaction between an amine group and a carboxylic anhydride group. A comparison between the MC simulation results and the predictions of the Flory-Stockmayer theory on MWD shows that the rates of the reactions are determined by the concentrations of the functional groups on the monomers involved in each reaction. It further shows that the Flory-Stockmayer theory predicts MWD well for systems below the gel point but starts to fail for systems around or above the gel point. However, for all the systems, the MC method can be used to reliably predict MWD no matter if they are below or above the gel point. Even for a macroscopic system, a converging distribution can be quickly obtained through MC simulations on a system of only a few hundred to a few thousand monomers that have the same molar ratios as in the macroscopic system. Monte Carlo method ; Statistical physics ; Polymer ; Molecular dynamics ; Materials science ; Molar mass distribution ; Thermodynamics ; Computational chemistry ; Chemistry ; Physics ; Mathematics ; Statistics Polymer crystallization and properties ; Advanced Polymer Synthesis and Characterization ; Organometallic Complex Synthesis and Catalysis
Authors: Min Cao | Junhang Tian | Weidong Zhuang | Ronghui Liu | Yuanhong Liu | Guantong Chen | Limin Wang | Jianwei Wang
Source: Journal of the American Ceramic Society (article, 2023-05-18)
Field: Materials Science — Materials Chemistry

Efficient, stable, broadband cyan‐emitting Ca‐substituted Ba <sub>9</sub> Lu <sub>2</sub> Si <sub>6</sub> O <sub>24</sub> :Eu <sup>2+</sup> with multisite luminescence for NUV‐wLEDs Abstract In order to develop an efficient and stable broadband cyan phosphor for full spectrum white lighting emitting diodes (wLEDs), novel Ba 9 Lu 2 Si 6 O 24 :Eu 2+ , xCa 2+ is designed and synthesized. Ca‐substitution induces Eu 2+ ions into Lu 3+ crystallographic site, which achieve rare nonequivalent cation substitution of Eu 2+ . Effects of Ca‐substitution on crystal structure of matrix and phosphor are investigated by X‐ray photoelectron spectroscopy, X‐ray powder diffraction, transmission electron microscopy, and density functional thoery (DFT). Ba 9 Lu 2 Si 6 O 24 :Eu 2+ , xCa 2+ can be effectively excited by with near‐ultraviolet (NUV) and exhibit broadband cyan emission with full width at half maximum (FWHM) of 119.7 nm at x = 0.2, due to the multisite luminescence centers. For the sample x = 0.2, the internal quantum efficiency is 92.61%, and the luminous intensity at 423 K remains 89% of that measured at room temperature. The rigid structure of [SiO4]‐[LuO6]‐[SiO4] doped with Eu2+ ion makes Ca‐substituted samples exhibit excellent luminescence efficiency and thermal stability. Our work develops a significant strategy based on multisite cation regulation to explore NUV‐excited broadband cyan phosphors for full spectrum wLEDs. Phosphor ; Cyan ; Luminescence ; Full width at half maximum ; Materials science ; Excited state ; Orthosilicate ; Analytical Chemistry (journal) ; Ion ; Quantum efficiency ; Emission spectrum ; Chemistry ; Optoelectronics ; Optics ; Spectral line ; Physics ; Atomic physics ; Nanotechnology Luminescence Properties of Advanced Materials ; Luminescence and Fluorescent Materials ; Advanced Photocatalysis Techniques
Authors: Julius Seumer | Jonathan Kirschner Solberg Hansen | Mogens Brøndsted Nielsen | Jan H. Jensen
Source: Angewandte Chemie (article, 2023-02-14)
Field: Chemistry — Organic Chemistry

Computational Evolution Of New Catalysts For The Morita–Baylis–Hillman Reaction** Abstract We present a de novo discovery of an efficient catalyst of the Morita–Baylis–Hillman (MBH) reaction by searching chemical space for molecules that lower the estimated barrier of the rate‐determining step using a genetic algorithm (GA) starting from randomly selected tertiary amines. We identify 435 candidates, virtually all of which contain an azetidine N as the catalytically active site, which is discovered by the GA. Two molecules are selected for further study based on their predicted synthetic accessibility and have predicted rate‐determining barriers that are lower than that of a known catalyst. Azetidines have not been used as catalysts for the MBH reaction. One suggested azetidine is successfully synthesized and showed an eightfold increase in activity over a commonly used catalyst. We believe this is the first experimentally verified de novo discovery of an efficient catalyst using a generative model. Azetidine ; Catalysis ; Chemistry ; Chemical space ; Molecule ; Stereoisomerism ; Combinatorial chemistry ; Organic chemistry ; Drug discovery Synthesis and Catalytic Reactions ; Asymmetric Hydrogenation and Catalysis ; Asymmetric Synthesis and Catalysis
Authors: Sandra Sefa | Jonathan Espiritu | Hanna Ćwieka | Imke Greving | Silja Flenner | Olga Will | Susanne Beuer | D. C. Florian Wieland | Regine Willumeit‐Römer | Berit Zeller‐Plumhoff
Source: Bioactive Materials (article, 2023-08-01)
Field: Materials Science — Biomaterials

Multiscale morphological analysis of bone microarchitecture around Mg-10Gd implants The utilization of biodegradable magnesium (Mg)-based implants for restoration of bone function following trauma represents a transformative approach in orthopaedic application. One such alloy, magnesium-10 weight percent gadolinium (Mg-10Gd), has been specifically developed to address the rapid degradation of Mg while enhancing its mechanical properties to promote bone healing. Previous studies have demonstrated that Mg-10Gd exhibits favorable osseointegration; however, it exhibits distinct ultrastructural adaptation in comparison to conventional implants like titanium (Ti). A crucial aspect that remains unexplored is the impact of Mg-10Gd degradation on the bone microarchitecture. To address this, we employed hierarchical three-dimensional imaging using synchrotron radiation in conjunction with image-based finite element modelling. By using the methods outlined, the vascular porosity, lacunar porosity and the lacunar-canaliculi network (LCN) morphology of bone around Mg-10Gd in comparison to Ti in a rat model from 4 weeks to 20 weeks post-implantation was investigated. Our investigation revealed that within our observation period, the degradation of Mg-10Gd implants was associated with significantly lower (p < 0.05) lacunar density in the surrounding bone, compared to Ti. Remarkably, the LCN morphology and the fluid flow analysis did not significantly differ for both implant types. In summary, a more pronounced lower lacunae distribution rather than their morphological changes was detected in the surrounding bone upon the degradation of Mg-10Gd implants. This implies potential disparities in bone remodelling rates when compared to Ti implants. Our findings shed light on the intricate relationship between Mg-10Gd degradation and bone microarchitecture, contributing to a deeper understanding of the implications for successful osseointegration. Osseointegration ; Materials science ; Biomedical engineering ; Implant ; Medicine ; Surgery Magnesium Alloys: Properties and Applications ; Orthopaedic implants and arthroplasty ; Bone Tissue Engineering Materials
Authors: Jungkap Park | Christopher Wilkins | Dmitry M. Avtonomov | Jiwon Hong | Seunghoon Back | Hokeun Kim | Nicholas Shulman | Brendan MacLean | Sang‐Won Lee | Sangtae Kim
Source: Cell Reports Methods (article, 2023-07-01)
Field: Chemistry — Spectroscopy

Targeted proteomics data interpretation with DeepMRM Targeted proteomics is widely utilized in clinical proteomics; however, researchers often devote substantial time to manual data interpretation, which hinders the transferability, reproducibility, and scalability of this approach. We introduce DeepMRM, a software package based on deep learning algorithms for object detection developed to minimize manual intervention in targeted proteomics data analysis. DeepMRM was evaluated on internal and public datasets, demonstrating superior accuracy compared with the community standard tool Skyline. To promote widespread adoption, we have incorporated a stand-alone graphical user interface for DeepMRM and integrated its algorithm into the Skyline software package as an external tool. Computer science ; Skyline ; Software ; Scalability ; Transferability ; Proteomics ; Data mining ; Data science ; Machine learning ; Database ; Programming language Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Machine Learning in Bioinformatics
Authors: Annex Ifeanyi Ogbu | Prosper Eguono Ovuoraye | Regina O. Ajemba | Mohammad Hadi Dehghani
Source: Scientific Reports (article, 2023-11-10)
Field: Chemistry — Organic Chemistry

Functionality and mechanistic parametric study of the potential of waste plantain peels and commercial bentonite for soybean oil refining The consumption of unrefined vegetable oil poses acute and chronic health issues, yet improper disposal of waste plantain peels is not environmentally sustainable. This research investigates the feasibility, mechanism and thermodynamics of waste plantain peels, and commercial bentonite clay for soybean oil refining. Experiment was carried out using masses (1-4 g) of commercial bentonite clay, and unripe plantain peel ash (UPPA) to degummed and neutralized free fatty acid (FFA) contents in crude soybean oil at varying temperatures (50-120 °C), and time (15-35 min) for treatment of soybean oil. FTIR spectroscopy, SEM, and XRF techniques were applied to characterize the sample. The results established that at optimum 4.0 g dosage, the UPPA (97.73%) was more effective in the removal of FFA from oil at 50 °C and 20 min, while the clay (90%) was more effective in the removal of colour pigment from the vegetable oil 100 °C, and 25 min. The optimum efficiency of Clay-Ash-composite (70:30) in adsorbing pigment from soybean oil corresponds to 80%. The impact of changing viscosities, densities, and acid values on the performance of UPPA, clay, and clay-UPPA composite was investigated. Mechanistic studies confirmed the pseudo-second-order kinetics at 5 × 10<sup>-2</sup> g/mg min<sup>-1</sup> and 1.87 × 10<sup>-1</sup> g/mg min<sup>-1</sup>, with corresponding adsorption capacity of 30.40 mg/g and 4.91 mg/g, at R<sup>2</sup> ≤ 0.9982. The UPPA-driven sorption of FFA occurred as a physisorption and exothermic process (- 620.60 kJ/mol), while colour pigment removal occurred by chemisorption and endothermic process (22.40 kJ/mol). The finding recommends UPPA and composite as economically feasible for refining soybean oil. Bentonite ; Chemistry ; Pulp and paper industry ; Soybean oil ; Adsorption ; Sorption ; Refining (metallurgy) ; Physisorption ; Nuclear chemistry ; Chemical engineering ; Food science ; Organic chemistry Edible Oils Quality and Analysis ; Dye analysis and toxicity ; Ginkgo biloba and Cashew Applications
Authors: Marìck Manrho | Sundar Raj Krishnaswamy | Björn Kriete | Ilias Patmanidis | Alex H. de Vries | ‪Siewert J. Marrink | Thomas L. C. Jansen | Jasper Knoester | Maxim S. Pshenichnikov
Source: Journal of the American Chemical Society (article, 2023-10-06)
Field: Materials Science — Biomaterials

Watching Molecular Nanotubes Self-Assemble in Real Time Molecular self-assembly is a fundamental process in nature that can be used to develop novel functional materials for medical and engineering applications. However, their complex mechanisms make the short-lived stages of self-assembly processes extremely hard to reveal. In this article, we track the self-assembly process of a benchmark system, double-walled molecular nanotubes, whose structure is similar to that found in biological and synthetic systems. We selectively dissolved the outer wall of the double-walled system and used the inner wall as a template for the self-reassembly of the outer wall. The reassembly kinetics were followed in real time using a combination of microfluidics, spectroscopy, cryogenic transmission electron microscopy, molecular dynamics simulations, and exciton modeling. We found that the outer wall self-assembles through a transient disordered patchwork structure: first, several patches of different orientations are formed, and only on a longer time scale will the patches interact with each other and assume their final preferred global orientation. The understanding of patch formation and patch reorientation marks a crucial step toward steering self-assembly processes and subsequent material engineering. Molecular dynamics ; Nanotechnology ; Chemistry ; Self-assembly ; Chemical physics ; Microfluidics ; Transmission electron microscopy ; Materials science ; Computational chemistry Supramolecular Self-Assembly in Materials ; Supramolecular Chemistry and Complexes ; Polydiacetylene-based materials and applications
Authors: Kaili Yin | Liping Shi | Xiaoliang Ma | Yesheng Zhong | Mingwei Li | Xiaodong He
Source: Nanomaterials (article, 2023-07-28)
Field: Materials Science — Materials Chemistry

Thermal Conductivity of 3C/4H-SiC Nanowires by Molecular Dynamics Simulation Silicon carbide (SiC) is a promising material for thermoelectric power generation. The characterization of thermal transport properties is essential to understanding their applications in thermoelectric devices. The existence of stacking faults, which originate from the "wrong" stacking sequences of Si-C bilayers, is a general feature of SiC. However, the effects of stacking faults on the thermal properties of SiC are not well understood. In this study, we evaluated the accuracy of Tersoff, MEAM, and GW potentials in describing the thermal transport of SiC. Additionally, the thermal conductivity of 3C/4H-SiC nanowires was investigated using non-equilibrium molecular dynamics simulations (NEMD). Our results show that thermal conductivity exhibits an increase and then saturation as the total lengths of the 3C/4H-SiC nanowires vary from 23.9 nm to 95.6 nm, showing the size effect of molecular dynamics simulations of the thermal conductivity. There is a minimum thermal conductivity, as a function of uniform period length, of the 3C/4H-SiC nanowires. However, the thermal conductivities of nanowires weakly depend on the gradient period lengths and the ratio of 3C/4H. Additionally, the thermal conductivity of 3C/4H-SiC nanowires decreases continuously from compressive strain to tensile strain. The reduction in thermal conductivity suggests that 3C/4H-SiC nanowires have potential applications in advanced thermoelectric devices. Our study provides insights into the thermal transport properties of SiC nanowires and can guide the development of SiC-based thermoelectric materials. Nanowire ; Thermal conductivity ; Materials science ; Stacking ; Thermoelectric effect ; Molecular dynamics ; Silicon carbide ; Seebeck coefficient ; Thermoelectric materials ; Nanotechnology ; Condensed matter physics ; Composite material ; Thermodynamics ; Computational chemistry ; Chemistry Thermal properties of materials ; Silicon Carbide Semiconductor Technologies