jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xiangzhe Kong | Jia, Yinjun | Wenbing Huang | Yang Liu
Source: arXiv (Cornell University) (preprint, 2024-02-21)
Field: Materials Science — Materials Chemistry

Full-Atom Peptide Design with Geometric Latent Diffusion Peptide design plays a pivotal role in therapeutics, allowing brand new possibility to leverage target binding sites that are previously undruggable. Most existing methods are either inefficient or only concerned with the target-agnostic design of 1D sequences. In this paper, we propose a generative model for full-atom \textbf{Pep}tide design with \textbf{G}eometric \textbf{LA}tent \textbf{D}iffusion (PepGLAD) given the binding site. We first establish a benchmark consisting of both 1D sequences and 3D structures from Protein Data Bank (PDB) and literature for systematic evaluation. We then identify two major challenges of leveraging current diffusion-based models for peptide design: the full-atom geometry and the variable binding geometry. To tackle the first challenge, PepGLAD derives a variational autoencoder that first encodes full-atom residues of variable size into fixed-dimensional latent representations, and then decodes back to the residue space after conducting the diffusion process in the latent space. For the second issue, PepGLAD explores a receptor-specific affine transformation to convert the 3D coordinates into a shared standard space, enabling better generalization ability across different binding shapes. Experimental Results show that our method not only improves diversity and binding affinity significantly in the task of sequence-structure co-design, but also excels at recovering reference structures for binding conformation generation. Diffusion ; Atom (system on chip) ; Peptide ; Computer science ; Chemistry ; Physics ; Thermodynamics ; Biochemistry ; Parallel computing Machine Learning in Materials Science ; Chemical Synthesis and Analysis ; Advanced Chemical Physics Studies
Authors: Shreyas Arvindekar | Kartik Majila | Shruthi Viswanath
Source: arXiv (Cornell University) (preprint, 2024-01-31)
Field: Materials Science — Materials Chemistry

Recent methods from statistical inference and machine learning to improve integrative modeling of macromolecular assemblies Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from complementary experiments along with physical principles, statistics of known structures, and prior models, for structure determination. Here, we review recent methods for integrative modeling based on statistical inference and machine learning. These methods improve over the current state-of-the-art by enhancing the data collection, optimizing coarse-grained model representations, making scoring functions more accurate, sampling more efficient, and model analysis more rigorous. We also discuss three new frontiers in integrative modeling: incorporating recent deep learning-based methods, integrative modeling with in situ data, and metamodeling. Inference ; Statistical inference ; Computer science ; Artificial intelligence ; Machine learning ; Statistical learning ; Management science ; Engineering ; Mathematics ; Statistics Machine Learning in Materials Science ; Protein Structure and Dynamics
Authors: Narcis Anghel | Iuliana Spiridon | Maria Valentina Dinu | Stelian Vlad | Mihaela Perţea
Source: Polymers (article, 2024-06-19)
Field: Materials Science — Polymers and Plastics

Xanthan–Polyurethane Conjugates: An Efficient Approach for Drug Delivery The antifungal agent, ketoconazole, and the anti-inflammatory drug, piroxicam, were incorporated into matrices of xanthan or oleic acid-esterified xanthan (Xn) and polyurethane (PU), to develop topical drug delivery systems. Compared to matrices without bioactive compounds, which only showed a nominal compressive stress of 32.18 kPa (sample xanthan-polyurethane) at a strain of 71.26%, the compressive resilience of the biomaterials increased to nearly 50.04 kPa (sample xanthan-polyurethane-ketoconazole) at a strain of 71.34%. The compressive strength decreased to around 30.67 kPa upon encapsulating a second drug within the xanthan-polyurethane framework (sample xanthan-polyurethane-piroxicam/ketoconazole), while the peak sustainable strain increased to 87.21%. The Weibull model provided the most suitable fit for the drug release kinetics. Unlike the materials based on xanthan-polyurethane, those made with oleic acid-esterified xanthan-polyurethane released the active ingredients more slowly (the release rate constant showed lower values). All the materials demonstrated antimicrobial effectiveness. Furthermore, a higher volume of piroxicam was released from oleic acid-esterified xanthan-polyurethane-piroxicam (64%) as compared to xanthan-polyurethane-piroxicam (44%). Considering these results, materials that include polyurethane and either modified or unmodified xanthan showed promise as topical drug delivery systems for releasing piroxicam and ketoconazole. Drug delivery ; Conjugate ; Polyurethane ; Drug ; Materials science ; Nanotechnology ; Pharmacology ; Medicine ; Composite material Polymer composites and self-healing ; Polysaccharides and Plant Cell Walls ; Synthetic Organic Chemistry Methods
Authors: Zhennan Kou | Dmitry Tolmachev | Maisa Vuorte | Maria Sammalkorpi
Source: Cellulose (article, 2024-12-22)
Field: Materials Science — Biomaterials

Component size dependent lignin-carbohydrate complex adsorption at crystalline cellulose surfaces Abstract The materials characteristics of natural wood but also the properties of artificial cellulose/hemicellulose-based wood-inspired composite materials result from the molecular level organization and interactions between cellulose, hemicellulose, and lignin. Here, we use atomistic detail molecular dynamics simulations to examine the adsorption of model lignin-carbohydrate complexes (LCCs) consisting of a glucomannan polysaccharide chain with differing lignin fragment linkages to the crystalline facets of cellulose nanocrystals. The findings show that on crystalline cellulose surfaces exceeding in surface dimensions the length of the adsorbed hemicellulose chain, the LCCs can adopt orientations both parallel and perpendicular to the surface chains with response depending on the crystalline facet. The observation of perpendicular orientations is unexpected, as previous molecular level modelling studies systematically report parallel LCC adsorption orientation, however on cellulose interfaces modelling the narrow natural wood cellulose fibrils. Here, the perpendicular adsorption orientation is stabilized by extensive hydrogen bonding and adsorption of the hemicellulose chain with negligible chain bending. Overall, the results show that component dimensions (hemicellulose chain length vs cellulose crystalline surface dimensions) combined with understanding the differences of adsorption response at the difference crystal facets are crucial in understanding wood-inspired materials. Graphical abstract Hemicellulose ; Cellulose ; Lignin ; Adsorption ; Chemical engineering ; Materials science ; Composite material ; Organic chemistry ; Chemistry Advanced Cellulose Research Studies ; Lignin and Wood Chemistry ; Polysaccharides and Plant Cell Walls
Authors: Abdul Ghaffar | Peng Song | Ryo Maezono | Kenta Hongo
Source: ACS Omega (article, 2024-12-01)
Field: Materials Science — Materials Chemistry

Theoretical Insights into High-<i>T</i><sub>c</sub> Superconductivity of Structurally Ordered YThH<sub>18</sub>: A First-Principles Study There has been a marked increase in interest in high-temperature superconductors over the past few years, sparked by their potential to revolutionize multiple fields, including energy generation and transportation. A particularly promising avenue of exploration has emerged in the form of ternary superhydrides, compounds composed of hydrogen along with two other rare-earth elements. Our investigation focuses on the search for Y-Th-H ternary compounds; employing an evolutionary search methodology complemented by electron-phonon calculations reveals a stable superhydride, <i>P</i>6̅<i>m</i>2-YThH<sub>18</sub>, capable of exhibiting a critical temperature (<i>T</i> <sub>c</sub>) as high as 222 K at 200 GPa along a few low-<i>T</i> <sub>c</sub> novel hydrides. Our analysis explores the possibility of alloyed structure formation from the disordered condition of Th-doped YH<sub>9</sub> and establishes that the <i>P</i>6̅<i>m</i>2-YThH<sub>18</sub> is indeed a structurally ordered structure. This opens up an exciting avenue for research on multinary superhydrides, which could facilitate experimental synthesis and provides potential implications for high-temperature superconductivity research. Superconductivity ; Ternary operation ; Condensed matter physics ; Doping ; Materials science ; Rare earth ; Crystallography ; Nanotechnology ; Physics ; Chemistry ; Computer science ; Metallurgy Hydrogen Storage and Materials ; High-pressure geophysics and materials ; Rare-earth and actinide compounds
Authors: Xavier Davoy | Julien Devémy | Sébastien Garruchet | Alain Dequidt | Patrice Hauret | Patrice Malfreyt
Source: Langmuir (article, 2024-05-20)
Field: Chemistry — Organic Chemistry

Toward a Better Understanding of the Poly(glycerol sebacate)–Water Interface Molecular simulations were conducted to provide a better description of the poly(glycerol sebacate) (PGS)-water interface. The density and the glass-transition temperature as well as their dependencies on the degree of esterification were examined in close connection with the available experimental data. The work of adhesion and water contact angle were calculated as a function of the degree of esterification. A direct correlation was established between the strength of the hydrogen bond network in the interfacial region and the change in the water contact angle with respect to the degree of esterification. The interfacial region was described by local density profiles and orientations of the water molecules. Contact angle ; Glass transition ; Hydrogen bond ; Work (physics) ; Degree (music) ; Molecule ; Glycerol ; Adhesion ; Materials science ; Chemical engineering ; Chemistry ; Polymer chemistry ; Composite material ; Chemical physics ; Organic chemistry ; Thermodynamics ; Polymer ; Physics Surfactants and Colloidal Systems ; Polymer Surface Interaction Studies ; Material Dynamics and Properties
Authors: Lukáš Pečínka | Lukáš Moráň | Petra Kovačovicová | Francesca Meloni | Josef Havel | Tiziana Pivetta | Petr Vaňhara
Source: Heliyon (article, 2024-04-22)
Field: Chemistry — Spectroscopy

Intact cell mass spectrometry coupled with machine learning reveals minute changes induced by single gene silencing Intact (whole) cell MALDI TOF mass spectrometry is a commonly used tool in clinical microbiology for several decades. Recently it was introduced to analysis of eukaryotic cells, including cancer and stem cells. Besides targeted metabolomic and proteomic applications, the intact cell MALDI TOF mass spectrometry provides a sufficient sensitivity and specificity to discriminate cell types, isogenous cell lines or even the metabolic states. This makes the intact cell MALDI TOF mass spectrometry a promising tool for quality control in advanced cell cultures with a potential to reveal batch-to-batch variation, aberrant clones, or unwanted shifts in cell phenotype. However, cellular alterations induced by change in expression of a single gene has not been addressed by intact cell mass spectrometry yet. In this work we used a well-characterized human ovarian cancer cell line SKOV3 with silenced expression of a tumor suppressor candidate 3 gene (TUSC3). TUSC3 is involved in co-translational N-glycosylation of proteins with well-known global impact on cell phenotype. Altogether, this experimental design represents a highly suitable model for optimization of intact cell mass spectrometry and analysis of spectral data. Here we investigated five machine learning algorithms (k-nearest neighbors, decision tree, random forest, partial least squares discrimination, and artificial neural network) and optimized their performance either in pure populations or in two-component mixtures composed of cells with normal or silenced expression of TUSC3. All five algorithms reached accuracy over 90 % and were able to reveal even subtle changes in mass spectra corresponding to alterations of TUSC3 expression. In summary, we demonstrate that spectral fingerprints generated by intact cell MALDI-TOF mass spectrometry coupled to a machine learning classifier can reveal minute changes induced by alteration of a single gene, and therefore contribute to the portfolio of quality control applications in routine cell and tissue cultures. Mass spectrometry ; Cell ; Gene silencing ; Gene expression ; Proteomics ; Cell culture ; Phenotype ; Biology ; Computational biology ; Single-cell analysis ; Chemistry ; Cell biology ; Gene ; Biochemistry ; Genetics ; Chromatography Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Markus Paramahasti | Valentinus Galih Vidia Putra | Yusril Yusuf
Source: Journal of Measurements in Engineering (article, 2024-08-22)
Field: Materials Science — Polymers and Plastics

Biomechanical surface roughness analysis of ramie-low melt polyester nonwovens exposed to plasma This study aims to characterize ramie-low melt polyester nonwoven fabrics treated with low-temperature plasma and to analyze 3-D images based on object-depth mapping (ODM) using the MATLAB ® R2022a software. We examined the low-temperature plasma treatment of nonwoven ramie fabrics using a plasma generator with 30 kV output power, six-minute treatment times, and a 4.5 cm distance between electrodes. The fabric’s chemical properties and surface topography were investigated using scanning electron microscopy (SEM) and infrared spectroscopy (FTIR). An analysis of the SEM images was performed using a statistical approach and image processing to determine the level of surface roughness. FTIR analysis revealed that fabrics exposed for six minutes differed from those that were not. Our findings indicated that plasma treatment caused the following: 1) Ramie fabrics to become more hydrophilic, as shown by their increased T% in the FTIR of hydrophilic functional groups such as hydroxyl (O-H), carboxyl (-COOH), and carbonyl (C=O); 2) A higher surface roughness was observed in nonwoven fabric during SEM testing and image processing; 3) Plasma treatment of fabrics resulted in a higher coefficient of variation (CV) than untreated fabrics; 4) Nonwoven fabric mass reduction. Based on this study, we found the relationship between plasma-treated ramie fabric and textiles in biomechanics. Plasma treatment reduced the mass of ramie fabric by 0.11 %, according to our findings. We found that the greater the mass reduction, the greater the surface roughness value. The novelty of this study is the use of 3-D images based on object-depth mapping (ODM) using the MATLAB ® R2022a software in SEM to observe surface roughness to the physical properties of ramie fabric for the first time. Ramie ; Polyester ; Surface roughness ; Materials science ; Composite material ; Surface finish ; Polymer science ; Fiber Textile materials and evaluations ; Natural Fiber Reinforced Composites ; Additive Manufacturing and 3D Printing Technologies
Authors: Duško Kostić | Sreċko Stopić | Monika Keutmann | Elif Emil-Kaya | Tatjana Volkov‐Husović | Mitar Perušić | Bernd Friedrich
Source: Materials (article, 2024-09-28)
Field: Materials Science — Materials Chemistry

Synthesis of Titanium-Based Powders from Titanium Oxy-Sulfate Using Ultrasonic Spray Pyrolysis Method Submicron and nanosized powders have gained significant attention in recent decades due to their broad applicability in various fields. This work focuses on ultrasonic spray pyrolysis, an efficient and flexible method that employs an aerosol process to synthesize titanium-based nanoparticles by transforming titanium oxy-sulfate. Various parameters are monitored to better optimize the process and obtain better results. Taking that into account, the influence of temperature on the transformation of titanium oxy-sulfate was monitored between 700 and 1000 °C. In addition to the temperature, the concentration of the starting solution was also changed, and the flow of hydrogen and argon was studied. The obtained titanium-based powders had spherical morphology with different particle sizes, from nanometer to submicron, depending on the influence of reaction parameters. The control of the oxygen content during synthesis is significant in determining the structure of the final powder. Titanium ; Materials science ; Chemical engineering ; Nanoparticle ; Ultrasonic sensor ; Titanium powder ; Particle size ; Sulfate ; Particle (ecology) ; Pyrolysis ; Nanometre ; Metallurgy ; Composite material ; Nanotechnology Nanoparticles: synthesis and applications ; Laser-Ablation Synthesis of Nanoparticles ; TiO2 Photocatalysis and Solar Cells
Authors: Lata Deso Abo | Sintayehu Mekuria Hailegiorgis | Gadissa Tokuma Gindaba | Mani Jayakumar | Sundramurthy Venkatesa Prabhu
Source: Environmental Quality Management (review, 2024-12-01)
Field: Materials Science — Biomaterials

A Comprehensive Review on Fouling of Heat Transfer Units in Sugar Factory Ethanol Plant: Mechanisms and Mitigation Methods ABSTRACT Fouling in heat transfer units has a negative economic impact. Many scale‐forming impurities are present in cane molasses generated by sugar cane production technology, including cations of aluminum (Al), calcium (Ca), iron (Fe), magnesium (Mg), potassium (K), sodium (Na), as well as anions of carbonates, sulfites, phosphates, sulfate, silicates, and chlorides. Ca cations, in particular, form insoluble complexes with many other chemical constituents, making them a scale‐forming impurity. The accumulation of Ca ion on the heat exchanger's surface could increase heat transfer resistance and reduce its overall efficiency. This article reviews many types of heat‐transmitting unit fouling and their successive fouling occurrences. Identifying the chemicals found in scale deposits helps to determine which cleaning products will effectively clean heat transfer units and which scale inhibitors will drastically lower scale formation rates. Furthermore, numerous unit operations and unit processes, such as molasses pre‐treatment and pre‐fermentation practice (inoculation of yeast), followed by fermentation practice, and product purification practice distillation, are used to limit deposit formation and boost ethanol production efficiency. Molasses pre‐treatment and treatment such as chemical treatment, heat treatment, acid centrifugation, and mechanical treatment are critical in decreasing scale development during heat exchange operations. Fouling ; Chemistry ; Fermentation ; Heat exchanger ; Pulp and paper industry ; Distillation ; Sugar ; Chemical engineering ; Heat transfer ; Ethanol fuel ; Waste management ; Chromatography ; Biochemistry ; Membrane Calcium Carbonate Crystallization and Inhibition ; Polysaccharides Composition and Applications ; Biodiesel Production and Applications
Authors: Mitsuo Niinomi | Takayuki Narushima | Takayoshi Nakano
Source: MATERIALS TRANSACTIONS (article, 2024-11-24)
Field: Materials Science — Materials Chemistry

Recent Research and Development in the Processing, Microstructure, and Properties of Titanium and Its Alloy The special issue on recent research and development in the processing, microstructure, and properties of titanium and its alloy contains four review articles on metal additive manufacturing (AM) focusing on the processing, microstructural and/or crystallographic control, and biomedical applications of titanium and its alloys, and seventeen regular articles on metal AM, refining, microstructural evolution, and mechanical and fatigue properties related to the microstructure, and biomedical applications of titanium and its alloys, which have been published in Materials Transactions in 2023. This study briefly addresses this issue. Materials science ; Microstructure ; Titanium alloy ; Alloy ; Metallurgy ; Development (topology) ; Titanium Titanium Alloys Microstructure and Properties ; Additive Manufacturing Materials and Processes ; Metallurgy and Material Forming
Authors: Konstantin Pikula | Seyed Ali Johari | Ralph Santos‐Oliveira | Kirill S. Golokhvast
Source: International Journal of Molecular Sciences (review, 2024-11-02)
Field: Materials Science — Materials Chemistry

Joint Toxicity and Interaction of Carbon-Based Nanomaterials with Co-Existing Pollutants in Aquatic Environments: A Review This review paper focuses on the joint toxicity and interaction of carbon-based nanomaterials (CNMs) with co-existing pollutants in aquatic environments. It explores the potential harmful effects of chemical mixtures with CNMs on aquatic organisms, emphasizing the importance of scientific modeling to predict mixed toxic effects. The study involved a systematic literature review to gather information on the joint toxicity and interaction between CNMs and various co-contaminants in aquatic settings. A total of 53 publications were chosen and analyzed, categorizing the studies based on the tested CNMs, types of co-contaminants, and the used species. Common test models included fish and microalgae, with zebrafish being the most studied species. The review underscores the necessity of conducting mixture toxicity testing to assess whether the combined effects of CNMs and co-existing pollutants are additive, synergistic, or antagonistic. The development of in silico models based on the solid foundation of research data represents the best opportunity for joint toxicity prediction, eliminating the need for a great quantity of experimental studies. Pollutant ; Aquatic toxicology ; Environmental science ; Fish <Actinopterygii> ; Environmental chemistry ; Environmental toxicology ; Joint (building) ; Biochemical engineering ; Toxicity ; Aquatic ecosystem ; Ecology ; Chemistry ; Biology ; Fishery ; Engineering Nanoparticles: synthesis and applications ; Environmental Toxicology and Ecotoxicology ; Electrochemical Analysis and Applications