jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yoshihiro Hayashi
Source: NIPPON GOMU KYOKAISHI (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Sim2Real Materials Informatics Transforming Data-Driven Polymer Materials Research The most important resource of data-driven research is data. However, the amount of data available on polymeric materials is overwhelmingly small compared to other material systems. To address this data scarcity, we describe a simulation-to-real (Sim2Real) transfer learning methodology, in which a large dataset of polymer property data generated through molecular simulations is leveraged to enhance a smaller set of experimental data. Additionally, we introduce the development of RadonPy, a Python library that fully automates all-atom classical molecular dynamics simulations of polymer properties, serving as the materials informatics (MI) foundation for Sim2Real transfer learning. We also discuss the industry-academia collaboration to develop the world's largest database of computational polymer properties using the RadonPy. As of July 2024, more than 80,000 polymers have been calculated, establishing this as the world's largest such database. Using the RadonPy database as training data, we have constructed a calibration model that compensates for the gap between calculated and experimental data through Sim2Real transfer learning. Furthermore, we observed a scaling law in Sim2Real transfer learning, where the generalization performance to experimental values improves according to a power law as the amount of simulation data increases. Informatics ; Materials informatics ; Polymer ; Materials science ; Data science ; Health informatics ; Computer science ; Engineering ; Political science ; Composite material ; Engineering informatics ; Electrical engineering Machine Learning in Materials Science
Authors: Nikhil Bharambe | Zhuowen Li | David Seiferth | Asha Manikkoth Balakrishna | Philip C. Biggin | Sandip Basak
Source: Biophysical Journal (article, 2024-02-01)
Field: Chemistry — Spectroscopy

Cryo-EM structures of nanodisc reconstituted ligand-gated ion channel GLIC in various conformations reveal state-dependent protein-lipid interactions and gating mechanism Protonation ; Chemistry ; KcsA potassium channel ; Gating ; Crystallography ; Biophysics ; Ion channel ; Nanodisc ; Ligand (biochemistry) ; Molecular dynamics ; Ion ; Helix bundle ; Ligand-gated ion channel ; Protein structure ; Lipid bilayer ; Stereochemistry ; Biochemistry ; Computational chemistry ; Membrane ; Receptor ; Biology Molecular Sensors and Ion Detection ; Antimicrobial Peptides and Activities ; Chemical Synthesis and Analysis
Authors: Pérez Sanz Fernando | Pedro Navarro | Egea Gutiérrez-Cortines Marcos | Weiss Julia Rosl
Source:  (article, 2024-02-29)
Field: Chemistry — Analytical Chemistry

Aprendizaje automatizado basado en transformadas wavelet para la segmentación de hojas en imágenes infrarrojas In this work we present an algorithm to segment leaves in NIR images captured inside a growth chamber. The proposed method uses a features vector composed by four elements extracted from different levels of wavelets transform. We have tested three classifiers: knearest neighbour (kNN), Naive Bayes classifier (NBC) and Support Vector Machine to determine the optimal machine learning algorithm to carry out the leaf segmentation. Method developed has been validated by means of the Receiver Operating Characteristic (ROC) curve and it has obtained a maximum performance of 98.33% in the leaf segmentation using SVM classifier. Computer science Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies
Authors: Ge Bai | Francesco Buscemi | Valerio Scarani
Source: arXiv (Cornell University) (preprint, 2024-10-01)
Field: Chemistry — Physical and Theoretical Chemistry

Quantum Bayes' rule and Petz transpose map from the minimum change principle Bayes' rule, which is routinely used to update beliefs based on new evidence, can be derived from a principle of minimum change. This principle states that updated beliefs must be consistent with new data, while deviating minimally from the prior belief. Here, we introduce a quantum analog of the minimum change principle and use it to derive a quantum Bayes' rule by minimizing the change between two quantum input-output processes, not just their marginals. This is analogous to the classical case, where Bayes' rule is obtained by minimizing several distances between the joint input-output distributions. When the change maximizes the fidelity, the quantum minimum change principle has a unique solution, and the resulting quantum Bayes' rule recovers the Petz transpose map in many cases. Transpose ; Bayes' theorem ; Mathematics ; Quantum ; Computer science ; Algorithm ; Statistics ; Physics ; Bayesian probability ; Quantum mechanics ; Eigenvalues and eigenvectors History and advancements in chemistry ; Bayesian Modeling and Causal Inference ; Computational Drug Discovery Methods
Authors: Dirk Bartel
Source: Lubricants (article, 2024-12-02)
Field: Materials Science — Materials Chemistry

Tribology in Germany: Latest Research and Development Sixty-five years ago, in November 1959, the “Gesellschaft für Schmiertechnik” (GST, Society for Lubrication Technology), the predecessor organization of today’s German Society for Tribology, was founded in the form of a non-profit technical scientific association [...] Tribology ; German ; Lubrication ; Engineering ; Engineering ethics ; Mechanical engineering ; Engineering management ; Manufacturing engineering ; Forensic engineering ; Geography Metal Alloys Wear and Properties ; Engineering and Materials Science Studies ; Tribology and Wear Analysis
Authors: S. V. Kondakov | M. A. Asfandiyarov | I. E. Levshin
Source: Bulletin of the South Ural State University series Mechanical Engineering Industry (article, 2024-01-01)
Field: Materials Science — General Materials Science

Review of modern methods for composite materials compacting The article discusses various methods of compaction of composite materials: static, vibration, shock, as well as combined action. The designs of mechanisms for compaction are given: a vibrating press, a vibrating plate, a mechanism with a ramming bar, a continuous press for molding products from powdery masses with a connecting rod-rocker impact mechanism, a machine for compacting rigid concrete mixtures, and others. Their principle of operation is considered, advantages and disadvantages are indicated. The analysis of existing compacting methods allows synthesizing the accumulated knowledge in this field, combining them into a single system, finding shortcomings and ways to improve the applied compacting methods in order to increase the productivity of the process, reduce the required drive power of the mechanism, improve the operational characteristics of products. The works of Russian researchers are considered: E.A. Shishkin, A.A. Smolyakov, O.G. Klevtsova, V.I. Ivanchura, A.P. Prokopyev and others. The works of foreign researchers are also considered: Donghai Liu, Ning Wang, Erbo Song, Carl Wersall, K. Rainer Massarsch, Johan Spross and others. The research examines modern methods of compaction, including practical experiments aimed at identifying the most optimal parameters of equipment operation and refining the designs of existing mechanisms. The authors note that many processes related to compaction require additional experimental studies, and the existing methods of compaction are not effective enough and have disadvantages that cannot be eliminated without making significant changes. Thus, it is necessary to apply new methods that meet the requirements of modern technological processes. Materials science ; Composite number ; Composite material Material Properties and Applications ; Polymer Science and Applications ; Epoxy Resin Curing Processes
Authors: Altair C. Hernández | Laura Betancur | Andrea Picco | Oriol Gallego
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-03-30)
Field: Materials Science — Materials Chemistry

Use of Protein interactions from Imaging Complexes after Translocation (PICT) to characterise <i>in situ</i> the spatial configuration of proteins interacting with the exocyst ABSTRACT Although the structure of the exocyst has been successfully resolved by cryo-electron microscopy, multiple studies showed that exocyst function requires the transient interaction with additional proteins. Unfortunately, the exocyst-interacting network could not be collectively reconstituted, challenging the understanding of how the exocyst complex is coordinated within the network of proteins involved in exocytosis. In a previous work, we described an approach that combines Protein interactions from Imaging Complexes after Translocation (PICT) and centroid localization analysis of diffraction-limited fluorescence signals to estimate the distance between a labelled protein and a spatial reference. This approach allows resolving the spatial organisation of protein interactions directly in living cells, both for intra-complex (i.e. between exocyst subunits) and inter-complex (i.e. between exocyst and transient binding proteins) interactions. In this chapter, we present the protocol to reproduce the sample preparation and image acquisition for PICT experiments. We also describe the computational image analysis pipeline to estimate the distance in PICT experiments. As illustration of the approach, we measure the distance from the spatial reference where the exocyst is anchored to 1) an intra-complex interaction (i.e. Sec5 exocyst subunit) and 2) an inter-complex interaction (Sec2, a guanyl-nucleotide exchange factor mediating vesicle tethering). Exocyst ; In situ ; Chromosomal translocation ; Cell biology ; Chemistry ; Biology ; Biochemistry Enzyme Structure and Function
Authors: Chaoyang Fan | Yi Wang | Min Huang | Jianming Cao | Xiangjun Li | Xiehua Ouyang | Hao Wu
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-04-20)
Field: Chemistry — Spectroscopy

WITHDRAWN: Proteonano™ coupled with Orbitrap Astral™: A robust and standardized workflow for large-cohort clinical plasma proteomics studies Withdrawal Statement The authors have withdrawn their manuscript owing to [INCOMPLETE DATA ANALYSIS]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. Workflow ; Orbitrap ; Proteomics ; Medicine ; Computer science ; Chemistry ; Database ; Chromatography ; Mass spectrometry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Advanced Biosensing Techniques and Applications
Authors: Ferran Gonzalez Hernandez | Victoria Smith | Quang Nguyen | Palang Chotsiri | Thanaporn Wattanakul | J. Cordero | María Rosa Ballester | Albert Sole‐Guitart | Gill Mundin | Watjana Lilaonitkul | Joseph F. Standing | Frank Kloprogge
Source:  (article, 2024-01-01)
Field: Chemistry — Spectroscopy

End-to-End Relation Extraction of Pharmacokinetic Estimates from the Scientific Literature Ferran Gonzalez Hernandez, Victoria Smith, Quang Nguyen, Palang Chotsiri, Thanaporn Wattanakul, José Antonio Cordero, Maria Rosa Ballester, Albert Sole, Gill Mundin, Watjana Lilaonitkul, Joseph F. Standing, Frank Kloprogge. Proceedings of the 23rd Workshop on Biomedical Natural Language Processing. 2024. Relation (database) ; Computer science ; Extraction (chemistry) ; Relationship extraction ; Data mining ; Chromatography ; Chemistry Analytical Chemistry and Chromatography ; Pharmacogenetics and Drug Metabolism
Authors: Yachen Liu | Li Mei | Chenyu Liang | Chuan‐Qi Zhong | Mengsha Tong | Rongshan Yu
Source: ACS Omega (article, 2024-11-04)
Field: Chemistry — Spectroscopy

Cross-Run Hybrid Features Improve the Identification of Data-Independent Acquisition Proteomics The analysis of data-independent acquisition (DIA) mass spectrometry data is crucial for comprehensive proteomics studies. However, traditional single-run methods often fall short in terms of identification depth and consistency. We present HFDiscrim, a specialized multirun DIA analysis tool aimed at enhancing the depth and consistency of reliable peptide identifications of DIA analysis tools. HFDiscrim was extensively benchmarked on multiple data sets, including the MCB data set, the ccRCC data set, and a three-species benchmark mixture. Compared to PyProphet, HFDiscrim identified 22.04% more precursors, 19.1% more peptides, and 13.2% more proteins while maintaining a controllable false discovery rate. Furthermore, HFDiscrim demonstrated higher identification rates and improved reproducibility across multiple runs. HFDiscrim is publicly available at https://github.com/yachliu/HFDiscrim. Identification (biology) ; Computer science ; Proteomics ; Chemistry ; Biology Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; vaccines and immunoinformatics approaches
Authors: Natebaye NGOIDITA | Amir Moungache | Stéphane Robert | S. Capraro
Source:  (preprint, 2024-12-27)
Field: Chemistry — Analytical Chemistry

CONTRIBUTION OF THE HIERARCHICAL GENETIC ALGORITHM TO ELLIPSOMETRIC SPECTROSCOPIC CHARACTERIZATION In spectroscopic ellipsometric characterization, different dispersion models are generally used to accurately determine the opto-geometric parameters of a Sample. However, all current methods use a single dispersion law. The appropriate dispersion law is chosen on the experience basis. This makes conventional methods less flexible and potentially leads to erroneous results. In this paper, we develop an algorithm capable of characterizing the sample without a priori knowledge of a dispersion law describing the refractive indexes Hierarchical Genetic Algorithm (HGA) automatically selects the best law from a set of models on the basis of the Root Mean Square Error (RMSE) between the simulation with the chosen law and the measurement. The algorithm was applied on 2 silicon samples with a layer of silicon dioxide and a layer of resist. The HGA results are more robust than the conventional optimization method. Characterization (materials science) ; Algorithm ; Genetic algorithm ; Computer science ; Materials science ; Nanotechnology ; Machine learning Spectroscopy and Chemometric Analyses
Authors: Klas Feike | Patrick Kurzeja | Jörn Mosler | Kai Langenfeld
Source: arXiv (Cornell University) (preprint, 2024-06-03)
Field: Materials Science — Materials Chemistry

Limits of isotropic damage models for complex load paths -- beyond stress triaxiality and Lode angle parameter The stress triaxiality and the Lode angle parameter are two well established stress invariants for the characterization of damage evolution. This work assesses the limits of this tuple by using it for damage predictions in a continuum damage mechanics framework. Isotropic and anisotropic formulations of two well-established models are used to avoid model-specific restrictions. The damage evolution is analyzed for different load paths, while the stress triaxiality and the Lode angle parameter are controlled. The equivalent plastic strain is moreover added as a third parameter, but still does not suffice to uniquely define the damage state. As a consequence, well-established concepts such as fracture surfaces depending on this triple have to be taken with care, if complex paths are to be investgated. These include, e.g., load paths observed during metal forming applications with varying load directions or multiple stages. Lode ; Isotropy ; Stress (linguistics) ; Materials science ; Physics ; Optics High-Velocity Impact and Material Behavior ; Fluid Dynamics Simulations and Interactions ; Rock Mechanics and Modeling
Authors: Ali Mahamoud Ghlaio | Imhemmed Hasan Algott | Abdalkrem khalifa Altresh | عبد الله علي شفتر
Source: Journal of Pure & Applied Sciences (article, 2024-02-21)
Field: Materials Science — Materials Chemistry

العلاقة بين مقاومة الضغط ومقاومة الشد في الخرسانة عالية المقاومة تم في هذا البحث إجراء اختبارات معملية على عينات خرسانية لحساب كل من مقاومة الضغط ومقاومة الشد في الخرسانة علية المقاومة، حيث تم حساب مقاومة الضغط باختبار عدد (12) مكعب مقاس cm(10*10*10) لكل تشغيلية (منخفضة – متوسطة – مرتفعة)، وتم حساب مقاومة الشد بإستخدام اختبار القص المباشر باختبار عدد (8) اسطوانات مقاس )cm15*15) لكل تشغيلية، حيث تم رسم منحنيات للعلاقة بين مقاومة الضغط ومقاومة الشد للخرسانة عالية المقاومة عند كل تشغيلية، وكانت النتائج تشير إلى أنّ مقاومة الضغط تزداد كلما قلت نسبة الماء إلى الإسمنت عند جميع التشغيليات، وأشارت النتائج أيضاً إلى أنّ مقاومة الشد تزداد كلما قلت نسبة الماء إلى الإسمنت، ولكن عند التشغيلية المنخفضة كانت مقاومة الشد تقل كلما قلت نسبة الماء إلى الإسمنت W/C حتى نسبة (0.45 = (W/C ثم تبدأ مقاومة الشد في الإزدياد عند النسبة الأقل من (0.45 = (W/C، كما أشارت النتائج أيضا إلى أنّ مقاومة الشد تتراوح بين 6% إلى 8% من مقاومة الضغط عند جميع التشغيليات، وأشارت النتائج أخيراً إلى أنّه كلما زادت التشغيلية قلّ معامل الاختلاف لكل من مقاومة الشد ومقاومة الضغط ونسبة مقاومة الشد إلى مقاومة الضغط أي أنّ النتائج تكون أكثر تجانس، بينما نسبة الماء إلى الإسمنت W/C ratio تكون أكثر تجانس كلما قلّت التشغيلية. Physics Material Selection and Properties ; Tribology and Wear Analysis ; Erosion and Abrasive Machining
Authors: Matthew G. Boebinger | Kevin M. Roccapriore | Ayana Ghosh | Kai Xiao | Andrew R. Lupini | Maxim Ziatdinov | Sergei V. Kalinin | Raymond R. Unocic
Source: Microscopy and Microanalysis (article, 2024-07-01)
Field: Materials Science — Materials Chemistry

Precision Defect Engineering in 2D Materials via Automated STEM Atomic Fabrication Fabrication ; Materials science ; Nanotechnology ; Medicine Electronic and Structural Properties of Oxides ; Integrated Circuits and Semiconductor Failure Analysis ; Semiconductor materials and devices
Authors: Prashant Kaushal | Manisha R Ummadi | Gwendolyn Μ. Jang | Yennifer Delgado | Sara K Makanani | Sophie F Blanc | Decan M Winters | Jiewei Xu | Benjamin J. Polacco | Yuan Zhou | Erica Stevenson | Manon Eckhardt | Lorena Zuliani-Alvarez | Robyn M. Kaake | Danielle L. Swaney | Nevan Krogan | Mehdi Bouhaddou
Source: PubMed (preprint, 2024-05-15)
Field: Chemistry — Spectroscopy

Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein-coding mutations or cellular signaling changes in response to molecular cues. Here, we present an affinity purification-mass spectrometry (APMS) proteomics protocol to quantify and visualize global changes in protein-protein interaction (PPI) networks between pairwise conditions. We describe steps for expressing affinity-tagged "bait" proteins in mammalian cells, identifying purified protein complexes, quantifying differential PPIs, and visualizing differential PPI networks. Specifically, this protocol details steps for designing affinity-tagged "bait" gene constructs, transfection, affinity purification, mass spectrometry sample preparation, data acquisition, database search, data quality control, PPI confidence scoring, cross-run normalization, statistical data analysis, and differential PPI visualization. Our protocol discusses caveats and limitations with applicability across cell types and biological areas. For complete details on the use and execution of this protocol, please refer to Bouhaddou et al. 2023<sup>1</sup>. Computational biology ; Proteomics ; Normalization (sociology) ; Protein–protein interaction ; Mass spectrometry ; Affinity chromatography ; Biology ; Chemistry ; Gene ; Biochemistry ; Chromatography ; Enzyme Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Microbial Metabolic Engineering and Bioproduction
Authors: Naoya Egawa | Kaoru Mizuta | Joji Nasu
Source: arXiv (Cornell University) (preprint, 2024-12-10)
Field: Materials Science — Materials Chemistry

Controlling discrete time crystals via single-site operations in zero-field diamond quantum simulators Discrete time crystals (DTCs) have emerged as novel nonequilibrium phases of matter that spontaneously break discrete time-translation symmetry in periodically driven systems. Rigorous experimental validation of DTCs, which requires highly controllable quantum simulators, has stimulated extensive research across diverse fields in condensed matter physics and quantum information technologies. Among these advances, DTCs were demonstrated in a hybrid spin register within diamond, comprising a processor spin and surrounding memory spins. However, in conventional strategies involving a bias magnetic field, the field application effectively restricts the controllability of the processor spin. This limitation can be a significant barrier to the next goal of DTCs: achieving multifunctionality through enhanced local controllability. In this study, we theoretically propose multiple DTC protocols through the design of specific single-site control within the entire system. To this end, we consider a concrete model of a diamond-based quantum simulator operating without a bias magnetic field, thereby eliminating the restrictions on the processor spin. Our findings demonstrate that single-site operations enable access to DTCs with multiple distinct features in terms of periodicity and lifetime. Therefore, this approach provides a promising platform for creating diverse DTCs induced by single-site operations. Diamond ; Zero (linguistics) ; Quantum ; Discrete time and continuous time ; Computer science ; Physics ; Quantum mechanics ; Materials science ; Mathematics ; Composite material Diamond and Carbon-based Materials Research
Authors: Yisheng Qiu | Tianwei Zhang | Thomas Möller | XueJian Jiang | Zihao Song | Huaxi Chen | Donghui Quan
Source: arXiv (Cornell University) (preprint, 2024-08-12)
Field: Chemistry — Spectroscopy

Spectuner: A Framework for Automated Line Identification of Interstellar Molecules Interstellar molecules, which play an important role in astrochemistry, are identified using observed spectral lines. Despite the advent of spectral analysis tools in the past decade, the identification of spectral lines remains a tedious task that requires extensive manual intervention, preventing us from fully exploiting the vast amounts of data generated by large facilities such as ALMA. This study aims to address the aforementioned issue by developing a framework of automated line identification. We introduce a robust spectral fitting technique applicable for spectral line identification with minimal human supervision. Our method is assessed using published data from five line surveys of hot cores, including W51, Orion-KL, Sgr B2(M), and Sgr B2(N). By comparing the identified lines, our algorithm achieves an overall recall of ~ 74% - 93%, and an average precision of ~ 78% - 92%. Our code, named Spectuner, is publicly available on GitHub. Identification (biology) ; Line (geometry) ; Astrobiology ; Molecule ; Interstellar medium ; Physics ; Astronomy ; Geometry ; Mathematics ; Quantum mechanics ; Biology ; Ecology ; Galaxy Spectroscopy and Laser Applications ; Scientific Research and Discoveries