jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Şule Gürsoy | Elif Oztürk | Bayan Zoatier | Mahmut Ülger | Öztekin Algül
Source: Erzincan Üniversitesi Fen Bilimleri Enstitüsü Dergisi (article, 2024-08-27)
Field: Chemistry — Organic Chemistry

Synthesis and antitubercular activities of acetamide-substituted benzazole derivatives Multidrug-resistant Mycobacterium tuberculosis strains' increasing emergence and rapid spread necessitate the urgent development of innovative antimycobacterial agents. In pursuit of novel agents, a series of N-(benzazole-2-ylmethyl)-2-substituted phenylacetamide or N-(benzazole-2-ylmethyl)-2-(thiophen-2-yl)acetamide compounds (6-11) were synthesized. Their efficacy against multidrug-resistant Mycobacterium tuberculosis was assessed. Compounds exhibited potent antimycobacterial activity with minimum inhibitory concentrations (MIC) ranging from 1.05 to 4.10 µM and demonstrated low cytotoxicity towards fibroblast cell line (L929). ADMET predictions suggested that these synthesized compounds possess drug-like properties. Our findings offer a promising starting point for designing more selective and potent antimycobacterial agents. Antimycobacterial ; Acetamide ; Mycobacterium tuberculosis ; Minimum inhibitory concentration ; Cytotoxicity ; Tuberculosis ; Chemistry ; Pharmacology ; Mycobacterium ; Multiple drug resistance ; Combinatorial chemistry ; Stereochemistry ; Microbiology ; Medicine ; Biology ; Drug resistance ; Biochemistry ; In vitro ; Organic chemistry Synthesis and biological activity ; Chemical Synthesis and Analysis ; Click Chemistry and Applications
Authors: Maksud J. Jumaniyazov | Rasulbek Jabbiev
Source:  (article, 2024-12-19)
Field: Materials Science — Materials Chemistry

GOSSYPOL RESIN - IN THE FUTURE A VALUABLE MATERIAL FOR BUILDING BITUMEN WITHOUT OIL The article presents the results of evaluating the effectiveness of treatment of patients with osteoarthritis of the knee joint of 1-3 degrees using platelet-rich plasma.According to the results of the study, it was found that the maximum decrease in indicators on the WOMAC and YOUR scales, in the form of relief of pain, reduction of stiffness and increase in range of motion, occurred in patients after 3 procedures of intraarticular injection of PRP. Gossypol ; Asphalt ; Petroleum engineering ; Materials science ; Environmental science ; Process engineering ; Computer science ; Waste management ; Composite material ; Pulp and paper industry ; Engineering ; Chemistry Structural mechanics and materials ; Innovations in Concrete and Construction Materials ; Fire effects on concrete materials
Authors: K. Nepal | Chinonso Ugwumadu | K. N. Subedi | K. Kappagantula | D. A. Drabold
Source: arXiv (Cornell University) (preprint, 2024-01-04)
Field: Materials Science — Materials Chemistry

Physical origin of enhanced electrical conduction in aluminum-graphene composites The electronic and transport properties of aluminum-graphene composite materials were investigated using ab initio plane wave density functional theory. The interfacial structure is reported for several configurations. In some cases, the face-centered aluminum (111) surface relaxes in a nearly ideal registry with graphene, resulting in a remarkably continuous interface structure. The Kubo-Greenwood formula and space-projected conductivity were employed to study electronic conduction in aluminum single- and double-layer graphene-aluminum composite models. The electronic density of states at the Fermi level is enhanced by the graphene for certain aluminum-graphene interfaces, thus, improving electronic conductivity. In double-layer graphene composites, conductivity varies non-monotonically with temperature, showing an increase between 300-400 K at short aluminum-graphene distances, unlike the consistent decrease in single-layer composites. Graphene ; Materials science ; Composite number ; Composite material ; Aluminium ; Conductivity ; Electrical resistivity and conductivity ; Thermal conduction ; Density functional theory ; Graphene nanoribbons ; Fermi level ; Graphene foam ; Ab initio ; Electronic structure ; Condensed matter physics ; Electron ; Nanotechnology ; Computational chemistry ; Chemistry ; Physics Graphene research and applications ; Surface and Thin Film Phenomena ; Chemical and Physical Properties of Materials
Authors: Fang Pan | Lin Yang | Zhuangde Jiang | Wei Ren | Zuo‐Guang Ye | Jingrui Li
Source: arXiv (Cornell University) (preprint, 2024-06-26)
Field: Chemistry — Inorganic Chemistry

Effects of model size in density-functional-theory study of alloys: A case study of CsPbBr$_2$Cl The primary challenge of density-functional-theory exploration of alloy systems concerns the size of computational model. Small alloy models can hardly exhibit the chemical disorder properly, while large models induce difficulty in sampling the alignments within the massive material space. We study this problem with the γ phase of the mixed halide inorganic perovskite alloy CsPbBr$_2$Cl. The distribution of alloy formation energy becomes narrower when the size of the model system increases along $\sqrt{2}\times\sqrt{2}\times2$, $2\times2\times2$, and $2\sqrt{2}\times2\sqrt{2}\times2$ models. This is primarily because the distribution of Br distribution parameters, which plays a leading role in determining the formation energy range, is more narrow for larger models. As a result, larger entropy stability effect can be observed with larger models especially at high temperatures, for which the approximation using mixing entropy based on the ideal solution model becomes better. Density functional theory ; Materials science ; Thermodynamics ; Chemistry ; Physics ; Computational chemistry Inorganic Chemistry and Materials ; nanoparticles nucleation surface interactions ; Advanced Chemical Physics Studies
Authors: Guzel Minibaeva | Pavel Polishchuk
Source: ChemRxiv (preprint, 2024-12-30)
Field: Chemistry — Organic Chemistry

CReM-dock: de novo design of synthetically feasible compounds guided by molecular docking De novo generation of compounds is an attractive strategy allowing to explore much broader chemical space than virtual screening. Fragment-based approaches suffer from low synthetic accessibility of generated compounds. In this study we combined the previously developed fragment-based generator CReM and molecular docking to guide the exploration of chemical space. The developed approach is very flexible and allows to indirectly control synthetic accessibility of generated compounds, their diversity by choosing one of selection strategies, augmentation of an objective function to generate more drug-like compounds, control over preserving important protein-ligand interactions and ligand poses. The generated compounds demonstrated high novelty and were competitive to compounds generated with REINVENT4. We demonstrated in different case studies flexibility of the developed approach and its applicability to de novo generation as well as fragment expansion tasks. DOCK ; Docking (animal) ; Computational biology ; Computer science ; Chemistry ; Combinatorial chemistry ; Biology ; Biochemistry ; Medicine Inorganic and Organometallic Chemistry
Authors: Guanxuan Wu | Allison Sullivan
Source: arXiv (Cornell University) (preprint, 2024-02-29)
Field: Materials Science — Materials Chemistry

AlloyASG: Alloy Predicate Code Representation as a Compact Structurally Balanced Graph Writing declarative models has numerous benefits, ranging from automated reasoning and correction of design-level properties before systems are built to automated testing and debugging of their implementations after they are built. Unfortunately, the model itself needs to be correct to gain these benefits. Alloy is a commonly used modeling language that has several existing efforts to repair faulty models automatically. Currently, these efforts are search-based methods that use an Abstract Syntax Tree (AST) representation of the model and do not scale. One issue is that ASTs themselves suffer from exponential growth in their data size due to the limitation that ASTs will often have identical nodes separately listed in the tree. To address this issue, we introduce a novel code representation schema, Complex Structurally Balanced Abstract Semantic Graph (CSBASG), which represents code as a complex-weighted directed graph that lists a semantic element as a node in the graph and ensures its structural balance for almost finitely enumerable code segments. We evaluate the efficiency of our CSBASG representation for Alloy models in terms of it's compactness compared to ASTs, and we explore if a CSBASG can ease the process of comparing two Alloy predicates. Moreover, with this representation in place, we identify several future applications of CSBASG, including Alloy code generation and automated repair. Predicate (mathematical logic) ; Graph ; Computer science ; Programming language ; Theoretical computer science Machine Learning in Materials Science ; Natural Language Processing Techniques
Authors: Zhangwei Guo | Qun Feng | Na Guo | Yansheng Yin | Tao Liu
Source: Frontiers in Microbiology (article, 2024-08-30)
Field: Materials Science — Biomaterials

Positive effects of molybdenum on the biomineralization process on the surface of low-alloy steel catalyzed by Bacillus subtilis The adhesion of microorganisms and the subsequent formation of mineralized layers in biofilms are of great significance in inhibiting the corrosion of metal materials. In this work, we found that the adhesion and subsequent mineralization of <i>Bacillus subtilis</i> on the surface of low-alloy steel are influenced by the molybdenum in the material. The addition of molybdenum will lead to increased adhesion of <i>B. subtilis</i> on the material surface, and the subsequent biomineralization ability has also been improved. Through transcriptome and physiological and biochemical tests, we found that molybdenum can affect the chemotaxis, mobility and carbonic anhydrase secretion related genes of <i>B. subtilis</i>, and then affect the formation and mineralization of the biofilm of <i>B. subtilis</i>. Bacillus subtilis ; Biomineralization ; Molybdenum ; Catalysis ; Metallurgy ; Alloy ; Chemistry ; Materials science ; Chemical engineering ; Bacteria ; Biology ; Biochemistry ; Engineering Calcium Carbonate Crystallization and Inhibition ; Microbial Applications in Construction Materials ; Bone Tissue Engineering Materials
Authors: José Ángel Castellanos-Reyes | Paul Zeiger | Ján Rusz
Source: arXiv (Cornell University) (preprint, 2024-01-28)
Field: Materials Science — Materials Chemistry

Dynamical theory of angle-resolved electron energy loss and gain spectroscopies of phonons and magnons in transmission electron microscopy including multiple scattering effects We present a method for computing angle-resolved electron-energy-loss and gain spectroscopies for phonon and magnon excitations in transmission electron microscopy. Fractional scattering intensities are derived from the temperature-dependent time auto-correlation of the electron beam wave function. This method captures both single and multiple scattering processes, as well as dynamical diffraction effects. Our method remains computationally efficient, and it is easy to parallelize. Magnon ; Scattering ; Electron ; Phonon ; Physics ; Condensed matter physics ; Energy (signal processing) ; Atomic physics ; Optics ; Quantum mechanics Electronic and Structural Properties of Oxides ; Mechanical and Optical Resonators ; Semiconductor materials and devices
Authors: Fileto Rodriguez | Robin Francotte | Beata Taudul | Jianing Wang | Ionut Trancă | Diane Sorgeloos | Enrique Lozano Diz | Mónica Calatayud | Frederik Tielens
Source: SSRN Electronic Journal (preprint, 2024-01-01)
Field: Chemistry — Spectroscopy

Advanced Spectroscopic Characterization of Calcium Carbonate Polymorphs: Ab Initio Dynamic Approaches and Experimental Raman Raman spectroscopy ; Characterization (materials science) ; Ab initio ; Materials science ; Ab initio quantum chemistry methods ; Computational chemistry ; Chemistry ; Nanotechnology ; Physics ; Molecule ; Optics ; Organic chemistry Molecular spectroscopy and chirality
Authors: Hongfeng Zhang | Aritra Sarkar | Koen Bertels
Source: ArXiv.org (preprint, 2024-04-23)
Field: Chemistry — Spectroscopy

A resource-efficient variational quantum algorithm for mRNA codon optimization Optimizing the mRNA codon has an essential impact on gene expression for a specific target protein. It is an NP-hard problem; thus, exact solutions to such optimization problems become computationally intractable for realistic problem sizes on both classical and quantum computers. However, approximate solutions via heuristics can substantially impact the application they enable. Quantum approximate optimization is an alternative computation paradigm promising for tackling such problems. Recently, there has been some research in quantum algorithms for bioinformatics, specifically for mRNA codon optimization. This research presents a denser way to encode codons for implementing mRNA codon optimization via the variational quantum eigensolver algorithms on a gate-based quantum computer. This reduces the qubit requirement by half compared to the existing quantum approach, thus allowing longer sequences to be executed on existing quantum processors. The performance of the proposed algorithm is evaluated by comparing its results to exact solutions, showing well-matching results. Quantum ; Algorithm ; Computer science ; Quantum mechanics ; Physics Mass Spectrometry Techniques and Applications
Authors: Lorenzo A. Mariano | Nguyen Vu Ha Anh | Jonatan B. Petersen | Magnus Bjørnsson | Jesper Bendix | Gareth R. Eaton | Sandra S. Eaton | Alessandro Lunghi
Source: arXiv (Cornell University) (preprint, 2024-07-01)
Field: Chemistry — Physical and Theoretical Chemistry

The role of electronic excited states in the spin-lattice relaxation of spin-1/2 molecules Magnetic resonance is a prime method for the study of chemical and biological structures and their dynamical processes. The interpretation of these experiments relies on considering the spin of electrons as the sole relevant degree of freedom. By applying ab inito open quantum systems theory to the full electronic wavefunction, here we show that contrary to this widespread framework the thermalization of the unpaired electron spin of two Cr(V) coordination compounds is driven by virtual transitions to excited states with energy higher than 20,000 cm$^{-1}$ instead of solely involving low-energy spin interactions such as Zeeman and hyperfine ones. Moreover, we found that a window of low-energy THz phonons contributes to thermalization, rather than a small number of high-energy vibrations. This work provides a drastic reinterpretation of relaxation in spin-1/2 systems and its chemical control strategies, and ultimately exemplifies the urgency of further advancing an ab initio approach to relaxometry. Excited state ; Condensed matter physics ; Spin (aerodynamics) ; Relaxation (psychology) ; Molecule ; Lattice (music) ; Spin states ; Spin–lattice relaxation ; Materials science ; Physics ; Atomic physics ; Quantum mechanics ; Medicine Photochemistry and Electron Transfer Studies ; Spectroscopy and Quantum Chemical Studies ; Molecular Junctions and Nanostructures
Authors: Ahtsham Ulhaq | Kristina Lilova | Virgel Torremocha
Source: Journal of Student Research (article, 2024-11-30)
Field: Materials Science — Biomaterials

Exploring the Optimized Function of Polymer Coated Nanoparticles: Applications in Drug Delivery Systems Nanoparticles (NPs) have gained traction throughout the recent years for their usage in many applications, including as drug delivery carriers. With their advantages - high surface area to volume ratio, surface functionalization, permeability, come with a downside of toxicity. Most of the inorganic NPs can cause ion leakage through core dissolution, leading to reactive oxygen species (ROS) production and ultimately to an extended damage to the liver and kidneys. Those side effects can be avoided by a polymer coating on the surface of the NPs. This paper aims to answer a rarely discussed question - what NPs - polymers system offers most benefits and least side effects. Throughout all the compiled findings, two strong candidates for NPs and two strong candidates for polymers stand out. Superparamagnetic iron oxide nanoparticles (SPIONs) and mesoporous silica nanoparticles (MSNs) are two of the most exceptional NPs for their unique magnetic properties and mesoporous structures, respectively, and paired with the enhanced properties of the natural polymer chitosan (Ch) and the synthetic poly(ethylene glycol) (PEG), can theoretically become the most suitable candidates for drug delivery. Drug delivery ; Nanoparticle ; Materials science ; Drug ; Function (biology) ; Polymer ; Nanotechnology ; Pharmacology ; Composite material ; Medicine Nanoparticle-Based Drug Delivery ; Nanomaterials for catalytic reactions
Authors: Robert M. Raddi | Vincent A. Voelz
Source: arXiv (Cornell University) (preprint, 2024-02-17)
Field: Materials Science — Materials Chemistry

Automated optimization of force field parameters against ensemble-averaged measurements with Bayesian Inference of Conformational Populations Accurate force fields are essential for reliable molecular simulations. These models are refined against quantum mechanical calculations and experimental measurements, which are subject to random and systematic errors. Bayesian Inference of Conformational Populations (BICePs) is a reweighting algorithm that reconciles simulated ensembles with sparse or noisy observables by sampling the full posterior distribution of conformational populations and experimental uncertainty. In this method, a metric called the BICePs score is used to perform model selection, by calculating the free energy of "turning on" the conformational populations under experimental restraints. This approach, when used with improved likelihood functions to deal with experimental outliers, can be used for force field validation (Raddi et al. 2025). Here, we extend the BICePs approach to perform automated force field refinement while simultaneously sampling the full distribution of uncertainties, using a variational method to minimize the BICePs score. To demonstrate the utility of this method, we refine multiple interaction parameters for a 12-mer HP lattice model using ensemble-averaged distance measurements as restraints. To illustrate the resilience of BICePs in the presence of unknown random and systematic errors, we assess the performance of our algorithm through repeated optimizations and under various extents of experimental error. Our results suggest that variational optimization of the BICePs score is a promising direction for robust and automatic parameterization of molecular potentials. Inference ; Force field (fiction) ; Bayesian inference ; Bayesian probability ; Field (mathematics) ; Computer science ; Artificial intelligence ; Statistical physics ; Mathematics ; Physics Machine Learning in Materials Science
Authors: Rui Liu | Bo Ma | Xin Zhao | Kefei Tan | Jifang Hu | Ming Yuan | Lianxia Wang | Hongbo Xiang | Dongxue Mi | Yongcai Lai | Kai Liu | Shibo Wang
Source: Research Square (preprint, 2024-09-09)
Field: Chemistry — Analytical Chemistry

Artificial Intelligence Identification of Japonica Rice varieties Based on Raman Spectroscopic Identification Mechanism of Saline-alkali Tolerance Identification (biology) ; Japonica rice ; Mechanism (biology) ; Japonica ; Alkali metal ; Raman spectroscopy ; Saline ; Chemistry ; Artificial intelligence ; Botany ; Computer science ; Biology ; Physics ; Optics ; Organic chemistry Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; GABA and Rice Research
Authors: Rongshan Qin
Source: Materials (article, 2024-06-11)
Field: Materials Science — Materials Chemistry

Visual Computation of Material Microstructure and Deformation The experimentally obtained material microstructure can be used to calculate a material's properties and identify microstructure-property relationships. The key procedure to enable this is to interpret the observed microstructure accurately. This work reports on a newly developed computational method to serve such a purpose. The method is based on cubic spline interpolation and a simple search algorithm. Parameterisation was accomplished via the comparison between its preliminary statistical results and the information in a phase diagram. The method was applied to analyse the quenched microstructure of multicomponent and multiphase metallic-oxide materials. The importance of adequate parameterisation is demonstrated. The results provide a good explanation for the experimentally measured electric conductance behaviour. Further application of the method to the deformation of materials is discussed. The algorithms are directly available for the analysis of the three-dimensional microstructure of materials. Microstructure ; Materials science ; Deformation (meteorology) ; Computation ; Composite material ; Computer science ; Algorithm Machine Learning in Materials Science ; Computer Graphics and Visualization Techniques ; High-Velocity Impact and Material Behavior
Authors: Steven R. Spurgeon
Source: OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (article, 2024-08-16)
Field: Materials Science — Surfaces, Coatings and Films

Accelerating Interface Science Through NREL's New Electron Microscopy Suite Presentation on NREL's new capabilities in electron microscopy and AI-guided interface that are relevant to the Si PV community. Suite ; Interface (matter) ; Electron microscope ; Computer science ; Nanotechnology ; Computational science ; Computer graphics (images) ; Engineering physics ; Materials science ; Engineering ; Physics ; Optics ; Operating system ; Geography ; Archaeology Electron and X-Ray Spectroscopy Techniques
Authors: W. Koch
Source: Journal of Molecular Modeling (article, 2024-01-24)
Field: Materials Science — Materials Chemistry

Quantum chemical “Aufbau” principles: how to estimate the shape of highly flexible (bio-)polymers? A recursively extendable “chemion picture” of Euler-Hückel-type An outline is given of how to split the n-dimensional space of torsion angles occurring in flexible (bio-)polymers (like alkanes, nucleic acids, or proteins, for instance) into n one-dimensional potential curves. Forthcoming applications will focus on the "protein folding problem," beginning with polyglycine. CONTEXT: In accordance with Euler's topology rules, molecules are considered to be composed of "vertices" (atoms, ligands, bonding sites, functional groups, and bigger fragments). Following Hückel, each vertex is represented by only one basis function. Starting from the "monofocal" hydrids CH[Formula: see text], NH[Formula: see text], OH[Formula: see text], FH, and SiH[Formula: see text], PH[Formula: see text], SH[Formula: see text], ClH as anchor units, "chemionic" Hamiltonians (of individual "chemion ensembles" and proportional nuclear charges) are constructed recursively, together with an appropriate basis set for the first five (normal) alkanes and some related oligomers like primary alcohols, alkyl amines, and alkyl chlorides. METHODS: Standard methods ("Restricted Hartree-Fock RHF" and "Full Configuration Interaction FCI") are used to solve the various stationary Schrödinger equations. Two software packages are indispensable: "SMILES" for integral evaluations over Slater-type orbitals (STO), and "Numerical Recipes" for matrix diagonalizations and inversions. While managing with only two-center repulsion integrals, "implicit multi-center integrations" lead us to the non-empirical fundament of Hoffmann's "Extended-Hückel Theory." Fock matrix ; Euler's formula ; Context (archaeology) ; Chemistry ; Type (biology) ; Computational chemistry ; Basis set ; Physics ; Quantum mechanics ; Mathematics ; Hartree–Fock method ; Density functional theory ; Mathematical analysis Enzyme Structure and Function ; Protein Structure and Dynamics ; Molecular spectroscopy and chirality