jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jinho Chang | Jong Chul Ye
Source: arXiv (Cornell University) (preprint, 2024-05-28)
Field: Materials Science — Materials Chemistry

LDMol: A Text-to-Molecule Diffusion Model with Structurally Informative Latent Space Surpasses AR Models With the emergence of diffusion models as a frontline generative model, many researchers have proposed molecule generation techniques with conditional diffusion models. However, the unavoidable discreteness of a molecule makes it difficult for a diffusion model to connect raw data with highly complex conditions like natural language. To address this, here we present a novel latent diffusion model dubbed LDMol for text-conditioned molecule generation. By recognizing that the suitable latent space design is the key to the diffusion model performance, we employ a contrastive learning strategy to extract novel feature space from text data that embeds the unique characteristics of the molecule structure. Experiments show that LDMol outperforms the existing autoregressive baselines on the text-to-molecule generation benchmark, being one of the first diffusion models that outperforms autoregressive models in textual data generation with a better choice of the latent domain. Furthermore, we show that LDMol can be applied to downstream tasks such as molecule-to-text retrieval and text-guided molecule editing, demonstrating its versatility as a diffusion model. Space (punctuation) ; Diffusion ; Chemical space ; Computer science ; Physics ; Statistical physics ; Chemistry ; Thermodynamics ; Biochemistry ; Drug discovery Machine Learning in Materials Science ; Computational Drug Discovery Methods
Authors: Marzoqa M. Alnairi | Mosab Jaser Banısalman
Source: International Journal of Molecular Sciences (article, 2024-10-07)
Field: Materials Science — Materials Chemistry

Local Strain Effects on Lattice Defect Dynamics and Interstitial Dislocation Loop Formation in Irradiated Tungsten–Molybdenum Alloys: A Molecular Dynamics Study In this study, molecular dynamics (MD) simulations were used to investigate how alloying tungsten (W) with molybdenum (Mo) and local strain affect the primary defect formation and interstitial dislocation loops (IDLs) in W-Mo alloys. While the number of Frenkel pairs (FPs) in the W-Mo alloy is similar to pure W, it is half that of pure Mo. The W-20% Mo alloy, chosen for further analysis, showed minimal FP variance after collision cascades induced by primary knock-on atoms (PKAs) at 10 to 80 keV. The research examined hydrostatic strains from -1.4% to 1.6%, finding that higher strains correlated with increased FP counts and cluster formation, including IDLs. The following two types of IDLs were identified: majority ½ <111> loops as well as <100> IDLs that formed within the initial picoseconds of the simulations under higher tensile strain (1.6%) and larger PKA energies (80 keV). The strain effects also correlated with changes in threshold displacement energy (TDE), with higher FP formation under tensile strain. This study highlights the impact of strain and alloying on radiation damage, particularly in low-temperature, high-energy environments. Tungsten ; Molecular dynamics ; Molybdenum ; Materials science ; Alloy ; Irradiation ; Dislocation ; Strain (injury) ; Crystallography ; Molecular physics ; Chemistry ; Metallurgy ; Composite material ; Physics ; Computational chemistry Fusion materials and technologies ; Nuclear Materials and Properties ; Advanced materials and composites
Authors: Wei Wang | Uwe Hübner | Tao Chen | Anne Gärtner | Joseph Köbel | Franka Jahn | Henrik Schneidwind | Andrea Dellith | Jan Dellith | Torsten Wieduwilt | Matthias Zeisberger | Tanveer Ahmed Shaik | Astrid Bingel | Markus A. Schmidt | Jer‐Shing Huang | Volker Deckert
Source: arXiv (Cornell University) (preprint, 2024-01-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Grayscale Electron Beam Lithography Direct Patterned Antimony Sulfide The rise of micro/nanooptics and lab-on-chip devices demands the fabrication of three-dimensional structures with decent resolution. Here, we demonstrate the combination of grayscale electron beam lithography and direct forming methodology to fabricate antimony sulfide structures with free form for the first time. The refractive index of the electron beam patterned structure was calculated based on an optimization algorithm that is combined with genetic algorithm and transfer matrix method. By adopting electron irradiation with variable doses, 4-level Fresnel Zone Plates and metalens were produced and characterized. This method can be used for the fabrication of three-dimensional diffractive optical elements and metasurfaces in a single step manner. Electron-beam lithography ; Materials science ; Lithography ; Fabrication ; Optics ; Antimony ; Resist ; Grayscale ; Optoelectronics ; Next-generation lithography ; Refractive index ; X-ray lithography ; Nanotechnology ; Physics Metamaterials and Metasurfaces Applications ; Optical Coatings and Gratings ; Photonic and Optical Devices
Authors: Jiaxin Gao | Yi Sheng Ng | Hao Cheng | Hui‐Qiong Wang | Tie‐Yu Lü | Jin‐Cheng Zheng
Source: Physical Chemistry Chemical Physics (article, 2024-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Local symmetry-driven interfacial magnetization and electronic states in (ZnO)<sub><i>n</i></sub>/(w-FeO)<sub><i>n</i></sub> superlattices Superlattices constructed with the wide-band-gap semiconductor ZnO and magnetic oxide FeO, both in the wurtzite structure, have been investigated using spin-polarized first-principles calculations. The structural, electronic and magnetic properties of the (ZnO)<sub><i>n</i></sub>/(w-FeO)<sub><i>n</i></sub> superlattices were studied in great detail. Two different interfaces in the (ZnO)<sub><i>n</i></sub>/(w-FeO)<sub><i>n</i></sub> superlattices were identified and they showed very different magnetic and electronic properties. Local symmetry-driven interfacial magnetization and electronic states can arise from different Fe/Zn distributions at different interfaces or spin ordering of Fe in the superlattice. The local symmetry-driven interfacial magnetization and electronic states, originating either from different Fe/Zn distribution across interfaces I and II, or by spin ordering of Fe in the superlattice, can be identified. It was also found that, in the case of the ferromagnetic phase, the electrons are more delocalized for the majority spin but strongly localized for the minority spin, which resulted in interesting spin-dependent transport properties. Our results will pave the way for designing novel spin-dependent electronic devices through the construction of superlattices from semiconductors and multiferroics. Superlattice ; Condensed matter physics ; Magnetization ; Materials science ; Delocalized electron ; Ferromagnetism ; Wurtzite crystal structure ; Electronic structure ; Spin (aerodynamics) ; Magnetic semiconductor ; Physics ; Magnetic field ; Zinc Multiferroics and related materials ; ZnO doping and properties ; Magnetic and transport properties of perovskites and related materials
Authors: Zuo‐Feng Zhang | Haisen Zhou | Zhun Xu | Guangqi Wu | Hua Lu | Huan Wang
Source: JACS Au (article, 2024-12-16)
Field: Chemistry — Organic Chemistry

Chemical Reactions on a Single Linear Chain Show Cooperativity Individual molecules dissolved in a dilute solution are usually considered not to correlate with each other as they undergo chemical reactions due to the mismatch of the diffusion and reaction time scales. Recent studies suggest otherwise, especially for reactions involving macromolecules. With selenopolypeptides as a model system, we used ensemble measurements and single-molecule direct imaging to investigate the correlation between physically constrained chemical reaction sites on a linear polymer chain and the coupling effects between conformation changes and reaction kinetics. We used graphene liquid cells to encapsulate and image the reaction of selenopolypeptides and observed helix-to-coil transitions as Se atoms are oxidized under liquid-phase electron microscopy. Three common pathways were identified among three kinds of selenopolypeptides that differ only in the side groups attached to the Se atoms, which were found to critically determine the observed cooperativity. A more hydrophobic side group appeared to slow the reaction rate, which allowed us to quantify the reaction kinetics in detail and observe the correlation between the reaction sites on a single chain. Cooperativity ; Chemical reaction ; Chemistry ; Kinetics ; Molecule ; Chemical kinetics ; Macromolecule ; Chemical physics ; Reaction rate ; Polymer ; Crystallography ; Organic chemistry ; Catalysis ; Physics Fullerene Chemistry and Applications ; Selenium in Biological Systems ; Quantum Dots Synthesis And Properties
Authors: Federico Giannessi | Simone Di Cataldo | Santanu Saha | Lilia Boeri
Source: Scientific Data (article, 2024-07-12)
Field: Chemistry — Physical and Theoretical Chemistry

A database of high-pressure crystal structures from hydrogen to lanthanum This paper introduces the HEX (High-pressure Elemental Xstals) database, a complete database of the ground-state crystal structures of the first 57 elements of the periodic table, from H to La, at 0, 100, 200 and 300 GPa. HEX aims to provide a unified reference for high-pressure research, by compiling all available experimental information on elements at high pressure, and complementing it with the results of accurate evolutionary crystal structure prediction runs based on Density Functional Theory. Besides offering a much-needed reference, our work also serves as a benchmark of the accuracy of current ab-initio methods for crystal structure prediction. We find that, in 98% of the cases in which experimental information is available, ab-initio crystal structure prediction yields structures which either coincide or are degenerate in enthalpy to within 300 K with experimental ones. The main manuscript contains synthetic tables and figures, while the Crystallographic Information File (cif) for all structures can be downloaded from the related figshare online repository. Crystal structure prediction ; Ab initio ; Crystal structure ; Degenerate energy levels ; Database ; Benchmark (surveying) ; Computer science ; Crystal (programming language) ; Density functional theory ; Table (database) ; Crystallography ; Data mining ; Chemistry ; Thermodynamics ; Physics ; Computational chemistry ; Geology ; Quantum mechanics Crystallography and molecular interactions ; High-pressure geophysics and materials ; X-ray Diffraction in Crystallography
Authors: Bei Li | Yilun Zhang | Meng Wang | Xu Zhang | Xiaofeng Zhang | Kai Liu
Source: Materials (article, 2024-07-11)
Field: Materials Science — Materials Chemistry

Insights into Antisite Defect Complex Induced High Ferro-Piezoelectric Properties in KNbO3 Perovskite: First-Principles Study Improving ferro-piezoelectric properties of niobate-based perovskites is highly desirable for developing eco-friendly high-performance sensors and actuators. Although electro-strain coupling is usually obtained by constructing multiphase boundaries via complex chemical compositions, defect engineering can also create opportunities for novel property and functionality advancements. In this work, a representative tetragonal niobate-based perovskite, i.e., KNbO<sub>3</sub>, is studied by using first-principles calculations. Two intrinsic types of Nb antisite defect complexes are selected to mimic alkali-deficiency induced excess Nb antisites in experiments. The formation energy, electronic profiles, polarization, and piezoelectric constants are systematically analyzed. It is shown that the structural distortion and chemical heterogeneity around the energetically favorable antisite pair defects, i.e., (NbK4·+KNb4'), lower the crystal symmetry of KNbO<sub>3</sub> from tetragonal to triclinic phase, and facilitate polarization emergence and reorientation to substantially enhance intrinsic ferro-piezoelectricity (i.e., spontaneous polarization <i>P</i><sub>s</sub> of 68.2 μC/cm<sup>2</sup> and piezoelectric strain constant <i>d</i><sub>33</sub> of 228.3 pC/N) without complicated doping and alloying. Materials science ; Piezoelectricity ; Tetragonal crystal system ; Polarization (electrochemistry) ; Perovskite (structure) ; Condensed matter physics ; Doping ; Ferroelectricity ; Dielectric ; Chemical physics ; Nanotechnology ; Crystal structure ; Optoelectronics ; Crystallography ; Composite material ; Physical chemistry ; Chemistry Ferroelectric and Piezoelectric Materials ; Multiferroics and related materials ; Microwave Dielectric Ceramics Synthesis
Authors: Mahnaz Ahmadi | Elham Asadian | Mona Mosayebnia | Simin Dadashzadeh | Soraya Shahhosseini | Fateme Ghorbani-Bidkorpeh
Source: Iranian journal of pharmaceutical research (article, 2024-04-08)
Field: Chemistry — Inorganic Chemistry

Optimization of the Synthesis and Radiolabeling of ZIF-8 Nanoparticles In this study, the optimum conditions were successfully identified for synthesizing and labeling ZIF-8 nanoparticles. These nanoparticles have the potential to serve as effective carriers for diagnostic and therapeutic agents. Nanoparticle ; Chemistry ; Combinatorial chemistry ; Nanotechnology ; Chemical engineering ; Materials science ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Characterization ; Radioactive element chemistry and processing
Authors: Lilliana Brandão | C. Reece
Source: Catalysis Science & Technology (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Non-steady state validation of kinetic models for ethylene epoxidation over silver catalysts A two-site kinetic model for ethylene epoxidation most accurately recreates the selectivity trends observed during transient pressure pulse experiments of ethylene over oxidized silver. Catalysis ; Ethylene ; Kinetic energy ; Chemistry ; Steady state (chemistry) ; Thermodynamics ; Organic chemistry ; Physics Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Catalysis and Hydrodesulfurization Studies
Authors: Sarmad Saadi Hussein | Karima F. Ali | Fouad A. Al-Saady
Source: Palestinian medical and pharmaceutical journal/Palestinian medical & pharmaceutical journal (article, 2024-06-01)
Field: Chemistry — Organic Chemistry

Synthesis, Characterization, Molecular Docking, and Preliminary Antimicrobial Evaluation of Thiazolidinone Derivatives Several derivatives carrying thiazolidine-4-one pharmacophore were prepared to evaluate their antimicrobial activities. The set of compounds were shown to possess potential activities as determined by molecular docking studies for both candidal (14-alpha demethylase) and bacterial enzymes (Penicillin binding protein of E. coli). In vitro antimicrobial activities were also performed to confirm the molecular docking results. Molecular characterization by spec-tral techniques (FT-IR, 13C NMR and 1H NMR) was carried out to confirm the identity of the synthesized compounds. The synthesized compounds were evaluated for antibacterial and anticandidal activity by comparing them with the reference drugs (positive controls) ceftriax-one and fluconazole respectively. Four bacterial species (Klebsiella pneumonia, Escherichia coli, Staphylococcus epidermis, Staphylococcus aureus) and one fungal species (Candida albicans) were inoculated into petri dishes and were expose to the synthesized compounds by well diffusion method. The series of the proposed compounds were successfully synthesized and some of them were proven to have antibacterial activities comparable to the reference drug. Particularly, the compounds 2c and 2a posessed activities against K. pneumomia being higher than ceftriaxone with average inhibition zone diameters of 17 mm and 16 mm at highest concentration respectively. Compound 2b was effective against E. Coli also yielding higher activity than ceftriaxone achieving an average diameter of 17 mm at the highest concentration. Antimicrobial ; Combinatorial chemistry ; Docking (animal) ; Chemistry ; Computational biology ; Organic chemistry ; Biology ; Medicine Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Click Chemistry and Applications
Authors: Md Faizul Islam | Gamage Isuri P. Wijesekera | Ammon J. Sindt | Mark D. Smith | Linda S. Shimizu
Source: CrystEngComm (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Examination of photoinduced radicals in two crystal forms of triphenylamine bis-urea macrocycles The structures and photoinduced radical (PIR) percentages of two crystalline solvates of unsubstituted triphenylamine bis-urea macrocycles are compared. Upon activation, both afford similar structures with higher PIR %. Radical ; Urea ; Chemistry ; Photochemistry ; Organic chemistry Luminescence and Fluorescent Materials ; Photochromic and Fluorescence Chemistry ; Photochemistry and Electron Transfer Studies
Authors: M. Taş | E. Şaşıoğlu | I. Galanakis
Source: Magnetism (article, 2024-12-10)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Magnetic Properties of All-d Metallic Heusler Compounds: A First-Principles Study All-d metallic Heusler compounds are promising materials for nanoelectronic applications. Such materials combining 3d, 4d, and 5d atoms have not yet been studied. In this respect, we perform ab initio electronic structure calculations and focus on Co2MnZ, Rh2MnZ, and Ru2MnZ compounds, where Z represents transition metal atoms from groups 3B, 4B, 5B, and 6B of the periodic table. Our results demonstrate that most of these compounds exhibit a distinctive region of very low minority-spin state density at the Fermi level when crystallized in the L21 lattice structure. The Co-based compounds follow a Slater–Pauling behavior for their total spin magnetic moments, while the Ru-based compounds consistently deviate from the predicted Slater–Pauling values. Rh-based compounds show similarities to Co-based compounds for lighter Z atoms and to Ru-based compounds for heavier Z atoms. We find that the choice of the Z element within the same periodic table column has only a minor effect on the results, except for the Rh2Mn(Cr, Mo, W) compounds. Our findings suggest that these compounds hold significant promise for applications in spintronics and magnetoelectronics. Condensed matter physics ; Metal ; Materials science ; Heusler compound ; Metallurgy ; Physics Heusler alloys: electronic and magnetic properties ; MXene and MAX Phase Materials ; Intermetallics and Advanced Alloy Properties
Authors: A N M Nafiz Abeer | Sanket Jantre | Nathan M. Urban | Byung-Jun Yoon
Source:  (article, 2024-09-22)
Field: Materials Science — Materials Chemistry

Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design Deep generative models have been accelerating the inverse design process in material and drug design. Unlike their counterpart property predictors in typical molecular design frameworks, generative molecular design models have seen fewer efforts on uncertainty quantification (UQ) d ue to computational challenges in Bayesian inference posed by their large number of parameters. In this work, we focus on the junction-tree variational autoencoder (JT-VAE), a popular model for generative molecular design, and address this issue by leveraging the low dimensional active subspace (AS) to capture the uncertainty in the model parameters. Specifically, we approximate the posterior distribution over the active subspace parameters to estimate the epistemic model uncertainty in an extremely high dimensional parameter space. The proposed UQ scheme does not require any alteration of the model architecture, making it readily applicable to any pre-trained model. Our experiments demonstrate the efficacy o f t he AS-based UQ and its potential impact on molecular optimization by exploring the model diversity under epistemic uncertainty. Uncertainty quantification ; Linear subspace ; Computer science ; Generative model ; Generative grammar ; Artificial intelligence ; Machine learning ; Mathematics Machine Learning in Materials Science ; Advanced Multi-Objective Optimization Algorithms ; Machine Learning and Algorithms
Authors: Indu Saxena | Syed Mohammad Ejaz | Aditya K. Gupta
Source: Heliyon (article, 2024-03-21)
Field: Materials Science — Materials Chemistry

Synthesis characterization and application of butyl acrylate mediated eco-friendly silver nanoparticles using ultrasonic radiation In the present investigation, with an effort to provide appropriate material for future applications, we have touched on two viable advancement targets: the production of silver nanoparticles (Ag-NPs) employing an ultrasonic approach and the use of Ag-NPs in environmental remediation. A green economical method was involved to prepare Ag-NPs using butyl acrylate as a stabilizer. The following techniques were used for analysing Ag-NPs: energy dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM), powder X-ray diffraction (XRD), and Fourier transformed infrared (FT-IR) spectroscopy. X-ray diffraction (XRD) analysis for the lattice characteristics showed that Ag-NPs have a face-centered structure with an average crystallite size of 9.51–11.83 nm. FE-SEM and TEM analysis were used for morphological investigations, and revealed that Ag-NPs had a spherical shape with an average particle size of 16.27 nm. The EDX profile displayed a strong signal at ∼3.0 keV, which indicated that the samples comprised silver. UV–Visible spectrophotometer with the absorption maximum occurring between 401 and 411 nm further confirmed the formation of Ag-NPs. The dye degradation effect of synthesized Ag-NPs on methylene blue and Rhodamine B was analyzed to assess their ability for environmental remediation, and results showed that around 100% of the dye degradation effect. This study has provided a most plausible mechanism for the dye degradation. Environmentally friendly ; Ultrasonic sensor ; Characterization (materials science) ; Acrylate ; Nanoparticle ; Materials science ; Silver nanoparticle ; Nanotechnology ; Chemical engineering ; Nuclear chemistry ; Chemistry ; Composite material ; Polymer ; Engineering ; Copolymer ; Physics Nanoparticles: synthesis and applications ; Laser-Ablation Synthesis of Nanoparticles ; Nanomaterials for catalytic reactions