jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mustafa Şamıl Argun | F. J. Turk | Abdullah Kurt
Source: Bitlis Eren Üniversitesi Fen Bilimleri Dergisi (article, 2023-09-21)
Field: Chemistry — Analytical Chemistry

Non-Destructive Prediction of Bread Staling Using Artificial Intelligence Methods In foods with limited shelf life and in new product development studies, it is important for producers and consumers to estimate the degree of staling with easy methods. Staling of bread, which has an essential role in human nutrition, is an important physicochemical phenomenon that affects consumer preference. Costly technologies, such as rheological, thermal, and spectroscopic approaches, are used to determine the degree of staling. This research suggests that an artificial intelligence-based method is more practical and less expensive than these methods. Using machine learning and deep learning algorithms, it was attempted to predict how many days old breads are, which provides information on the freshness status and degree of staling, from photos of whole bread and pieces of bread. Among the machine learning algorithms, the highest accuracy rate for slices of bread was calculated as 62.84% with Random Forest, while the prediction accuracy was lower for all bread images. The training accuracy rate for both slice and whole bread was determined to be 99% when using the convolutional neural network (CNN) architecture. While the test results for whole breads were around 56.6%, those for sliced breads were 92.3%. The results of deep learning algorithms were superior to those of machine learning algorithms. The results indicate that crumb images reflect staling more accurately than whole bread images. Artificial intelligence ; Machine learning ; Convolutional neural network ; Degree (music) ; Food science ; Deep learning ; Computer science ; Artificial neural network ; Mathematics ; Chemistry Spectroscopy and Chemometric Analyses ; Nutritional Studies and Diet ; Food composition and properties
Authors: Jiangxue Fan | Meng Zhang | Xiaofei Hou | Fang Wang | Mengyuan Bai | Ruoxi Jiao | Zhongyu Yang | Erhong Duan | Fengfei Cheng | Wen Zhou
Source: Polish Journal of Chemical Technology (article, 2023-12-01)
Field: Materials Science — Materials Chemistry

Study on safe disposal of cephalosporins based on kinetic pyrolysis mechanism Abstract Based on the global goals for cleaner production and sustainable development, the pyrolysis behavior of cephalosporin residues was studied by TG-MS method. The influence of full temperature window on the safe disposal of residues was analyzed based on the “3-2-2” and “1+1” of thermal analysis kinetics, and the gas by-products of thermal degradation were monitored. Results showed that the pyrolysis of distillation residues were divided into low and high-temperature zones, including six stages. Maximum error rate (8.55%) by multiple scan rate was presented based on “3-2-2” pattern and maximum total fluctuation (33.7) by single scan rate was presented based on “1+1” pattern, which implied that the comprehensive multi-level comparison method was very reliable. The E value “E” of six stages showed an increasing trend ranging 166.8 to 872.8 kJ/mol. Lg A (mean) was 27.28. Most mechanism function of stage 1, 2 were Z-L-T equation (3D), stage 3, 4, 6 were Avrami-Erofeev equation (AE3, AE4, AE2/3) and stage 5 was Reaction Order (O2). In addition, various small molecular micromolecule substances were detected such as C 2 H 4 O, C 2 H 6 , NH 3 , CH 4 , CO 2 under full temperature windows and a possible pyrolysis path of residues was provided. Pyrolysis ; Kinetics ; Chemistry ; Rate equation ; Degradation (telecommunications) ; Reaction mechanism ; Analytical Chemistry (journal) ; Materials science ; Chromatography ; Organic chemistry ; Catalysis ; Physics Thermal and Kinetic Analysis ; Energetic Materials and Combustion ; Thermochemical Biomass Conversion Processes
Authors: Pengwei Jin | Di Huang | Rui Zhang | Xing Hu | Ziyuan Nan | Zidong Du | Qi Guo | Yunji Chen
Source: arXiv (Cornell University) (preprint, 2023-02-21)
Field: Materials Science — Materials Chemistry

Online Symbolic Regression with Informative Query Symbolic regression, the task of extracting mathematical expressions from the observed data $\{ \vx_i, y_i \}$, plays a crucial role in scientific discovery. Despite the promising performance of existing methods, most of them conduct symbolic regression in an \textit{offline} setting. That is, they treat the observed data points as given ones that are simply sampled from uniform distributions without exploring the expressive potential of data. However, for real-world scientific problems, the data used for symbolic regression are usually actively obtained by doing experiments, which is an \textit{online} setting. Thus, how to obtain informative data that can facilitate the symbolic regression process is an important problem that remains challenging. In this paper, we propose QUOSR, a \textbf{qu}ery-based framework for \textbf{o}nline \textbf{s}ymbolic \textbf{r}egression that can automatically obtain informative data in an iterative manner. Specifically, at each step, QUOSR receives historical data points, generates new $\vx$, and then queries the symbolic expression to get the corresponding $y$, where the $(\vx, y)$ serves as new data points. This process repeats until the maximum number of query steps is reached. To make the generated data points informative, we implement the framework with a neural network and train it by maximizing the mutual information between generated data points and the target expression. Through comprehensive experiments, we show that QUOSR can facilitate modern symbolic regression methods by generating informative data. Symbolic regression ; Computer science ; Expression (computer science) ; Regression ; Task (project management) ; Process (computing) ; Regression analysis ; Symbolic data analysis ; The Symbolic ; Data mining ; Data point ; Theoretical computer science ; Artificial intelligence ; Machine learning ; Mathematics ; Statistics ; Programming language Machine Learning in Materials Science ; Machine Learning and Data Classification ; Machine Learning and Algorithms
Authors: Sayan Maity | Surajpal Verma | Lavanya M. Ramaniah | Varadharajan Srinivasan
Source: ChemRxiv (preprint, 2023-02-20)
Field: Materials Science — Materials Chemistry

Clarifying the Nature of Pressure-Induced Phases of MAPbBr3 by ab initio Molecular Dynamics Pressure-induced phases of hybrid perovskite MAPbBr3 are investigated at room temperature in a pressure range 0-2.8 GPa by ab initio molecular dynamics. Through appropriately designed MA (MA=methylammonium cation) orientational distribution functions and other order parameters, including a nematic scalar-tensor, we show two transitions at 0.7 and 1.1 GPa involving confinement of MA orientational fluctuations to a crystal plane. The first transition (cubic to cubic) involves dynamic disordering over the plane whereas the second one (cubic to tetragonal) corresponds to a static disordering of MA dipoles along two crystal axes on the same plane. This is similar to isotropic to isotropic and isotropic to oblate transition from the perspective of nematic transitions of liquid crystal. In the latter phase, both local anti-polar and polar domains, consisting of at least two units, are formed. The static disordering of MA dipoles along two crystal axes is stabilized by H-bonding interactions which are also responsible for strong organic-inorganic coupling. The primary order of the pressure-induced phase transitions comes from lattice degrees of freedom most notably octahedral tilting, which is associated with a displacive type transition. These phase transitions are also accompanied by changes in coupled modes between organic and inorganic components such as MA orientations/translations and octahedral tilting/lattice scissoring. Interestingly, the high-pressure phase transition is also driven by suppression of CH3 torsional motion, unlike temperature variation. Phase transition ; Liquid crystal ; Tetragonal crystal system ; Isotropy ; Condensed matter physics ; Ab initio ; Dipole ; Molecular dynamics ; Octahedron ; Chemistry ; Lattice (music) ; Materials science ; Crystal structure ; Crystallography ; Computational chemistry ; Physics ; Optics Solid-state spectroscopy and crystallography ; Perovskite Materials and Applications ; Material Dynamics and Properties
Authors: Kaixin Li | Zhanghao Chen | Xin Jin | Haoting Tian | Song Zhen-xia | Qingyun Zhang | Dayong Xu | Ran Hong
Source: Research Square (preprint, 2023-01-31)
Field: Chemistry — Physical and Theoretical Chemistry

Electronic manipulating in hydrated electron simulation of the carbon-halogen bond reductive cleavage Abstract Hydrated electron e − ( aq ) reaction with the alkyl halide and aryl halide was simulated synergistically with ab initial molecular dynamics (AIMD) in this study to reveal the morphological and dynamics mechanism. An original method was developed for preparing the proper initial wavefunction guess of AIMD, in which the extra electron was curled properly in a tetrahedral cavity of four water molecules. Our results indicated that the tetrahedral structure of e − ( aq ) (THE*) is more stable than the prism structure e − ( aq ) (PHE*) from the energy aspect. The interior weak interaction in THE* is mainly between the hydroxyl group with the extra electron, while the PHE* structure stability is attributed to the weak H-H interaction. The extra electron, with a significant sigma characteristic, collapses in a cavity composed of water molecules in these two structures and has a probability of collapsing to a certain sole water, this probability is inversely proportional to the number of waters; Organic halides prefer the direct reaction with e − ( aq ) in a neutral or alkaline environment while the hydrogen radical would be the dominant reaction species in an acidic solution. Fluorobenzene and fluoromethane are the hardest molecules to accept the extra electron and also have the highest reaction barriers during the hydrogen radical reactions; AIMD suggested that the LUMO or higher orbitals were the e − ( aq ) migration destination. The transplanted electron enhanced C-halogen bond vibration before the cleavage actually occurred. The solvation of the departing halogen anions was observed in both fluorobenzene and fluoromethane AIMD, indicating it might have a significant effect on enthalpy. A deformation of fluoromethane product, the methane radical, was detected from the sp3 structure to the sp2 plane structure, resulting in larger energy differences during the reaction than aryl halides. The study provided theoretical insight into the pollutant environmental fate and placed a methodological foundation for AIMD simulation of analogous free radical reactions. Chemistry ; Molecule ; Halogen ; Halide ; Solvation ; Solvated electron ; Fluorobenzene ; Photochemistry ; Hydrogen bond ; Alkyl ; Computational chemistry ; Physical chemistry ; Inorganic chemistry ; Organic chemistry ; Aqueous solution ; Radiolysis Photochemistry and Electron Transfer Studies ; Spectroscopy and Quantum Chemical Studies ; Free Radicals and Antioxidants
Authors: Advika Vidhyadhiraja | Arun Thiagarajan | Shang Zhu | Venkat Viswanathan | Bharath Ramsundar
Source: arXiv (Cornell University) (preprint, 2023-09-27)
Field: Materials Science — Materials Chemistry

Open Source Infrastructure for Differentiable Density Functional Theory Learning exchange correlation functionals, used in quantum chemistry calculations, from data has become increasingly important in recent years, but training such a functional requires sophisticated software infrastructure. For this reason, we build open source infrastructure to train neural exchange correlation functionals. We aim to standardize the processing pipeline by adapting state-of-the-art techniques from work done by multiple groups. We have open sourced the model in the DeepChem library to provide a platform for additional research on differentiable quantum chemistry methods. Differentiable function ; Pipeline (software) ; Open source software ; Computer science ; Open source ; Software ; Work (physics) ; Density functional theory ; Quantum ; Data science ; Theoretical computer science ; Physics ; Quantum mechanics ; Programming language ; Mathematics ; Pure mathematics Machine Learning in Materials Science
Authors: Olga S. Bokareva | Oliver Kühn
Source: arXiv (Cornell University) (preprint, 2023-05-12)
Field: Chemistry — Inorganic Chemistry

Quantum Dynamics of Photoactive Transition Metal Complexes. A Case Study of Model Reduction Transition metal complexes for photochemical applications often feature a high density of electron-vibrational states characterized by nonadiabatic and spin-orbit couplings. Overall, the dynamics after photoexcitation is shaped by rapid transitions between states of different character and multiplicity. Even though transient absorption experiments enable characterization in terms of kinetic rates, the complexity of the systems usually prevents a more detailed analysis. Quantum dynamics simulations using quantum chemically determined model Hamiltonians may provide such details. In particular, one is tempted to pursue a model reduction, such as to identify couplings or vibrational modes most relevant for the dynamics. Here, we address how such an endeavor is challenged by the particular nature of transition metal complexes. For that purpose, we performed quantum dynamics simulations for a recently studied iron(II) homoleptic complex. Photoexcitation ; Quantum dynamics ; Homoleptic ; Quantum ; Transition metal ; Chemistry ; Chemical physics ; Physics ; Metal ; Quantum mechanics ; Excited state Metal-Catalyzed Oxygenation Mechanisms ; Magnetism in coordination complexes ; Metal complexes synthesis and properties
Authors: Sharkov M.D. | Prasolov N.D. | Levin A.A. | Brunkov P.N.
Source: Физика твердого тела (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Simulating 2D-Diffraction Patterns of Model Gallium Arsenide Whisker Crystals A set of GaAs whisker crystallites in the shape of hexagonal prism with the axisalong the [111] direction have been modeled as well as constructions consisting of such prisms. For these model samples XRD patterns have been calculated. Basing on the calculated XRD pattern analysis, a fitting configuration of prismatic fragments has been built for an atomic array obtained with the help of applying molecular dynamics techniques to the initial model prismatic GaAs crystallite. Keywords: whiskers, XRD pattern simulation, A III B V semiconductors, gallium arsenide. Crystallite ; Gallium arsenide ; Whisker ; Materials science ; Gallium ; Diffraction ; Hexagonal crystal system ; Semiconductor ; Crystallography ; Whiskers ; Optics ; Optoelectronics ; Composite material ; Chemistry ; Physics ; Metallurgy X-ray Diffraction in Crystallography ; Crystallography and Radiation Phenomena ; Electron and X-Ray Spectroscopy Techniques
Authors: Nathan Garland | D. L. Muccignat | Greg Boyle | Ronald D. White
Source: arXiv (Cornell University) (preprint, 2023-12-07)
Field: Materials Science — Materials Chemistry

Robust approximation rules for critical electric field of dielectric gas mixtures A semi-analytic method for quickly approximating the density-reduced critical electric field for arbitrary mixtures of gases is proposed and validated. Determination of this critical electric field is crucial for designing and testing alternatives to SF$_6$ for insulating high voltage electrical equipment. We outline the theoretical basis of the approximation formula from electron fluid conservation equations, and demonstrate how for binary mixtures the critical electric field can be computed from the transport data of electrons in the pure gases. We demonstrate validity of the method in mixtures of N$_2$ and O$_2$, and SF$_6$ and O$_2$. We conclude with an application of the method to approximate the critical electric field for mixtures of SF$_6$ and HFO1234ze(E), which is a high interest mixture being actively studied for high voltage insulation applications. Electric field ; Dielectric ; Field (mathematics) ; Electron ; Voltage ; Sulfur hexafluoride ; Physics ; Condensed matter physics ; Materials science ; Thermodynamics ; Mathematics ; Quantum mechanics High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Plasma Diagnostics and Applications
Authors: Xiang Sun | Xiaofang Zhang | Zengkui Liu
Source: ChemRxiv (preprint, 2023-10-05)
Field: Chemistry — Physical and Theoretical Chemistry

Generalized Nonequilibrium Fermi’s Golden Rule and Its Semiclassical Approximations for Electronic Transitions between Multiple States Nonequilibrium Fermi’s golden rule (NE-FGR) approach is developed to simulate the electronic transitions between multiple excited states in complex condensed-phase systems described by the recently proposed multi-state harmonic (MSH) model Hamiltonian. The MSH models were constructed for faithfully capturing the photoinduced charge transfer dynamics in a prototypical organic photovoltaic carotenoid-porphyrin-C60 molecular triad dissolved in tetrahydrofuran. A general expression of the fully quantum-mechanical NE-FGR rate coefficients for transitions between all pairs of states in the MSH model is obtained with the path-integral formalism. Besides, the linearized semiclassical NE-FGR formula and a series of semiclassical approximations featuring Wigner and classical nuclear sampling choices and different dynamics during the quantum coherence period for the MSH model are derived. The current approach enables all the possible population transfer pathways between the excited states of the triad, in contrast to the previous applications that only addressed donor-to-acceptor transition. Our simulations for two triad conformations serve as a demonstration for benchmarking different NE-FGR approximations and show that the difference between all levels of approximation is small for the current system, especially at room temperature. By comparing with nonadiabatic semiclassical dynamics, we observe similar timescales of the electronic population transfer predicted by NE-FGR. It is believed that the general formulation of NE-FGR for the MSH Hamiltonian enables a variety of applications in realistic systems. Semiclassical physics ; Fermi's golden rule ; Non-equilibrium thermodynamics ; Population ; Hamiltonian (control theory) ; Excited state ; Physics ; Quantum mechanics ; Quantum ; Chemistry ; Statistical physics ; Fermi Gamma-ray Space Telescope ; Mathematics Photochemistry and Electron Transfer Studies ; Spectroscopy and Quantum Chemical Studies ; Porphyrin and Phthalocyanine Chemistry
Authors: Subarna Sasmal | Martin McCullagh | Glen M. Hocky
Source: arXiv (Cornell University) (preprint, 2023-01-09)
Field: Chemistry — Spectroscopy

Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule are a direct representation of a macromolecular configuration, and yet they have not been used in enhanced sampling studies due to a lack of rotational and translational invariance. We resolve this issue using the technique of our prior work, where a molecular configuration is considered a member of an equivalence class in size-and-shape space, which is the set of all configurations that can be translated and rotated to a single point within a reference multivariate Gaussian distribution characterizing a single molecular state. The reaction coordinates produced by LDA applied to positions are shown to be good reaction coordinates both in terms of characterizing the transition between two states of a system within a long molecular dynamics (MD) simulation, and also ones that allow us to readily produce free energy estimates along that reaction coordinate using enhanced sampling MD techniques. Reaction coordinate ; Gaussian ; Molecular dynamics ; Configuration space ; Transition state ; Log-polar coordinates ; Representation (politics) ; Chemistry ; Work (physics) ; Statistical physics ; Computational chemistry ; Generalized coordinates ; Physics ; Classical mechanics ; Thermodynamics ; Quantum mechanics Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Metabolomics and Mass Spectrometry Studies
Authors: Ádám Mechler | Óscar Vicente | Monica Boşcaiu | Sara González-Orenga | Şehime Gülsün Temel | Irmak Sakin | Gülten Tuncel | Ha- Esoo Kim | Stephen L. Viviano | Sebiha Çevik | Ferhan Yenisert | Oktay I. Kaplan | Aslı Karaman | Miray Çakıroğlu | Şükrü Sadik Öner | Mustafa K. Khokha | Şebnem Özemri Sağ | Fatma Sılan | Munis Dündar | Cerkez Ergoren | Engin Deniz | Şehime Te- Mel | Marmarare Group | Michele Maffia | Debora Musarò | Anas Munir | Alessandra Ingus- Cio | Chiara Coppola | Antonio Danieli | Marco Greco | Maria Rachele Ceccarini | Irene Chiesa | Silvia Bittolo Bon | Carmelo De Maria | Tommaso Beccari | Luca Valentini | Kristina Gruden
Source: The EuroBiotech Journal (article, 2023-12-01)
Field: Materials Science — Biomaterials

Invited Speaker Abstracts Nature abounds in self-assembling systems that include cell membranes, actin fibres and the flagellum rotor.Nature inspired design attempts to learn from the organizing principles of these structures while introducing novel molecular designs.It is highly desirable to develop a versatile, small molecule based system that incorporates a universal self-assembly motif that allows the design and seamsless spontaneous assembly of functionally different molecules.This concept is often described as a molecular LEGO system.Here a substituted oligoamide (SO) based molecular LEGO system is described.SOs are artificial analogues of natural peptides, yielding small helical (i.e.topologically cylindrical) molecules that can self-assemble head to tail into fibres where each monomer retains the helical fold; these supramolecular nanorods can grow up to millimeters in length.It was demonstrated that a broad range of chemical function can be implemented in the monomers, they can co-assemble, and they can be assembled by the use of a secondary motif into metallosupramolecular framework materials.This platform allows the design of geometrically and chemically well defined nanostructured materials, opening new avenues to design molecular electronics and to build molecular machines. Computer science ; Speech recognition Supramolecular Self-Assembly in Materials ; Supramolecular Chemistry and Complexes ; Synthesis and Properties of Aromatic Compounds
Authors: Toreshettahally R. Swaroop | Chalya Shivaprasad | Kanchugarakoppal S. Rangappa | G Sugai | K Harsha | S Rangappa | H Preetham | T Swaroop | M Gilandoust | K Rakesh | K Rangappa | A Vinayaka | P Chikkade | M Sadashiva | K Kiran | N Rajeev | S Anil | R Roopashree | C Mohan | S Jagadish | Y Bommegowda | K Kumar | G Lingaraju | K Sukrutha | J Shruthi | C Shivaprasad | D Mohan | K Narasimhamurthy | S Chandrappa
Source: Journal of Chemistry Education Research and Practice (article, 2023-01-19)
Field: Chemistry — Physical and Theoretical Chemistry

Art of Writing Flowchart in Organic Chemistry Practicals Induces Logical Thinking in Chemistry Students In this article we present an art of writing flowcharts in organic chemistry preparation practicals. We divided students into two groups. One group of students was trained to write procedural flowchart and the other group of students was educated to write chemical flowchart for the preparation of p-nitroacetanilde from acetanilde and preparation of hippuric acid from glycine. The procedural flowchart simply represents the steps involved in an organic preparation. While, chemical flowchart describes chemical species involved in each step of preparation. We found that students educated to write chemical flowchart have gained superior knowledge in chemistry over the students who were trained to write procedural flowchart. Flowchart ; Chemistry ; Computer science ; Mathematics education ; Programming language ; Psychology Various Chemistry Research Topics