jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: You Li | Yu Zhai | Hui Li
Source: ChemRxiv (preprint, 2022-10-18)
Field: Materials Science — Materials Chemistry

MLRNet: Combining physics-motivated potential model with neural network for intermolecular potential energy surface construction A physics-based machine learning model called MLRNet has been developed to construct the high-accuracy two-body intermolecular potential energy surface (IPES). The outputs of the neural network are integrated into the physically realistic Morse/Long Range (MLR) function, which ensures that the MLRNet has meaningful extrapolation at both short and long ranges and solves the asymptotic problem in common neural network potential (NNP) models. The neural network representation of the MLR parameters is more flexible and more efficient than the polynomials expansion in the conventional mdMLR model, especially for systems containing non-rigid monomer(s). The present work illustrates the basic framework of the current MLRNet model, including (i) how to combine the physically meaningful MLR function with different possible NN structures, (ii) the preservation of permutation symmetry, and (iii) the predetermination of the long-range function uLR. We choose two realistic systems to demonstrate the performance of MLRNet: the 3-dimensional IPES of CO2-He including CO2 anti-symmetric vibration Q3, and the 6-dimensional IPES of H2O-Ar system. In both cases, the fitting errors of the MLRNet are several times smaller than those of the conventional mdMLR model. Both the short-range and long-range extrapolation tests have been performed to illustrate the extrapolation ability of the MLRNet and its damping function version. Moreover, for the 6-D H2O-Ar system, the MLRNet only needs 1596 trainable parameters which are almost equal 5-D mdMLR model (1509) and half of the PIP-NN model (3501) with similar accuracy, which illustrates the model efficiency in high-dimensional IPES fitting. Extrapolation ; Artificial neural network ; Range (aeronautics) ; Function (biology) ; Benchmark (surveying) ; Statistical physics ; Representation (politics) ; Physics ; Computer science ; Applied mathematics ; Algorithm ; Mathematics ; Artificial intelligence ; Mathematical analysis ; Engineering ; Aerospace engineering Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Advanced Physical and Chemical Molecular Interactions
Authors: Anupam Mondal | Arghadip Mondal | Kamalesh Sen | Priyanka Debnath | Naba Kumar Mondal
Source: Research Square (preprint, 2022-01-24)
Field: Materials Science — Materials Chemistry

Synthesis, Characterization and Optimization of Chicken-Bile Mediated Silver Nanoparticles: A Mechanistic Insight Into Antibacterial and Antibiofilm Activity Abstract The fast-growing urbanization and slow progress in the field of waste management have led to the accumulation of large quantities of animal wastes. Present work focused on the synthesis of low-cost and eco-friendly chicken bile juice mediated silver nanoparticles (BJ-AgNP). Results reveals that bile juices have enough potentiality towards the synthesis of almost uniform sizes (average size &lt; 50 nm) of BJ-AgNPs which remains stable for more than 6 months. Response surface methodology (RSM) successfully demonstrated the optimised condition of AgNP-BJ synthesis. Factor like concentration of salt and bile extract and temperature are significantly responsible for the synthesis of nanoparticle which was further characterized using UV-Vis, TEM, FESEM, XRD, FTIR, TGA, and EDS. The synthesised nanoparticle showed excellent bactericidal activity against both Gram positive and Gram negative bacteria with MIC and MBC of 40 and 50 µg/mL for Bacillus subtilis (MTCC-441) and 60 and 60 µg/mL for Eschecheria coli (MTCC-1687) respectively. The synthesized nanoparticle also acted as an antibiofilm agent against Bacillus subtilis , with ~89% biofilm inhibition efficacy at 4 X MIC, having optimal bacterial concentration of 10 6 CFU/mL. Therefore, present findings clearly demonstrated that an absolute animal waste could be a valuable ingredient in the field of therapeutic nanoscience. Characterization (materials science) ; Chemistry ; Nanotechnology ; Nanoparticle ; Biofilm ; Silver nanoparticle ; Antibacterial activity ; Combinatorial chemistry ; Biochemical engineering ; Materials science ; Biology ; Bacteria ; Engineering Nanoparticles: synthesis and applications ; Advanced Nanomaterials in Catalysis ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Entao Yang | Robert A. Riggleman
Source: Physical Review Letters (preprint, 2022-03-01)
Field: Materials Science — Materials Chemistry

Role of Local Structure in the Enhanced Dynamics of Deformed Glasses External stress can accelerate molecular mobility of amorphous solids by several orders of magnitude. The changes in mobility are commonly interpreted through the Eyring model, which invokes an empirical activation volume. Here, we analyze constant-stress molecular dynamics simulations and propose a structure-dependent Eyring model, connecting activation volume to a machine-learned field, softness. We show that stress has a heterogeneous effect on the mobility that depends on local structure through softness. The barrier impeding relaxation reduces more for well-packed particles, which explains the narrower distribution of relaxation time observed under stress. Molecular dynamics ; Relaxation (psychology) ; Statistical physics ; Dynamics (music) ; Stress (linguistics) ; Amorphous solid ; Constant (computer programming) ; Stress relaxation ; Volume (thermodynamics) ; Materials science ; Stress field ; Field (mathematics) ; Chemical physics ; Physics ; Classical mechanics ; Thermodynamics ; Computer science ; Kinetics ; Chemistry ; Mathematics ; Crystallography ; Quantum mechanics ; Psychology Material Dynamics and Properties ; Theoretical and Computational Physics ; Glass properties and applications
Authors: Alfredo De Biasio | Kerry Blair | Muhammad Tehseen | Vlad‐Stefan Raducanu | Taha Shahid | Claudia Lancey | Ramón Crehuet | Samir M. Hamdan
Source: Research Square (preprint, 2022-02-22)
Field: Materials Science — Materials Chemistry

Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing Abstract During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Flap endonuclease 1 (FEN1), but the structural basis of this mechanism is unknown. We present cryo-EM structures of human Lig1 bound to nicked DNA and PCNA in absence and presence of FEN1. Lig1 and PCNA form a two-ring complex encircling the DNA substrate. The ligase DNA binding domain (DBD) dynamically tethers Lig1 to one PCNA protomer, leaving one protomer fully accessible for FEN1 engagement. Ligation assays argue that Lig1 binding to PCNA is critical for substrate handoff from FEN1 preassembled with nicked DNA and PCNA. Consistently, cryo-EM data show that when Lig1 and FEN1 are simultaneously bound to one PCNA ring, the nicked DNA is trapped within the ligase active site and poised for the end-joining reaction. Thus, PCNA functions as a bivalent platform for the synchronous coordination of Lig1 and FEN1 in Okazaki fragment sealing. Okazaki fragments ; Proliferating cell nuclear antigen ; Fragment (logic) ; Mechanism (biology) ; Obfuscation ; Cell biology ; Computer science ; Biology ; Computer security ; Philosophy ; DNA ; Genetics ; Programming language ; Epistemology Enzyme Structure and Function ; RNA Research and Splicing ; DNA Repair Mechanisms
Authors: López-Correa Juan Manuel | K ouml nig Caroline | Alfredo Vellido
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2022-06-14)
Field: Chemistry — Spectroscopy

Long Short-Term Memory to predict 3D Amino acids Positions in GPCR Molecular Dynamics G-Protein Coupled Receptors (GPCRs) are a big family of eukaryotic<br> cell transmembrane proteins, responsible for numerous biological processes. From<br> a practical viewpoint around 34% of the drugs approved by the US Food and<br> Drug Administration target these receptors. They can be analyzed from their sim-<br> ulated molecular dynamics, including the prediction of their behavior in the pres-<br> ence of drugs. In this paper, the capability of Long Short-Term Memory Networks<br> (LSTMs) are evaluated to learn and predict the molecular dynamic trajectories of<br> a receptor. Several models were trained with the 3D position of the amino acids<br> of the receptor considering different transformations on the position of the amino<br> acid, such as their centers of mass, the geometric centers and the position of the<br> α–carbon for each amino acid. The error of the prediction of the position was eval-<br> uated by the mean average error (MAE) and root-mean-square deviation (RMSD).<br> The LSTM models show a robust performance, with results comparable to the state-<br> of-the-art in non-dynamic 3D predictions. The best MAE and RMSD values were<br> found for the mass center of the amino acids with 0.078 ̊A and 0.156 ̊A respec-<br> tively. This work shows the potential of LSTM to predict the molecular dynamics<br> of GPRCs. Term (time) ; G protein-coupled receptor ; Memory formation ; Computational biology ; Computer science ; Biological system ; Biology ; Neuroscience ; Receptor ; Physics ; Genetics Mass Spectrometry Techniques and Applications ; Receptor Mechanisms and Signaling ; Pharmacological Effects and Assays
Authors: Abdulhammed K. Hamzat | Ally Memon | Luai M. Alhems | F Almutairi | D Davies | A Khormali | D Petrakov | R Moghaddam | S Naseri | J Moghadasi | M Jamialahmadi | T Yi | Z Jin | X Chuan-Li | W Wei-Ying | J Macadam | S Parsons | J Baat Doelman | B Senthilmurugan | B Ghosh | S Sanker | X Wang | C Zhang | P Ouyang | Z Amjad | J Hooley | L Sanders | X Hu | E Mavredaki | V Eroini | R Barker | A Neville | M El-Said | M Ramzi | T Abdel-Moghny | A Quddus | L Al-Hadrami | M Crabtree | D Eslinger | P Fletcher | M Miller | A Johnson | G King | M Vazirian | T Charpentier | M De Oliveira Penna | O Vazquez | E Fursov | O Vetter | R Kippersund | P Lunde | K Frysa | J Smith | M Yuan | U Lopez | M Means | J Przybylinski | J Poyet | G Sgral | E Toskey | M Jelbuldina | H Younes | I Saadat | L Tizani | S Sofela | A Ghaferi | P Rostron | D Oliveira | R Santos | A Machado | M Silva | R Anjos | Lopes | F Echeverra | J Castao | C Arroyave | G Peuela | A Ramrez | J Morat | Y Cui | S Liu | K Smith | K Yu | H Hu | Y Li | W Jiang | C East | W Doherty | C Fellows | H Yu | A Olufade | C Simonson | Z Yin | W Zhao | Y Feng | S Zhu | C Ding | K Gao | C Chen
Source: International Journal of Corrosion and Scale Inhibition (article, 2022-12-02)
Field: Materials Science — Materials Chemistry

Novel assessment of in-operations mapped stainless steel elbow pipe internal wall for detection of corrosion and scale deposition Corrosion and deposition of scale onto the pipelines pose a great risk in the petroleum industry. If proper detection and monitoring techniques are not employed, scale deposits can lead to a reduction of flow area as well as obstruction of entire sections in pipeline infrastructure. In this work, ultrasonic testing, visual inspection, and spectroscopic techniques have been combined to investigate the influence of simulated seawater on corrosion and scale deposition on 316L stainless steel elbow. Specifically, ultrasonic thickness gauge was used externally to study the changes in wall thickness of the elbow pipe, which was then visually inspected using a borehole camera. To characterize the morphology and composition of the scale deposit, a sample was extracted and characterized using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), X-ray fluorescence (XRF), and Fourier transform infrared spectroscopy (FT-IR). Scales accumulation on the pipe internal wall prompted a slight increase in the wall thickness before cleaning and a maximum decrease of 14% after cleaning. The extracted scale sample characterization reveals the formation of CaCO3 scale of the Aragonite phase and is traced to the composition of the simulated seawater. Multiple techniques deployments for assessment of corrosion and scale deposition in elbow help stop both processes and ultimately assist in the oil and gas industry. Corrosion ; Deposition (geology) ; Elbow ; Materials science ; Metallurgy ; Scale (ratio) ; Geology ; Physics ; Surgery ; Medicine Corrosion Behavior and Inhibition ; Non-Destructive Testing Techniques ; Concrete Corrosion and Durability
Authors: Joseph Selvi Binoj | Shukur Abu Hassan | Reefat Arefin Khan | Alamry Ali
Source: Journal of Nanomaterials (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

Applications of Mobile Information Processor Edge‐Over‐Edge Molecular Wires with High‐Performance Thermoelectric Generators If high‐efficiency organic isotherm models for mobile processors can be found, a variety of energy harvesting devices, such as Peltier coolers composed of flexible and transparent thin‐film materials, might be manufactured. The thermoelectric characteristics of three zinc porphyrins (ZnP) were studied. Theoretical analyses of electron transport across a potassium (Zn‐Diphenyl porphyrin: Zn‐DPP) molecular sandwiched between electrode surface with three distinct connections were investigated. The contribution of this research is to see what happens because once pyridine is added above the surface of the zinc‐porphyrin skeleton, the “edge‐over‐edge” dimer created from stacked formed rings has a high electrical conductance, minimal exciton thermal conductance, and a large thermal diffusivity on the order of 300 V K1. At room temperature, these variables add up to a projected ZT 4 figure of merit, the greatest ZT for a single organic molecule ever seen. The stacked arrangement of the porphyrin rings causes low phonon thermal conductance, which delays phonon transport across the edge‐over‐edge molecule and increases the Seebeck coefficient, resulting in a higher ZT value. Porphyrin ; Thermoelectric effect ; Materials science ; Thermal diffusivity ; Optoelectronics ; Thin film ; Thermal conductivity ; Condensed matter physics ; Chemical physics ; Nanotechnology ; Chemistry ; Composite material ; Thermodynamics ; Photochemistry Advanced Thermoelectric Materials and Devices ; Molecular Junctions and Nanostructures ; Green IT and Sustainability
Authors: Nicolas Castel | François‐Xavier Coudert
Source: ChemRxiv (preprint, 2022-10-26)
Field: Chemistry — Inorganic Chemistry

Challenges in Molecular Dynamics of Amorphous ZIFs using Reactive Force Fields While amorphous metal–organic frameworks (a-MOFs) form an emerging class of materials of growing interest, their structural characterization remains experimentally and computationally challenging challenging. Out of the many molecular simulation methods that exist to model these disordered materials, one strategy consists in simulating the phase transition from a crystalline MOF to the amorphous state using molecular dynamics. ReaxFF reactive force fields have been proposed for this purpose in several studies to generate models of zeolitic imidazolate frameworks (ZIFs) glasses by melt-quenching. In this work, we investigate in detail the accuracy and reliability of this approach by reproducing the published procedures and comparing the structure of the resulting glasses to other data, including ab initio modeling. We find that the in silico melt-quench procedure is extremely sensitive to the choice of methodology and parameters, and suggest adaptations to improve the scheme. We also show that the glass models generated with ReaxFF are markedly different from their ab initio counterparts, as well as known experimental characteristics, and feature an unphysical description of the local coordination environment, which in term affects the medium-range and bulk properties. ReaxFF ; Molecular dynamics ; Amorphous solid ; Zeolitic imidazolate framework ; Materials science ; Force field (fiction) ; Ab initio ; Chemical physics ; Glass transition ; Quenching (fluorescence) ; Statistical physics ; Nanotechnology ; Computational chemistry ; Computer science ; Chemistry ; Physics ; Polymer ; Interatomic potential ; Physical chemistry ; Metal-organic framework ; Crystallography Metal-Organic Frameworks: Synthesis and Applications ; Lanthanide and Transition Metal Complexes ; Magnetism in coordination complexes
Authors: Hiroki Matsuo | Masashi Utsunomiya | Yuji Noguchi
Source: Research Square (preprint, 2022-03-09)
Field: Materials Science — Materials Chemistry

Utilizing ferrorestorable polarization in energy storage ceramic capacitors Abstract A self-powered system with a long lifetime offers an opportunity to develop a next-generation, standalone Internet of Things. Ceramic capacitors are promising candidates for energy storage components because of their stability and fast charge/discharge capability. Even for state-of-the-art capacitors, the energy density needs to be increased markedly. Improving breakdown electric fields provides a potential solution, but operations at such high fields relying on unchanged dielectric permittivity sacrifice the lifetime to some degree. Here, we report a ferrorestorable polarization engineering capable of enhancing effective permittivity over twice. Our experiments and ab initio calculations demonstrate that a defect dipole composed of Cu 3+ and oxygen vacancy in a prototypical ferroelectric BaTiO 3 ceramic is coupled with spontaneous polarization. The resultant ferrorestorable polarization delivers an extraordinarily large effective relative permittivity beyond 7,000 with a high energy efficiency up to 89%. Our work paves the way to realizing efficient ceramic capacitors for self-powered applications. Capacitor ; Energy storage ; Materials science ; Ceramic ; Polarization (electrochemistry) ; Ceramic capacitor ; Electrical engineering ; Engineering physics ; Optoelectronics ; Engineering ; Composite material ; Voltage ; Physics ; Chemistry Ferroelectric and Piezoelectric Materials ; Dielectric materials and actuators ; Multiferroics and related materials
Authors: Priyabrata Karmakar | Shyh Wei Teng. Manzur Murshed | Paul Pang | Cuong Van Bui
Source: arXiv (Cornell University) (review, 2022-09-13)
Field: Chemistry — Analytical Chemistry

A Guide to Employ Hyperspectral Imaging for Assessing Wheat Quality at Different Stages of Supply Chain in Australia: A Review Wheat is one of the major staple crops across the globe. Therefore, it is mandatory to measure, maintain and improve the wheat quality for human consumption. Traditional wheat quality measurement methods are mostly invasive, destructive and limited to small samples of wheat. In a typical supply chain of wheat, there are many receival points where bulk wheat arrives, gets stored and forwarded as per the requirements. In this receival points, the application of traditional quality measurement methods is difficult and often very expensive. Therefore, there is a need for non-invasive, non-destructive real-time methods for wheat quality assessments. One such method that fulfils the above-mentioned criteria is hyperspectral imaging (HSI) for food quality measurement and it can also be applied to bulk samples. In this paper, we have investigated how HSI has been used in the literature for assessing stored wheat quality. So that the required information to implement real-time digital quality assessment methods at the different stages of Australian supply chain can be made available in a single and compact document. Hyperspectral imaging ; Quality (philosophy) ; Supply chain ; Agricultural engineering ; Computer science ; Quality assessment ; Environmental science ; Artificial intelligence ; Business ; Engineering ; Reliability engineering ; Evaluation methods ; Marketing Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Food Science and Nutritional Studies
Authors: Emmanuel Ren | François‐Xavier Coudert
Source: ChemRxiv (preprint, 2022-11-23)
Field: Materials Science — Materials Chemistry

Rapid Adsorption Enthalpy Surface Sampling (RAESS) to Characterize Nanoporous Materials Molecular adsorption in nanoporous materials has many large-scale industrial applications ranging from separation to storage. To design the best materials, computational simulations are key in guiding the experimentation and engineering processes. Because nanoporous materials exist in a plethora of forms, we need to speed up the existing simulation tools to be able to screen databases of hundreds of thousands structures. Here, we describe a new algorithm that quickly calculates adsorption enthalpies by sampling the surface of the material instead of the whole porous space. This surface sampling has been tested on the CoRE MOF 2019 database and has been proven to be more than 2 orders of magnitude faster than the gold standard method (Widom insertion), with an acceptable level of error on the enthalpy value of 0.34 kJ/mol, and is therefore proposed as a valuable addition to the high-throughput screening toolbox. Nanoporous ; Toolbox ; Adsorption ; Sampling (signal processing) ; Porosity ; Enthalpy ; Materials science ; Computer science ; Surface (topology) ; Porous medium ; Nanotechnology ; Computational science ; Process engineering ; Chemistry ; Thermodynamics ; Physics ; Engineering ; Physical chemistry ; Mathematics Catalytic Processes in Materials Science ; Machine Learning in Materials Science ; Metal-Organic Frameworks: Synthesis and Applications
Authors: Mohammed Nooraldeen Mahmod Al-Qattan | Mohd N Mordi
Source: Research Square (preprint, 2022-04-25)
Field: Chemistry — Organic Chemistry

Development and application of Fragment-based De novo inhibitors against Plasmodium falciparum GST Abstract Modulation of disease progression is frequently started by identifying biochemical pathway catalyzed by biomolecule that is prone to inhibition by small molecular weight ligands. Such ligands (leads) can be obtained from natural resources or synthetic libraries. However de novo design based on fragments assembly and optimization is showing increasing success. In this research, fragment-based approaches were used to design molecules that can fit glutathione (GSH) binding site of P lasmodium falciparum GST ( PfGST ). The involved approaches build molecules from fragments that are either isosteric to GSH sub-moieties (ligand-based) or successfully docked to GSH binding sub-pockets (structure-based). Selected fragments are joined to create ligands that were explored using molecular docking, Cartesian coordinate’s optimization, and simplified free energy determination as well as MD simulation and MMPBSA calculations. Compared to reference GST inhibitor of S-hexyl GSH, ligands with improved rigidity, synthetic accessibility and affinity to receptor were successfully designed. Small molecule ; Glutathione ; Chemistry ; Stereochemistry ; Plasmodium falciparum ; Molecular model ; Ligand efficiency ; Combinatorial chemistry ; In silico ; Docking (animal) ; Computational biology ; Ligand (biochemistry) ; Molecule ; Fragment (logic) ; Biochemistry ; Receptor ; Enzyme ; Biology ; Computer science ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds ; Computational Drug Discovery Methods ; Click Chemistry and Applications
Authors: Peter Blaha | Henry Chermette
Source: Computation (article, 2022-05-23)
Field: Chemistry — Inorganic Chemistry

Dedication: Commemorative Issue in Honor of Professor Karlheinz Schwarz on the Occasion of His 80th Birthday Karlheinz Schwarz was born in January 1941 in Vienna (Austria), and he married Christine Schwarz in 1969 [...] Honor ; Art history ; Art ; Classics ; Philosophy ; Computer science Inorganic Chemistry and Materials ; Heusler alloys: electronic and magnetic properties ; Rare-earth and actinide compounds