jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Nicodemo Di Pasquale | Thomas Hudson | Matteo Icardi
Source: Physical review. E (article, 2019-01-07)
Field: Materials Science — Materials Chemistry

Systematic derivation of hybrid coarse-grained models Molecular dynamics represents a key enabling technology for applications ranging from biology to the development of new materials. However, many real-world applications remain inaccessible to fully resolved simulations due to their unsustainable computational costs and must therefore rely on semiempirical coarse-grained models. Significant efforts have been devoted in the last decade towards improving the predictivity of these coarse-grained models and providing a rigorous justification of their use, through a combination of theoretical studies and data-driven approaches. One of the most promising research efforts is the (re)discovery of the Mori-Zwanzig projection as a generic, yet systematic, theoretical tool for deriving coarse-grained models. Despite its clean mathematical formulation and generality, there are still many open questions about its applicability and assumptions. In this work, we propose a detailed derivation of a hybrid multiscale system, generalizing and further investigating the approach developed in Español [Europhys. Lett. 88, 40008 (2009)10.1209/0295-5075/88/40008]. Issues such as the general coexistence of atoms (fully resolved degrees of freedom) and beads (larger coarse-grained units), the role of the fine-to-coarse mapping chosen, and the approximation of effective potentials are discussed. The theoretical discussion is supported by numerical simulations of a monodimensional nonlinear periodic benchmark system with an open-source parallel Julia code, easily extensible to arbitrary potential models and fine-to-coarse mapping functions. The results presented highlight the importance of introducing, in the macroscopic model, nonconstant fluctuating and dissipative terms, given by the Mori-Zwanzig approach, to correctly reproduce the reference fine-grained results, without requiring ad hoc calibration of interaction potentials and thermostats. Generality ; Benchmark (surveying) ; Computer science ; Nonlinear system ; Code (set theory) ; Dissipative system ; Statistical physics ; Degrees of freedom (physics and chemistry) ; Theoretical computer science ; Projection (relational algebra) ; Ranging ; Algorithm ; Computational science ; Physics ; Programming language Material Dynamics and Properties ; Block Copolymer Self-Assembly ; Theoretical and Computational Physics
Authors: Song Ya | Zhiyu Zhang | Lamei Yan | Ling Zhang | Simin Liu | Shaowen Xie | Lijian Xu | Jingjing Du
Source: Nanomaterials (article, 2019-12-17)
Field: Materials Science — Polymers and Plastics

Electrodeposition of Ti-Doped Hierarchically Mesoporous Silica Microspheres/Tungsten Oxide Nanocrystallines Hybrid Films and Their Electrochromic Performance In this paper, a novel Ti-doped hierarchically mesoporous silica microspheres/tungsten oxide (THMS/WO<sub>3</sub>) hybrid film was prepared by simultaneous electrodeposition of Ti-doped hierarchically mesoporous silica microspheres (THMSs) and WO<sub>3</sub> nanocrystallines onto the fluoride doped tin dioxide (FTO) coated glass substrate. It is demonstrated that the incorporation of THMSs resulted in the hybrid film with improved electrochromic property. Besides, the content of THMSs plays an important role on the electrochromic property of the hybrid film. An excellent electrochromic THMS/WO<sub>3</sub> hybrid film with good optical modulation (52.00% at 700 nm), high coloration efficiency (88.84 cm<sup>2</sup> C<sup>-1</sup> at 700 nm), and superior cycling stability can be prepared by keeping the weight ratio of Na<sub>2</sub>WO<sub>4</sub>·2H<sub>2</sub>O (precursor of WO<sub>3</sub>):THMSs at 15:1. The outstanding electrochromic performances of the THMS/WO<sub>3</sub> hybrid film were mainly attributed to the porous structure, which facilitates the charge-transfer, promotes the electrolyte infiltration and alleviates the expansion of the film during Li<sup>+</sup> insertion. This kind of porous THMS/WO<sub>3</sub> hybrid film is promising for a wide range of applications in smart homes, green buildings, airplanes, and automobiles. Electrochromism ; Materials science ; Mesoporous material ; Chemical engineering ; Tin oxide ; Tungsten trioxide ; Doping ; Nanotechnology ; Electrolyte ; Tin dioxide ; Mesoporous silica ; Substrate (aquarium) ; Tungsten ; Electrode ; Optoelectronics ; Organic chemistry ; Chemistry ; Catalysis ; Metallurgy Transition Metal Oxide Nanomaterials ; Gas Sensing Nanomaterials and Sensors ; Conducting polymers and applications
Authors: Hugues Prevet | Ian Collins
Source: Future Medicinal Chemistry (review, 2019-05-01)
Field: Chemistry — Organic Chemistry

Labelled Chemical Probes for Demonstrating Direct Target Engagement in Living Systems Demonstrating target engagement in living systems can help drive successful drug discovery. Target engagement and occupancy studies in cells confirm direct binding of a ligand to its intended target protein and provide the binding affinity. Combined with biomarkers to measure the functional consequences of target engagement, these experiments can increase confidence in the relationship between <i>in vitro</i> pharmacology and observed biological effects. In this review, we focus on chemically and radioactively labelled probes as key reagents for performing such experiments. Using recent examples, we examine how the labelled probes have been employed in combination with unlabelled ligands to quantify target engagement in cells and in animals. Finally, we consider future developments of this emerging methodology. Computational biology ; Drug discovery ; Drug target ; Ligand (biochemistry) ; Target protein ; Chemistry ; Pharmacology ; Biochemistry ; Biology ; Receptor Click Chemistry and Applications ; Synthesis and Biological Evaluation ; Monoclonal and Polyclonal Antibodies Research
Authors: Daehyun Wee | Jeeyoung Kim | Semi Bang | Ge. G. Samsonidze | Boris Kozinsky
Source: Physical Review Materials (article, 2019-03-25)
Field: Materials Science — Materials Chemistry

Quantification of uncertainties in thermoelectric properties of materials from a first-principles prediction method: An approach based on Gaussian process regression We present the electron-phonon averaged via Gaussian process regression (EPA-GPR) method, in which the electron-phonon coupling matrix is represented as a function of two energies and is in turn modeled as a Gaussian process. The EPA-GPR method can be used as an efficient method to estimate thermoelectric properties of materials for fast-screening applications, comparable to the original electron-phonon averaged (EPA) method and the electron-phonon averaged via moving-least-squares (EPA-MLS) method. The EPA-GPR method does not require specification of any open parameter, unlike the other EPA-related methods, since all the hyperparameters in the model can be unambiguously estimated within the type II maximum likelihood (ML-II) approximation. Thus, the EPA-GPR method is a parameter-free estimation method. Additionally, the concept of Gaussian processes in the EPA-GPR method allows us to quantify the uncertainty in estimated properties of thermoelectric materials. One can randomly realize the electron-phonon coupling coefficients from the identified Gaussian process, and those realized samples can be further analyzed in the solution process of the semiclassical Boltzmann transport equation for charge carriers. The results of the semiclassical Boltzmann transport equation provide the statistical properties of the thermoelectric properties of interest. The means, standard deviations, histograms, and confidence intervals of the Seebeck coefficient, the electrical conductivity, and the power factor can be constructed and analyzed. The proposed EPA-GPR method is applied to a $p$-type half-Heusler compound, i.e., HfCoSb, as a case example, the results of which clearly present the advantages of the method. Semiclassical physics ; Boltzmann equation ; Seebeck coefficient ; Kriging ; Ground-penetrating radar ; Gaussian ; Gaussian process ; Phonon ; Thermoelectric effect ; Materials science ; Statistical physics ; Applied mathematics ; Computational physics ; Physics ; Mathematics ; Computer science ; Condensed matter physics ; Thermodynamics ; Statistics ; Quantum mechanics ; Radar ; Quantum Machine Learning in Materials Science ; Advanced Thermoelectric Materials and Devices ; Thermal properties of materials
Authors: Meysam Hassanipour | Shinta Watanabe | Kyosuke Hirayama | Hiroyuki Toda | Kentaro Uesugi | Akihisa Takeuchi
Source: Materials Science and Engineering A (article, 2019-08-06)
Field: Materials Science — Materials Chemistry

Effects of 3D microstructural distribution on short crack growth behavior in two bimodal Ti–6Al–4V alloys Materials science ; Microstructure ; Crack closure ; Volume fraction ; Composite material ; Alloy ; Crack growth resistance curve ; Phase (matter) ; Metallurgy ; Fracture mechanics ; Chemistry Titanium Alloys Microstructure and Properties ; Hydrogen embrittlement and corrosion behaviors in metals ; Welding Techniques and Residual Stresses
Authors: Vineeth Venugopal | Scott Broderick | Krishna Rajan
Source: MRS Communications (article, 2019-09-25)
Field: Materials Science — Materials Chemistry

A picture is worth a thousand words: applying natural language processing tools for creating a quantum materials database map Computer science ; Natural language processing ; Domain (mathematical analysis) ; Visualization ; Heuristic ; Information retrieval ; Artificial intelligence ; Natural (archaeology) ; Database ; History Machine Learning in Materials Science ; Topic Modeling ; Advanced Text Analysis Techniques
Authors: Pengpeng Hu | Edmond S. L. Ho | Nauman Aslam | Taku Komura | Hubert P. H. Shum
Source: Textile Research Journal (article, 2019-02-13)
Field: Materials Science — Polymers and Plastics

A new method to evaluate the dynamic air gap thickness and garment sliding of virtual clothes during walking With the development of e-shopping, there is a significant growth in clothing purchases online. However, the virtual clothing fit evaluation is still under-researched. In the literature, the thickness of the air layer between the human body and clothes is a dominant geometric indicator to evaluate the clothing fit. However, such an approach has only been applied to the stationary positions of the mannequin/human body. Physical indicators such as the pressure/tension of a virtual garment fitted on the virtual body in a continuous motion are also proposed for clothing fit evaluation. Neither geometric nor physical evaluations consider the interaction of the garment with the body, e.g., the sliding of the garment along the human body. In this study, a new framework was proposed to automatically determine the dynamic air gap thickness. First, the dynamic dressed character sequence was simulated in three-dimensional (3D) clothing software via importing the body parameters, cloth parameters, and a walking motion. Second, a cost function was defined to convert the garment in the previous frame to the local coordinate of the next frame. The dynamic air gap thickness between clothes and the human body was determined. Third, a new metric, the 3D garment vector field was proposed to represent the movement flow of the dynamic virtual garment, whose directional changes are calculated by cosine similarity. Experimental results show that our method is more sensitive to the small air gap thickness changes compared with state-of-the-art methods, allowing it to more effectively evaluate clothing fit in a virtual environment. Clothing ; Metric (unit) ; Frame (networking) ; Computer science ; Computer vision ; Simulation ; Engineering ; Mechanical engineering Textile materials and evaluations ; 3D Shape Modeling and Analysis ; Human Motion and Animation
Authors: Chandra Ade‐Browne | Arnab Dawn | Marzieh Mirzamani | Shuo Qian | Harshita Kumari
Source: Journal of Colloid and Interface Science (article, 2019-02-25)
Field: Chemistry — Organic Chemistry

Differential behavior of sodium laurylsulfate micelles in the presence of nonionic polymers Micelle ; Polymer ; Sodium ; Nonionic surfactant ; Chemistry ; Differential (mechanical device) ; Polymer chemistry ; Chemical engineering ; Organic chemistry ; Pulmonary surfactant ; Aqueous solution ; Thermodynamics ; Biochemistry ; Engineering ; Physics Surfactants and Colloidal Systems ; Analytical Chemistry and Chromatography ; Chemical and Physical Properties in Aqueous Solutions
Authors: Hongyu Wang | Yunquan Man | Yanan Xiang | Kaiye Wang | Na Li | Bo Tang
Source: Chemical Communications (article, 2019-01-01)
Field: Chemistry — Organic Chemistry

Regioselective intramolecular Markovnikov and anti-Markovnikov hydrofunctionalization of alkenes <i>via</i> photoredox catalysis Highly regioselective Markovnikov hydrofunctionalization of alkenes was successfully realized via photoredox catalysis by introducing a urea group and fine tuning the hydrogen atom transfer catalysts. The anti-Markovnikov hydroamination of alkenes was also achieved with high yields and stereoselectivities in this work. Markovnikov's rule ; Hydroamination ; Regioselectivity ; Chemistry ; Intramolecular force ; Catalysis ; Combinatorial chemistry ; Hydrogen atom ; Photoredox catalysis ; Organic chemistry ; Group (periodic table) ; Photocatalysis Radical Photochemical Reactions ; Sulfur-Based Synthesis Techniques ; Catalytic C–H Functionalization Methods
Authors: Tharindu Kankanam Kapuge | Wimalika R.K. Thalgaspitiya | Dinithi Rathnayake | Junkai He | Peter Kerns | Steven L. Suib
Source: Applied Catalysis B: Environmental (article, 2019-11-05)
Field: Materials Science — Materials Chemistry

Photo-generated reactive oxygen species assisted tandem amine homocoupling and amine-alcohol cross-coupling reaction on mesoporous spinel cobalt oxide Chemistry ; Inorganic chemistry ; Mesoporous material ; Cobalt oxide ; Amine gas treating ; Cobalt ; Photochemistry ; Catalysis ; Organic chemistry Catalytic Processes in Materials Science ; CO2 Reduction Techniques and Catalysts ; Oxidative Organic Chemistry Reactions
Authors: Sara Novak | Thiago F. Chaves | Leandro Martins | Celso V. Santilli
Source: Colloids and Surfaces A Physicochemical and Engineering Aspects (article, 2019-10-14)
Field: Chemistry — Inorganic Chemistry

Preparation of hydrophobic MFI zeolites containing hierarchical micro-mesopores using seeds functionalized with octyltriethoxysilane Thermogravimetric analysis ; Mesoporous material ; Materials science ; Chemical engineering ; Grafting ; Contact angle ; Surface modification ; Zeolite ; Crystallization ; Hydrothermal synthesis ; Steric effects ; Hydrothermal circulation ; Organic chemistry ; Catalysis ; Chemistry ; Composite material ; Polymer Zeolite Catalysis and Synthesis ; Mesoporous Materials and Catalysis ; Supercapacitor Materials and Fabrication
Authors: Elena Romero‐Ben | Teresa Mena Barragán | E. García de Dionisio | Elena M. Sánchez‐Fernández | José M. Garcı́a Fernández | Emilio Guillén-Mancina | Miguel López‐Lázaro | Noureddine Khiar
Source: Journal of Materials Chemistry B (article, 2019-01-01)
Field: Chemistry — Organic Chemistry

Mannose-coated polydiacetylene (PDA)-based nanomicelles: synthesis, interaction with concanavalin A and application in the water solubilization and delivery of hydrophobic molecules Carbohydrate-lectin interactions are involved in a number of relevant biological events including fertilization, immune response, cell adhesion, tumour cell metastasis, and pathogen infection. Lectins are also tissue specific, making carbohydrates not only promising drug candidates but also excellent low molecular weight ligands for active drug delivery system decorations. In order for these interactions to be effective multivalency is essential, as the interaction of a lectin with its cognate monovalent carbohydrate epitope usually takes place with low affinity. Unlike the covalent approach, supramolecular self-assembly of glyco-monomers mediated by non-covalent forces allows accessing multivalent systems with diverse topology, composition, and assembly dynamics in a single step. In order to fine-tune the size and sugar adaptability of spherical micelles at the nanoscale for an optimal glycoside cluster effect, herein we report the synthesis of mannose-coated static micelles from diacetylene-based mannopyranosyl glycolipids differing in the length of the poly(ethyleneglycol) (PEG) chains and the oxidation state of the anomeric sulfur atom. The reported shot-gun like synthetic approach for the synthesis of dilution-insensitive micelles is based on the ability of diacetylenic-based neoglycolipids to self-assemble into micelles in water and to undergo an easy photopolymerization by a simple irradiation at 254 nm. The affinity of the obtained 6 nanosystems was assessed by enzyme-linked lectin assay (ELLA) using the mannose-specific concanavalin A lectin as a model receptor. Relative binding potency enhancements, compared to methyl α-d-mannopyranoside used as control, from 20-, to 29- to 300-fold on a sugar molar basis were observed for micelles derived from sulfonyl-, sulfinyl- and thioglycoside monomers with a tatraethyleneglycol spacer, respectively, indicative of a significant cluster glycoside effect. Moreover, pMic1 micelles are able to solubilize and slowly liberate lipophilic clinically relevant drugs, and show the enhanced cytotoxic effect of docetaxel toward prostate cancer cells. These findings highlight the potential of mannose-coated photopolymerized micelles pMic1 as an efficient nanovector for active delivery of cytotoxic hydrophobic molecules. Lectin ; Concanavalin A ; Micelle ; Chemistry ; Mannose ; Monomer ; Diacetylene ; Drug delivery ; Targeted drug delivery ; Biophysics ; Covalent bond ; Combinatorial chemistry ; Biochemistry ; Organic chemistry ; Aqueous solution ; Biology Polydiacetylene-based materials and applications ; Supramolecular Self-Assembly in Materials ; Carbohydrate Chemistry and Synthesis
Authors: Zhaoying Li | Iek Man Lei | Pooya Davoodi | Luai Huleihel | Yan Yan Shery Huang
Source: ACS Biomaterials Science & Engineering (article, 2019-06-07)
Field: Materials Science — Biomaterials

Solution Formulation and Rheology for Fabricating Extracellular Matrix-Derived Fibers Using Low-Voltage Electrospinning Patterning Composite formation and chemical cross-linking are common strategies in tuning the functionality and performance of biologically derived fibers fabricated by electrospinning. The modification to the initial polymeric solution changes the fiber-processing parameters and the associated fiber morphologies. Here, we investigated the gelatin solution formulation and how the addition of homogenized decellularized matrix particles (dCMps) can alter the processability of gelatin fibers produced by low-voltage electrospinning patterning. To produce water-insoluble fibers, the effect of a cross-linker addition was also separately investigated. In particular, we found that the electrospinnability of the solutions formulated with different concentrations of gelatin and dCMps and the morphology of the electrospun fibers were dependent on the rheological properties of the solutions. The solution dispersion rheology can be used as a useful indicator for guiding fiber processability and the fabrication strategy for patterning. The loss tangent associated with an oscillatory rheological test can be used to indicate the switch from an "extrusion-patterning" to a "drag-patterning" configuration. Fine-tuning of the cross-linking time can switch the thin fibrous film between a woven and a nonwoven structure. This study can be used as a guide to producing extracellular matrix fibers and films with specific microstructures suitable for tissue engineering applications. Electrospinning ; Materials science ; Gelatin ; Rheology ; Fiber ; Nanofiber ; Extrusion ; Composite material ; Fabrication ; Polymer ; Nanotechnology ; Chemistry Electrospun Nanofibers in Biomedical Applications ; Advanced Sensor and Energy Harvesting Materials ; Tissue Engineering and Regenerative Medicine
Authors: Kalyanasundaram Subramanian | Karolina Mitusińska | John Raedts | Feras Almourfi | Henk-Jan Joosten | Sjon Hendriks | Svetlana E. Sedelnikova | Servé W. M. Kengen | Wilfred R. Hagen | Artur Góra | Vítor A. P. Martins dos Santos | Patrick J. Baker | John van der Oost | Peter J. Schaap
Source: Biomolecules (article, 2019-05-31)
Field: Materials Science — Materials Chemistry

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon <i>Pyrococcus furiosus</i> catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools to select functionally-important residues based on correlated mutation analyses. A pair of amino acids in the periphery of PfPGI was found to be the dominant co-evolving mutation. The position of these selected residues was found to be non-obvious to conventional protein engineering methods. We designed a small smart library of variants by substituting the co-evolved pair and screened their biochemical activity, which revealed their functional relevance. Four mutants were further selected from the library for purification, measurement of their specific activity, crystal structure determination, and metal cofactor coordination analysis. Though the mutant structures and metal cofactor coordination were strikingly similar, variations in their activity correlated with their fine-tuned dynamics and solvent access regulation. Alternative, small smart libraries for enzyme optimization are suggested by our approach, which is able to identify non-obvious yet beneficial mutations. Pyrococcus furiosus ; Glucose-6-phosphate isomerase ; Isomerase ; Biochemistry ; Mutant ; Cofactor ; Chemistry ; Mutation ; Protein engineering ; Biology ; Enzyme ; Gene ; Archaea Enzyme Structure and Function ; Biochemical and Molecular Research ; Protein Structure and Dynamics