jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Alicia Plourde | Jacquelyn C. Ogata-Bean | Siavash Vahidi
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-12-17)
Field: Chemistry — Spectroscopy

Probing the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry ABSTRACT The Pup-proteasome system (PPS) is a unique bacterial proteolytic pathway found in some bacterial species, including in Mycobacterium tuberculosis , that plays a vital role in maintaining proteome integrity and survival during infection. Pupylation is the process of tagging substrates with Pup for degradation and is catalyzed by PafA, the sole Pup ligase in bacteria. However, how PafA interacts with diverse targets and its oligomeric state remain poorly understood. Although X-ray crystal structures have characterized PafA as a domain-swapped dimer, it is widely regarded as functionally active in its monomeric form. It remains to be established whether PafA dimerizes in solution, and how dimerization influences its function. In this study, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) alongside complementary biophysical techniques to explore the oligomeric states and conformational dynamics of PafA. We show that recombinantly-produced PafA exists in a monomeric and a domain-swapped dimeric state in solution. While PafA dimer is stabilized by nucleotide, it predominately resides in a catalytically inactive conformation. Our HDX-MS highlighted regions throughout the N- and C-terminal domains that facilitate the PafA dimerization process. HDX-MS also revealed nucleotide binding induces global conformational changes on the PafA monomer , underscoring the structural plasticity of this promiscuous enzyme. Our findings provide insight into the structure-function-dynamics relationship of PafA, shedding light on how its oligomeric states and conformational flexibility might influence its role in the PPS. Mass spectrometry ; Chemistry ; Chromatography Mass Spectrometry Techniques and Applications ; Enzyme Structure and Function ; Peptidase Inhibition and Analysis
Authors: Yuto Watanabe | Ceren Tayran | Md. Riad Kasem | Aichi Yamashita | M. Çakmak | Takayoshi Katase | Yoshikazu Mizuguchi
Source: arXiv (Cornell University) (preprint, 2024-06-26)
Field: Materials Science — Materials Chemistry

Specific heat analyses on optical-phonon-derived uniaxial negative thermal expansion system $Tr$Zr$_{2}$ ($Tr$ = Fe and Co$_{1-x}$Ni$_{x}$) Recently, huge uniaxial negative thermal expansion (NTE) along a $c$-axis has been observed in transition-metal ($Tr$) zirconides $Tr$Zr$_{2}$ with a tetragonal CuAl$_{2}$-type structure. In a recent study on FeZr$_{2}$ [M. Xu et al., Nat. Commun. 14, 4439 (2023)], the importance of optical phonons to the emergence of the $c$-axis NTE in FeZr$_{2}$ has been proposed. In this study, the physical properties of $Tr$Zr$_{2}$ ($Tr$ = Fe and Co$_{1-x}$Ni$_{x}$) have been studied by specific heat, sound velocity measurements, and theoretical phonon calculations to discuss the importance of optical phonons to the emergence of the $c$-axis NTE in CoZr$_{2}$ and FeZr$_{2}$. From analyses of lattice specific heat, we found that Ni substitution results in a systematic decrease in oscillator strength for the Einstein modes with 8.74 meV (CoZr$_{2}$). From phonon calculations, the low-energy optical phonon branches at the $Γ$ point were observed for CoZr$_{2}$ and FeZr$_{2}$ with $c$-axis NTE, but not in NiZr$_{2}$ with positive thermal expansion. The enhancement of phonon density of states near the above-mentioned optical phonon energy in CoZr$_{2}$ and FeZr$_{2}$ is consistent with the specific heat analyses. We propose the importance of the low-energy optical phonons to the emergence of the $c$-axis NTE in TrZr$_{2}$. Phonon ; Thermal expansion ; Materials science ; Condensed matter physics ; Negative thermal expansion ; Thermal ; Analytical Chemistry (journal) ; Chemistry ; Thermodynamics ; Physics ; Metallurgy ; Organic chemistry Thermal Expansion and Ionic Conductivity ; Inorganic Chemistry and Materials ; Thermodynamic and Structural Properties of Metals and Alloys
Authors: Sanjay Kumar Mire | Jitendra Kumar Sinha
Source: South Eastern European Journal of Public Health (article, 2024-09-02)
Field: Materials Science — Biomaterials

Design of Nanocarriers for Chemotherapy of Prostate Cancer Any part of the body might become cancerous. It begins when regular cells are pushed out by out-of-control cells. This can spread to other parts of the body and interfere with normal bodily functions. Globally, cancer is considered to be a huge burden that will only get worse as the population ages and grows. Given the various drawbacks and adverse effects of the traditional formulations, novel strategies for medication delivery to prostate cancer cells are being researched and explored. With their many advantages over traditional chemotherapy, including improved drug solubility, protection from macrophage uptake, which lengthens the drug's blood residence time, and controlled drug delivery to the target prostate cancer, polymeric nanoparticles have been identified as promising candidates for drug delivery to prostate cancer. Prostate cancer ; Nanocarriers ; Medicine ; Drug delivery ; Cancer ; Drug ; Population ; Prostate ; Targeted drug delivery ; Adverse effect ; Chemotherapy ; Pharmacology ; Internal medicine ; Nanotechnology ; Materials science Nanoparticle-Based Drug Delivery ; RNA Interference and Gene Delivery ; Nanoplatforms for cancer theranostics
Authors: Nicolás Salas | Justin López ansd Carlos A. Arango | Arango, Carlos A.
Source: arXiv (Cornell University) (preprint, 2024-05-15)
Field: Chemistry — Organic Chemistry

The Graph automorphism group of the dissociation microequilibrium of polyprotic acids The dissociation micro-states (DMS) of an $N$-protic acid are described using set theory notation. This facilitates the mathematical description of the dissociation micro-equilibrium (DME). In particular, the DME constants are easily obtained in terms of the dissociation equilibrium constants and the molar fractions of the DMSs. Representing of the DMEs in terms of graph theory allows to identify permutations between DMSs that preserve the vertex-edge connectivity of the graph. These permutations, along with their composition, allow us to identify the direct product of the cyclic group $C_2$, and the symmetric group $S_N$, $C_2\times S_N$, as the graph automorphism group of the micro-dissociation of $N$-protic acids. Dissociation (chemistry) ; Chemistry ; Graph ; Stereochemistry ; Combinatorics ; Organic chemistry ; Mathematics Chemical Thermodynamics and Molecular Structure ; Adsorption, diffusion, and thermodynamic properties of materials ; Chemistry and Stereochemistry Studies
Authors: Apilak Worachartcheewan | Ratchanok Pingaew | Veda Prachayasittikul | Setthawut Apiraksattayakul | Supaluk Prachayasittikul | Somsak Ruchirawat | Virapong Prachayasittikul
Source: PubMed (article, 2024-09-19)
Field: Chemistry — Organic Chemistry

Synthesis, biological investigation, and in silico studies of 2-aminothiazole sulfonamide derivatives as potential antioxidants Antioxidant compounds have gained current interest as potential protective agents for several therapeutic applications. Antimicrobial drug resistance and infectious diseases also still be concerning globally health issues. Accordingly, the discovery of new antioxidative and antimicrobial agents is essential for human well-being. Thiazole and sulfonamide are privileged scaffolds in drug discovery due to their various bioactive properties. In this study, a series of 2-aminothiazole sulfonamide derivatives (<b>1</b> <b>-</b> <b>12</b>) were synthesized and investigated for their antioxidant (i.e., DPPH and SOD-mimic) and antimicrobial activities. Among tested compounds, compound <b>8</b> was the most promising one with potent DPPH and SOD (%DPPH = 90.09 %, %SOD = 99.02 %). However, none of these compounds are active antimicrobial agents. Quantitative structure-activity relationship (QSAR) modeling was performed in which the key findings were further used to guide the rational design of additional derivatives. Two antioxidant QSAR models (i.e., DPPH and SOD) were constructed using multiple linear regression (MLR) with good predictive performance. An additional set of structurally modified compounds were designed based on QSAR findings to finally obtain 112 newly designed compounds in which their activities (DPPH and SOD) were predicted. Most of the modified compounds performed better activities than their prototypes. Mass, polarizability, electronegativity, the presence of C-F bond, van der Waals volume, and structural symmetry were revealed as key properties influencing antioxidant activities. In summary, this study demonstrated the combination used of chemical synthesis, experimental assays, and computer-aided drug design for developing novel antioxidants for potential medicinal applications. See also the graphical abstract(Fig. 1). Sulfonamide ; In silico ; Chemistry ; Computational biology ; Combinatorial chemistry ; Pharmacology ; Medicine ; Biochemistry ; Biology ; Organic chemistry Synthesis and biological activity
Authors: Shreya Gupta | Ethan F. Bull-Vulpe | Henry Agnew | Shishir Iyer | Xuanyu Zhu | Ruihan Zhou | Chris Knight | Francesco Paesani
Source: ChemRxiv (preprint, 2024-12-26)
Field: Materials Science — Materials Chemistry

MBX v1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the ``gold standard'' coupled cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. These advancements enable simulations on nanosecond timescales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions. Molecular dynamics ; Dynamics (music) ; Statistical physics ; Physics ; Quantum mechanics Machine Learning in Materials Science ; Quantum many-body systems ; Protein Structure and Dynamics
Authors: Budhijanto Budhijanto | Tirto Wahyu Widodo | Gilang Afif Setya Ramadhani
Source: Eksergi (article, 2024-08-21)
Field: Chemistry — Organic Chemistry

Effects of Kaolin Powder and Borax Addition on Adhesion Properties of Soy Protein Isolate-Based Adhesives A low-cost strategy was developed to improve the adhesion properties and long shelf life of soy protein isolate-based adhesive, by using kaolin powder as filler and borax as an antifungal. Soy protein bioadhesive will be synthesized through denaturation using Sodium Lauryl Sulfate, followed by crosslinking using epoxy resin as a crosslinker, kaolin powder addition as filler, and borax addition to inhibit the fungal growth. Some analysis such as viscosity, solid content, dry shear strength, wet shear strength, FTIR Spectroscopy, SEM analysis, and shelf life were done to measure the adhesion properties of the bioadhesive. The result shows that the best shear strength, both dry and wet was obtained by adding 1.5% w/w kaolin powder with shear strength resulted 2,2684 MPa and with addition 2% w/w borax increased the shear strength up to 2,3207 MPa. Borax addition had been proven in improving the water resistance of the adhesive also inhibit fungal growth resulting extended the shelf life of the adhesive. Borax ; Soy protein ; Adhesive ; Soy flour ; Food science ; Adhesion ; Chemistry ; Materials science ; Composite material ; Raw material ; Organic chemistry ; Layer (electronics) Plant-Derived Bioactive Compounds ; biodegradable polymer synthesis and properties
Authors: Ajayi O.O. | Nwodo D.C. | T. Adedeji | Ogwugua V.H. | Mahamadi Dianda | Fagade O.E.
Source: African Research Journal of Biosciences (article, 2024-01-25)
Field: Chemistry — Analytical Chemistry

Diagnostic and portable point-of-use technologies as plant monitoring tools for plant awareness &lt;p&gt;An increasing need for better agricultural practices that are sustainable to provide increased yields of crops for the ever increasing food demand to be met for the growing world population is a current necessity. It is estimated by the UN that in 2050 the world&rsquo;s populace may be as much as 9.8 billion global, yet, farmers still face several obstacles, which includes soil degradation, extreme temperatures, and drought which as increasingly becoming more severe with climate changes. Plant health monitoring is a method that will help to increase awareness about plant enhancing by studying how to increase crop yields while decreasing the environmental impacts. The use of low-cost, controlled environments, soil quality, water levels, and pathogenic and pests attacks can be regularly monitored. Currently, several diagnostic technologies and portable point-of-use methods and technologies are employed for detection of diseases, although, the current available lab-based methods used for plant&rsquo;s diagnostics test are inadequate for plant point-of-use monitoring. The promotion of use of these point of use methods will enable pathogen detection, poor plant growth, unsuitable environmental conditions and nutrient use efficiency allowing for immediate and timely corrective actions to ensure minimal damage to the plants with maximal yield. Increase in the use of sustainable agri practices are required for ensuring higher yields with minimal inputs and that are non-destructive to the land and the use of improved methodologies and technologies will be useful tools for achieving sustainable agriculture.&lt;/p&gt; Point (geometry) ; Computer science ; Engineering Spectroscopy and Chemometric Analyses
Authors: Mansoor Ani Najeeb | Robbie Morrison | Ahmed H. Mokhtar | D. G. Porter | F. Lichtenberg | A. Bombardi | Mary Newton
Source: Discover Nano (article, 2024-12-15)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Imaging of electric-field-induced domain structure in DyMnO$$_{3}$$ nanocrystals Multiferroic materials that exhibit interacting and coexisting properties, like ferroelectricity and ferromagnetism, possess significant potential in the development of novel technologies that can be controlled through the application of external fields. They also exhibit varying regions of polarity, known as domains, with the interfaces that separate the domains referred to as domain walls. In this study, using three-dimensional (3D) bragg coherent diffractive imaging (BCDI), we investigate the dynamics of multiferroic domain walls in a single hexagonal dysprosium manganite (h-DyMnO <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mmultiscripts><mml:mrow></mml:mrow> <mml:mn>3</mml:mn> <mml:mrow></mml:mrow></mml:mmultiscripts> </mml:math> ) nanocrystal under varying applied electric field. Our analysis reveals that domain wall motion is influenced by the pinning effects, and a threshold voltage of +3 V is required to overcome them. Using circular mean analysis and phase gradient mapping, we identified localised phase realignment and high-gradient regions corresponding to domain walls, providing insights into the behaviour of multiferroic systems under external stimuli. Multiferroics ; Ferroelectricity ; Manganite ; Electric field ; Materials science ; Condensed matter physics ; Domain (mathematical analysis) ; Field (mathematics) ; Nanocrystal ; Ferromagnetism ; Phase (matter) ; Nanotechnology ; Physics ; Optoelectronics ; Mathematics ; Mathematical analysis Multiferroics and related materials ; Magneto-Optical Properties and Applications ; Ferroelectric and Piezoelectric Materials
Authors: Yuhan Zhang | Zehua Huang | Tianrui Li | Peilin Li
Source: Applied and Computational Engineering (article, 2024-11-08)
Field: Materials Science — Surfaces, Coatings and Films

Innovations and Insights in Superhydrophobicity: Learning from Nature to Surpass It Abstract. Superhydrophobic surfaces, inspired by natural examples, have emerged as a promising area of research due to their unique properties. This paper reviews the characteristics and challenges of creating surfaces that can exceed the capabilities of natural counterparts. Key aspects include surface tension, contact angle, and morphology, with a focus on natural models such as lotus leaves and gecko feet. The paper highlights knowledge gaps in durability and manufacturing, and discusses design challenges in achieving roughness, hierarchy, and balance between hydrophobicity and durability. Methods for enhancing durability, such as chemical and roughness restoration, are explored, alongside the potential of AI in optimizing material and design choices. The paper concludes with recommendations for future research directions in the field. Nanotechnology ; Human–computer interaction ; Psychology ; Computer science ; Materials science Surface Modification and Superhydrophobicity
Authors: 泰英 望月 | Yasuhide Mochizuki | 宏喜 小磯 | Hiroki Koiso | 楓 永松 | Kaede Nagamatsu | 敏宏 磯部 | Toshihiro Isobe | 章 中島 | Akira Nakajima
Source: Institutional Repositories DataBase (IRDB) (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Thermal Properties of the Element and Binary Oxides toward Negative Thermal Expansion: A First-Principles Lattice-Dynamics Study To establish the design principles of thermal properties of solids, we performed comprehensive calculations of volume thermal expansion coefficients V , bulk moduli B T , average atomic volumes V, and Gruneisen parameters in the finite temperature for the 46 elements and 45 binary oxides using first-principles lattice-dynamics calculations.We clarified that (i) a crystal possessing large V tends to have small B T ; (ii) the major role of is the determination of the sign of V , the value of which is ruled by the crystal structures and coordination numbers; (iii) the transverse-acoustic (TA) and/ or low-frequency phonons are responsible for the negative thermal expansion (NTE) behaviors; (iv) the NTE materials prefer the relatively large V with the void space, possessing negative mode-Gruneisen parameters q ; and (v) the common feature of the NTE materials is the phonons vibrating forward to the void space.Our study provides a wide perspective on designing low and/or negative thermal expansion materials. Thermal ; Binary number ; Thermal conductivity ; Binary system ; Element (criminal law) ; Thermal conduction Thermal Expansion and Ionic Conductivity ; High-pressure geophysics and materials ; High-Temperature Coating Behaviors
Authors: Umar Faruk Hassan | Abubakar Habib Idris | Jamila Ibrahim Shekaru
Source: Earthline Journal of Chemical Sciences (article, 2024-11-11)
Field: Materials Science — Materials Chemistry

Biosynthesis of gold and silver nanoparticle using water hyacinth (Eichhornia crassipes) extract for photocatalytic degradation of organophosphate and organochlorine pesticide The study aimed to assess the efficiency of synthesized gold (Au) and silver (Ag) nanoparticles in the degradation of organochlorine and organophosphate pesticides through photocatalysis. The synthesis of gold and silver nanoparticles was achieved using Eichhornia crassipes (water hyacinth extract). Photocatalytic degradation tests were conducted on organochlorine and organophosphate pesticides using gold and silver nanoparticles, with the absorbance of the samples measured by a UV spectrophotometer. The photocatalytic degradation rates of organochlorine and organophosphate were determined, with varied concentrations of the synthesized nanoparticles. The results showed high degradation rates at lower concentrations (10–20 ppm), with degradations of 51.789%, 47.954%, 47.983%, 44.088%, 41.565%, and 36.749% for 25/75, 50/50, and 75/25 Au nanoparticle ratios, respectively. The results also revealed that higher degradation rates were observed at longer reaction times (70–80 minutes), with percentage degradations of 44.344% and 49.987%, 41.754% and 45.937%, 36.773% and 40.458% for 25/75, 50/50, and 75/25 Au nanoparticle ratios, respectively. Lower degradation efficiencies were observed at shorter reaction times (10–20 minutes), with percentage degradations of 15.356% and 19.982%, 13.746% and 17.082%, and 10.976% and 15.167% for 25/75, 50/50, and 75/25 ratios, respectively. Additionally, the results showed high degradation rates at lower concentrations (10–20 ppm) for Ag nanoparticles, with percentage degradations ranging from 40.814% to 44.822% across AgNP ratios (25/75, 50/50, 75/25), indicating efficient degradation at lower concentrations. Conversely, at higher concentrations (60–80 ppm), the degradation efficiency was notably lower, with percentage degradations ranging from 7.004% to 13.539% across different AgNP ratios. In conclusion, Au nanoparticles exhibited higher photocatalytic efficiency than Ag nanoparticles, particularly in degrading organophosphate (Sniper) pesticides. It is recommended that these synthesized nanoparticles be considered as environmentally friendly and cost-effective options for pesticide degradation. Eichhornia crassipes ; Hyacinth ; Organophosphate ; Pesticide ; Environmental chemistry ; Degradation (telecommunications) ; Photocatalysis ; Organochlorine pesticide ; Chemistry ; Environmental science ; Aquatic plant ; Biology ; Organic chemistry ; Agronomy ; Ecology Nanoparticles: synthesis and applications
Authors: Taimo Priinits | Artjom Vargunin | Aleksandr Liivand
Source: arXiv (Cornell University) (preprint, 2024-06-02)
Field: Chemistry — Inorganic Chemistry

Peculiarities of niobium-based superconducting alloys in the light of crystal chemistry: A brief survey In this survey, we focus on Nb-based binary intermetallic compounds, which have been widely used over the last 40 years to develop a range of superconducting applications, including non-standard engineering solutions in the design of large magnets. However, since the 1980s, when it became apparent that the mechanical and superior superconducting properties of ordered intermetallic alloys such as Nb$_{3}$Sn were largely due to their unique structural features, much of the research interest in the science of superconducting intermetallic alloys has been redirected to the development of necessary engineering applications in high magnetic field technology. Accordingly, the important role of crystal chemistry in understanding the fundamental aspects of the material properties of the Nb$_{3}$Sn family of intermetallics has been little explored. In the paper, we try to fill this gap by investigating the relationships between composition, microstructure and properties, highlighting their relevance to technological applications. Our goal is to link aspects of crystal chemistry with materials application issues. We shed light on the atomic assembly mechanisms and processes in terms of changes in the chemical environment, lattice structure, crystallization pathway, and macroscale phase textures, which can help in interpreting and explaining the prospects and limitations of the superconducting properties of Nb$_{3}$Sn. In the context of past and present prospects and limitations we briefly overview most important technological applications and discuss the various interrelations between superconductivity and structural properties of Nb-based A-15 intermetallic alloys. We argue that these interrelations can be used to find the Nb-based superconductors with more superior properties and stronger technological usability. Niobium ; Superconductivity ; Crystal (programming language) ; Materials science ; Chemistry ; Physics ; Condensed matter physics ; Metallurgy ; Computer science Inorganic Fluorides and Related Compounds ; Rare-earth and actinide compounds ; Superconductivity in MgB2 and Alloys