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Machine-learning (ML) has become a key workhorse in molecular simulations. Building an ML model in this context involves encoding the information on chemical environments using local atomic descriptors. In this work, we focus on the Smooth Overlap of Atomic Positions (SOAP) and their application in studying the properties of liquid water both in the bulk and at the hydrophobic air-water interface. By using a statistical test aimed at assessing the relative information content of different distance measures defined on the same data space, we investigate if these descriptors provide the same information as some of the common order parameters that are used to characterize local water structure such as hydrogen bonding, density, or tetrahedrality to name a few. Our analysis suggests that the ML description and the standard order parameters of the local water structure are not equivalent. In particular, a combination of these order parameters probing local water environments can predict SOAP similarity only approximately, and vice versa, the environments that are similar according to SOAP are not necessarily similar according to the standard order parameters. We also elucidate the role of some of the metaparameters in the SOAP definition in encoding chemical information.
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http://dx.doi.org/10.1021/acs.jctc.2c01205 | DOI Listing |
Environ Monit Assess
September 2025
Department of Civil Engineering, Faculty of Engineering, Karpagam Academy of Higher Education, Pollachi Main Road, Eachanari Post, Coimbatore, Tamil Nadu, 641021, India.
Synthetic dyes, such as Congo red (CR), pose serious threats to human health and aquatic ecosystems because of their carcinogenicity and resistance to degradation, necessitating the development of efficient and eco-friendly remediation strategies. In this study, silver nanoparticles (AgNPs) were synthesized via a green method using Ocimum sanctum (holy basil) leaf extract and applied for CR dye removal from aqueous solutions. The adsorption process was optimized using response surface methodology (RSM) based on Box-Behnken design (BBD), evaluating the influence of key parameters including pH, AgNP dosage, initial dye concentration, contact time, and temperature.
View Article and Find Full Text PDFNature
September 2025
National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA.
Controlling spin currents, that is, the flow of spin angular momentum, in small magnetic devices, is the principal objective of spin electronics, a main contender for future energy-efficient information technologies. A pure spin current has never been measured directly because the associated electric stray fields and/or shifts in the non-equilibrium spin-dependent distribution functions are too small for conventional experimental detection methods optimized for charge transport. Here we report that resonant inelastic X-ray scattering (RIXS) can bridge this gap by measuring the spin current carried by magnons-the quanta of the spin wave excitations of the magnetic order-in the presence of temperature gradients across a magnetic insulator.
View Article and Find Full Text PDFBiosystems
September 2025
IVIRMA Global Research Alliance, The Health Research Institute La Fe (IIS La Fe), Edificio Biopolo. Av. Fernando Abril Martorell, 106 - Torre A, Planta 1, Valencia, 46026, Spain; Rey Juan Carlos University, Department of Medical Specialties and Public Health, Edificio Departamental II. Av. de Atenas
Cellular aging associated with telomeric shortening plays an important role in female fertility. In addition to natural decline, due to the loss of telomeric repeats during cell division, other factors such oxidative stress (OS), accelerate telomere shortening by causing a dramatic loss of telomeric repeats. Thus, mathematical models to better understand the accelerated aging leading to infertility are lacking in the literature.
View Article and Find Full Text PDFTalanta
September 2025
School of Chemistry, Damghan University, 36716-45667, Damghan, Iran.
Flavonoids are a major class of natural polyphenolic compounds with potent antioxidant, anti-inflammatory and anticancer properties. Among them, quercetin and catechin have been widely studied due to their significant health benefits and potent free radical scavenging activity. The efficient extraction and separation of these structurally similar antioxidants remains challenging, necessitating the development of high-performance adsorbents.
View Article and Find Full Text PDFJ Chem Theory Comput
September 2025
Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States.
The Slater-type F12 geminal length scales originally tuned for the second-order Mo̷ller-Plesset F12 method are too large for higher-order F12 methods formulated using the SP (diagonal fixed-coefficient spin-adapted) F12 ansatz. The new geminal parameters reported herein reduce the basis set incompleteness errors (BSIEs) of absolute coupled-cluster singles and doubles F12 correlation energies by a significant─and increase with the cardinal number of the basis─margin. The effect of geminal reoptimization is especially pronounced for the cc-pVZ-F12 basis sets (specifically designed for use with F12 methods) relative to their conventional aug-cc-pVZ counterparts.
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