Many-body descriptors are widely used to represent atomic environments in the construction of machine-learned interatomic potentials and more broadly for fitting, classification, and embedding tasks on atomic structures. There is a widespread belief in the community that three-body correlations are likely to provide an overcomplete description of the environment of an atom. We produce several counterexamples to this belief, with the consequence that any classifier, regression, or embedding model for atom-centered properties that uses three- (or four)-body features will incorrectly give identical results for different configurations. Writing global properties (such as total energies) as a sum of many atom-centered contributions mitigates the impact of this fundamental deficiency-explaining the success of current "machine-learning" force fields. We anticipate the issues that will arise as the desired accuracy increases, and suggest potential solutions.
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http://dx.doi.org/10.1103/PhysRevLett.125.166001 | DOI Listing |
Int J Mol Sci
January 2025
Research Institute for Systems Biology and Medicine (RISBM), Nauchnyi proezd 18, 117246 Moscow, Russia.
SARS-CoV-2 viral entry requires membrane fusion, which is facilitated by the fusion peptides within its spike protein. These predominantly hydrophobic peptides insert into target membranes; however, their precise mechanistic role in membrane fusion remains incompletely understood. Here, we investigate how FP1 (SFIEDLLFNKVTLADAGFIK), the N-terminal fusion peptide, modulates membrane stability and barrier function across various model membrane systems.
View Article and Find Full Text PDFAstrobiology
January 2025
NASA Goddard Space Flight Center, Greenbelt, Maryland, USA.
Meteoritic impacts on planetary surfaces deliver a significant amount of energy that can produce prebiotic organic compounds such as cyanides, which may be a key step to the formation of biomolecules. To study the chemical processes of impact-induced organic synthesis, we simulated the physicochemical processes of hypervelocity impacts (HVI) in experiments with both high-speed C projectiles and laser ablation. In the first approach, a C beam was accelerated to collide with ammonium nitrate (NHNO) to reproduce the shock process and plume generation of meteoritic impacts on nitrogen-rich planetary surfaces.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
National Center for International Research on Green Optoelectronics, Guangdong Provincial Key Laboratory of Optical Information Materials and Technology, Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou 510006, China.
Ice melting, a common yet complex phenomenon, remains incompletely understood. While theoretical studies suggest that preexisting defects in ice generate "off-lattice" water molecules, triggering bulk ice melting, direct experimental evidence of their form has been lacking as the transparent and transient nature of ice poses significant challenges for observation with current techniques. Here, we introduce an ice-melting-induced lyophilization (IMIL) technique that employs graphene-based nanoprobes to replicate and track liquid evolution within melting bulk ice.
View Article and Find Full Text PDFJ Phys Chem Lett
January 2025
School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
Photochemistry-based silica formation offers a pathway toward energy-efficient and controlled fabrication processes. While the transformation of poly(dimethylsiloxane) (PDMS) to silica (often referred to as SiO due to incomplete conversion) under deep ultraviolet (DUV) irradiation in the presence of oxygen/ozone has experimentally been validated, the detailed mechanism remains elusive. This study demonstrates the underlying molecular-level mechanism of PDMS-to-silica conversion using density functional theory (DFT) calculations.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France.
The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.
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