The free energy landscape of mean-field marginal glasses is ultrametric. We demonstrate that this feature persists in finite three-dimensional systems that are out of equilibrium by finding sets of minima, which are nearby in configuration space. By calculating the distance between these nearby minima, we produce a small region of the distance metric. This metric exhibits a clear hierarchical structure and shows the signature of an ultrametric space. That such a hierarchy exists for the jamming energy landscape provides direct evidence for the existence of a marginal phase along the zero temperature jamming line.
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http://dx.doi.org/10.1103/PhysRevLett.124.078002 | DOI Listing |
Sci Rep
January 2025
Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, El‑Sadat, Egypt.
Sci Adv
January 2025
School of Materials Science and Engineering, Peking University, Beijing 100871, P.R. China.
Microcavity exciton polaritons (polaritons) as part-light part-matter quasiparticles garner considerable attention for Bose-Einstein condensation at elevated temperatures. Recently, halide perovskites have emerged as promising room-temperature polaritonic platforms because of their large exciton binding energies and superior optical properties. However, currently, inducing room-temperature nonequilibrium polariton condensation in perovskite microcavities requires optical pulsed excitations with high excitation densities.
View Article and Find Full Text PDFPLoS One
January 2025
Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
The ongoing increase in the prevalence and mutation rate of the influenza virus remains a critical global health issue. A promising strategy for antiviral drug development involves targeting the RNA-dependent RNA polymerase, specifically the PB2-cap binding domain of Influenza A H5N1. This study employs an in-silico approach to inhibit this domain, crucial for viral replication, using potential inhibitors derived from marine bacterial compounds.
View Article and Find Full Text PDFActa Crystallogr B Struct Sci Cryst Eng Mater
February 2025
Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, United Kingdom.
We present an approach to reduce this computational cost substantially, based on the partitioning of the molecule into geometrically separated torsional groups, with the dependence of the intramolecular energy and atomic point charges and dependent degrees of freedom on molecular conformation being computed as a linear combination of the contributions of these groups. This can lead to large savings in computational cost without a significant impact on accuracy, as demonstrated in the cases of N-acetyl-para-aminophenol (paracetamol) and methyl 4-hydroxybenzoate (methyl paraben). The approach is also applied successfully to two larger molecules, benzyl [4-(4-methyl-5-[(4-methylphenyl)sulfonyl]-1,3-thiazol-2-yl)phenyl]carbamate (molecule XX from the fifth CSP blind test) and (2S)-2-[4-(3-fluorobenzyloxy)benzylamino]propionamide (safinamide), for which we conduct the first reported CSP study.
View Article and Find Full Text PDFProtein Sci
February 2025
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
We have recently demonstrated a novel anaerobic NADH-dependent haem breakdown reaction, which is carried out by a range of haemoproteins. The Yersinia enterocolitica protein, HemS, is the focus of further research presented in the current paper. Using conventional experimental methods, bioinformatics, and energy landscape theory (ELT), we provide new insight into the mechanism of the novel breakdown process.
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