The DNLS model including Kac-Baker long-range interactions and nonlinear damping exhibits prominent effects in computer simulations. The combination of long-range forces and damping yields a periodic pattern of stationary breathers from an originally uniformly distributed background. The inverse interaction radius determines the periodicity which can be understood in the quasicontinuum approximation of the system. For the undamped system, we investigate the impact of the long-range interactions on the transition to the persistent-breather phase, which only depends on the energy and the norm of the DNLS. Using Monte Carlo techniques, we can monitor the localization strength as a function of the the long-range radius and the system temperature, which is formally negative in the persistent-breather phase.
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http://dx.doi.org/10.1103/PhysRevE.73.056610 | DOI Listing |
Biomolecules
January 2025
School of Computer Science, University College Dublin (UCD), D04 V1W8 Dublin, Ireland.
Predicting the relative solvent accessibility (RSA) of a protein is critical to understanding its 3D structure and biological function. RSA prediction, especially when homology transfer cannot provide information about a protein's structure, is a significant step toward addressing the protein structure prediction challenge. Today, deep learning is arguably the most powerful method for predicting RSA and other structural features of proteins.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
CuO octahedra usually show elongated distortion, leading to active orbitals and planar exchange interactions, while compressed CuO octahedra with active orbitals and unidirectional exchange interactions are exceptionally rare. Here, we design and synthesize a new frustrated antiferromagnet CaCuFeO through a high-pressure and high-temperature approach, in which robust compressed CuO octahedra are realized, separating the FeO sheets that comprise zigzag spin ladders. Magnetic susceptibility and specific heat measurements exhibit a long-range antiferromagnetic order below the Néel temperature of 165 K, which is further confirmed by neutron diffraction.
View Article and Find Full Text PDFG3 (Bethesda)
January 2025
Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics.
View Article and Find Full Text PDFACS Nano
January 2025
School of Medicine and Health, Harbin Institute of Technology, Harbin 150080, China.
Modularly organizing active micromachines into high-grade metamachines makes a great leap for operating the microscopic world in a biomimetic way. However, modulating the nonreciprocal interactions among different colloidal motors through chemical reactions to achieve the controllable construction of active colloidal metamachines with specific dynamic properties remains challenging. Here, we report the phototactic active colloidal metamachines constructed by shape-directed dynamic self-assembly of chemically driven peanut-shaped TiO colloidal motors and Janus spherical Pt/SiO colloidal motors.
View Article and Find Full Text PDFRSC Adv
January 2025
College of Agriculture and Biological Science, Dali University Dali 671000 China
The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models.
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