Preferential attachment (PA) is a widely observed behavior in many living systems and has been used in modeling many networks. The aim of this work is to show that the mechanism of PA is a consequence of the fundamental principle of least effort. We derive PA directly from this principle in maximizing an efficiency function. This approach not only allows a better understanding of the different PA mechanisms already reported but also naturally extends these mechanisms with a non-power law probability of attachment. The possibility of using the efficiency function as a general measure of attachment efficiency is also investigated.
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http://dx.doi.org/10.3390/e25020305 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Science, Peking University, Beijing 100871, People's Republic of China.
Phycobilisomes (PBS) are the major photosynthetic light-harvesting complexes in cyanobacteria and red algae. While the structures of PBS have been determined in atomic resolutions, how PBS are attached to the reaction centers of photosystems remains less clear. Here, we report that a linker protein (LcpA) is required for the attachment of PBS to photosystem II (PSII) in the cyanobacterium sp.
View Article and Find Full Text PDFNature
January 2025
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
The abundance and sequence of satellite DNA at and around centromeres is evolving rapidly despite the highly conserved and essential process through which the centromere directs chromosome inheritance. The impact of such rapid evolution is unclear. Here we find that sequence-dependent DNA shape dictates packaging of pericentromeric satellites in female meiosis through a conserved DNA-shape-recognizing chromatin architectural protein, high mobility group AT-hook 1 (HMGA1).
View Article and Find Full Text PDFACS Nano
January 2025
Physikalisches Institut, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany.
Biochimie
December 2024
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia. Electronic address:
Except for telomeres, G4 DNA structures in the human genome can be formed only within the context of double-stranded DNA. DNA duplexes flanking the G4 structure may potentially affect the G4 architecture and the binding of G4-specific ligands. Here, we examine the interaction of TMPyP4, NMM, and PDS ligands with three structures formed by the same DNA fragment containing the (GGGT) sequence: the G4 in duplex (dsG4), G4 in single-stranded DNA (ssG4) and perfect duplex DNA (ds).
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Chile.
This paper presents a theoretical study on the distinguishable regiodivergent C-C Myers-Saito and C-C Schmittel routes of benzannelated enyne-allene cycloaromatizations, in which substitutions on the terminal alkyne by alkyl (-CH, -CHCH, -CH(CH) and -C(CH)) and aryl (-CH and -CH(CH)) groups were included. Mechanistic differences were found between substituents attached to alkynes with and without α-H, whereas in the former the Schmittel cyclization proceeds together with 1,8-H migration, in the latter it does so as the sole primitive event. It was also observed that bulky substituents preferentially favor the C-C Schmittel route, and the statistical prediction of regioselectivity is greatly affected when the ratio of accessible vibrational microstates of the transition states is included, especially in highly competing routes, , ΔΔ → 0.
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