The ability of different correlation functions to shed some light onto the conformational dynamics of an amorphous polymer has been analyzed. The study has been performed on a polyethylene model polymer, which has been simulated at decreasing temperatures towards its glass transition, via the molecular dynamics technique. Three rotational isomers are allowed by the considered torsional potential. The correlation times associated with the evaluated transition rates have shown to be Arrhenius in nature, with activation energies resulting basically from internal rotation barriers. Overall torsional autocorrelation functions have been calculated. We have observed that they are dominated by slow events. Alternatively, a set of torsional autocorrelation functions associated with every isomeric state has been evaluated. Stretched exponential fits lead to correlation times that display Vogel-Fulcher temperature dependence.
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http://dx.doi.org/10.1063/1.2234775 | DOI Listing |
J Am Chem Soc
January 2025
State Key Laboratory of Molecular Reaction Dynamics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
Directly probing the heterogeneous conformations of intracellular proteins within their native cellular environment remains a significant challenge in mass spectrometry (MS). Here, we establish an in-cell MS and ultraviolet photodissociation (UVPD) strategy that directly ejects proteins from living cells into a mass spectrometer, followed by 193 nm UVPD for structural analysis. Applying this approach to calmodulin (CaM), we reveal that it adopts more extended conformations within living cells compared with purified samples , highlighting the unique influence of intracellular environments on protein folding.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202, United States.
Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
Division of Micro and Nanosystems, KTH Royal Institute of Technology, Malvinas väg 10, Stockholm 100 44, Sweden.
Solid-state nanopores offer unique possibilities for biomolecule sensing; however, scalable production of sub-5 nm pores with precise diameter control remains a manufacturing challenge. In this work, we developed a scalable method to fabricate sub-5 nm nanopores in silicon (Si) nanomembranes through metal-assisted chemical etching (MACE) using gold nanoparticles. Notably, we present a previously unreported self-limiting effect that enables sub-5 nm nanopore formation from both 10 and 40 nm nanoparticles in the 12 nm thick monocrystalline device layer of a silicon-on-insulator substrate.
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Clinical Physiology/Nutritional Medicine, Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.
The pore-forming enterotoxin (CPE), a common cause of foodborne diseases, facilitates Ca influx in enterocytes, leading to cell damage. Upon binding to certain claudins (e.g.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo-ku, Kyoto 606-8502, Japan.
V-shaped polyaromatic amphiphiles (s) form micelle-like nonbonded self-assemblies in aqueous solution and feature prominent properties of encapsulation and solubilization for various types of hydrophobic molecules. To understand microscopic molecular characteristics underlying the wide capability of solubilization, the atomic-level molecular structures of the self-assemblies of s were investigated by microsecond molecular dynamics (MD) simulations. The MD simulations showed that s spontaneously formed quasi-stable self-assemblies, in close agreement with experimental observations.
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