We compute by molecular simulation the energy/entropic partition of the force in a stretched double-stranded (ds)DNA molecule that is not yet available from the single-molecule measurements. Simulation using the coarse-grained wormlike chain (WLC) model predicts a gradual decrease in the internal (bending) energy of DNA at stretching. The ensuing negative energy contribution to force f is outweighed by the positive entropy contribution f . The ratio f /f, used to assess the polymer elasticity, is about -1 at the moderate extension of DNA. At the high extension, the extra energy expenses due to the contour length elongation make the ratio f /f less negative. The simulation findings of the hybrid energy/entropy nature of DNA elasticity at weak and moderate forces are supported by computations using the thermoelastic method mimicking the polymer experiments in bulk. It is contended that the observation of the negative energy elasticity in DNA can be generalized to other semiflexible polymers described by the WLC model.
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http://dx.doi.org/10.1002/bip.23487 | DOI Listing |
Environ Pollut
January 2025
Xi'an Jinborui Ecological Tech. Co., Ltd., Xi'an 710065, China.
As a crucial component of soil organic matter, humic acid (HA) persists in soil and exert a complex interaction with hydrophobic organic pollutants, yet its specific role still remains unclear. In this study, HA was obtained from weathered coal via alkaline dissolution and acidic precipitation for the adsorption of benzo[a]anthracene (BAA). Subsequently, an aging simulation was employed to assess its long-term performance.
View Article and Find Full Text PDFJ Exp Biol
January 2025
College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia.
Comparative finite element analysis involves standardising aspects of models to test equivalent loading scenarios across species. However, regarding feeding biomechanics of the vertebrate skull, what is considered "equivalent" can depend on the hypothesis. Using 13 diversely-shaped skulls of marsupial bettongs and potoroos (Potoroidae), we demonstrate that scaling muscle forces to standardise specific aspects of biting mechanics can produce clearly opposing comparisons of stress or strain that are differentially suited to address specific kinds of hypotheses.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
IBiTech - BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Entrance 98, 9000 Gent, Belgium.
Molecular oxygen (O) is essential for life, and continuous effort has been made to understand its pathways in cellular respiration with all-atom (AA) molecular dynamics (MD) simulations of, e.g., membrane permeation or binding to proteins.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
School of Environment and Safety Engineering, North University of China, Taiyuan, Shanxi 030051, China.
DNP (3,4-dinitropyrazole) has attracted much interest due to its promising melting characteristics and high detonation performances, such as low melting point, high density, high detonation velocity, and low sensitivity. In this work, first-principles molecular dynamics (MD) simulations were performed to investigate the anisotropic shock response of DNP in conjunction with the multiscale shock technique (MSST). The initial decomposition mechanism was revealed through the evolution of the chemical reaction and product analysis.
View Article and Find Full Text PDFEur Heart J Cardiovasc Imaging
January 2025
Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.
Background: Cardiac magnetic resonance (CMR) is essential for diagnosing cardiomyopathy, serving as the gold standard for assessing heart chamber volumes and tissue characterization. Hemodynamic forces (HDF) analysis, a novel approach using standard cine CMR images, estimates energy exchange between the left ventricular (LV) wall and blood. While prior research has focused on peak or mean longitudinal HDF values, this study aims to investigate whether unsupervised clustering of HDF curves can identify clinically significant patterns and stratify cardiovascular risk in non-ischemic LV cardiomyopathy (NILVC).
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