The reverse nonequilibrium molecular dynamics (RNEMD) method calculates the shear viscosity of a fluid by imposing a nonphysical exchange of momentum and measuring the resulting shear velocity gradient. In this study we investigate the range of momentum flux values over which RNEMD yields usable (linear) velocity gradients. We find that nonlinear velocity profiles result primarily from gradients in fluid temperature and density. The temperature gradient results from conversion of heat into bulk kinetic energy, which is transformed back into heat elsewhere via viscous heating. An expression is derived to predict the temperature profile resulting from a specified momentum flux for a given fluid and simulation cell. Although primarily bounded above, we also describe milder low-flux limitations. RNEMD results for a Lennard-Jones fluid agree with equilibrium molecular dynamics and conventional nonequilibrium molecular dynamics calculations at low shear, but RNEMD underpredicts viscosity relative to conventional NEMD at high shear.
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Biomark Res
January 2025
Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung, Taiwan.
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January 2025
Department of Materials Science and Metallurgical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India.
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View Article and Find Full Text PDFCommun Chem
January 2025
Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK.
Various photoactive molecules contain motifs built on aza-aromatic heterocycles, although a detailed understanding of the excited state photophysics and photochemistry in such systems is not fully developed. To help address this issue, the non-adiabatic dynamics operating in azanaphthalenes under hexane solvation was studied following 267 nm excitation using ultrafast transient absorption spectroscopy. Specifically, the species quinoline, isoquinoline, quinazoline, quinoxaline, 1,6-naphthyridine, and 1,8-naphthyridine were investigated, providing a systematic variation in the relative positioning of nitrogen heteroatom centres within a bicyclic aromatic structure.
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Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India.
Inward rectifying potassium (Kir) channels play a critical role in maintaining the resting membrane potential and cellular homeostasis. The high-resolution crystal structure of homotetrameric KirBac1.1 in detergent micelles provides a snapshot of the closed state.
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Obsidian Therapeutics, Cambridge, MA, USA.
Adoptive cell therapies (ACT) have shown reduced efficacy against solid tumor malignancies compared to hematologic malignancies, partly due to the immunosuppressive nature of the tumor microenvironment (TME). ACT efficacy may be enhanced with pleiotropic cytokines that remodel the TME; however, their expression needs to be tightly controlled to avoid systemic toxicities. Here we show T cells can be armored with membrane-bound cytokines with surface expression regulated using drug-responsive domains (DRDs) developed from the 260-amino acid protein human carbonic anhydrase 2 (CA2).
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