Permeation of metabolic substrates across biological membranes is a fundamental process in cellular life. This process is largely driven by the concentration gradient of various molecules between the outside and inside of a cell. To meet the need for creating such concentration gradients in MD simulation, and to calculate permeation under natural conditions, we developed a technique in NAMD to continually drive permeant molecules near the periphery of the simulation box across the periodic boundary, which results in a sustained gradient in the center of the simulation system where the membrane is located. This allows for purely diffusive motion of particles across a membrane, enabling one to directly calculate permeability the same way as in experiment. Read more in a recent paper.
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- Beyond nothingness in the formation and functional relevance of voids in polymer films. Nat. Commun., 15:2852. 2024.
- Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. Nat. Commun., 15:2750. 2024.
- Generating Concentration Gradients Across Membranes for Molecular Dynamics Simulations of Periodic Systems. Int. J. Mol. Sci., 25:3616. 2024.
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J. Mol. Biol., 18:168546. 2024.
- Elucidating the Mechanism of Metabolism of Cannabichromene by Human Cytochrome P450s. J. Nat. Prod., 2024.
- WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination. Nucleic Acids Res., gkae161. 2024.
- Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. Drug Resist. Updat., 73:101066. 2024.
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