Best practices in constant pH MD simulations: accuracy and sampling
Various approaches have been proposed to include the effect of [...]
Teixobactin kills bacteria by a two-pronged attack on the cell envelope
Antibiotics that use novel mechanisms are needed to combat antimicrobial [...]
Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons in Strongly Coupled Molecule–Cavity Systems
We performed multiscale molecular dynamics simulations of tetracene molecules strongly coupled to the confined light modes of an optical cavity. The results suggest that both mechanisms are driven by the same molecular vibrations that induce relaxation through nonadiabatic coupling between dark states and polaritonic states.
The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization
Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail.
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in [...]
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function
In Eukaryotic cells, DNA epigenetic modifications play an important role in gene expression and regulation, and protein recognition. In this work we investigate the physical implications of cytosine 5-hydroxymethylation on DNA, its structural and flexibility differences with methylated and unmodified cytosine using molecular dynamics, biophysical experiments and NMR spectroscopy.
