molecular dynamics

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. [...]

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. [...]