Path Sampling of Rare Events
Path sampling methodologies offer a means to augment the efficiency of simulating infrequent occurrences, such as protein folding, protein binding and unbinding, as well as cellular signaling processes. Among these approaches, the Weighted Ensemble (WE) method stands out as a particularly potent and versatile technique. In our research pursuits, we have harnessed WE simulations to delve into the fundamental mechanisms governing an array of biological systems. Notably, our investigations have encompassed subjects such as membrane proteins and cell-penetrating peptides (CPPs).
Publications
Insights into translocation of arginine-rich cell-penetrating peptides across a model membrane
It is well-known that membrane deformation and water pores contribute to the spontaneous translocation of arginine-rich …
Spontaneous translocation of cell-penetrating peptides across a model membrane using molecular dynamics simulations
Observing the spontaneous translocation of cell-penetrating peptides across a lipid bilayer in molecular dynamics simulations is …
Spontaneous translocation of cell-penetrating peptides using the weighted ensemble method within molecular dynamics simulations
Our findings demonstrate the occurrence of self-induced translocation of a specific cell-penetrating peptide (CPP) across a model …
Translocation of cell-penetrating peptides using the weighted ensemble method within molecular dynamics simulations approach
We report spontaneous translocation of a single cell-penetrating peptide (CPP) across a model membrane using the weighted ensemble (WE) …
Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method
It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few …
Translocation of cell-penetrating peptides across a model membrane using molecular dynamics simulations
In this study, we report a single Arg9(R9) peptide translocation across a DOPC/DOPG(4:1) model membrane within an order of a few tens …
Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method
A spontaneous translocation of cell-penetrating peptides(CPPs) in all-atom molecular dynamics(MD) simulations is not expected within a …
Free energy analyses of cell-penetrating peptides using the weighted ensemble method
Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they …
Free energy analyses of cell penetrating peptides using the weighted ensemble method
Cell penetrating peptides (CPPs) have been widely used for drug-delivery agents, however, it has not been fully understood how they …
Free energy analyses of cell penetrating peptides using the weighted ensemble method
Cell penetrating peptides (CPPs) have been widely used for drug-delivery agents, however, it has not been fully understood how they …
Enhancement of direct membrane penetration of cell-penetrating peptides (CPPs) by polyprolines
The transport mechanism of cell-penetrating peptides (CPPs) has not been fully understood and there seems no general rule to design …