AI and Advanced Sampling for Theoretical and Molecular Systems
Under the theme of AI and Advanced Sampling for Theoretical and Molecular Systems, we apply machine learning to theoretical physics and materials design while advancing molecular simulation methodologies for complex biological systems.
In particular, we integrate data-driven approaches with path sampling techniques, such as the Weighted Ensemble (WE) method, to efficiently capture rare events and elucidate mechanisms of processes including protein folding, binding and unbinding, membrane protein dynamics, and cell-penetrating peptides (CPPs).
Publications
Efficient Jet Tagging at the LHC Using Convolutional Neural Networks (CNNs)
Jet tagging is a central and challenging task in high-energy physics, aiming to identify and classify collimated sprays of particles …
Spontaneous penetration of carbon nanotubes through lipid bilayers: A computational perspective
Carbon nanotubes (CNTs) have been widely explored for applications ranging from drug delivery to energy conversion. To evaluate their …
Polyproline Modulates Membrane Translocation of Arginine-Rich Cell-Penetrating Peptides: Insights from Molecular Dynamics Simulationshe
Recent experiments have shown that incorporating polyproline segments into arginine (R)–rich cell-penetrating peptides (CPPs) markedly …
The role of polyproline in the membrane translocation of arginine-rich cell-penetrating peptides: A study based on molecular dynamics simulations
Recent experimental studies have demonstrated that incorporating polyproline segments into arginine (R)‑rich cell‑penetrating peptides …
Spontaneous translocation of carbon nanotubes across a model membrane
Carbon nanotubes (CNTs) have been utilized in various applications, including drug delivery and energy conversion. It is essential to …
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 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 …