Functional and Mechanical Properties of Biological Soft Matter
Mean curvature and Gaussian curvature of a DOPC/DOPG membrane
Understanding the functional and mechanical properties of fundamental structures, such as peptides, DNAs, and membranes (whether bilayer or monolayer), is crucial for unraveling the mechanisms that govern various biological functions at the molecular level. Our efforts have focused on developing theoretical models for these structures, enabling us to explore their mechanical properties as well as the interactions between these distinct entities.
Publications
Polyproline modulates membrane translocation of arginine-rich cell-penetrating peptides: Insights from molecular dynamics simulations
Recent experiments have shown that incorporating polyproline segments into arginine (R)-rich cell-penetrating peptides (CPPs) enhances …
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 …
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 …
Molecular dynamics studies of interactions between Arg9(nona-arginine) and a DOPC/DOPG(4:1) membrane
It has been known that the uptake mechanisms of cell-penetrating peptides (CPPs) depend on the experimental conditions such as the …
Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle
This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a …
A continuum method for determining membrane protein insertion energies and the problem of charged residues
Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they …
Bending elasticity of anti-parallel β-sheets
Using a coarse-grained elastic model, we examine the bending properties of anti-parallel β-sheets comprised of uniform amino-acid …
The elasticity of α-helices
The elasticity of α-helices is examined using equilibrium molecular-dynamics simulations. From the statistics of curvatures and twists, …
