Functional and Mechanical Properties of Biological Soft Matter
Mean curvature and Gaussian curvature of a DOPC/DOPG membrane
Recognizing the essential nature of comprehending the functional and mechanical characteristics of foundational structures like peptides, DNAs, and membranes (whether bilayer or monolayer), becomes paramount in unraveling the mechanisms governing diverse biological functions at the molecular level. Our efforts have been focused on formulating theoretical models for these structures, thereby enabling an exploration of their mechanical attributes as well as the interactions that transpire among these distinct entities.
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 …
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, …
