6 papers
IEPDYN: Integral-equation formalism of population dynamics
Kento Kasahara, Ryo Okabe, Chia-en A. Chang +2
We propose the integral-equation formalism of population dynamics (IEPDYN) to describe the population dynamics of distinct configurational states. According to classical reaction d…
Dual effect of cholesterol on interfacial water dynamics in lipid membranes: Interplay between membrane packing and hydration
Kokoro Shikata, Kento Kasahara, Nozomi Morishita Watanabe +3
Water contained within biological membranes plays a critical role in maintaining the separation between intracellular and extracellular environments and facilitating biochemical pr…
Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
Ryo Okabe, Natsuumi Ito, Yuya Matsubara +4
The physicochemical properties of lipid bilayers (membranes) are closely associated with various cellular functions and are often evaluated using absorption and fluorescence spectr…
Flexible framework of computing binding free energy using the energy representation theory of solution
Kazuya Okita, Yusei Maruyama, Kento Kasahara +1
Host-guest binding plays a crucial role in the functionality of various systems, and its efficiency is often quantified using the binding free energy, which represents the free-ene…
Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures
Kokoro Shikata, Kento Kasahara, Nozomi Morishita Watanabe +3
Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting considerable influence on water molecules proximal to the memb…
A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation
Yuya Matsubara, Ryo Okabe, Ren Masayama +4
We propose a theoretical approach to estimate the permeability coefficient of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of m…