Generalized Langevin Dynamics-based schemes
We work on the development of a Generalized Langevin Dynamics-based scheme to simulate membrane environments. Within this scheme, the lipid bilayer is represented in an effective way through a generalized (time-dependent) friction and a colored noise, related through the fluctuation dissipation theorem.
By representing the membrane as a viscoelastic material, we develop simple and flexible models able to describe all the dynamical regimes featured by a particle laterally diffusing in a lipid membrane - namely ballistic, subdiffusive, and Brownian - as well as the crossover from one regime to another. The aim is to create a computational platform for the simulation of diffusion limited protein-protein association/dissociation events occurring at the membrane.
The memory kernel (generalized friction) is represented in terms of a viscous (instantaneous) and an elastic (noninstantaneous) component modeled through a Dirac δ function and a three-parameter Mittag-Leffler type function, respectively [1]. The proposed model can be seen as a generalization of the diffusion in a transient confining harmonic potential, with a large distribution of escape times. The model parameters can be tuned by higher resolution molecular dynamics simulations in order to mimic different lipid compositions.
People involved
Dr. Vania Calandrini
Group leader
References
- L. Di Cairano, B. Stamm, V. Calandrini, Subdiffusive-Brownian crossover in membrane proteins: a generalized Langevin equation-based approach, Biophysical Journal 2021, 120(21), 4722-4737.