Adam Prada | Searcharxiv

arXiv2025

A tutorial for mesoscale computer simulations of lipid membranes: tether pulling, tubulation and fluctuation

Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations (CGMS) at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop CGMS. Lastly, we construct a hands-on tutorial on how to apply CGMS, by providing a pedagogical examination of tether pulling, tubulation and fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials.

physics.bio-ph↗

arXiv2022

Comparison of Matsubara dynamics with exact quantum dynamics for an oscillator coupled to a dissipative bath

Matsubara dynamics is the classical dynamics which results when imaginary-time path-integrals are smoothed; it conserves the quantum Boltzmann distribution and appears in drastically approximated form in path-integral dynamics methods such as (thermostatted) ring-polymer molecular dynamics (T)RPMD and centroid molecular dynamics (CMD). However, it has never been compared directly with exact quantum dynamics for non-linear operators, because the difficulty of treating the phase has limited the number of Matsubara modes to fewer than 10. Here, we treat up to $\sim$200 Matsubara modes in simulations of a Morse oscillator coupled to a dissipative bath of harmonic oscillators. This is done by expressing the Matsubara equations of motion in the form of a generalised Langevin equation, approximating the noise to be real, and analytically continuing the momenta to convert the Matsubara phase into ring-polymer springs. The resulting equations of motion are stable up to a maximum value of modes which increases with bath coupling strength and decreases with system anharmonicity. The dynamics of the tail of highly oscillatory Matsubara modes is found to be harmonic, and can thus be computed efficiently. For a moderately anharmonic oscillator with a strong but subcritical coupling to the bath, the Matsubara simulations yield non-linear $\large\langle{\hat q^2\hat q^2(t)}\large\rangle$ time-correlation functions in almost perfect agreement with the exact quantum results. Reasonable agreement is also obtained for weaker coupling strengths, where errors arise because of the real-noise approximation. These results give strong evidence that Matsubara dynamics correctly explains how classical dynamics arises in quantum systems which are in thermal equilibrium.

physics.chem-ph↗