PyRETIS 3: Conquering rare and slow events without boundaries.

We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data.

Path sampling with memory reduction and replica exchange to reach long permeation timescales.

Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. Next, recent and current developments in three RETIS aspects are discussed: several new Monte Carlo moves in the path-sampling algorithm, memory reduction by reducing pathlengths, and exploitation of parallel computing with CPU-imbalanced replicas. Finally, the memory reduction presenting a new replica exchange implementation, coined REPPTIS, is showcased with a permeant needing to pass a membrane with two permeation channels, either representing an entropic or energetic barrier. The REPPTIS results showed clearly that inclusion of some memory and enhancing ergodic sampling via replica exchange moves are both necessary to obtain correct permeability estimates. In an additional example, ibuprofen permeation through a dipalmitoylphosphatidylcholine membrane was modeled. REPPTIS succeeded in estimating the permeability of this amphiphilic drug molecule with metastable states along the permeation pathway. In conclusion, the presented methodological advances allow for deeper insight into membrane biophysics even if the pathways are slow, as RETIS and REPPTIS push the permeability calculations to longer timescales.

Oxygen Storage in Stacked Phospholipid Membranes Under an Oxygen Gradient as a Model for Myelin Sheaths.

Axons in the brain and peripheral nervous system are enveloped by myelin sheaths, which are composed of stacked membrane bilayers containing large fractions of cholesterol, phospholipids, and glycolipids. The oxygen availability to the nearby oxygen consuming cytochrome c oxidase in the mitochondria is essential for the well-functioning of a cell. By constructing a rate network model based on molecular dynamics simulations, and solving it for steady-state conditions, this work calculates the oxygen storage in stacked membranes under an oxygen gradient. It is found that stacking membranes increases the oxygen storage capacity, indicating that myelin can function as an oxygen reservoir. However, it is found that the storage enhancement levels out for stacks with a large number of bilayers, suggesting why myelin sheaths consist of only 10-300 membranes rather than thousands. The presence of additional water between the stacked bilayers, as seen in cancer cells, is shown to diminish myelin oxygen storage enhancement.