Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently

27 April 2023, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


Conformational changes underpin function and encode complex biomolecular mechanisms. Gaining atomic-level detail of how such changes occur has the potential to reveal these mechanisms and is of critical importance in identifying drug targets, facilitating rational drug design, and enabling bioengineering applications. While the past two decades have brought Markov State Model techniques to the point where practitioners can regularly use them to glimpse the long-time dynamics of slow conformations in complex systems, many systems are still beyond their reach. In this perspective, we discuss how memory can reduce the computational cost to predict the long-time dynamics in these complex systems by orders of magnitude and with greater accuracy and resolution than state-of-the-art Markov State Models. We illustrate how memory lies at the heart of successful and promising techniques, ranging from the Fokker-Planck and generalized Langevin equations to deep learning recurrent neural networks and generalized master equations. We delineate how these techniques work, identify insights that they can offer in biomolecular systems, and discuss their advantages and disadvantages in practical settings. We show how generalized master equations can enable the investigation of, for example, the gate-opening process in RNA polymerase II and demonstrate how our recent advances tame the deleterious influence of statistical underconvergence of the molecular dynamics simulations used to parameterize these techniques. This represents a significant leap forward that will enable our memory-based techniques to interrogate systems that are currently beyond the reach of even the best Markov State Models. We conclude by discussing some current challenges and future prospects for how exploiting memory will open the door to many exciting opportunities.


Non-Markovian dynamic models
Protein dynamics
Conformational changes
Generalized Master Equation


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