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Dinner, Aaron R.

Publications and source records attributed to Dinner, Aaron R..

Predicting rare events using neural networks and short-trajectory data

Estimating the likelihood, timing, and nature of events is a major goal of modeling stochastic dynamical systems. When the event is rare in comparison with the timescales of simulation and/or measurement needed to resolve the elemental dynamics, accurate prediction from direct observations becomes challenging. In such cases a more effective approach is to cast statistics of interest as solutions to Feynman-Kac equations (partial differential equations). Here, we develop an approach to solve Feynman-Kac equations by training neural networks on short-trajectory data. Our approach is based on a Markov approximation but otherwise avoids assumptions about the underlying model and dynamics. This makes it applicable to treating complex computational models and observational data. Additionally, we illustrate the advantages of our method using a low-dimensional model that facilitates visualization, and this analysis motivates an adaptive sampling strategy that allows on-the-fly identification of and addition of data to regions important for predicting the statistics of interest. Finally, we demonstrate that we can compute accurate statistics for a 75-dimensional model of sudden stratospheric warming. This system provides a stringent test bed for our method.

97 MATHEMATICS AND COMPUTING↗

Thermodynamic Control of Activity Patterns in Cytoskeletal Networks

Biological materials, such as the actin cytoskeleton, exhibit remarkable structural adaptability to various external stimuli by consuming different amounts of energy. In this Letter, we use methods from large deviation theory to identify a thermodynamic control principle for structural transitions in a model cytoskeletal network. Specifically, we demonstrate that biasing the dynamics with respect to the work done by nonequilibrium components effectively renormalizes the interaction strength between such components, which can eventually result in a morphological transition. Further, our work demonstrates how a thermodynamic quantity can be used to renormalize effective interactions, which in turn can tune structure in a predictable manner, suggesting a thermodynamic principle for the control of cytoskeletal structure and dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

A strong nonequilibrium bound for sorting of cross-linkers on growing biopolymers

Significance Understanding the connection between microscopic driving forces in biological systems and their emergent structures remains an outstanding challenge. We tackle this problem by deriving a fluctuation–response bound in the context of actin polymerization and bundling and verify its robustness far from equilibrium through simulation. Our results show how actin polymerization, molecular fluxes of cross-linker binding, and the morphology of the growing bundle are associated quantitatively; when the bound is saturated, it becomes a nonequilibrium linear-response relation. Molecular driving forces are difficult to measure directly in biological systems, and this work represents a first step toward estimating them from experimentally accessible quantities such as molecular fluxes and compositions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatiotemporal control of liquid crystal structure and dynamics through activity patterning

Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means of controlling and manipulating transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. In this work, simulations and experiments are used to demonstrate that topological defects can be generated at will and then constrained to move along specified trajectories by inducing local stresses in an otherwise passive material. These results provide a foundation for the design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Error Bounds for Dynamical Spectral Estimation

Dynamical spectral estimation is a well-established numerical approach for estimating eigenvalues and eigenfunctions of the Markov transition operator from trajectory data. Although the approach has been widely applied in biomolecular simulations, its error properties remain poorly understood. Here we analyze the error of a dynamical spectral estimation method called “the variational approach to conformational dynamics" (VAC). We bound the approximation error and estimation error for VAC estimates. Our analysis establishes VAC's convergence properties and suggests new strategies for tuning VAC to improve accuracy.

97 MATHEMATICS AND COMPUTING↗