An Exploration Algorithm for Stochastic Simulators Driven by Energy Gradients
AbstractIn recent work, we have illustrated the construction of an exploration geometry on free energy surfaces: the adaptive computer-assisted discovery of an approximate low-dimensional manifold on which the effective dynamics of the system evolves. Constructing such an exploration geometry involves geometry-biased sampling (through both appropriately-initialized unbiased molecular dynamics and through restraining potentials) and, machine learning techniques to organize the intrinsic geometry of the data resulting from the sampling (in particular, diffusion maps, possibly enhanced through the appropriate Mahalanobis-type metric). In this contribution, we detail a method for exploring the conformational space of a stochastic gradient system whose effective free energy surface depends on a smaller number of degrees of freedom than the dimension of the phase space. Our approach comprises two steps. First, we study the local geometry of the free energy landscape using diffusion maps on samples computed through stochastic dynamics. This allows us to automatically identify the relevant coarse variables. Next, we use the information garnered in the previous step to construct a new set of initial conditions for subsequent trajectories. These initial conditions are computed so as to explore the accessible conformational space more efficiently than by continuing the previous, unbiased simulations. We showcase this method on a representative test system. View Full-Text
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Georgiou, A.S.; Bello-Rivas, J.M.; Gear, C.W.; Wu, H.-T.; Chiavazzo, E.; Kevrekidis, I.G. An Exploration Algorithm for Stochastic Simulators Driven by Energy Gradients. Entropy 2017, 19, 294.
Georgiou AS, Bello-Rivas JM, Gear CW, Wu H-T, Chiavazzo E, Kevrekidis IG. An Exploration Algorithm for Stochastic Simulators Driven by Energy Gradients. Entropy. 2017; 19(7):294.Chicago/Turabian Style
Georgiou, Anastasia S.; Bello-Rivas, Juan M.; Gear, Charles W.; Wu, Hau-Tieng; Chiavazzo, Eliodoro; Kevrekidis, Ioannis G. 2017. "An Exploration Algorithm for Stochastic Simulators Driven by Energy Gradients." Entropy 19, no. 7: 294.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.