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Stochastic dynamics is generated by a matrix of transition probabilities. Certain eigenvectors of this matrix provide observables, and when these are plotted in the appropriate multi-dimensional space the phases (in the sense of phase transitions) of the underlying system become manifest as extremal points. This geometrical construction, which we call an textit{observable-representation of state space}, can allow hierarchical structure to be observed. It also provides a method for the calculation of the probability that an initial points ends in one or another asymptotic state.
For diffusive stochastic dynamics, the probability to observe any individual trajectory is vanishingly small, making it unclear how to experimentally validate theoretical results for ratios of path probabilities. We provide the missing link between t
We introduce a simple nearest-neighbor spin model with multiple metastable phases, the number and decay pathways of which are explicitly controlled by the parameters of the system. With this model we can construct, for example, a system which evolves
An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale perspective. The supr
Freidlin-Wentzell theory of large deviations can be used to compute the likelihood of extreme or rare events in stochastic dynamical systems via the solution of an optimization problem. The approach gives exponential estimates that often need to be r
We study single crystals of Dy$_2$Ti$_2$O$_7$ and Ho$_2$Ti$_2$O$_7$ under magnetic field and stress applied along their [001] direction. We find that many of the features that the emergent gauge field of spin ice confers to the macroscopic magnetic p