Measurements and characterization of the dynamics of tracer particles in an actin network.

The underlying physics governing the diffusion of a tracer particle in a viscoelastic material is a topic of some dispute. The long-term memory in the mechanical response of such materials should induce diffusive motion with a memory kernel, such as fractional Brownian motion (fBM). This is the reason that microrheology is able to provide the shear modulus of polymer networks.

Learning algorithms allow for improved reliability and accuracy of global mean surface temperature projections.

Climate predictions are only meaningful if the associated uncertainty is reliably estimated. A standard practice is to use an ensemble of climate model projections. The main drawbacks of this approach are the fact that there is no guarantee that the ensemble projections adequately sample the possible future climate conditions.

Gradual regime shifts in fairy circles.

Large responses of ecosystems to small changes in the conditions--regime shifts--are of great interest and importance. In spatially extended ecosystems, these shifts may be local or global. Using empirical data and mathematical modeling, we investigated the dynamics of the Namibian fairy circle ecosystem as a case study of regime shifts in a pattern-forming ecosystem.

Theory of single molecule emission spectroscopy.

A general theory and calculation framework for the prediction of frequency-resolved single molecule photon counting statistics is presented. Expressions for the generating function of photon counts are derived, both for the case of naive "detection" based solely on photon emission from the molecule and also for experimentally realizable detection of emitted photons, and are used to explicitly calculate low-order photon-counting moments. The two cases of naive detection versus physical detection are compared to one another and it is demonstrated that the physical detection scheme resolves certain inconsistencies predicted via the naive detection approach.

Interplay between Turing mechanisms can increase pattern diversity.

We use the context of dryland vegetation to study a general problem of complex pattern-forming systems: multiple pattern-forming instabilities that are driven by distinct mechanisms but share the same spectral properties. We find that the co-occurrence of two Turing instabilities when the driving mechanisms counteract each other in some region of the parameter space results in the growth of a single mode rather than two interacting modes. The interplay between the two mechanisms compensates for the simpler dynamics of a single mode by inducing a wider variety of patterns, which implies higher biodiversity in dryland ecosystems.

Regime shifts in models of dryland vegetation.

Drylands are pattern-forming systems showing self-organized vegetation patchiness, multiplicity of stable states and fronts separating domains of alternative stable states. Pattern dynamics, induced by droughts or disturbances, can result in desertification shifts from patterned vegetation to bare soil. Pattern formation theory suggests various scenarios for such dynamics: an abrupt global shift involving a fast collapse to bare soil, a gradual global shift involving the expansion and coalescence of bare-soil domains and an incipient shift to a hybrid state consisting of stationary bare-soil domains in an otherwise periodic pattern.

Regime shifts in models of dryland vegetation.

Drylands are pattern-forming systems showing self-organized vegetation patchiness, multiplicity of stable states and fronts separating domains of alternative stable states. Pattern dynamics, induced by droughts or disturbances, can result in desertification shifts from patterned vegetation to bare soil. Pattern formation theory suggests various scenarios for such dynamics: an abrupt global shift involving a fast collapse to bare soil, a gradual global shift involving the expansion and coalescence of bare-soil domains and an incipient shift to a hybrid state consisting of stationary bare-soil domains in an otherwise periodic pattern.

The simplicity of completion time distributions for common complex biochemical processes.

Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the precise construction of specific macromolecules. In this work, we study the transient properties of such systems and fully characterize their first passage (completion) time distributions.

Specificity and completion time distributions of biochemical processes.

In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this high specificity is kinetic proofreading, which has been extended to a variety of systems from detection of DNA mismatch to cell signaling processes. While the specification properties of kinetic proofreading models are well known and were studied in various contexts, very little is known about their temporal behavior.

Theory for wavelength-resolved photon emission statistics in single-molecule fluorescence spectroscopy.

We derive the moment generating function for photon emissions from a single molecule driven by laser excitation. The frequencies of the fluoresced photons are explicitly considered. Calculations are performed for the case of a two-level dye molecule, showing that measured photon statistics will display a strong and nonintuitive dependence on detector bandwidth.

Single molecule photon counting statistics for quantum mechanical chromophore dynamics.

We extend the generating function technique for calculation of single molecule photon emission statistics (Zheng, Y.; Brown, F. L.