David A. Adams

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state of the globular histone core. The mechanism is relevant to several classes of posttranslational modifications such as histone acetylation and phosphorylation; several specific scenarios consistent with recent in vivo experiments are considered. The model integrates a description based on an idealized geometry with one based on the atomistic structure of the nucleosome, and the model consistently accounts for both the electrostatic and nonelectrostatic contributions to the nucleosome free energy. Under physiological conditions, isolated nucleosomes are predicted to be very stable (38 +/- 7 kcal/mol). However, a decrease in the charge of the globular histone core by one unit charge, for example due to acetylation of a single lysine residue, can lead to a significant decrease in the strength of association with its DNA. In contrast to the globular histone core, comparable changes in the charge state of the histone tail regions have relatively little effect on the nucleosomes stability. The combination of high stability and sensitivity explains how the nucleosome is able to satisfy the seemingly contradictory requirements for thermodynamic stability while allowing quick access to its DNA informational content when needed by specific cellular processes such as transcription.

Far-from-equilibrium transport with constrained resources

The totally asymmetric simple exclusion process (TASEP) is a well studied example of far-from-equilibrium dynamics. Here, we consider a TASEP with open boundaries but impose a global constraint on the total number of particles. In other words, the boundary reservoirs and the system must share a finite supply of particles. Using simulations and analytic arguments, we obtain the average particle density and current of the system, as a function of the boundary rates and the total number of particles. Our findings are relevant to biological transport problems if the availability of molecular motors becomes a rate-limiting factor.

Computation of nucleation at a nonequilibrium first-order phase transition using a rare-event algorithm

We introduce a new forward flux sampling in time algorithm to efficiently measure transition times in rare-event processes in nonequilibrium systems and apply it to study the first-order (discontinuous) kinetic transition in the Ziff-Gulari-Barshad model of catalytic surface reaction. The average time for the transition to take place, as well as both the spinodal and transition points, is efficiently found by this method.

Harmonic measure for percolation and ising clusters including rare events.

We obtain the harmonic measure of the hulls of critical percolation clusters and Ising-model Fortuin-Kastelyn clusters using a biased random-walk sampling technique which allows us to measure probabilities as small as 10{-300}. We find the multifractal D(q) spectrum including regions of small and negative q. Our results for external hulls agree with Duplantiers theoretical predictions for D(q) and his exponent -23/24 for the harmonic measure probability distribution for percolation. For the complete hull, we find the probability decays with an exponent of -1 for both systems.

Fractal dimensions of the Q-state Potts model for the complete and external hulls

Fortuin–Kastelyn clusters in the critical Q-state Potts model are conformally invariant fractals. We obtain simulation results for the fractal dimension of the complete and external (accessible) hulls for Q = 1, 2, 3, and 4, on clusters that wrap around a cylindrical system. We find excellent agreement between these results and theoretical predictions. We also obtain the probability distributions of the hull lengths and maximal heights of the clusters in this geometry and provide a conjecture for their form.

The harmonic measure of diffusion-limited aggregates including rare events

We obtain the harmonic measure of diffusion-limited aggregate (DLA) clusters using a biased random-walk sampling technique which allows us to measure probabilities of random walkers hitting sections of clusters with unprecedented accuracy; our results include probabilities as small as 10- 80. We find the multifractal D(q) spectrum including regions of small and negative q. Our algorithm allows us to obtain the harmonic measure for clusters more than an order of magnitude larger than those achieved using the method of iterative conformal maps, which is the previous best method. We find a phase transition in the singularity spectrum f(α) at α≈14 and also find a minimum q of D(q), qmin=0.9±0.05.

Fractal dimensions of the Q-state Potts model for complete and external hulls

Fortuin–Kastelyn clusters in the critical Q-state Potts model are conformally invariant fractals. We obtain simulation results for the fractal dimension of the complete and external (accessible) hulls for Q = 1, 2, 3, and 4, on clusters that wrap around a cylindrical system. We find excellent agreement between these results and theoretical predictions. We also obtain the probability distributions of the hull lengths and maximal heights of the clusters in this geometry and provide a conjecture for their form.

Fractal dimensions of the

Fortuin–Kastelyn clusters in the critical Q-state Potts model are conformally invariant fractals. We obtain simulation results for the fractal dimension of the complete and external (accessible) hulls for Q = 1, 2, 3, and 4, on clusters that wrap around a cylindrical system. We find excellent agreement between these results and theoretical predictions. We also obtain the probability distributions of the hull lengths and maximal heights of the clusters in this geometry and provide a conjecture for their form.