Joshua E. S. Socolar

Global control of cell-cycle transcription by coupled CDK and network oscillators

A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically during the cell division cycle, indicating that properly timed gene expression is important for regulating cell-cycle events. Genomic analyses of the localization and expression dynamics of transcription factors suggest that a network of sequentially expressed transcription factors could control the temporal programme of transcription during the cell cycle. However, directed studies interrogating small numbers of genes indicate that their periodic transcription is governed by the activity of cyclin-dependent kinases (CDKs). To determine the extent to which the global cell-cycle transcription programme is controlled by cyclin–CDK complexes, we examined genome-wide transcription dynamics in budding yeast mutant cells that do not express S-phase and mitotic cyclins. Here we show that a significant fraction of periodic genes are aberrantly expressed in the cyclin mutant. Although cells lacking cyclins are blocked at the G1/S border, nearly 70% of periodic genes continued to be expressed periodically and on schedule. Our findings reveal that although CDKs have a function in the regulation of cell-cycle transcription, they are not solely responsible for establishing the global periodic transcription programme. We propose that periodic transcription is an emergent property of a transcription factor network that can function as a cell-cycle oscillator independently of, and in tandem with, the CDK oscillator.

STABILITY OF PERIODIC ORBITS CONTROLLED BY TIME-DELAY FEEDBACK

Abstract Extended time-delay auto-synchronization (ETDAS) is a promising technique for stabilizing unstable periodic orbits in low-dimensional dynamical systems. The technique involves continuous feedback of signals delayed by multiples of the orbits period in a manner that is especially well-suited for fast systems and optical implementation. We show how to analyze the stability of a given implementation of ETDAS without explicit integration of time-delay equations. To illustrate the method and point out some nontrivial features of ETDAS, we obtain the domain of control for a period-one orbit of the driven, damped pendulum.

Binary colloidal structures assembled through Ising interactions

New methods for inducing microscopic particles to assemble into useful macroscopic structures could open pathways for fabricating complex materials that cannot be produced by lithographic methods. Here we demonstrate a colloidal assembly technique that uses two parameters to tune the assembly of over 20 different pre-programmed structures, including kagome, honeycomb and square lattices, as well as various chain and ring configurations. We programme the assembled structures by controlling the relative concentrations and interaction strengths between spherical magnetic and non-magnetic beads, which behave as paramagnetic or diamagnetic dipoles when immersed in a ferrofluid. A comparison of our experimental observations with potential energy calculations suggests that the lowest energy configuration within binary mixtures is determined entirely by the relative dipole strengths and their relative concentrations.

Mutual information in random Boolean models of regulatory networks

The amount of mutual information contained in the time series of two elements gives a measure of how well their activities are coordinated. In a large, complex network of interacting elements, such as a genetic regulatory network within a cell, the average of the mutual information over all pairs, , is a global measure of how well the system can coordinate its internal dynamics. We study this average pairwise mutual information in random Boolean networks (RBNs) as a function of the distribution of Boolean rules implemented at each element, assuming that the links in the network are randomly placed. Efficient numerical methods for calculating show that as the number of network nodes, N, approaches infinity, the quantity N exhibits a discontinuity at parameter values corresponding to critical RBNs. For finite systems it peaks near the critical value, but slightly in the disordered regime for typical parameter variations. The source of high values of N is the indirect correlations between pairs of elements from different long chains with a common starting point. The contribution from pairs that are directly linked approaches zero for critical networks and peaks deep in the disordered regime.

Graph fission in an evolving voter model

We consider a simplified model of a social network in which individuals have one of two opinions (called 0 and 1) and their opinions and the network connections coevolve. Edges are picked at random. If the two connected individuals hold different opinions then, with probability 1 - α, one imitates the opinion of the other; otherwise (i.e., with probability α), the link between them is broken and one of them makes a new connection to an individual chosen at random (i) from those with the same opinion or (ii) from the network as a whole. The evolution of the system stops when there are no longer any discordant edges connecting individuals with different opinions. Letting ρ be the fraction of voters holding the minority opinion after the evolution stops, we are interested in how ρ depends on α and the initial fraction u of voters with opinion 1. In case (i), there is a critical value αc which does not depend on u, with ρ ≈ u for α > αc and ρ ≈ 0 for α < αc. In case (ii), the transition point αc(u) depends on the initial density u. For α > αc(u), ρ ≈ u, but for α < αc(u), we have ρ(α,u) = ρ(α,1/2). Using simulations and approximate calculations, we explain why these two nearly identical models have such dramatically different phase transitions.

Controlling chaos in a fast diode resonator using extended time-delay autosynchronization: Experimental observations and theoretical analysis

We stabilize unstable periodic orbits of a fast diode resonator driven at 10.1 MHz (corresponding to a drive period under 100 ns) using extended time-delay autosynchronization. Stabilization is achieved by feedback of an error signal that is proportional to the difference between the value of a state variable and an infinite series of values of the state variable delayed in time by integral multiples of the period of the orbit. The technique is easy to implement electronically and it has an all-optical counterpart that may be useful for stabilizing the dynamics of fast chaotic lasers. We show that increasing the weights given to temporally distant states enlarges the domain of control and reduces the sensitivity of the domain of control on the propagation delays in the feedback loop. We determine the average time to obtain control as a function of the feedback gain and identify the mechanisms that destabilize the system at the boundaries of the domain of control. A theoretical stability analysis of a model of the diode resonator in the presence of time-delay feedback is in good agreement with the experimental results for the size and shape of the domain of control. (c) 1997 American Institute of Physics.

An aperiodic hexagonal tile

We show that a single prototile can fill space uniformly but not admit a periodic tiling. A two-dimensional, hexagonal prototile with markings that enforce local matching rules is proven to be aperiodic by two independent methods. The space-filling tiling that can be built from copies of the prototile has the structure of a union of honeycombs with lattice constants of 2^na, where a sets the scale of the most dense lattice and n takes all positive integer values. There are two local isomorphism classes consistent with the matching rules and there is a nontrivial relation between these tilings and a previous construction by Penrose. Alternative forms of the prototile enforce the local matching rules by shape alone, one using a prototile that is not a connected region and the other using a three-dimensional prototile.

Network growth models and genetic regulatory networks

We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with the innovation of new links, allowing for the possibility that input and output links from a newly created node may have different probabilities of survival. We find some counterintuitive trends as the parameters are varied, including the broadening of the in-degree distribution when the probability for retaining input links is decreased. We also find that both the scaling of transcription factors with genome size and the measured degree distributions for genes in yeast can be reproduced by the growth algorithm if and only if a special seed is used to initiate the process.

AVERAGE STRESSES AND FORCE FLUCTUATIONS IN NONCOHESIVE GRANULAR MATERIALS

A lattice model is presented for investigating the fluctuations in static granular materials under gravitationally induced stress. The model is similar in spirit to the scalar

Trajectory Divergence for Coupled Relaxation Oscillators: Measurements and Models

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