arXiv subjects

Björn Samuelsson

Publications and source records attributed to Björn Samuelsson.

10 recordsLinked to original sources

arXiv2007

Mutual information in random Boolean models of regulatory networks

The amount of mutual information contained in 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.

q-bio.OT↗

arXiv2007

Attractors in continuous and Boolean networks

We study the stable attractors of a class of continuous dynamical systems that may be idealized as networks of Boolean elements, with the goal of determining which Boolean attractors, if any, are good approximations of the attractors of generic continuous systems. We investigate the dynamics in simple rings and rings with one additional self-input. An analysis of switching characteristics and pulse propagation explains the relation between attractors of the continuous systems and their Boolean approximations. For simple rings, "reliable" Boolean attractors correspond to stable continuous attractors. For networks with more complex logic, the qualitative features of continuous attractors are influenced by inherently non-Boolean characteristics of switching events.

q-bio.MN↗

arXiv2007

Network Analysis of the State Space of Discrete Dynamical Systems

We study networks representing the dynamics of elementary 1-d cellular automata (CA) on finite lattices. We analyze scaling behaviors of both local and global network properties as a function of system size. The scaling of the largest node in-degree is obtained analytically for a variety of CA including rules 22, 54 and 110. We further define the \emph{path diversity} as a global network measure. The co-appearance of non-trivial scaling in both hub size and path diversity separates simple dynamics from the more complex behaviors typically found in Wolfram's Class IV and some Class III CA.

cond-mat.stat-mech↗

arXiv2006

Exhaustive percolation on random networks

We consider propagation models that describe the spreading of an attribute, called "damage", through the nodes of a random network. In some systems, the average fraction of nodes that remain undamaged vanishes in the large system limit, a phenomenon we refer to as exhaustive percolation. We derive scaling law exponents and exact results for the distribution of the number of undamaged nodes, valid for a broad class of random networks at the exhaustive percolation transition and in the exhaustive percolation regime. This class includes processes that determine the set of frozen nodes in random Boolean networks with indegree distributions that decay sufficiently rapidly with the number of inputs. Connections between our calculational methods and previous studies of percolation beginning from a single initial node are also pointed out. Central to our approach is the observation that key aspects of damage spreading on a random network are fully characterized by a single function specifying the probability that a given node will be damaged as a function of the fraction of damaged nodes. In addition to our analytical investigations of random networks, we present a numerical example of exhaustive percolation on a directed lattice.

nlin.CG↗

arXiv2005

Random maps and attractors in random Boolean networks

Despite their apparent simplicity, random Boolean networks display a rich variety of dynamical behaviors. Much work has been focused on the properties and abundance of attractors. The topologies of random Boolean networks with one input per node can be seen as graphs of random maps. We introduce an approach to investigating random maps and finding analytical results for attractors in random Boolean networks with the corresponding topology. Approximating some other non-chaotic networks to be of this class, we apply the analytic results to them. For this approximation, we observe a strikingly good agreement on the numbers of attractors of various lengths. We also investigate observables related to the average number of attractors in relation to the typical number of attractors. Here, we find strong differences that highlight the difficulties in making direct comparisons between random Boolean networks and real systems. Furthermore, we demonstrate the power of our approach by deriving some results for random maps. These results include the distribution of the number of components in random maps, along with asymptotic expansions for cumulants up to the 4th order.

cond-mat.dis-nn↗

arXiv2004

Counting attractors in synchronously updated random Boolean networks

Despite their apparent simplicity, random Boolean networks display a rich variety of dynamical behaviors. Much work has been focused on the properties and abundance of attractors. We here derive an expression for the number of attractors in the special case of one input per node. Approximating some other non-chaotic networks to be of this class, we apply the analytic results to them. For this approximation, we observe a strikingly good agreement on the numbers of attractors of various lengths. Furthermore, we find that for long cycle lengths, there are some properties that seem strange in comparison to real dynamical systems. However, those properties can be interesting from the viewpoint of constraint satisfaction problems.

q-bio.MN↗

arXiv2004

Genetic networks with canalyzing Boolean rules are always stable

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are dynamically stable. Furthermore, for architectures with few inputs per node, the dynamics of the networks is close to critical. In addition, the fraction of genes that are active decreases with the number of inputs per node. These results are based upon investigating ensembles of networks using analytical methods. Also, for different in-degree distributions, the numbers of fixed points and cycles are calculated, with results intuitively consistent with stability analysis; fewer inputs per node implies more cycles, and vice versa. There are hints that genetic networks acquire broader degree distributions with evolution, and hence our results indicate that for single cells, the dynamics should become more stable with evolution. However, such an effect is very likely compensated for by multicellular dynamics, because one expects less stability when interactions among cells are included. We verify this by simulations of a simple model for interactions among cells.

q-bio.MN↗

arXiv2004

Random Boolean Network Models and the Yeast Transcriptional Network

The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.

q-bio.MN↗

arXiv2003

Two-state folding over a weak free-energy barrier

We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described in terms of a simple two-state system, and that the relaxation behavior is close to single exponential. The motion along individual reaction coordinates is roughly diffusive on timescales beyond the reconfiguration time for an individual helix. A simple estimate based on diffusion in a square-well potential predicts the relaxation time within a factor of two.

q-bio.BM↗

arXiv2003

Thermodynamics of alpha- and beta-structure formation in proteins

An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-state character of the melting curves, the energy distributions are found to lack a clear bimodal shape, which is discussed in some detail. We also perform a Monte Carlo-based kinetic study and find, in accord with experimental data, that the alpha-helix forms faster than the beta-hairpin.

q-bio.BM↗