Origin of compartmentalization in food webs.

The response of an ecosystem to perturbations is mediated by both antagonistic and facilitative interactions between species. It is thought that a community's resilience depends crucially on the food web--the network of trophic interactions--and on the food web's degree of compartmentalization. Despite its ecological importance, compartmentalization and the mechanisms that give rise to it remain poorly understood. Here we investigate several definitions of compartments, propose ways to understand the ecological meaning of these definitions, and quantify the degree of compartmentalization of empirical food webs. We find that the compartmentalization observed in empirical food webs can be accounted for solely by the niche organization of species and their diets. By uncovering connections between compartmentalization and species' diet contiguity, our findings help us understand which perturbations can result in fragmentation of the food web and which can lead to catastrophic effects. Additionally, we show that the composition of compartments can be used to address the long-standing question of what determines the ecological niche of a species.

A network-based method for target selection in metabolic networks.

MOTIVATION: The lack of new antimicrobials, combined with increasing microbial resistance to old ones, poses a serious threat to public health. With hundreds of genomes sequenced, systems biology promises to help in solving this problem by uncovering new drug targets. RESULTS: Here, we propose an approach that is based on the mapping of the interactions between biochemical agents, such as proteins and metabolites, onto complex networks. We report that nodes and links in complex biochemical networks can be grouped into a small number of classes, based on their role in connecting different functional modules. Specifically, for metabolic networks, in which nodes represent metabolites and links represent enzymes, we demonstrate that some enzyme classes are more likely to be essential, some are more likely to be species-specific and some are likely to be both essential and specific. Our network-based enzyme classification scheme is thus a promising tool for the identification of drug targets. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mesoscopic modeling for nucleic acid chain dynamics.

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin--a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop--studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.

Micro-bias and macro-performance.

We use agent-based modeling to investigate the effect of conservatism and partisanship on the efficiency with which large populations solve the density classification task - a paradigmatic problem for information aggregation and consensus building. We find that conservative agents enhance the populations' ability to efficiently solve the density classification task despite large levels of noise in the system. In contrast, we find that the presence of even a small fraction of partisans holding the minority position will result in deadlock or a consensus on an incorrect answer. Our results provide a possible explanation for the emergence of conservatism and suggest that even low levels of partisanship can lead to significant social costs.