Related papers: Protein Interaction Networks are Fragile against R…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
We consider a cyber-physical system consisting of two interacting networks, i.e., a cyber-network overlaying a physical-network. It is envisioned that these systems are more vulnerable to attacks since node failures in one network may…
The observed structure of protein interaction networks is corrupted by many false positive/negative links. This observational incompleteness is abstracted as random link removal and a specific, experimentally motivated (spoke) link…
Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
Adaptation to dynamic conditions requires a certain degree of diversity. If all agents take the best current action, learning that the underlying state has changed and behavior should adapt will be slower. Diversity is harder to maintain…
With increasingly ambitious initiatives such as GENI and FIND that seek to design the future Internet, it becomes imperative to define the characteristics of robust topologies, and build future networks optimized for robustness. This paper…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Many infrastructure networks have a modular structure and are also interdependent. While significant research has explored the resilience of interdependent networks, there has been no analysis of the effects of modularity. Here we develop a…
Given a connected network, it can be augmented by applying a growing strategy (e.g. random or scale-free rules) over the previously existing structure. Another approach for augmentation, recently introduced, involves incorporating a direct…
Computer infections such as viruses and worms spread over networks of contacts between computers, with different types of networks being exploited by different types of infections. Here we analyze the structures of several of these…
We investigate the dynamics of a simple epidemiological model for the invasion by a pathogen strain of a population where another strain circulates. We assume that reinfection by the same strain is possible but occurs at a reduced rate due…
Multi-strain competition on networks is observed in many contexts, including infectious disease ecology, information dissemination or behavioral adaptation to epidemics. Despite a substantial body of research has been developed considering…
This paper studies network resilience against structured additive perturbations to its topology. We consider dynamic networks modeled as linear time-invariant systems subject to perturbations of bounded energy satisfying specific sparsity…
Here we propose a generic mechanism - networked buffering - for generating robust traits in complex systems that requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role…
Most complex systems are nonlinear, relying on emergent behavior from interacting subsystems, often characterized by oscillatory dynamics. Collective oscillatory behavior is essential for the proper functioning of many real world systems.…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally…