Related papers: Network analysis of protein dynamics
Real-world networks are composed of diverse interacting and evolving entities, while most of existing researches simply characterize them as particular static networks, without consideration of the evolution trend in dynamic networks.…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
The importance of studying properties of networks is manifest in diverse fields ranging from biology, engineering, physics, chemistry, neuroscience, and medicine. The functionality of networks with regard to performance, throughput,…
Epidemic spreading on complex networks depends on the topological structure as well as on the dynamical properties of the infection itself. Generally speaking, highly connected individuals play the role of hubs and are crucial to channel…
The connection between network topology and stability remains unclear. General approaches that clarify this relationship and allow for more efficient stability analysis would be desirable. Inspired by chemical reaction networks, I…
A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics…
Understanding conformational change is crucial for programming and controlling the function of many mechanical systems such as allosteric enzymes and tunable metamaterials. Of particular interest is the relationship between the network…
The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of…
Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Impact of an intruder on granular matter leads to formation of mesoscopic force networks seen particularly clearly in the recent experiments carried out with photoelastic particles, e.g., Clark et al., Phys. Rev. Lett., 114 144502 (2015).…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
Interconnected networks describe the dynamics of important systems in a wide range such as biological systems and electrical power grids. Some important features of these systems were successfully studied and understood through simplified…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
We present a simple model of network dynamics that can be solved analytically for uniform networks. We obtain the dynamics of response of the system to perturbations. The analytical solution is an excellent approximation for random…
We study the robustness of complex networks subject to edge removal. Several network models and removing strategies are simulated. Rather than the existence of the giant component, we use total connectedness as the criterion of breakdown.…
Many real-world complex systems, such as epidemic spreading networks and ecosystems, can be modeled as networked dynamical systems that produce multivariate time series. Learning the intrinsic dynamics from observational data is pivotal for…
The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional…
Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…