相关论文: Target search on networks-within-networks with app…

Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…

Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…

Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…

The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…

In most natural and engineered systems, a set of entities interact with each other in complicated patterns that can encompass multiple types of relationships, change in time, and include other types of complications. Such systems include…

Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…

Complex networks are ubiquitous in nature and play a role of paramount importance in many contexts. Internet and the cyberworld, which permeate our everyday life, are self-organized hierarchical graphs. Urban traffic flows on intricate road…

This review examines intermittent target search strategies, which combine phases of slow motion, allowing the searcher to detect the target, and phases of fast motion during which targets cannot be detected. We first show that intermittent…

Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…

We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA…

Multilayer networks provide a more advanced and comprehensive framework for modeling real-world systems compared to traditional single-layer and multiplex networks. Unlike single-layer models, multilayer networks have multiple interacting…

In the past years, network theory has successfully characterized the interaction among the constituents of a variety of complex systems, ranging from biological to technological, and social systems. However, up until recently, attention was…

Complex network theory aims to model and analyze complex systems that consist of multiple and interdependent components. Among all studies on complex networks, topological structure analysis is of the most fundamental importance, as it…

We investigate the searchability of complex systems in terms of their interconnectedness. Associating searchability with the number and size of branch points along the paths between the nodes, we find that scale-free networks are relatively…

A network representation is useful for describing the structure of a large variety of complex systems. However, most real and engineered systems have multiple subsystems and layers of connectivity, and the data produced by such systems is…

For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…

We analyze velocity-jump process models of persistent search for a single target on a bounded domain. The searcher proceeds along ballistic trajectories and is absorbed upon collision with the target boundary. When reaching the domain…

Real networks often form interacting parts of larger and more complex systems. Examples can be found in different domains, ranging from the Internet to structural and functional brain networks. Here, we show that these multiplex systems are…

Efficient techniques to navigate networks with local information are fundamental to sample large-scale online social systems and to retrieve resources in peer-to-peer systems. Biased random walks, i.e. walks whose motion is biased on…

Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…