Related papers: The protein folding network
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
We interpret the subgraph centrality as the partition function of a network. The entropy, the internal energy and the Helmholtz free energy are defined for networks and molecular graphs on the basis of graph spectral theory. Various…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
The configuration space network (CSN) of a dynamical system is an effective approach to represent the ensemble of configurations sampled during a simulation and their dynamic connectivity. To elucidate the connection between the CSN…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Complex network topologies and hyperbolic geometry seem specularly connected, and one of the most fascinating and challenging problems of recent complex network theory is to map a given network to its hyperbolic space. The Popularity…
We report on parallel observations in two seemingly unrelated areas of dynamical network research. The one is the so-called small world phenomenon and/or the observation of scale freeness in certain types of large (empirical) networks and…
Transportation and distribution networks are a class of spatial networks that have been of interest in recent years. These networks are often characterized by the presence of complex structures such as central loops paired with peripheral…
Community structures have been identified in various complex real-world networks, for example, communication, information, internet and shareholder networks. The scaling of community size distribution indicates the heterogeneity in the…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
In this paper we present the first mathematical analysis of the protein interaction network found in the yeast, S. cerevisiae. We show that, (a) the identified protein network display a characteristic scale-free topology that demonstrate…
We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
Temporal gene expression data (Wen, et. al.) was analyzed using the recently introduced inverse modeling technique of Embedded Complex Logistic Maps (ECLM). Preliminary results indicate scale-free structure in the gene regulatory network…
Adaptive networks have been recently introduced in the context of disease propagation on complex networks. They account for the mutual interaction between the network topology and the states of the nodes. Until now, existing models have…
A network is scale-free if its connectivity density function is proportional to a power-law distribution. Scale-free networks may provide an explanation for the robustness observed in certain physical and biological phenomena, since the…
A small-world topology characterizes many complex systems including the structural and functional organization of brain networks. The topology allows simultaneously for local and global efficiency in the interaction of the system…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
Free-energy landscapes for short peptides -- specifically for variants of the pH Low Insertion Peptide (pHLIP) -- in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant…