We study the robustness and stability of the yeast cell regulatory network by using a general inhomogeneous discrete model. We find that inhomogeneity, on average, enhances the stability of the biggest attractor of the dynamics and that the large size of the basin of attraction is robust against changes in the parameters of inhomogeneity. We find that the most frequent orbit, which represents the cell-cycle pathway, has a better biological meaning than the one exhibited by the homogeneous model.
We have uncovered that the non-equilibrium network dynamics and global properties are determined by two essential features: the potential landscape and the flux landscape. We have found that the funneled potential landscape is crucial for the stability of the states on the cell cycle, however, the stabilities of the oscillation states cannot guarantee the stable directional flows. We have uncovered that the funneled flux landscape is important for the emergence and maintenance of the stable limit cycle oscillation flow. This work will allow us to identify the key factors and structure elements…
The biological processes that execute complex multiple functions, such as cell cycle, must ensure the order of sequential events and keep the dynamic robustness against various fluctuations. Here, we examine the dynamic mechanism and the fundamental structure to achieve these properties in the cell-cycle process of budding yeast Saccharomyces cerevisiae. We show that the budding yeast cell-cycle process behaves like an excitable system containing three well-coupled saddle-node bifurcations to execute DNA replication and mitosis events. The yeast cell-cycle regulatory network can be separated i…
Study of network dynamics is very active area in biological and social sciences. However, the relationship between the network structure and the attractors of the dynamics has not been fully understood yet. In this study, we numerically investigated the role of degenerate self-loops on the attractors and its basin size using the budding yeast cell-cycle network model. In the network, all self-loops negatively surpress the node (self-inhibition loops) and the attractors are only fixed points, i.e. point attractors. It is found that there is a simple division rule of the state space by removing …
We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for regulation of the cell cycle of the fission yeast Schizosaccharomyces Pombe. We compare calculated values of local and global information measures for the fission yeast cell cycle to the same measures as applied to two different classes of random networks: random and scale-free. We report patterns in local information processing and storage that do indeed distinguish…
Organisms across all domains of life regulate the size of their cells. However, the means by which this is done is poorly understood. We study two abstracted "molecular" models for size regulation: inhibitor dilution and initiator accumulation. We apply the models to two settings: bacteria like Escherichia coli, that grow fully before they set a division plane and divide into two equally sized cells, and cells that form a bud early in the cell division cycle, confine new growth to that bud, and divide at the connection between that bud and the mother cell, like the budding yeast Saccharomyces …
Regulatory networks and connected components of the neutral space
活细胞的功能在很大程度上由其调控网络的结构决定，该网络包括调控基因之间的非线性相互作用。这种监管系统的稳定性和可演变性的一个重要因素是中立性-通常大量的备选网络结构会产生必要的动态。在这里，我们研究了酵母细胞周期的离散化调控动力学[Li et al.，PNAS，2004]和能够复制它的网络集合，我们称之为功能性。其中，经验酵母野生型网络是接近最佳的稀疏布线。在建立或删除单个相互作用的点突变下，功能网络的中性空间被分割成4.7 * 10^8个分量。其中一个较小的包含野生型网络。平均而言，从野生型突变可达的功能网络是稀疏的，具有更高的噪声弹性和更少的固定点吸引子相比，该野生型组件之外的网络。
The dynamics of a mathematical model of the Calvin cycle, which is part of photosynthesis, is analysed. Since diffusion of ATP is included in the model a system of reaction-diffusion equations is obtained. It is proved that for a suitable choice of parameters there exist spatially inhomogeneous positive steady states, in fact infinitely many of them. It is also shown that all positive steady states, homogeneous and inhomogeneous, are nonlinearly unstable. The only smooth steady state which could be stable is a trivial one, where all concentrations except that of ATP are zero. It is found that …
Gene expression data, or transcription data, are surrogates for actual protein concentrations in the cells. In addition protein-protein interactions are static diagrams of all the protein-protein interactions in the cell. These interactions may consist of covalent bonding or maybe just secondary bonding such as hydrogen bonding. Given these two surrogate data types we show a technique to compute the Gibbs free energy of a cell. We apply this to yeast cell cycle and to cancer.
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data available and the recent discoveries showing that many diseases are related to the disruption of cellular signal transduction cascades, in silico discovery of signaling pathways in cell biology has become an active research topic in past years. However, reconstruction of signaling pathways remains a challenge mainly because of the need for systematic approac…
Control of complex networks requires both structure and dynamics
School of Informatics and Computing, Indiana University（印第安纳大学信息学与计算学院）；Program in Cognitive Science, Indiana University（印第安纳大学认知科学项目）；Instituto Gulbenkian de Ciencia（古尔本基安科学研究所）
