Communication dynamics in finite capacity social networks

In communication networks structure and dynamics are tightly coupled. The structure controls the flow of information and is itself shaped by the dynamical process of information exchanged between nodes. In order to reconcile structure and dynamics, a generic model, based on the local interaction between nodes, is considered for the communication in large social networks. In agreement with data from a large human organization, we show that the flow is non-Markovian and controlled by the temporal limitations of individuals. We confirm the versatility of our model by predicting simultaneously the degree-dependent node activity, the balance between information input and output of nodes and the degree distribution. Finally, we quantify the limitations to network analysis when it is based on data sampled over a finite period of time.Comment: Physical Review Letter, accepted (5 pages, 4 figures

Modeling the spatio-temporal organization and segregation of bacterial chromosomes

This work examined the spatio-temporal organization and segregation of bacterial DNA in order to investigate the fundamental processes regulating the inheritance of genetic material and the proliferation of life. For the investigation of the spatio-temporal organization of genetic material in the cell fundamental physical principles were used in this work. The aim was to use concepts of polymer physics to formulate physical models of the complex biological reality. These models were evaluated in computer simulations and compared with experimental data. In the first project of this thesis, the spatial organization of DNA in multipartite bacteria (= bacteria with multiple replicons) was investigated. The results of this work reveal high order of spatial organization even for multipartite bacteria. The organization could be reproduced using a physical model of compacted DNA and geometric constraints on individual genes. Furthermore, it was possible to make accurate predictions for different mutants and to predict interactions between replicons with the developed model. The second project focused on the study of simultaneous replication and segregation of bacterial DNA. Segregation patterns of the ori were analyzed in the model organism Bacillus subtilis. Using Molecular Dynamics simulations, it was shown that entropic segregation of chromosomes is a plausible mechanism for the segregation of genetic material that would also explain the observed variability in the experimental data. The model of entropic segregation of bacterial chromosomes was extended in the third project by the implementation of additional segregation mechanisms, so that a large data set of different trajectories of the ori through the cell could be generated. Thus, machine learning models could be used to classify the different segregation movements. The evaluation of the predictions showed very good results and encourages future classification of experimental data based on the developed models. This work is intended to provide new perspectives on the organization of DNA in the bacterial cell as well as a better understanding of the physical basis of cellular processes

Present state of knowledge of the upper atmosphere: An assessment report; processes that control ozone and other climatically important trace gases

The state of knowledge of the upper atmosphere was assessed as of January 1986. The physical, chemical, and radiative processes which control the spatial and temporal distribution of ozone in the atmosphere; the predicted magnitude of ozone perturbations and climate changes for a variety of trace gas scenarios; and the ozone and temperature data used to detect the presence or absence of a long term trend were discussed. This assessment report was written by a small group of NASA scientists, was peer reviewed, and is based primarily on the comprehensive international assessment document entitled Atmospheric Ozone 1985: Assessment of Our Understanding of the Processes Controlling Its Present Distribution and Change, to be published as the World Meteorological Organization Global Ozone Research and Monitoring Project Report No. 16

Functional Integrative Levels in the Human Interactome Recapitulate Organ Organization

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This ‘Largest Common Interactome Network’ represents a ‘functional interactome core’. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization

Spatial re-organization of myogenic regulatory sequences temporally controls gene expression

During skeletal muscle differentiation, the activation of some tissue-specific genes occurs immediately while others are delayed. The molecular basis controlling temporal gene regulation is poorly understood. We show that the regulatory sequences, but not other regions of genes expressed at late times of myogenesis, are in close physical proximity in differentiating embryonic tissue and in differentiating culture cells, despite these genes being located on different chromosomes. Formation of these inter-chromosomal interactions requires the lineage-determinant MyoD and functional Brg1, the ATPase subunit of SWI/SNF chromatin remodeling enzymes. Ectopic expression of myogenin and a specific Mef2 isoform induced myogenic differentiation without activating endogenous MyoD expression. Under these conditions, the regulatory sequences of late gene loci were not in close proximity, and these genes were prematurely activated. The data indicate that the spatial organization of late genes contributes to temporal regulation of myogenic transcription by restricting late gene expression during the early stages of myogenesis. The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research

Fractals in the Nervous System: conceptual Implications for Theoretical Neuroscience

This essay is presented with two principal objectives in mind: first, to document the prevalence of fractals at all levels of the nervous system, giving credence to the notion of their functional relevance; and second, to draw attention to the as yet still unresolved issues of the detailed relationships among power law scaling, self-similarity, and self-organized criticality. As regards criticality, I will document that it has become a pivotal reference point in Neurodynamics. Furthermore, I will emphasize the not yet fully appreciated significance of allometric control processes. For dynamic fractals, I will assemble reasons for attributing to them the capacity to adapt task execution to contextual changes across a range of scales. The final Section consists of general reflections on the implications of the reviewed data, and identifies what appear to be issues of fundamental importance for future research in the rapidly evolving topic of this review

Spatiotemporal organization of energy release events in the quiet solar corona

Using data from STEREO and SOHO spacecraft, we show that temporal organization of energy release events in the quiet solar corona is close to random, in contrast to the clustered behavior of flaring times in solar active regions. The locations of the quiet-Sun events follow the meso- and supergranulation pattern of the underling photosphere. Together with earlier reports of the scale-free event size statistics, our findings suggest that quiet solar regions responsible for bulk coronal heating operate in a driven self-organized critical state, possibly involving long-range Alfv\'{e}nic interactions.Comment: 5 pages, 4 figures, 1 tabl