Tag: physics.bio-ph

🔖 Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity

Bookmarked Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity (arxiv.org)
Neuroengineering is faced with unique challenges in repairing or replacing complex neural systems that are composed of many interacting parts. These interactions form intricate patterns over large spatiotemporal scales, and produce emergent behaviors that are difficult to predict from individual elements. Network science provides a particularly appropriate framework in which to study and intervene in such systems, by treating neural elements (cells, volumes) as nodes in a graph and neural interactions (synapses, white matter tracts) as edges in that graph. Here, we review the emerging discipline of network neuroscience, which uses and develops tools from graph theory to better understand and manipulate neural systems, from micro- to macroscales. We present examples of how human brain imaging data is being modeled with network analysis and underscore potential pitfalls. We then highlight current computational and theoretical frontiers, and emphasize their utility in informing diagnosis and monitoring, brain-machine interfaces, and brain stimulation. A flexible and rapidly evolving enterprise, network neuroscience provides a set of powerful approaches and fundamental insights critical to the neuroengineer's toolkit.
17 pages, 6 figures. Manuscript accepted to the journal Annual Review of Biomedical Engineering [1]

References

[1]
D. Bassett S., A. Khambhati N., and S. Grafton T., “Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity,” arXiv, 23-Dec-2016. [Online]. Available: https://arxiv.org/abs/1612.08059. [Accessed: 03-Jan-2017]

🔖 100 years after Smoluchowski: stochastic processes in cell biology

Bookmarked 100 years after Smoluchowski: stochastic processes in cell biology (arxiv.org)
100 years after Smoluchowski introduces his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from large number (tens of thousands) of single molecular trajectories or to study the diffusive motion of molecules, proteins or receptors. Stochastic modeling is a new step in large data analysis that serves extracting cell biology concepts. We review here the Smoluchowski's approach to stochastic processes and provide several applications for coarse-graining diffusion, studying polymer models for understanding nuclear organization and finally, we discuss the stochastic jump dynamics of telomeres across cell division and stochastic gene regulation.
65 pages, J. Phys A 2016 [1]

References

[1]
D. Holcman and Z. Schuss, “100 years after Smoluchowski: stochastic processes in cell biology,” arXiv, 26-Dec-2016. [Online]. Available: https://arxiv.org/abs/1612.08381. [Accessed: 03-Jan-2017]
Bookmarked Selective pressures on genomes in molecular evolution by Charles Ofria, Christoph Adami, Travis C. Collier (arXiv.org, 15 Jan 2003)
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms.
To be published in J. theor. Biology 222 (2003) 477-483
DOI: 10.1016/S0022-5193(03)00062-6