scholarly journals A Computational Approach to Increase Time Scales in Brownian Dynamics–Based Reaction-Diffusion Modeling

2012 ◽  
Vol 19 (6) ◽  
pp. 606-618 ◽  
Author(s):  
Zachary Frazier ◽  
Frank Alber
2014 ◽  
Vol 20 (1) ◽  
pp. 55-76 ◽  
Author(s):  
Tom Froese ◽  
Nathaniel Virgo ◽  
Takashi Ikegami

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an ximpoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively.


2016 ◽  
Author(s):  
Davide Michieletto ◽  
Davide Marenduzzo ◽  
Ajazul H. Wani

Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its faithful transmission through disruptive events of cell-cycle, like mitosis, are not fully understood. By using Brownian dynamics simulations of Drosophila chromosome 3R up to time-scales of minutes, we show that chromatin binding profile of Polycomb-repressive-complex-1 robustly predicts a sub-set of topologically associated domains (TADs), and inclusion of other factors recapitulates the profile of all TADs, as observed experimentally. Our simulations show that chromosome 3R attains interphase organization from mitotic state by a two-step process in which formation of local TADs is followed by long-range interactions. Our model also explains statistical features and tracks the assembly kinetics of polycomb subnuclear clusters. In conclusion, our approach can be used to predict structural and kinetic features of 3D chromosome folding and its associated proteins in biological relevant genomic and time scales.


2010 ◽  
Vol 96 (6) ◽  
pp. 061103 ◽  
Author(s):  
Jianhua Liu ◽  
Haihui Pu ◽  
Bin Gao ◽  
Hongyue Gao ◽  
Dejin Yin ◽  
...  

2006 ◽  
Vol 39 (3) ◽  
pp. 1279-1289 ◽  
Author(s):  
Ajay S. Panwar ◽  
Satish Kumar

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Kaihong Zhao ◽  
Yongkun Li

The existence of equilibrium solutions to reaction-diffusion recurrent neural networks with Dirichlet boundary conditions on time scales is proved by the topological degree theory and M-matrix method. Under some sufficient conditions, we obtain the uniqueness and global exponential stability of equilibrium solution to reaction-diffusion recurrent neural networks with Dirichlet boundary conditions on time scales by constructing suitable Lyapunov functional and inequality skills. One example is given to illustrate the effectiveness of our results.


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