Stochastic Dynamics in Computational Biology

2020 ◽  
Author(s):  
Stefanie Winkelmann ◽  
Christof Schütte
2017 ◽  
Author(s):  
Debasish Roy ◽  
G. Visweswara Rao
Keyword(s):  

2018 ◽  
Vol 26 (2) ◽  
Author(s):  
Dean A. Forbes

In a recent essay published in this journal, I illustrated the limitations one may encounter when sequencing texts temporally using s-curve analysis. I also introduced seriation, a more reliable method for temporal ordering much used in both archaeology and computational biology. Lacking independently ordered Biblical Hebrew (BH) data to assess the potential power of seriation in the context of diachronic studies, I used classic Middle English data originally compiled by Ellegård. In this addendum, I reintroduce and extend s-curve analysis, applying it to one rather noisy feature of Middle English. My results support Holmstedt’s assertion that s-curve analysis can be a useful diagnostic tool in diachronic studies. Upon quantitative comparison, however, the five-feature seriation results derived in my former paper are found to be seven times more accurate than the single-feature s-curve results presented here. 


2015 ◽  
Vol 16 (8) ◽  
pp. 701-717 ◽  
Author(s):  
Izabella Pena Neshich ◽  
Leticia Nishimura ◽  
Fabio de Moraes ◽  
Jose Salim ◽  
Fabian Villalta-Romero ◽  
...  

Author(s):  
Sauro Succi

Dense fluids and liquids molecules are in constant interaction; hence, they do not fit into the Boltzmann’s picture of a clearcut separation between free-streaming and collisional interactions. Since the interactions are soft and do not involve large scattering angles, an effective way of describing dense fluids is to formulate stochastic models of particle motion, as pioneered by Einstein’s theory of Brownian motion and later extended by Paul Langevin. Besides its practical value for the study of the kinetic theory of dense fluids, Brownian motion bears a central place in the historical development of kinetic theory. Among others, it provided conclusive evidence in favor of the atomistic theory of matter. This chapter introduces the basic notions of stochastic dynamics and its connection with other important kinetic equations, primarily the Fokker–Planck equation, which bear a complementary role to the Boltzmann equation in the kinetic theory of dense fluids.


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