Journal of Theoretical Biology
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Journal of Theoretical Biology 359:IFC (2014)
Journal of Theoretical Biology 354:IFC (2014)
Feature extraction by statistical contact potentials and wavelet transform for predicting subcellular localizations in gram negative bacteri...
We propose a protein representation based on the structural information contained in the pairwise statistical contact potentials. The wavelet transform decodes the information contained in the primary structure of the proteins, allowing the identification of patterns along the proteins, which are us...
The origin and spread of a cooperative replicase in a prebiotic chemical system.
We consider a trans-acting replicase that catalyses replication of a template (either a copy of itself or another sequence). Our model includes alternating plus/minus strand replication where only the plus strand is a catalyst. Prebiotic chemistry generates random sequences and allows for non-cataly...
Fidelity drive: a mechanism for chaperone proteins to maintain stable mutation rates in prokaryotes over evolutionary time.
We show a mechanism by which chaperone proteins can play a key role in maintaining the long-term evolutionary stability of mutation rates in prokaryotes with perfect genetic linkage. Since chaperones can reduce the phenotypic effects of mutations, higher mutation rate, by affecting chaperones, can i...
Determining equilibrium osmolarity in poly(ethylene glycol)/chondrotin sulfate gels mimicking articular cartilage.
We present an experimentally guided, multi-phase, multi-species polyelectrolyte gel model to make qualitative predictions on the equilibrium electro-chemical properties of articular cartilage. The mixture theory consists of two different types of polymers: poly(ethylene gylcol) (PEG), chondrotin sul...
Speed of evolution in large asexual populations with diminishing returns.
We propose a phenomenological model that generalizes the fixed-advantage framework to include this negative epistasis in a simple way. We evaluate analytically as well as with direct simulations the quantitative consequences of diminishing returns on the evolutionary dynamics. The speed of adaptatio...
Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation.
We examine the difference of gene expression noise and correlation when tuning the expression level at the transcriptional or translational level in a bicistronic operon driven by a constitutive or a two-state promoter. We get analytic results for the noise and correlation of gene expression levels,...
Network impact on persistence in a finite population dynamic diffusion model: Application to an emergent seed exchange network.
Dynamic extinction colonisation models (also called contact processes) are widely studied in epidemiology and in metapopulation theory. Contacts are usually assumed to be possible only through a network of connected patches. This network accounts for a spatial landscape or a social organization of i...
Mathematical modeling of tuberculosis data of China.
We set up a mathematical model to fit those data with the goodness of fit and obtain the optimal parameter values of the model. By the Chi-square test of the statistical inference, the optimal parameter values of the model are reasonable. We get the effective reproductive number of the disease for e...