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The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Complexity is a signature quality of interest in artificial life systems. Alongside other dimensions of assessment, it is common to quantify genome sites that contribute to fitness as a complexity measure. However, limitations to the…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification, a gene expression pattern that achieves greater cell…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Evolutionary adaptation is the process that increases the fit of a population to the fitness landscape it inhabits. As a consequence, evolutionary dynamics is shaped, constrained, and channeled, by that fitness landscape. Much work has been…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable the investigator to pinpoint the sites…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…
Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of…