Related papers: System-Level Genetic Codes: An Explanation for Bio…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
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…
A software element defined in one place is typically used in many places. When it is changed, all its occurrences may need to be changed too, which can severely hinder software evolution. This has led to the support of encapsulation in…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
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…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Probabilistic biological network growth models have been utilized for many tasks including but not limited to capturing mechanism and dynamics of biological growth activities, null model representation, capturing anomalies, etc. Well-known…
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…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
While fields like Artificial Life have made huge strides in quantifying the mechanisms that distinguish living systems from non-living ones, particular mechanisms remain difficult to reproduce in silico. Known as open-endedness, we've been…
Complex systems are characterized by specific time-dependent interactions among their many constituents. As a consequence they often manifest rich, non-trivial and unexpected behavior. Examples arise both in the physical and non-physical…