Related papers: Protein Evolution as a Complex System
We consider networks of dynamical units that evolve in time according to different laws, and are coupled to each other in highly irregular ways. Studying how to steer the dynamics of such systems towards a desired evolution is of great…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in…
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…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
Deep learning has become a powerful tool in computational biology, revolutionising the analysis and interpretation of biological data over time. In our article review, we delve into various aspects of deep learning in computational biology.…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Complex Systems were identified and studied in different fields, such as physics, biology, and economics. These systems exhibit exciting properties such as self-organization, robust order, and emergence. In recent years, software systems…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…