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Nature's many varied complex systems (including galaxies, stars, planets, life, and society) are islands of order within the increasingly disordered universe. All organized systems are subject to physical, biological or cultural evolution,…
The study of system complexity primarily has two objectives: to explore underlying patterns and to develop theoretical explanations. Pattern exploration seeks to clarify the mechanisms behind the emergence of system complexity, while…
Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…
Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins…
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…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…
We compare the ability of a simulated annealing program and an evolutionary algorithm to find molecules with large molecular average hyperpolarizabilities. This property is an important component of nonlinear optical materials. Both…
In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of…
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…
A theory of aging based on the principles of the kinetics of chemical reactions and the rules of natural selection of organisms is proposed. The theory is based on a hypothesis that the biochemical processes in the organism can be described…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
The shape of a molecule determines its physicochemical and biological properties. However, it is often underrepresented in standard molecular representation learning approaches. Here, we propose using the Euler Characteristic Transform…
The emergence of life from inanimate matter presents a thermodynamic challenge: the Second Law of Thermodynamics dictates a global trend towards disorder, yet life constitutes localized pockets of profound organization. This paper presents…
Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Motivated by present activities in (statistical) physics directed towards biological evolution, we review the interplay of three evolutionary forces: mutation, selection, and genetic drift. The review addresses itself to physicists and…
Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box…
An assembly is a large population of neurons whose synchronous firing is hypothesized to represent a memory, concept, word, and other cognitive categories. Assemblies are believed to provide a bridge between high-level cognitive phenomena…
The Semantic Theory of Evolution (STE) takes the existence of a number of arbitrary communication codes as a fundamental feature of life, from the genetic code to human cultural communication codes. Their arbitrariness enables, at each…