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We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…

Statistical Mechanics · Physics 2007-05-23 Stefan Bornholdt , Kim Sneppen

Predicting the response of nonlinear dynamical systems subject to random, broadband excitation is important across a range of scientific disciplines, such as structural dynamics and neuroscience. Building data-driven models requires…

Machine Learning · Computer Science 2024-09-27 Joseph Massingham , Ole Nielsen , Tore Butlin

A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early…

Populations and Evolution · Quantitative Biology 2009-11-13 Kalin Vetsigian , Carl Woese , Nigel Goldenfeld

Noise is one of the central obstacles to building useful quantum computers, and quantum error correction (QEC) provides the framework for protecting quantum information against it. Unlike classical error correction, QEC must preserve…

Like all natural systems, great societies and their cultures emerge by a growth process from their environments, developing, organized, and behaving as wholes with their internal designs linked with their external worlds. So the general…

Physics and Society · Physics 2022-08-16 Jessie Henshaw

Sensitivity of deep-neural models to input noise is known to be a challenging problem. In NLP, model performance often deteriorates with naturally occurring noise, such as spelling errors. To mitigate this issue, models may leverage…

Computation and Language · Computer Science 2021-11-18 Jakub Náplava , Martin Popel , Milan Straka , Jana Straková

Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…

Pattern Formation and Solitons · Physics 2020-11-18 Bram A. Siebert , Cameron L. Hall , James P. Gleeson , Malbor Asllani

A first-principles theory is developed for the general evolution of a key structural characteristic of planar granular systems - the cell order distribution. The dynamic equations are constructed and solved in closed form for a number of…

Materials Science · Physics 2015-05-04 Raphael Blumenfeld

During development of biological organisms, multiple complex structures are formed. In many instances, these structures need to exhibit a high degree of order to be functional, although many of their constituents are intrinsically…

Biological Physics · Physics 2019-03-06 George Courcoubetis , Sammi Ali , Sergey V Nuzhdin , Paul Marjoram , Stephan Haas

Information theoretic analysis of large evolved programs produced by running genetic programming for up to a million generations has shown even functions as smooth and well behaved as floating point addition and multiplication loose entropy…

Neural and Evolutionary Computing · Computer Science 2021-12-03 W. B. Langdon

In complex ecosystems such as microbial communities, there is constant ecological and evolutionary feedback between the residing species and the environment occurring on concurrent timescales. Species respond and adapt to their surroundings…

Populations and Evolution · Quantitative Biology 2023-10-17 Jim Wu , David J. Schwab , Trevor GrandPre

This paper investigates the behavior of the Min-Sum decoder running on noisy devices. The aim is to evaluate the robustness of the decoder in the presence of computation noise, e.g. due to faulty logic in the processing units, which…

Information Theory · Computer Science 2014-05-27 Christiane L. Kameni Ngassa , Valentin Savin , Elsa Dupraz , David Declercq

Some biological systems operate at the critical point between stability and instability and this requires a fine-tuning of parameters. We bring together two examples from the literature that illustrate this: neural integration in the…

Optimization and Control · Mathematics 2007-05-23 Luc Moreau , Eduardo Sontag

Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…

Molecular Networks · Quantitative Biology 2009-08-26 Thimo Rohlf , Stefan Bornholdt

What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…

Systems and Control · Electrical Eng. & Systems 2022-07-12 Sebastian Mayer , Leo Francoso Dal Piccol Sotto , Jochen Garcke

How the very first nervous systems evolved remains a fundamental open question. Molecular and genomic techniques have revolutionized our knowledge of the molecular ingredients behind this transition but not yet provided a clear picture of…

Neurons and Cognition · Quantitative Biology 2017-10-31 Ronald A. J. van Elburg , Oltman O. de Wiljes , Michael Biehl , Fred A. Keijzer

Synchronization is a widespread phenomenon observed in physical, biological, and social networks, which persists even under the influence of strong noise. Previous research on oscillators subject to common noise has shown that noise can…

Adaptation and Self-Organizing Systems · Physics 2021-06-02 Zachary G. Nicolaou , Michael Sebek , Istvan Z. Kiss , Adilson E. Motter

Many biological phenomena or social events critically depend on how information evolves in complex networks. However, a general theory to characterize information evolution is yet absent. Consequently, numerous unknowns remain about the…

Biological Physics · Physics 2022-07-20 Yang Tian , Guoqi Li , Pei Sun

The automatic design of robots has existed for 30 years but has been constricted by serial non-differentiable design evaluations, premature convergence to simple bodies or clumsy behaviors, and a lack of sim2real transfer to physical…

Robotics · Computer Science 2024-05-28 Luke Strgar , David Matthews , Tyler Hummer , Sam Kriegman

Quantum systems, in general, output data that cannot be simulated efficiently by a classical computer, and hence is useful for solving certain mathematical problems and simulating quantum many-body systems. This also implies, unfortunately,…

Quantum Physics · Physics 2017-10-04 Keisuke Fujii , Masahito Hayashi