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Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown…

Biomaterial systems have allowed for the in vitro production of complex, emergent tissue behaviors that were not possible with conventional 2D culture systems allowing for analysis of the normal development as well as disease processes. We…

The control of manufacturing processes must satisfy high quality and efficiency requirements while meeting safety requirements. A broad spectrum of monitoring and control strategies, such as model- and optimization-based controllers, are…

Over the last decade, significant progress has been made in understanding complex biological systems, however there have been few attempts at incorporating this knowledge into nature inspired optimization algorithms. In this paper, we…

Can we allow humans to pick among different, yet reasonably similar, decisions? Are we able to construct optimization problems whose outcome are sets of feasible, close-to-optimal decisions for human users to pick from, instead of a single,…

Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…

Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of…

As automatic optimization techniques find their way into industrial applications, the behavior of many complex systems is determined by some form of planner picking the right actions to optimize a given objective function. In many cases,…

A challenge in global change biology is to predict how species will respond to future environmental change and to manage these responses. To make such predictions and management actions robust to novel futures, we need to accurately…

Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…

Living systems self-organize in ways that conventional physical frameworks-based on forces, energies, and continuous fields-cannot fully capture. Processes like gene regulation and cellular decision-making involve rule-based logic and…

The design of control systems for the spatial self-organization of mobile agents is an open challenge across several engineering domains, including swarm robotics and synthetic biology. Here, we propose a bio-inspired leader-follower…

Technology is increasingly shaping our social structures and is becoming a driving force in altering human biology. Besides, human activities already proved to have a significant impact on the Earth system which in turn generates complex…

Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…

Combining a spatiotemporal, multi-agent based model of a foraging ecosystem with linear, genetically programmed rules for the agents' behaviors results in implicit, endogenous, objective functions and selection algorithms based on "natural…

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…

Self-organized criticality has been proposed to be a universal mechanism for the emergence of scale-free dynamics in many complex systems, and possibly in the brain. While such scale-free patterns were identified experimentally in many…

One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…

The search for universal laws that help establish a relationship between dynamics and computation is driven by recent expansionist initiatives in biologically inspired computing. A general setting to understand both such dynamics and…

In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…