Related papers: A bioreactor-based architecture for in vivo model-…
A key problem toward the use of microorganisms as bio-factories is reaching and maintaining cellular communities at a desired density and composition so that they can efficiently convert their biomass into useful compounds. Promising…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Controlling microalgae cultivation, i.e., a crucial industrial topic today, is a challenging task since the corresponding modeling is complex, highly uncertain and time-varying. A model-free control setting is therefore introduced in order…
Dynamic flux balance analysis of a bioreactor is based on the coupling between a dynamic problem, which models the evolution of biomass, feeding substrates and metabolites, and a linear program, which encodes the metabolic activity inside…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
A looming challenge for agriculture is sustainable intensification of food production to feed the growing human population. Current chemical and genetic technologies used to manage plant diseases are highly vulnerable to pathogen evolution…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
When developing a biotechnological process, the microorganism is first designed, e.g., using metabolic engineering. Then, the optimum fermentation parameters are determined on a laboratory scale, and lastly, they are transferred to the…
Biomolecules composed of a limited set of chemical building blocks can co-localize into distinct, spatially segregated compartments known as biomolecular condensates. While many condensates are known to form spontaneously via phase…
We investigate optimization of an algal-bacterial consortium, where an exogenous control input modulates bacterial resource allocation between growth and synthesis of a resource that is limiting for algal growth. Maximization of algal…
The experimental control of synergistic chemomechanical dynamics of catalytically active microgels (microreactors) is a key prerequisite for the design of adaptive and biomimetic materials. Here, we report a minimalistic model of…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Bio-hybrid systems---close couplings of natural organisms with technology---are high potential and still underexplored. In existing work, robots have mostly influenced group behaviors of animals. We explore the possibilities of mixing…
Proposed here is a dynamic Monte-Carlo algorithm that is efficient in simulating dense systems of long flexible chain molecules. It expands on the configurational-bias Monte-Carlo method through the simultaneous generation of a large set of…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
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…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
Large-scale manufacturing of induced pluripotent stem cells (iPSCs) is essential for cell therapies and regenerative medicines. Yet, iPSCs form large cell aggregates in suspension bioreactors, resulting in insufficient nutrient supply and…
Bacteria live in environments that are continuously fluctuating and changing. Exploiting any predictability of such fluctuations can lead to an increased fitness. On longer timescales bacteria can "learn" the structure of these fluctuations…