Related papers: Directed Evolution of Microorganisms for Engineere…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
Hierarchically modular organization is a canonical network topology that is evolutionarily conserved in the nervous systems of animals. Within the network, neurons form directional connections defined by the growth of their axonal…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
With conventional silicon-based computing approaching its physical and efficiency limits, biocomputing emerges as a promising alternative. This approach utilises biomaterials such as DNA and neurons as an interesting alternative to data…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…
Active systems of self-propelled agents, e.g., birds, fish, and bacteria, can organize their collective motion into myriad autonomous behaviors. Ubiquitous in nature and across length scales, such phenomena are also amenable to artificial…
Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods.…
Many research fields, reaching from social networks and epidemiology to biology and physics, have experienced great advance from recent developments in random graphs and network theory. In this paper we propose to view percolation on a…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
Understanding how living organisms spontaneously develop complex functional structures inspires innovative approaches in engineering design. Here, we introduce a decentralized generative model based on morphogenesis to autonomously grow…
We introduce EvoFlows, a variable-length protein sequence-to-sequence modeling approach designed for protein engineering. Existing protein language models are poorly suited for optimization tasks: autoregressive models require full sequence…
Creating autonomous, self-supporting, self-replicating, sustainable systems is a great challenge. To some extent, understanding life means not only being able to create it from scratch, but also improving, supporting, saving it, or even…
The process of self-morphing in curved surfaces found in nature, such as with the growth of flowers and leaves, has generated interest in the study of self-morphing bilayers, which has been used in many soft robots or switchers. However,…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…
Protein evolution through amino acid mutations is a cornerstone of life sciences. Recent advances in protein language models have shown rich evolutionary patterns, offering unprecedented potential for in-silicon directed evolution. However,…
The recent interest in using microorganisms for biofuels is motivation enough to study bioconvection and cell dispersion in tubes subject to imposed flow. To optimize light and nutrient uptake, many microorganisms swim in directions biased…