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Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
To make sense of their surroundings, intelligent systems must transform complex sensory inputs to structured codes that are reduced to task-relevant information such as object category. Biological agents achieve this in a largely autonomous…
We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute…
Collective cellular movement plays a crucial role in many processes fundamental to health, including development, reproduction, infection, wound healing, and cancer. The emergent dynamics that arise in these systems are typically thought to…
There is growing recognition in both the experimental and modelling literature of the importance of spatial structure to the dynamics of viral infections in tissues. Aided by the evolution of computing power and motivated by recent…
The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Masked AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various…
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…
Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock…
The host immune response can often efficiently suppress a virus infection, which may lead to selection for immune-resistant viral variants within the host. For example, during HIV infection, an array of CTL immune response populations…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
This chapter investigates the evolutionary ecology of software, focusing on the symbiotic relationship between software and innovation. An interplay between constraints, tinkering, and frequency-dependent selection drives the complex…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
The experiments involving a slider moving on top of granular media consisting of photoelastic particles in two dimensions have uncovered elaborate dynamics that may vary from continuous motion to crackling, periodic motion, and stick-slip…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
Designing controllers for robot swarms is challenging, because human developers have typically no good understanding of the link between the details of a controller that governs individual robots and the swarm behavior that is an indirect…
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
Most studies of disease spreading consider the underlying social network as obtained without the contagion, though epidemic influences people's willingness to contact others: A "friendly" contact may be turned to "unfriendly" to avoid…
The effective mixing behavior of solutes in porous media is fundamentally connected to the development of a local mixing interface between the two initial solutions, which is characterized by a complex lamellar structure. The deformation of…