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We introduce a numerical scheme to evolve functional materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures and the correlations among them can be computed. As an…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
In an increasingly interconnected world, a key scientific challenge is to examine mechanisms that lead to the widespread propagation of contagions, such as misinformation and pathogens, and identify risk factors that can trigger large-scale…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
Dynamical patterns in complex networks of coupled oscillators are both of theoretical and practical interest, yet to fully reveal and understand the interplay between pattern emergence and network structure remains to be an outstanding…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the sharp differences in virus distributions across…
Proteins are shaped by gradual evolution under biophysical and functional constraints. Protein language models learn rich evolutionary constraints from large-scale sequences, and discrete diffusion-based protein language models~(\eg, DPLMs)…
Predicting the fitness impact of mutations is central to protein engineering but constrained by limited assays relative to the size of sequence space. Protein language models (pLMs) trained with masked language modeling (MLM) exhibit strong…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Log-based detection rules remain central to modern security operations, encoding domain expertise that analysts iteratively refine to balance detection coverage against alert volume. Yet while prior work has examined the evolution of…
While safety-aligned large language models (LLMs) are increasingly used as the cornerstone for powerful systems such as multi-agent frameworks to solve complex real-world problems, they still suffer from potential adversarial queries, such…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
We introduce novel sets of measures with the goal of describing dynamical properties of force networks in dense particulate systems. The presented approach is based on persistent homology and allows for extracting precise, quantitative…
Are foundation models secure against malicious actors? In this work, we focus on the image input to a vision-language model (VLM). We discover image hijacks, adversarial images that control the behaviour of VLMs at inference time, and…
Coordination of cytoplasmic flows on large scales in space and time are at the root of many cellular processes, including growth, migration or division. These flows are driven by organized contractions of the actomyosin cortex. In order to…
In past work, we developed a computational model of the evolution of symbiotic entities (Model-S), based on Conway's Game of Life. In this article, we examine three trends that biologists have observed in the evolution of symbiotes. (1)…