Related papers: Tunable kinetic proofreading in a model with molec…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
Finetuning can significantly modify the behavior of large language models, including introducing harmful or unsafe behaviors. To study these risks, researchers develop model organisms: models finetuned to exhibit specific known behaviors…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence,…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To…
When mathematicians present proofs they usually adapt their explanations to their didactic goals and to the (assumed) knowledge of their addressees. Modern automated theorem provers, in contrast, present proofs usually at a fixed level of…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
Double phosphorylation of protein kinases is a common feature of signalling cascades. This motif may reduce cross-talk between signalling pathways, as the second phosphorylation site allows for proofreading, especially when phosphorylation…
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a…
In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this…
In contrast to engineering applications, in which the structure of control laws are designed to satisfy prescribed function requirements, in biology it is often necessary to infer gene-circuit function from incomplete data on gene-circuit…
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologically relevant rates with remarkable precision and efficiency.…
Geometric frustration appears in a broad range of systems, generally emerging as disordered ground configurations, thereby impeding understanding of the phenomenon's underlying mechanics. We report on a continuum system featuring locally…
Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities…
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the…
Adapting pre-trained models to specialized tasks often leads to catastrophic forgetting, where new knowledge overwrites foundational capabilities. Existing methods either compromise performance on the new task or struggle to balance…
Despite the increasing effectiveness of language models, their reasoning capabilities remain underdeveloped. In particular, causal reasoning through counterfactual question answering is lacking. This work aims to bridge this gap. We first…
The wayward quality of continuous prompts stresses the importance of their interpretability as unexpected and unpredictable behaviors appear following training, especially in the context of large language models automating people-sensitive…