Related papers: Protein overabundance is driven by growth robustne…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Quantifying the effects of amino acid mutations in proteins presents a significant challenge due to the vast combinations of residue sites and amino acid types, making experimental approaches costly and time-consuming. The Potts model has…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
The prevalence of sexual reproduction ("sex") in eukaryotes is an enigma of evolutionary biology. Sex increases genetic variation only tells its long-term superiority in essence. The accumulation of harmful mutations causes an immediate and…
Embryonic development relies on the formation of sharp, precise gene expression boundaries. In the fruit fly Drosophila melanogaster, boundary formation has been proposed to occur at a dynamical critical point. Yet, in the paradigmatic case…
We study an optimal control problem arising from a resource allocation problem in cellular metabolism. A minimalistic model that describes the production of enzymatic vs. non-enzymatic biomass components from a single nutrient source is…
Increasing model size has unlocked a dazzling array of capabilities in modern language models. At the same time, even frontier models remain vulnerable to jailbreaks and prompt injections, despite concerted efforts to make them robust. As…
Regular expression is important for many natural language processing tasks especially when used to deal with unstructured and semi-structured data. This work focuses on automatically generating regular expressions and proposes a novel…
We study a minimal model for the growth of a phenotypically heterogeneous population of cells subject to a fluctuating environment in which they can replicate (by exploiting available resources) and modify their phenotype within a given…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
We investigate the fitness advantage associated with the robustness of a phenotype against deleterious mutations using deterministic mutation-selection models of quasispecies type equipped with a mesa shaped fitness landscape. We obtain…
We derive the boundary condition for a subdiffusive particle interacting with a reactive boundary with finite reaction rate. Molecular crowding conditions, that are found to cause subdiffusion of larger molecules in biological cells, are…
Many of the existing stochastic models of gene expression contain the first-order decay reaction term that may describe active protein degradation or dilution. If the model variable is interpreted as the molecule number, and not…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
Gene regulatory networks (GRNs) are complex systems in which many genes regulate mutually to adapt the cell state to environmental conditions. In addition to function, the GRNs possess several kinds of robustness. This robustness means that…
We consider a power system with $N$ transmission lines whose initial loads (i.e., power flows) $L_1, \ldots, L_N$ are independent and identically distributed with $P_L(x)$. The capacity $C_i$ defines the maximum flow allowed on line $i$,…
Biological machine learning is often bottlenecked by a lack of scaled data. One promising route to relieving data bottlenecks is through high throughput screens, which can experimentally test the activity of $10^6-10^{12}$ protein sequences…