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Mitochondrial function relies on the coordinated expression of mitochondrial and nuclear genes, exhibiting remarkable resilience regardless the susceptibility of mitochondrial DNA (mtDNA) to accumulate harmful mutations. A suggested…
In this work, we study non-equilibrium dynamics in Floquet conformal field theories (CFTs) in 1+1D, in which the driving Hamiltonian involves the energy-momentum density spatially modulated by an arbitrary smooth function. This generalizes…
Individuals of different types, may it be genetic, cultural, or else, with different levels of fitness often compete for reproduction and survival. A fitter type generally has higher chances of disseminating their copies to other…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling…
Extensions of linear models are very commonly used in the analysis of biological data. Whereas goodness of fit measures such as the coefficient of determination (R2) or the adjusted R2 are well established for linear models, it is not…
This paper provides synchronization conditions for networks of nonlinear systems. The components of the network (referred to as "compartments'' in this paper) are made up of an identical interconnection of subsystems, each represented as an…
While generative models have recently become ubiquitous in many scientific areas, less attention has been paid to their evaluation. For molecular generative models, the state-of-the-art examines their output in isolation or in relation to…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
Bayes' rule tells us how to invert a causal process in order to update our beliefs in light of new evidence. If the process is believed to have a complex compositional structure, we may ask whether composing the inversions of the component…
The inclusion process is a stochastic lattice gas, which is a natural bosonic counterpart of the well-studied exclusion process and has strong connections to models of heat conduction and applications in population genetics. Like the…
One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which…
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases of mild stress,…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
Conformational isomers or conformers of molecules play a decisive role in chemistry and biology. However, experimental methods to investigate chemical reaction dynamics are typically not conformer-sensitive. Here, we report on a gas-phase…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
We study a continuous-time dynamical system that models the evolving distribution of genotypes in an infinite population where genomes may have infinitely many or even a continuum of loci, mutations accumulate along lineages without…
A living cell actively generates traction forces on its environment with its actin cytoskeleton. These forces deform the cell elastic substrate which, in turn, affects the traction forces exerted by the cell and can consequently modify the…