Related papers: Conformational selection or induced fit? New insig…
Most sensor calibrations rely on the linearity and steadiness of their response characteristics, but practical sensors are nonlinear, and their response drifts with time, restricting their choices for adoption. To broaden the realm of…
Within a mathematical model, the metabolic process of glycolysis is studied. The general scheme of glycolysis is considered as a natural result of the biochemical evolution. By using the theory of dissipative structures, the conditions of…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while…
Weak selection, which means a phenotype is slightly advantageous over another, is an important limiting case in evolutionary biology. Recently it has been introduced into evolutionary game theory. In evolutionary game dynamics, the…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a…
Molecular isomerization kinetics in liquid solvents are determined by a complex interplay between the friction acting on a rotating dihedral due to interactions with the solvent, internal dissipation effects (also known as internal…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation…
This paper introduces a simulation preorder among lifted systems, a generalization of finite-dimensional Koopman approximations (also known as approximate immersions) to systems with inputs. It is proved that this simulation relation…
The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c)…
Matching is a widely used causal inference design that aims to approximate a randomized experiment using observational data by forming matched sets of treated and control units based on similarities in their covariates. Ideally, treated…
Bayesian model selection is a tool to decide whether the introduction of a new parameter is warranted by data. I argue that the usual sampling statistic significance tests for a null hypothesis can be misleading, since they do not take into…
To insight the relationships between the self-organizing structures of cells, such as the cell clusters, and the properties of biotissues is helpful in revealing the function and designing biomaterial. Traditional random foam model neglects…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion…
At the fundamental conceptual level, two alternatives have traditionally been considered for how mutations arise and how evolution happens: 1) random mutation and natural selection, and 2) Lamarckism. Recently, the theory of…