Related papers: Conformational selection or induced fit? New insig…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
A decision-maker must consider cofounding bias when attempting to apply machine learning prediction, and, while feature selection is widely recognized as important process in data-analysis, it could cause cofounding bias. A causal Bayesian…
A theory of aging based on the principles of the kinetics of chemical reactions and the rules of natural selection of organisms is proposed. The theory is based on a hypothesis that the biochemical processes in the organism can be described…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamic simulations. In these models, the two…
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). We further consider the problem of inferring…
Structural transition induced by a local conformational change in biomolecules is formulated based on the generalized Langevin theory for the structural fluctuation of a molecule in solution, and the linear response theory, derived by Kim…
Matching mechanisms play a central role in operations management across diverse fields including education, healthcare, and online platforms. However, experimentally comparing a new matching algorithm against a status quo presents some…
Enzyme kinetics has historically been described by deterministic models, with the Michaelis-Menten (MM) equation serving as a paradigm. However, recent experimental and theoretical advances have made it clear that stochastic fluctuations,…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
The nucleation process of polyethylene under quiescent and shear flow conditions are comparatively studied with all_atom molecular dynamical simulations. At both conditions, nucleation are demonstrated to be two_step processes, which,…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…