Related papers: Ultrasensitivity and sharp threshold theorems for …
Iron-sulfur clusters conduct a wide variety of biochemical reactions that are conserved across all domains of life. The hyperfine structure of reactive ligands of these clusters can be studied experimentally and theoretically by means of…
Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding,…
Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior…
Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be…
We address characterization of many-body superradiant systems and establish a fundamental connection between quantum criticality and the possibility of locally estimating the coupling constant, i.e extracting its value by probing only a…
We put forward a phenomenological theory for entanglement dynamics in monitored quantum many-body systems with well-defined quasiparticles. Within this theory entanglement is carried by ballistically propagating non-Hermitian quasiparticles…
Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Multisite protein phosphorylation plays a prominent role in intracellular processes like signal transduction, cell-cycle control and nuclear signal integration. Many proteins are phosphorylated in a sequential and distributive way at more…
The parameter region of multistationarity of a reaction network contains all the parameters for which the associated dynamical system exhibits multiple steady states. Describing this region is challenging and remains an active area of…
The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and…
We illuminate the many-body effects underlying the structure, formation, and dissolution of cellular adhesion domains in the presence and absence of forces. We consider mixed Glauber-Kawasaki dynamics of a two-dimensional model of…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
Biochemical systems are inherently stochastic, particularly those with small-molecule populations. The spatial distribution of molecules plays a critical role and requires the inclusion of spatial coordinates in their analysis. Stochastic…
Sensitive detection of low-abundance molecular targets is widely assumed to require enzymatic amplification, such as PCR, to achieve low detection limits. In amplification-free platforms, sensitivity is traditionally constrained by…
We investigate the dynamics of a quantum system subjected to a time-dependent and conditional resetting protocol. Namely, we ask: what happens when the unitary evolution of the system is repeatedly interrupted at random time instants with…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Limits on a system's response to external perturbations inform our understanding of how physical properties can be shaped by microscopic characteristics. Here, we derive constraints on the steady-state nonequilibrium response of physical…
We introduce a new measure of the structure of a liquid which is the softness of the mean-field potential developed by us earlier. We find that this softness is sensitive to small changes in the structure. We then study its correlation with…
Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many…