Related papers: Dynamical hysteresis in multisite protein modifica…
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or more positive steady states with the same conserved quantities). Although deciding multistationarity for a polynomial dynamical system is an…
A theory is developed of the time-dependent magnetization of the metacrystal composed of magnetoferritin macromolecules. Such superstructures, comprising up to several millions of superparamagnetic nanoparticles encapsulated in protein…
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…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…
We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…
Cells achieve size homeostasis by regulating their division timing based on their size, added size, and cell cycle time. Previous research under steady-state conditions demonstrated the robustness of these mechanisms. However, their dynamic…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…
The mechanical properties of cells, which influence the properties of the tissue they belong to, are controlled by various mechanisms. Bi et al. theoretically demonstrated that density-independent rigidity transition occurs in…
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, one can change e.g. binding affinities, control allostery or temper with complex…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…
We briefly introduce hysteresis in spatially extended systems and the dynamic phase transition observed as the frequency of the oscillating field increases beyond a critical value. Hysteresis and the decay of metastable phases are closely…
The hysteresis or internal friction in the deformation of crystalline solids stressed cyclically is studied from the viewpoint of collective dislocation dynamics. Stress-controlled simulations of a dislocation dynamics model at various…
We study hysteresis for a two-dimensional, spin-1/2, nearest-neighbor, kinetic Ising ferromagnet in an oscillating field, using Monte Carlo simulations and analytical theory. Attention is focused on small systems and weak field amplitudes…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
We have studied the mobility of the folding catalyst, protein disulphide-isomerase (PDI), by molecular dynamics and by a rapid approach based on flexibility. We analysed our simulations using measures of backbone movement, relative…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…