Related papers: Synchronization as a unifying mechanism for protei…
Symmetry is closely intertwined with the function, genetics, and chemical properties of multiprotein complexes. Here, we explore the relation between structural symmetry and the ability of membrane proteins to sense and induce membrane…
This paper investigates synchronization phenomena in networks of coupled oscillators governed by three-time-scale dynamical systems exhibiting canard dynamics. A mathematical framework has been developed to analyze the synchronization of…
The basic phenomenology of experimentally observed synchronization (i.e., a stochastic phase locking) of identical, beating flagella of a biflagellate alga is known to be captured well by a minimal model describing the dynamics of coupled,…
Synchronization over networks depends strongly on the structure of the coupling between the oscillators. When the coupling presents certain regularities, the dynamics can be coarse-grained into clusters by means of External Equitable…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how…
Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
Synchronization of coupled dynamical systems is a widespread phenomenon in both biological and engineered networks, and understanding this behavior is crucial for controlling such systems. Considerable research has been dedicated to…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
Globally coupled phase oscillator models, such as the Kuramoto model, exhibit spontaneous collective synchronization. Such models can be restated in terms of interactions within and between subsets of oscillators. An approximation for the…
Brain networks typically exhibit characteristic synchronization patterns where several synchronized clusters coexist. On the other hand, neurological disorders are considered to be related to pathological synchronization such as excessive…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Synchronization is observed in many natural systems, with examples ranging from neuronal activation to walking pedestrians. The models proposed by Winfree and Kuramoto stand as the classic frameworks for investigating these phenomena. The…
Co-evolutionary adaptive mechanisms are not only ubiquitous in nature, but also beneficial for the functioning of a variety of systems. We here consider an adaptive network of oscillators with a stochastic, fitness-based, rule of…