Related papers: Asymptotics of Stochastic Protein Assembly Models
mRNA-protein assemblies play a fundamental role in forming membraneless compartments within cells, whose functions may include activating, inhibiting, and localizing reactions. Recruitment of proteins into droplets can diminish cell to cell…
Unfolded protein aggregation in cellular system is a problem causing various types of diseases depending on which type unfolded proteins aggregate. This phenomenon of aggregation may take place during production, storage, shipment or…
Self-replicability is the unique attribute observed in all the living organisms and the question how the life was physically initiated could be equivalent to the question how self-replicating informative polymers were formed in the abiotic…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
First order phase transitions proceed via nucleation. The rate of nucleation varies exponentially with the free-energy barrier to nucleation, and so is highly sensitive to variations in this barrier. In practice, very few systems are…
We propose a kinetic model for the self-aggregation by amyloid proteins. By extending several well-known models for protein aggregation, the time evolution of aggregate concentrations containing $r$ proteins, denoted $c_r(t)$, can be…
Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…
Model-based prediction of stochastic noise in biomolecular reactions often resorts to approximation with unknown precision. As a result, unexpected stochastic fluctuation causes a headache for the designers of biomolecular circuits. This…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
Nucleation is the onset of a first-order phase transition by which a metastable phase transforms into a more stable one. Such a phase transition occurs when an initial system initially in equilibrium is destabilized by the change of an…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
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…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…