Related papers: Bistable protein distributions in rod-shaped bacte…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
Diverse processes--e.g. bioremediation, biofertilization, and microbial drug delivery--rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown…
The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
We analyze the governing partial differential equations of a model of pole-to-pole oscillations of the MinD protein in a bacterial cell. The sensitivity to extrinsic noise in the parameters of the model is explored. Our analysis shows that…
Experiments have found that diffusion in metabolically active cells is much faster than in dormant cells, especially for large particles. However, the mechanism of this size-dependent diffusion enhancement in living cells is still unclear.…
Directed growth, anisotropic cell shapes, and confinement drive self-organization in multicellular systems. We investigate the influence of particle shape on the distribution and dynamics of nematic microdomains in a minimal in-silico model…
Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms of rod-shaped bacteria were observed at single-cell resolution and shown to develop from a disordered, two-dimensional layer of founder cells into a…
We derive a model describing spatio-temporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
Cells actively regulate their size during the cell cycle to maintain volume homeostasis across generations. While various mathematical models of cell size regulation have been proposed to explain how this is achieved, relating these models…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
We investigate pores in fluid membranes by molecular dynamics simulations of an amphiphile-solvent mixture, using a molecular coarse-grained model. The amphiphilic membranes self-assemble into a lamellar stack of amphiphilic bilayers…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…
Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…