Related papers: Thermodynamic pathways to genome spatial organizat…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
We propose a mathematical kinetic framework to investigate interactions between tumor cells and the immune system, focusing on the spatial dynamics of tumor progression and immune responses. We develop two kinetic models: one describes a…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Nucleocytoplasmic transport is essential for cellular function, presenting a canonical example of rapid molecular sorting inside cells. It consists of a coordinated interplay between import/export of molecules in/out the cell nucleus. Here,…
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of…
The contributions of active deformation dynamics in cell nuclei to the intra-nuclear positioning of hetero- and euchromatin are investigated. We analyzed the behaviors of model chains containing two types of regions, one with high and the…
Migratory and tissue resident cells exhibit highly branched morphologies to perform their function and to adapt to the microenvironment. Immune cells, for example, display transient branched shapes while exploring the surrounding tissues.…
The migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Cell invasion and spatial pattern formation are two distinct manifestations of cellular self-organisation in development, regeneration, and disease. Here, we develop and analyse a unified theoretical framework that links these two seemingly…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
The large-scale organization of complex networks, both natural and artificial, has shown the existence of highly heterogeneous patterns of organization. Such patterns typically involve scale-free degree distributions and small world,…
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…
Living systems are thermodynamically open but closed in their organization. In other words, even though their material components turn over constantly, a material-independent property persists, which we call organization. Moreover,…
Bacterial colonies growing on surfaces are shaped by mechanical stresses transmitted through the community, governed by the balance between cell growth and steric and cell-substrate interactions. Using overdamped dynamics simulations of…