亚细胞过程
In this paper, we develop further the theory of thermostated systems along the lines of our earlier paper. Two results are highlighted: 1) in the Markov limit of the contracted description, a least dissipation of Helmholtz free energy…
In cells, most of cargos are transported by motor proteins along microtubule. Biophysically, unidirectional motion of large number of motor proteins along a single track can be described by totally asymmetric simple exclusion process…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Mitochondrial research is important to ageing, apoptosis, and mitochondrial diseases. In previous works, mitochondria are usually stimulated indirectly by proapoptotic drugs to study mitochondrial development, which is in lack of…
Plasmodium falciparum aquaglyceroporin (PfAQP) is a multifunctional channel protein in the plasma membrane of the malarial parasite that causes the most severe form of malaria infecting more than a million people a year. Finding a novel way…
Epigenetics has captured the attention of scientists in the past decades, yet its scope has been continuously changing. In this paper, we give an overview on how and why its definition has evolved and suggest several clarification on the…
In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually…
Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to…
We present an experimentally guided, bi-phasic, multi-species ionic gel model to compare and make quantitative predictions on the viscoelastic properties of healthy mucus versus Cystic-Fibrosis infected mucus. The mixture theory consists of…
The aim of this paper is to give an introductory review of the cryoelectron microscopy as a complex data source for the most of the system biology branches, including the most perspective non-local approaches known as "localomics" and…
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene,…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…
A microtubule (MT) is a hollow tube of approximately 25 nm diameter. The two ends of the tube are dissimilar and are designated as `plus' and `minus' ends. Motivated by the collective push and pull exerted by a bundle of MTs during…
We formulate and analyze a theoretical model for the regulation of microtubule (MT) polymerization dynamics by the signaling proteins Rac1 and stathmin. In cells, the MT growth rate is inhibited by cytosolic stathmin, which, in turn, is…
We introduce a model for microtubule mechanics containing lateral bonds between dimers in neighboring protofilaments, bending rigidity of dimers, and repulsive interactions between protofilaments modeling steric constraints to investigate…
Endocytosis underlies many cellular functions including signaling and nutrient uptake. The endocytosed cargo gets redistributed across a dynamic network of endosomes undergoing fusion and fission. Here, a theoretical approach is reviewed…
Experiments show that cellular uptake of nanoparticles, via receptor-mediated endocytosis, strongly depends on nanoparticle size. There is an optimal size, approximately 50 nm in diameter, at which cellular uptake is the highest. In…
The molecular chaperone Hsp70 plays a central role in the import of cytoplasmic proteins into organelles, driving their translocation by binding them from the organellar interior. Starting from the experimentally-determined structure of the…
Ion transport is the major determining factor of salinity tolerance in plants. A simple scheme of a plant cell with ion fluxes provides basic understanding of ion transport and the corresponding changes of ion concentrations under salinity.…
We demonstrate how nanojunctions between lysosomes and sarcoplasmic reticulum (L-SR junctions) serve to couple lysosomal activation to regenerative, ryanodine receptor-mediated cellular calcium (Ca2+) waves. In pulmonary artery smooth…