Subcellular Processes
Rod-like bacteria maintain their cylindrical shapes with remarkable precision during growth. However, they are also capable to adapt their shapes to external forces and constraints, for example by growing into narrow or curved confinements.…
The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry,…
Modeling of ion transport via plasma membrane needs identification and quantitative understanding of the involved processes. Brief characterization of main ion transport systems of a yeast cell (Pma1, Ena1, TOK1, Nha1, Trk1, Trk2,…
The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth and survival. Sensory adaptation allows a cell to recover its sensitivity after a transient response to a shift in the…
This paper studies how patterns derived from a system of reaction-diffusion equations may vary significantly depending upon boundary and initial conditions, as well as in the spatial dependence of the coefficients involved. From an…
We discuss the implementation of a multiscale biophysico-chemical model able to cope with the main mechanisms underlying cumulative exocytosis in cells. The model is based on a diffusion equation in the presence of external forces that…
Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For…
In this paper we review and extend our earlier recent work on thermostated systems. A description of nano-biological systems by Markov chains in coordinate space in the strongly overdamped limit is presented. Characterization of the most…
It was proposed earlier that Pfcrmp (Plasmodium falciparum chloroquine resistance marker protein) may be the chloroquine's target protein in nucleus. In this communication, further evidence is presented to support the view that Pfcrmp may…
In this projecting work we propose a mass spectrometric patch-clamp equipment with the capillary performing both a local potential registration at the cell membrane and the analyte suction simultaneously. This paper provides a current…
Cellular internalization of nanoparticles requires the full wrapping of the nanoparticles by the cell membrane. This wrapping process can occur spontaneously if the adhesive interactions between the nanoparticles and the membranes are…
Recovering a stochastic process from noisy ensembles of single particle trajectories (SPTs) is resolved here using the Langevin equation as a model. The massive redundancy contained in SPTs data allows recovering local parameters of the…
Deprivation of essential nutrients can have stark consequences for many processes in a cell. We consider amino acid starvation, which can result in bottlenecks in mRNA translation when ribosomes stall due to lack of resources, i.e. tRNAs…
The physical limit with which a cell senses external ligand concentration corresponds to the perfect absorber, where all ligand particles are absorbed and overcounting of same ligand particles does not occur. Here we analyze how the lateral…
Motility is characteristic of life, but a common basis for movement has remained to be identified. Diverse systems in motion shift between two states depending on interactions that turnover at the rate of an applied cycle of force. Although…
Recent studies has revealed that Microtubules (MTs) exhibit three transition states of growth, shrinkage and pause. In this paper, we first introduce a three states random evolution model as a framework for studying MTs dynamics in three…
Influenza viruses enter a cell via endocytosis after binding to the surface. During the endosomal journey, acidification triggers a conformational change of the virus spike protein hemagglutinin (HA) that results in escape of the viral…
Protein assembly plays an important role in the regulation of biological systems. The cytoskeleton assembly activity is provided by the binding cofactors GTP (guanidine triphosphate) or ATP(adenosine triphosphate) to monomeric protein, and…
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…
Many cells contain non-centrosomal arrays of microtubules (MT), but the assembly, organisation and function of these arrays are poorly understood. We present the first theoretical model for the non-centrosomal MT cytoskeleton in…