Related papers: Structure and function of Enterotoxigenic Escheric…
Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…
Cellular contractility, migration, and extracellular matrix (ECM) mechanics are critical for a wide range of biological processes including embryonic development, wound healing, tissue morphogenesis, and regeneration. Even though the…
We have developed a 3D off-lattice stochastic polymerization model to study subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering.…
Controlling the phases of matter is a challenge that spans from condensed materials to biological systems. Here, by imposing a geometric boundary condition, we study controlled collective motion of Escherichia coli bacteria. A circular…
Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently several high-resolution imaging techniques…
We have developed a mathematical model of regulation of expression of the Escherichia coli lac operon, and have investigated bistability in its steady-state induction behavior in the absence of external glucose. Numerical analysis of…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and…
Simulations of tethered cells in viscous sub-layers are frequently performed using the Stokes drag force, but without taking into account contributions from surface corrections, lift forces, buoyancy, the Basset force, the cells finite…
Understanding mixing and transport of passive scalars in active fluids is important to many natural (e.g. algal blooms) and industrial (e.g. biofuel, vaccine production) processes. Here, we study the mixing of a passive scalar (dye) in…
Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single…
The current management of critical size bone defects (CSBDs) remains challenging and requires multiple surgeries. To reduce the number of surgeries, wrapping a biodegradable fibrous membrane around the defect to contain the graft and carry…
The outbreak of enterohemorrhagic Escherichia coli (EHEC) in May 2011 warns the potential threats of the world vegetables trade network (VTN) in spreading fatal infectious diseases. The heterogeneous weight distribution and multi-scale…
Anaerobic digestion enables the water industry to treat wastewater as a resource for generating energy and recovering valuable by-products. The complexity of the anaerobic digestion process has motivated the development of complex models.…
Bacteria populate the colon where they replicate and migrate in response to nutrient availability. Here I model the colon bacterial population as a sandpile model, the colon-pile. Sand addition mimics bacterial replication and grains…
We have investigated the correlation between structural and transport properties in sputtered $\beta$-FeSe films grown onto SrTiO$_3$ (100). The growth parameters, such as substrate temperature and thickness, have been varied in order to…
Exocytosis is a common transport mechanism via which cells transport out non-essential macro-molecules (cargo) into the extra cellular space. ESCRT-III proteins are known to help in this. They polymerize into a conical spring like structure…
Bacterial colonization ofimplanted biomedical devicesis themain cause of healthcare-associated infections, estimated to be 8.8 million per year in Europe. Many infections originate from damaged skin, which lets microorganisms exploit…
Clathrin-mediated endocytosis (CME) is a key pathway for transporting cargo into cells via membrane vesicles. It plays an integral role in nutrient import, signal transduction, neurotransmission and cellular entry of pathogens and…
Flow-Induced Self-Assembly (FISA) is the phenomena of particle chaining in viscoelastic fluids while experiencing shear flow. FISA has a large number of applications across many fields including material science, food processing and…