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Register a new userFCS diffusion laws on two-phases lipid membranes : experimental and Monte-carlo simulation determination of domain size
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For more than ten years now, many efforts have been done to identify and characterize nature of obstructed diffusion in model and cellular lipid membranes. Amongst all the techniques developed for this purpose, FCS, by means of determination of FCS diffusion laws, has been shown to be a very efficient approach. In this paper, FCS diffusion laws are used to probe the behavior of a pure lipid and a lipid mixture at temperatures below and above phase transitions, both numerically, using a full thermodynamic model, and experimentally. In both cases FCS diffusion laws exhibit deviation from free diffusion and reveal the existence of domains. The variation of these domains mean size with temperature is in perfect correlation with the enthalpy fluctuation.
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We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein--lipid complexes within the membrane voids, which are generated by hydrophobic mismatch or the transport of lipids by proteins.
Supported lipid bilayers have been studied intensively over the past two decades. In this work, we study the diffusion of single gold nanoparticles (GNPs) with diameter of 20 nm attached to GM1 ganglioside or DOPE lipids at different concentrations in supported DOPC bilayers. The indefinite photostability of GNPs combined with the high sensitivity of interferometric scattering microscopy (iSCAT) allows us to achieve 1.9 nm spatial precision at 1 ms temporal resolution, while maintaining long recording times. Our trajectories visualize strong transient confinements within domains as small as 20 nm, and the statistical analysis of the data reveals multiple mobilities and deviations from normal diffusion. We present a detailed analysis of our findings and provide interpretations regarding the effect of the supporting substrate and GM1 clustering. We also comment on the use of high-speed iSCAT for investigating diffusion of lipids, proteins or viruses in lipid membranes with unprecedented spatial and temporal resolution.
Studies of social and group behavior in interacting organisms require high-throughput analysis of the motion of a large number of individual subjects. Computer vision techniques offer solutions to specific tracking problems, and allow automated and efficient tracking with minimal human intervention. In this work, we adopt the open active contour model to track the trajectories of moving objects at high density. We add repulsive interactions between open contours to the original model, treat the trajectories as an extrusion in the temporal dimension, and show applications to two tracking problems. The walking behavior of Drosophila is studied at different population density and gender composition. We demonstrate that individual male flies have distinct walking signatures, and that the social interaction between flies in a mixed gender arena is gender specific. We also apply our model to studies of trajectories of gliding Myxococcus xanthus bacteria at high density. We examine the individual gliding behavioral statistics in terms of the gliding speed distribution. Using these two examples at very distinctive spatial scales, we illustrate the use of our algorithm on tracking both short rigid bodies (Drosophila) and long flexible objects (Myxococcus xanthus). Our repulsive active membrane model reaches error rates better than $5times 10^{-6}$ per fly per second for Drosophila tracking and comparable results for Myxococcus xanthus.
The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior of the DNA bundle is investigated. Experimentally, it is known that multivalent counterions have strong effect on the DNA condensation phenomenon. While tri- and tetra-valent counterions are shown to easily condense free DNA molecules in solution into toroidal bundles, the situation with divalent counterions are not as clear cut. Some divalent counterions like Mg$^{+2}$ are not able to condense free DNA molecules in solution, while some like Mn$^{+2}$ can condense them into disorder bundles. In restricted environment such as in two dimensional system or inside viral capsid, Mg$^{+2}$ can have strong effect and able to condense them, but the condensation varies qualitatively with different system, different coions. It has been suggested that divalent counterions can induce attraction between DNA molecules but the strength of the attraction is not strong enough to condense free DNA in solution. However, if the configuration entropy of DNA is restricted, these attractions are enough to cause appreciable effects. The variations among different divalent salts might be due to the hydration effect of the divalent counterions. In this paper, we try to understand this variation using a very simple parameter, the size of the divalent counterions. We investigate how divalent counterions with different sizes can leads to varying qualitative behavior of DNA condensation in restricted environments. Additionally a Grand canonical Monte-Carlo method for simulation of systems with two different salts is presented in detail.
Microbial-Induced Carbonate Precipitation (MICP) has been explored for more than a decade as a promising soil improvement technique. However, it is still challenging to predict and control the growth rate and characteristics of CaCO3 precipitates, which directly affect the engineering performance of MICP-treated soils. In this study, we employ a microfluidics-based pore scale model to observe the effect of bacterial density on the growth rate and characteristics of CaCO3 precipitates during MICP processes occurring at the sand particle scale. Results show that the precipitation rate of CaCO3 increases with bacterial density in the range between 0.6e8 and 5.2e8 cells/ml. Bacterial density also affects both the size and number of CaCO3 crystals. A low bacterial density of 0.6e8 cells/ml produced 1.1e6 crystals/ml with an average crystal volume of 8,000 um3, whereas a high bacterial density of 5.2e8 cells/ml resulted in more crystals (2.0e7 crystals/ml) but with a smaller average crystal volume of 450 um3. The produced CaCO3 crystals were stable when the bacterial density was 0.6e8 cells/ml. When the bacterial density was 4-10 times higher, the crystals were first unstable and then transformed into more stable CaCO3 crystals. This suggests that bacterial density should be an important consideration in the design of MICP protocols.
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