Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userUsing Multiscale Molecular Dynamics Simulations to Obtain Insights into Pore Forming Toxin Mechanisms
266
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse grained MARTINI models and structure based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.
rate research
Read More
We report on the results of a molecular dynamics simulation study of binodal glassy systems, formed in the process of isochoric rapid quenching from a high-temperature fluid phase. The transition to vitreous state occurs due to concurrent spinodal decomposition and solidification of the matter. The study is focused on topographies of the porous solid structures and their dependence on temperature and average density. To quantify the pore-size distributions, we put forth a scaling relation that provides a robust data collapse in systems with high porosity. We also find that the local density of glassy phases is broadly distributed, and, with increasing average glass density, a distinct peak in the local density distribution is displaced toward higher values.
As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types of molecules are simulated in a rather large system (1356 x 1356 x 67.8 A^3, corresponding to about 3.2 million atoms). Following the sudden system expansion, a complicated interplay between phase separation in the directions perpendicular and parallel to the walls is found: in the early stages the hexadecane molecules accumulate mostly in the center of the slit pore, but as the coarsening of the structure in the parallel direction proceeds, the inhomogeneity in the perpendicular direction gets much reduced. Studying then the structure factors and correlation functions at fixed distances from the wall, the densities are essentially not conserved at these distances, and hence the behavior differs strongly from spinodal decomposition in the bulk. Some of the characteristic lengths show a nonmonotonic variation with time, and simple coarsening described by power-law growth is only observed if the domain sizes are much larger than the film thickness.
A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of alpha-quartz are well-reproduced, showing the transferability of the new potential.
The heat flux autocorrelation functions of carbon nanotubes (CNTs) with different radius and lengths is calculated using equilibrium molecular dynamics. The thermal conductance of CNTs is also calculated using the Green-Kubo relation from the linear response theory. By pointing out the ambiguity in the cross section definition of single wall CNTs, we use the thermal conductance instead of conductivity in calculations and discussions. We find that the thermal conductance of CNTs diverges with the CNT length. After the analysis of vibrational density of states, it can be concluded that more low frequency vibration modes exist in longer CNTs, and they effectively contribute to the divergence of thermal conductance.
We study pore nucleation in a model membrane system, a freestanding polymer film. Nucleated pores smaller than a critical size close, while pores larger than the critical size grow. Holes of varying size were purposefully prepared in liquid polymer films, and their evolution in time was monitored using optical and atomic force microscopy to extract a critical radius. The critical radius scales linearly with film thickness for a homopolymer film. The results agree with a simple model which takes into account the energy cost due to surface area at the edge of the pore. The energy cost at the edge of the pore is experimentally varied by using a lamellar-forming diblock copolymer membrane. The underlying molecular architecture causes increased frustration at the pore edge resulting in an enhanced cost of pore formation.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
