SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Collective Effects on Single Particle Orientational Relaxation in Slow Dipolar Liquids

Theoretical and computer simulation studies of orientational relaxation in dense molecular liquids are presented. The emphasis of the study is to understand the effects of collective orientational relaxation on the single-particle orientational dynamics. The theoretical analysis is based on a recently developed molecular hydrodynamic theory which allows a self-consistent description of both the collective and the single-particle orientational relaxation. The molecular hydrodynamic theory can be used to derive a relation between the memory function for the collective orientational correlation function and the frequency-dependent dielectric function. A novel feature of the present work is the demonstration that this collective memory function is significantly different from the single-particle rotational friction. However, a microscopic expression for the single-particle rotational friction can be derived from the molecular hydrodynamic theory where the collective memory function can be used to obtain the single-particle orientational friction. This procedure allows, us to calculate the single-particle orientational correlation function near the alpha-beta transition in the supercooled liquid. The calculated correlation function shows an interesting bimodal decay below the bifurcation temperature as the glass transition is approached from above. Brownian dynamics simulations have been carried out to check the validity of the above procedure of translating the memory function from the dielectric relaxation data. We have also investigated the following two issues important in understanding the orientational relaxation in slow liquids. First, we present an analysis of the ''orientational caging'' of translational motion. The value of the translational friction is found to be altered significantly by the orientational caging. Second, we address the question of the rank dependence of the dielectric friction using both simulation and the molecular hydrodynamic theory.

The extended Enskog operator for simple fluids with continuous potentials: single particle and collective properties

We generalized the Enskog theory originally developed for the hard-sphere fluid to fluids with continuous potentials, such as the Lennard–Jones. We derived the expression for the k and ω dependent transport coefficient matrix which enables us to calculate the transport coefficients for arbitrary length and time scales. Our results reduce to the conventional Chapman–Enskog expression in the low density limit and to the conventional k dependent Enskog theory in the hard-sphere limit. As examples, the self-diffusion of a single atom, the vibrational energy relaxation, and the activated barrier crossing dynamics problem are discussed.

Single Particle and Packed Bed Combustion in Modern Gasifier Stoves—Density Effects

This article is concerned with a study of an unusual effect due to density of biomass pellets in modern stoves based on close-coupled gasification-combustion process. The two processes, namely, flaming with volatiles and glowing of the char show different effects. The mass flux of the fuel bears a constant ratio with the air flow rate of gasification during the flaming process and is independent of particle density; char glowing process shows a distinct effect of density. The bed temperatures also have similar features: during flaming, they are identical, but distinct in the char burn (gasification) regime. For the cases, wood char and pellet char, the densities are 350, 990 kg/m(3), and the burn rates are 2.5 and 3.5 g/min with the bed temperatures being 1380 and 1502 K, respectively. A number of experiments on practical stoves showed wood char combustion rates of 2.5 +/- 0.5 g/min and pellet char burn rates of 3.5 +/- 0.5 g/min. In pursuit of the resolution of the differences, experimental data on single particle combustion for forced convection and ambient temperatures effects have been obtained. Single particle char combustion rate with air show a near-d(2) law and surface and core temperatures are identical for both wood and pellet char. A model based on diffusion controlled heat release-radiation-convection balance is set up. Explanation of the observed results needs to include the ash build-up over the char. This model is then used to explain observed behavior in the packed bed; the different packing densities of the biomass chars leading to different heat release rates per unit bed volume are deduced as the cause of the differences in burn rate and bed temperatures.

Many-Body Localization in the Presence of a Single-Particle Mobility Edge

In one dimension, noninteracting particles can undergo a localization-delocalization transition in a quasiperiodic potential. Recent studies have suggested that this transition transforms into a many-body localization (MBL) transition upon the introduction of interactions. It has also been shown that mobility edges can appear in the single particle spectrum for certain types of quasiperiodic potentials. Here, we investigate the effect of interactions in two models with such mobility edges. Employing the technique of exact diagonalization for finite-sized systems, we calculate the level spacing distribution, time evolution of entanglement entropy, optical conductivity, and return probability to detect MBL. We find that MBL does indeed occur in one of the two models we study, but the entanglement appears to grow faster than logarithmically with time unlike in other MBL systems.

Effects of particle size ratio on single particle motion in colloidal dispersions

The motion of a single Brownian particle of arbitrary size through a dilute colloidal dispersion of neutrally buoyant bath spheres of another characteristic size in a Newtonian solvent is examined in two contexts. First, the particle in question, the probe particle, is subject to a constant applied external force drawing it through the suspension as a simple model for active and nonlinear microrheology. The strength of the applied external force, normalized by the restoring forces of Brownian motion, is the Péclet number, Pe. This dimensionless quantity describes how strongly the probe is upsetting the equilibrium distribution of the bath particles. The mean motion and fluctuations in the probe position are related to interpreted quantities of an effective viscosity of the suspension. These interpreted quantities are calculated to first order in the volume fraction of bath particles and are intimately tied to the spatial distribution, or microstructure, of bath particles relative to the probe. For weak Pe, the disturbance to the equilibrium microstructure is dipolar in nature, with accumulation and depletion regions on the front and rear faces of the probe, respectively. With increasing applied force, the accumulation region compresses to form a thin boundary layer whose thickness scales with the inverse of Pe. The depletion region lengthens to form a trailing wake. The magnitude of the microstructural disturbance is found to grow with increasing bath particle size -- small bath particles in the solvent resemble a continuum with effective microviscosity given by Einstein's viscosity correction for a dilute dispersion of spheres. Large bath particles readily advect toward the minimum approach distance possible between the probe and bath particle, and the probe and bath particle pair rotating as a doublet is the primary mechanism by which the probe particle is able to move past; this is a process that slows the motion of the probe by a factor of the size ratio. The intrinsic microviscosity is found to force thin at low Péclet number due to decreasing contributions from Brownian motion, and force thicken at high Péclet number due to the increasing influence of the configuration-averaged reduction in the probe's hydrodynamic self mobility. Nonmonotonicity at finite sizes is evident in the limiting high-Pe intrinsic microviscosity plateau as a function of bath-to-probe particle size ratio. The intrinsic microviscosity is found to grow with the size ratio for very small probes even at large-but-finite Péclet numbers. However, even a small repulsive interparticle potential, that excludes lubrication interactions, can reduce this intrinsic microviscosity back to an order one quantity. The results of this active microrheology study are compared to previous theoretical studies of falling-ball and towed-ball rheometry and sedimentation and diffusion in polydisperse suspensions, and the singular limit of full hydrodynamic interactions is noted.

Second, the probe particle in question is no longer subject to a constant applied external force. Rather, the particle is considered to be a catalytically-active motor, consuming the bath reactant particles on its reactive face while passively colliding with reactant particles on its inert face. By creating an asymmetric distribution of reactant about its surface, the motor is able to diffusiophoretically propel itself with some mean velocity. The effects of finite size of the solute are examined on the leading order diffusive microstructure of reactant about the motor. Brownian and interparticle contributions to the motor velocity are computed for several interparticle interaction potential lengths and finite reactant-to-motor particle size ratios, with the dimensionless motor velocity increasing with decreasing motor size. A discussion on Brownian rotation frames the context in which these results could be applicable, and future directions are proposed which properly incorporate reactant advection at high motor velocities.

Single-particle probing of edge-state formation in a graphene nanoribbon

We investigate the effect of a perpendicular magnetic field on the single-particle charging spectrum of a graphene quantum dot embedded inline with a nanoribbon. We observe uniform shifts in the single-particle spectrum which coincide with peaks in the magnetoconductance, implicating Landau level condensation and edge state formation as the mechanism underlying magnetic field-enhanced transmission through graphene nanostructures. The experimentally determined ratio of bulk to edge states is supported by single-particle band-structure simulations, while a fourfold beating of the Coulomb blockade transmission amplitude points to many-body interaction effects during Landau level condensation of the ν=0 state. © 2012 American Physical Society.

Collective and single-particle excitations in coupled quantum wires in magnetic fields

The full spectra of magnetoplasmons and single-particle excitations are obtained of coupled one-dimensional electron gases in parallel semiconductor quantum wires with tunneling. We show the effects of the interwire Coulomb interaction and the tunneling, as well as the magnetic-field-induced localization on the elementary excitations in symmetric and asymmetric coulped quantum wire structures. The interacton and resonance between the plasmon and the intersubband single-particle excitations are found in magnetic fields.

Shell model study of single-particle and collective structure in neutron-rich Cr isotopes

The structure of neutron-rich Cr isotopes is systematically investigated by using the spherical shell model. The calculations reproduce well the known energy levels for the even-even Cr52-62 and odd-mass Cr53-59 nuclei, and predict a lowering of excitation energies around neutron number N = 40. The calculated B(E2; 2(1)(+) -> 0(1)(+)) systematics shows a pronounced collectivity around N = 40; a similar characteristic behavior has been suggested for Zn and Ge isotopes. Causes for the sudden drop of the 9/2(1)(+) energy in Cr-59 and the appearance of very low 0(2)(+) states around N = 40 are discussed. We also predict a new band with strong collectivity built on the 0(2)(+) state in the N = 40 isotope Cr-64.