Christian D. Lorenz

PRECISE DETERMINATION OF THE BOND PERCOLATION THRESHOLDS AND FINITE-SIZE SCALING CORRECTIONS FOR THE SC, FCC, AND BCC LATTICES

Extensive Monte-Carlo simulations were performed to study bond percolation on the simple cubic (s.c.), face-centered cubic (f.c.c.), and body-centered cubic (b.c.c.) lattices, using an epidemic kind of approach. These simulations provide very precise values of the critical thresholds for each of the lattices: pc(s.c.) = 0.2488126 ± 0.0000005, pc(f.c.c.) = 0.1201635 ± 0.0000010, and pc(b.c.c.) = 0.1802875 ± 0.0000010. For p close to pc, the results follow the expected finite-size and scaling behavior, with values for the Fisher exponent � (2.189 ±0.002), the finite-size correction exponent (0.64 ±0.02), and the scaling function exponent � (0.445 ± 0.01) confirmed to be universal.

Precise determination of the critical percolation threshold for the three-dimensional “Swiss cheese” model using a growth algorithm

Precise values for the critical threshold for the three-dimensional “Swiss cheese” continuum percolation model have been calculated using extensive Monte Carlo simulations. These simulations used a growth algorithm and memory blocking scheme similar to what we used previously in three-dimensional lattice percolation. The simulations yield a value for the critical number density nc=0.652 960±0.000 005, which confirms recent work but extends the precision by two significant figures.

Simulations of Nanotribology with Realistic Probe Tip Models

We present the results of massively parallel molecular dynamics simulations aimed at understanding the nanotribological properties of alkylsilane self-assembled monolayers (SAMs) on amorphous silica. In contrast to studies with opposing flat plates, as found in the bulk of the simulation literature, we use a model system with a realistic AFM tip (radius of curvature ranging from 3 to 30 nm) in contact with a SAM-coated silica substrate. We compare the differences in response between systems in which chains are fully physisorbed, fully chemisorbed, and systems with a mixture of the two. Our results demonstrate that the ubiquitous JKR and DMT models do not accurately describe the contact mechanics of these systems. In shear simulations, we find that the chain length has minimal effects on both the friction force and coefficient. The tip radius affects the friction force only (i.e., the coefficient is unchanged) by a constant shift in magnitude due to the increase in pull-off force with increasing radius. We also find that at extremely low loads, on the order of 10 nN, shearing from the tip causes damage to the physisorbed monolayers by removal of molecules.

Targeting of two effector protein classes to the type III secretion system by a HpaC- and HpaB-dependent protein complex from Xanthomonas campestris pv. vesicatoria.

The Gram‐negative plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria translocates effector proteins via a specialized type III secretion (TTS) system into the host cell cytosol. The efficient secretion of many effector proteins depends on the global TTS chaperone HpaB. Here, we identified a novel export control protein, HpaC, which significantly contributes to bacterial pathogenicity. Deletion of hpaC leads to a severe reduction in secretion of effector proteins and the putative type III translocon proteins HrpF and XopA. By contrast, secretion of the TTS pilus protein HrpE is not affected. We provide experimental evidence that HpaC differentiates between two classes of effector proteins. Using an in vivo reporter assay, we found that HpaC specifically promotes the translocation of the effector proteins XopJ and XopF1 into the plant cell, whereas AvrBs3 and XopC are efficiently translocated even in the absence of HpaC. Similar findings were obtained for HpaB. Inhibition of protein synthesis suggests that HpaB is involved in the secretion of stored effector proteins. Furthermore, protein–protein interaction studies revealed that HpaB and HpaC form an oligomeric protein complex and that they interact with members of both effector protein classes and the conserved TTS system component HrcV. Taken together, our data indicate that HpaB and HpaC play a central role in recruiting TTS substrates to the secretion apparatus.

Universality of the excess number of clusters and the crossing probability function in three-dimensional percolation

Extensive Monte Carlo simulations were performed to evaluate the excess number of clusters and the crossing probability function for three-dimensional percolation on the simple cubic (s.c.), face-centred cubic (f.c.c.), and body-centred cubic (b.c.c.) lattices. Systems L L L0 with L0 L were studied for both bond (s.c., f.c.c., b.c.c.) and site (f.c.c.) percolation. The excess number of clusters Q b per unit length was confirmed to be a universal quantity with a value Q b 0:412. Likewise, the critical crossing probability in the L0 direction, with periodic boundary conditions in theLL plane, was found to follow a universal exponential decay as a function of r D L 0 =L for large r. Simulations were also carried out to find new precise values of the critical thresholds for site percolation on the f.c.c. and b.c.c. lattices, yielding pc.f:c:c:/D 0:199 2365 0:000 0010, pc.b:c:c:/D 0:245 9615 0:000 0010. We also report the value pc.s:c:/D 0:311 6080 0:000 0004 for site percolation.

Functional Characterization of the Type III Secretion ATPase HrcN from the Plant Pathogen Xanthomonas campestris pv. vesicatoria

Many gram-negative plant and animal pathogenic bacteria employ a type III secretion (T3S) system to inject effector proteins into the cytosol of eukaryotic host cells. The membrane-spanning T3S apparatus is associated with an ATPase that presumably provides the energy for the secretion process. Here, we describe the role of the predicted ATPase HrcN from the plant pathogenic bacterium Xanthomonas campestris pathovar vesicatoria. We show that HrcN hydrolyzes ATP in vitro and is essential for T3S and bacterial pathogenicity. Stability of HrcN in X. campestris pv. vesicatoria depends on the conserved HrcL protein, which interacts with HrcN in vitro and in vivo. Both HrcN and HrcL bind to the inner membrane protein HrcU and specifically localize to the bacterial membranes under T3S-permissive conditions. Protein-protein interaction studies revealed that HrcN also interacts with the T3S substrate specificity switch protein HpaC and the global T3S chaperone HpaB, which promotes secretion of multiple effector proteins. Using an in vitro chaperone release assay, we demonstrate that HrcN dissociates a complex between HpaB and the effector protein XopF1 in an ATP-dependent manner, suggesting that HrcN is involved in the release of HpaB-bound effectors. Effector release depends on a conserved glycine residue in the HrcN phosphate-binding loop, which is crucial for enzymatic activity and protein function during T3S. There is no experimental evidence that T3S can occur in the absence of the ATPase, in contrast to recent findings reported for animal pathogenic bacteria.

On the hydration of the phosphocholine headgroup in aqueous solution

The hydration of the phosphocholine headgroup in 1,2-dipropionyl-sn-glycero-3-phosphocholine (C(3)-PC) in solution has been determined by using neutron diffraction enhanced with isotopic substitution in combination with computer simulation techniques. The atomic scale hydration structure around this head group shows that both the -N(CH(3))(3) and -CH(2) portions of the choline headgroup are strongly associated with water, through a unique hydrogen bonding regime, where specifically a hydrogen bond from the C-H group to water and a strong association between the water oxygen and N(+) atom in solution have both been observed. In addition, both PO(4) oxygens (P=O) and C=O oxygens are oversaturated when compared to bulk water in that the average number of hydrogen bonds from water to both X=O oxygens is about 2.5 for each group. That water binds strongly to the glycerol groups and is suggestive that water may bind to these groups when phosophotidylcholine is embedded in a membrane bilayer.

HpaC controls substrate specificity of the Xanthomonas type III secretion system.

The Gram-negative bacterial plant pathogen Xanthomonas campestris pv. vesicatoria employs a type III secretion (T3S) system to inject bacterial effector proteins into the host cell cytoplasm. One essential pathogenicity factor is HrpB2, which is secreted by the T3S system. We show that secretion of HrpB2 is suppressed by HpaC, which was previously identified as a T3S control protein. Since HpaC promotes secretion of translocon and effector proteins but inhibits secretion of HrpB2, HpaC presumably acts as a T3S substrate specificity switch protein. Protein–protein interaction studies revealed that HpaC interacts with HrpB2 and the C-terminal domain of HrcU, a conserved inner membrane component of the T3S system. However, no interaction was observed between HpaC and the full-length HrcU protein. Analysis of HpaC deletion derivatives revealed that the binding site for the C-terminal domain of HrcU is essential for HpaC function. This suggests that HpaC binding to the HrcU C terminus is key for the control of T3S. The C terminus of HrcU also provides a binding site for HrpB2; however, no interaction was observed with other T3S substrates including pilus, translocon and effector proteins. This is in contrast to HrcU homologs from animal pathogenic bacteria suggesting evolution of distinct mechanisms in plant and animal pathogenic bacteria for T3S substrate recognition.

Forces between functionalized silica nanoparticles in solution.

To prevent the flocculation and phase separation of nanoparticles in solution, nanoparticles are often functionalized with short chain surfactants. Here we present fully atomistic molecular dynamics simulations which characterize how these functional coatings affect the interactions between nanoparticles and with the surrounding solvent. For 5-nm-diameter silica nanoparticles coated with poly(ethylene oxide) (PEO) oligomers in water, we determined the hydrodynamic drag on two approaching nanoparticles moving through solvent and on a single nanoparticle as it approaches a planar surface. In most circumstances, macroscale fluid theory accurately predicts the drag on these nanoscale particles. Good agreement is seen with Brenners analytical solutions for wall separations larger than the soft nanoparticle radius. For two approaching coated nanoparticles, the solvent-mediated (velocity independent) and lubrication (velocity-dependent) forces are purely repulsive and do not exhibit force oscillations that are typical of uncoated rigid spheres.

HpaA from Xanthomonas is a regulator of type III secretion

The Gram‐negative plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria employs a type III secretion (T3S) system to inject effector proteins into the host cell cytoplasm. Efficient secretion of several effector proteins depends on the cytoplasmic global T3S chaperone HpaB. In this study, we show that HpaB interacts with the virulence factor HpaA, which is secreted by the T3S system and translocated into the plant cell. HpaA promotes secretion of pilus, translocon and effector proteins and therefore appears to be an important control protein of the T3S system. Protein–protein interaction studies and the analysis of HpaA deletion derivatives revealed that the C‐terminal protein region, which contains a HpaB binding site, is crucial for the contribution of HpaA to T3S. Secretion of pilus and translocon proteins is not affected when HpaA is expressed as an N‐terminal deletion derivative that lacks the secretion and translocation signal. Our data suggest that binding of HpaA to HpaB within the bacterial cell favours secretion of extracellular components of the secretion apparatus. Secretion of HpaA presumably liberates HpaB and thus promotes effector protein secretion after assembly of the T3S apparatus.