Coarse-Grained Lattice Monte Carlo Simulations with Continuous Interaction Potentials

A coarse-grained lattice Metropolis Monte Carlo (CG-MMC) method is presented for simulating fluid systems described by standard molecular force fields. First, a thermodynamically consistent coarse-grained interaction potential is obtained numerically and automatically from a continuous force field such as Lennard-Jones. The coarse-grained potential then is used to driveCG-MMC simulations of vapor-liquid equilibrium in Lennard-Jones, square-well, and simple point chargewater systems. The CG-MMC predicts vapor-liquid phase envelopes, as well as the particle density distributions in both the liquid and vapor phases, in excellent agreement with full-resolution Monte Carlo simulations, at a fraction of the computational cost

Novel insights into host-fungal pathogen interactions derived from live-cell imaging

Acknowledgments The authors acknowledge funding from the Wellcome Trust (080088, 086827, 075470 and 099215) including a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377 and FP7-2007–2013 grant agreement HEALTH-F2-2010-260338–ALLFUN to NARG.Peer reviewedPublisher PD

Coarse-grained lattice kinetic Monte Carlo simulation of systems of strongly interacting particles

A general approach is presented for spatially coarse-graining lattice kinetic Monte Carlo (LKMC) simulations of systems containing strongly interacting particles. While previous work has relied on approximations that are valid in the limit of weak interactions, here we show that it is possible to compute coarse-grained transition rates for strongly interacting systems without a large computational burden. A two-dimensional square lattice is employed on which a collection of (supersaturated) strongly interacting particles is allowed to reversibly evolve into clusters. A detailed analysis is presented of the various approximations applied in LKMC coarse graining, and a number of numerical closure rules are contrasted and compared. In each case, the overall cluster size distribution and individual cluster structures are used to assess the accuracy of the coarse-graining approach. The resulting closure approach is shown to provide an excellent coarse-grained representation of the systems considered in this study

On-lattice kinetic Monte Carlo simulations of point defect aggregation in entropically influenced crystalline systems

An on-lattice kinetic Monte Carlo model of vacancy aggregation in crystalline silicon is parametrized using direct regression to evolution data from nonequilibrium molecular dynamics simulations. The approach bypasses the need to manually compute an energy barrier for each possible transition and leads to an excellent, robust representation of the molecular dynamics data. We show that the resulting lattice kinetic Monte Carlo model correctly captures the behavior of the real, continuous space system by properly accounting for continuous space entropic effects, which are often neglected in lattice-based models of atomistic processes. These contributions are particularly important at the high temperatures relevant to many steps in semiconductor materials processing

Confined jet mixing in the entrance of a tubular reactor

The equations for the conservation of momentum and mass were solved numerically for the region downstream from the exit of an axial jet into a confined annular stream of the same fluid. An implicit, alternating direction method was used. Numerical results were obtained for radius ratios of 0.281, 0.470, and 0.563 over a range of jet-to-annular velocities from 0.85 to 2.77. The values for the limiting case of the entrance region in pipe flow are in good agreement with the values of Christiansen and Lemmon and Ventras, Duda, and Bargeron. Solution of the equations for the conservation of chemical components produced results for component transfer in agreement with the experimental compositions obtained by Wood for jet mixing. Representative calculations were carried out for a chemical reaction. The results indicate the efficiency of the mixing process for this type of reactor. Experiments were carried out with water and dye to define the conditions under which the assumption of steady, laminar jet mixing is valid. The experiments also indicated the conditions and location of turbulent breakup of the jet.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/37362/1/690170338_ftp.pd

Software for analytical nonlinear controller design

Proceedings of the 2006 American Control Conference, pp. 4848-4853.This paper presents a new software package that carries out symbolic manipulations to generate automatically analytical, model-based controllers and subsequently test the performance of the designed controller implemented on the process model. The software package has a user-friendly interface that was developed using Visual Basic and linked to MATHEMATICA using MathLink. The user enters the process model (set of ordinary differential and algebraic equations), and the software generates an analytical modelbased controller (set of ordinary differential and algebraic equations), that can be in FORTRAN, C, or MATLAB format. The application and implementation of the software package are shown using a chemical reactor example

Identification of Candida glabrata genes involved in pH modulation and modification of the phagosomal environment in macrophages

notes: PMCID: PMC4006850types: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov'tCandida glabrata currently ranks as the second most frequent cause of invasive candidiasis. Our previous work has shown that C. glabrata is adapted to intracellular survival in macrophages and replicates within non-acidified late endosomal-stage phagosomes. In contrast, heat killed yeasts are found in acidified matured phagosomes. In the present study, we aimed at elucidating the processes leading to inhibition of phagosome acidification and maturation. We show that phagosomes containing viable C. glabrata cells do not fuse with pre-labeled lysosomes and possess low phagosomal hydrolase activity. Inhibition of acidification occurs independent of macrophage type (human/murine), differentiation (M1-/M2-type) or activation status (vitamin D3 stimulation). We observed no differential activation of macrophage MAPK or NFκB signaling cascades downstream of pattern recognition receptors after internalization of viable compared to heat killed yeasts, but Syk activation decayed faster in macrophages containing viable yeasts. Thus, delivery of viable yeasts to non-matured phagosomes is likely not triggered by initial recognition events via MAPK or NFκB signaling, but Syk activation may be involved. Although V-ATPase is abundant in C. glabrata phagosomes, the influence of this proton pump on intracellular survival is low since blocking V-ATPase activity with bafilomycin A1 has no influence on fungal viability. Active pH modulation is one possible fungal strategy to change phagosome pH. In fact, C. glabrata is able to alkalinize its extracellular environment, when growing on amino acids as the sole carbon source in vitro. By screening a C. glabrata mutant library we identified genes important for environmental alkalinization that were further tested for their impact on phagosome pH. We found that the lack of fungal mannosyltransferases resulted in severely reduced alkalinization in vitro and in the delivery of C. glabrata to acidified phagosomes. Therefore, protein mannosylation may play a key role in alterations of phagosomal properties caused by C. glabrata.Deutsche ForschungsgemeinschaftNational Institutes for HealthWellcome TrustBBSR

Parasite fate and involvement of infected cells in the induction of CD4+ and CD8+ T cell responses to Toxoplasma gondii

During infection with the intracellular parasite Toxoplasma gondii, the presentation of parasite-derived antigens to CD4+ and CD8+ T cells is essential for long-term resistance to this pathogen. Fundamental questions remain regarding the roles of phagocytosis and active invasion in the events that lead to the processing and presentation of parasite antigens. To understand the most proximal events in this process, an attenuated non-replicating strain of T. gondii (the cpsII strain) was combined with a cytometry-based approach to distinguish active invasion from phagocytic uptake. In vivo studies revealed that T. gondii disproportionately infected dendritic cells and macrophages, and that infected dendritic cells and macrophages displayed an activated phenotype characterized by enhanced levels of CD86 compared to cells that had phagocytosed the parasite, thus suggesting a role for these cells in priming naïve T cells. Indeed, dendritic cells were required for optimal CD4+ and CD8+ T cell responses, and the phagocytosis of heat-killed or invasion-blocked parasites was not sufficient to induce T cell responses. Rather, the selective transfer of cpsII-infected dendritic cells or macrophages (but not those that had phagocytosed the parasite) to naïve mice potently induced CD4+ and CD8+ T cell responses, and conferred protection against challenge with virulent T. gondii. Collectively, these results point toward a critical role for actively infected host cells in initiating T. gondii-specific CD4+ and CD8+ T cell responses

The Facultative Intracellular Pathogen Candida glabrata Subverts Macrophage Cytokine Production and Phagolysosome Maturation

Abstract Although Candida glabrata is an important human pathogenic yeast, its pathogenicity mechanisms are largely unknown. Immune evasion strategies seem to play key roles during infection, since very little inflammation is observed in mouse models. Furthermore, C. glabrata multiplies intracellularly after engulfment by macrophages. In this study, we sought to identify the strategies that enable C. glabrata to survive phagosome biogenesis and antimicrobial activities within human monocyte-derived macrophages. We show that, despite significant intracellular proliferation, macrophage damage or apoptosis was not apparent, and production of reactive oxygen species was inhibited. Additionally, with the exception of GM-CSF, levels of pro- and anti-inflammatory cytokines were only marginally increased. We demonstrate that adhesion to and internalization by macrophages occur within minutes, and recruitment of endosomal early endosomal Ag 1 and lysosomal-associated membrane protein 1 indicates phagosome maturation. However, phagosomes containing viable C. glabrata, but not heat-killed yeasts, failed to recruit cathepsin D and were only weakly acidified. This inhibition of acidification did not require fungal viability, but it had a heat-sensitive surface attribute. Therefore, C. glabrata modifies the phagosome into a nonacidified environment and multiplies until the host cells finally lyse and release the fungi. Our results suggest persistence of C. glabrata within macrophages as a possible immune evasion strategy.</jats:p