Elimination of MHD current sheets by modifications to the plasma wall in a fixed boundary model.

Models of magnetohydrodynamic (MHD) equilibia that for computational convenience assume the existence of a system of nested magnetic flux surfaces tend to exhibit singular current sheets. These sheets are located on resonant flux surfaces that are associated with rational values of the rotational transform. We study the possibility of eliminating these singularities by suitable modifications of the plasma boundary, which we prescribe in a fixed boundary setting. We find that relatively straightforward iterative procedures can be used to eliminate weak current sheets that are generated at resonant flux surfaces by the nonlinear interactions of resonating wall harmonics. These types of procedures may prove useful in the design of fusion devices with configurations that enjoy improved stability and transport properties.

Effect of vacancy creation and annihilation on grain boundary motion.

Interaction of vacancies with grain boundaries (GBs) is involved in many processes occurring in materials, including radiation damage healing, diffusional creep, and solid-state sintering. We analyze a model describing a set of processes occurring at a GB in the presence of a non-equilibrium, non-homogeneous vacancy concentration. Such processes include vacancy diffusion toward, away from, and across the GB, vacancy generation and absorption at the GB, and GB migration. Numerical calculations within this model reveal that the coupling among the different processes gives rise to interesting phenomena, such as vacancy-driven GB motion and accelerated vacancy generation/absorption due to GB motion. The key combinations of the model parameters that control the kinetic regimes of the vacancy-GB interactions are identified via a linear stability analysis. Possible applications and extensions of the model are discussed.

Model reduction of rigid-body molecular dynamics via generalized multipole potentials.

Motivated by the challenges of uncertainty quantification for coarse-grained (CG) molecular dynamics, we investigate the role of perturbation theory in model reduction of classical systems. In particular, we consider the task of coarse-graining rigid bodies in the context of generalized multipole potentials that have controllable levels of accuracy relative to their atomistic counterparts. We show how the multipole framework yields a hierarchy of models that systematically connects a CG "point molecule" approximation to the exact dynamics. We use these results to understand when and how the CG models fail to describe atomistic dynamics at the trajectory level and develop asymptotic error estimates for approximate molecular potential energies. Implications for other model-reduction strategies are also discussed. Key findings of this work are that (i) omitting rotational energy introduces significant error when coarse-graining and (ii) attention to symmetry can improve accuracy of "point-molecule" approximations. Analytical derivations and numerical results support these conclusions. Relevance to nonrigid bodies is also discussed.

Numerical Analysis and Simulation for a Generalized Planar Ginzburg-Landau Equation in a Circular Geometry.

In this paper, a numerical scheme for a generalized planar Ginzburg-Landau energy in a circular geometry is studied. A spectral-Galerkin method is utilized, and a stability analysis and an error estimate for the scheme are presented. It is shown that the scheme is unconditionally stable. We present numerical simulation results that have been obtained by using the scheme with various sets of boundary data, including those the form u(θ) = exp(idθ), where the integer d denotes the topological degree of the solution. These numerical results are in good agreement with the experimental and analytical results. Results include the computation of bifurcations from pure bend or splay patterns to spiral patterns for d = 1, and computations of metastable or unstable higher-energy solutions as well as the lowest energy ground state solutions for values of d ranging from two to five.

On the Stability of Rotating Drops.

We consider the equilibrium and stability of rotating axisymmetric fluid drops by appealing to a variational principle that characterizes the equilibria as stationary states of a functional containing surface energy and rotational energy contributions, augmented by a volume constraint. The linear stability of a drop is determined by solving the eigenvalue problem associated with the second variation of the energy functional. We compute equilibria corresponding to both oblate and prolate shapes, as well as toroidal shapes, and track their evolution with rotation rate. The stability results are obtained for two cases: (i) a prescribed rotational rate of the system ("driven drops"), or (ii) a prescribed angular momentum ("isolated drops"). For families of axisymmetric drops instabilities may occur for either axisymmetric or non-axisymmetric perturbations; the latter correspond to bifurcation points where non-axisymmetric shapes are possible. We employ an angle-arc length formulation of the problem which allows the computation of equilibrium shapes that are not single-valued in spherical coordinates. We are able to illustrate the transition from spheroidal drops with a strong indentation on the rotation axis to toroidal drops that do not extend to the rotation axis. Toroidal drops with a large aspect ratio (major radius to minor radius) are subject to azimuthal instabilities with higher mode numbers that are analogous to the Rayleigh instability of a cylindrical interface. Prolate spheroidal shapes occur if a drop of lower density rotates within a denser medium; these drops appear to be linearly stable. This work is motivated by recent investigations of toroidal tissue clusters that are observed to climb conical obstacles after self-assembly [Nurse et al., Journal of Applied Mechanics 79 (2012) 051013].

Equilibrium and stability of axisymmetric drops on a conical substrate under gravity.

Motivated by recent investigations of toroidal tissue clusters that are observed to climb conical obstacles after self-assembly [Nurse et al., Journal of Applied Mechanics 79 (2012) 051013], we study a related problem of the determination of the equilibrium and stability of axisymmetric drops on a conical substrate in the presence of gravity. A variational principle is used to characterize equilibrium shapes that minimize surface energy and gravitational potential energy subject to a volume constraint, and the resulting Euler equation is solved numerically using an angle/arclength formulation. The resulting equilibria satisfy a Laplace-Young boundary condition that specifies the contact angle at the three-phase trijunction. The vertical position of the equilibrium drops on the cone is found to vary significantly with the dimensionless Bond number that represents the ratio of gravitational and capillary forces; a global force balance is used to examine the conditions that affect the drop positions. In particular, depending on the contact angle and the cone half-angle, we find that the vertical position of the drop can either increase ("the drop climbs the cone") or decrease due to a nominal increase in the gravitational force. Most of the equilibria correspond to upward-facing cones, and are analogous to sessile drops resting on a planar surface; however we also find equilibria that correspond to downward facing cones, that are instead analogous to pendant drops suspended vertically from a planar surface. The linear stability of the drops is determined by solving the eigenvalue problem associated with the second variation of the energy functional. The drops with positive Bond number are generally found to be unstable to non-axisymmetric perturbations that promote a tilting of the drop. Additional points of marginal stability are found that correspond to limit points of the axisymmetric base state. Drops that are far from the tip are subject to azimuthal instabilities with higher mode numbers that are analogous to the Rayleigh instability of a cylindrical interface. We have also found a range of completely stable solutions that correspond to small contact angles and cone half-angles.

The viral tropism of two distinct oncolytic viruses, reovirus and myxoma virus, is modulated by cellular tumor suppressor gene status.

Replication-competent oncolytic viruses hold great potential for the clinical treatment of many cancers. Importantly, many oncolytic virus candidates, such as reovirus and myxoma virus, preferentially infect cancer cells bearing abnormal cellular signaling pathways. Reovirus and myxoma virus are highly responsive to activated Ras and Akt signaling pathways, respectively, for their specificity for viral oncolysis. However, considering the complexity of cancer cell populations, it is possible that other tumor-specific signaling pathways may also contribute to viral discrimination between normal versus cancer cells. Because carcinogenesis is a multistep process involving the accumulation of both oncogene activations and the inactivation of tumor suppressor genes, we speculated that not only oncogenes but also tumor suppressor genes may have an important role in determining the tropism of these viruses for cancer cells. It has been previously shown that many cellular tumor suppressor genes, such as p53, ATM and Rb, are important for maintaining genomic stability; dysfunction of these tumor suppressors may disrupt intact cellular antiviral activity due to the accumulation of genomic instability or due to interference with apoptotic signaling. Therefore, we speculated that cells with dysfunctional tumor suppressors may display enhanced susceptibility to challenge with these oncolytic viruses, as previously seen with adenovirus. We report here that both reovirus and myxoma virus preferentially infect cancer cells bearing dysfunctional or deleted p53, ATM and Rb tumor suppressor genes compared to cells retaining normal counterparts of these genes. Thus, oncolysis by these viruses may be influenced by both oncogenic activation and tumor suppressor status.

Fatty acid synthesis in protozoan parasites: unusual pathways and novel drug targets.

Fatty acid biosynthesis pathways in protozoan parasites are reviewed with a view to targeting this metabolism for drug therapy. The type II fatty acid biosynthesis pathways derived from bacteria in protozoan relict plastids and mitochondria are examined in different groups with emphasis on apicomplexa. The suitability of different enzymes from the type II fatty acid biosynthesis pathway for drug intervention, and the state-of-play with known and potential inhibitors is explored. The type I acid biosynthesis pathways that occur in select protozoan parasites and their potential for inhibition using anti-tumour and obesity management compounds currently in development are also examined. Pathways used by parasites to scavenge and modify host lipids are also described briefly and their potential for therapeutics discussed.

Instability in pipe flow.

The long-puzzling, unphysical result that linear stability analyses lead to no transition in pipe flow, even at infinite Reynolds number, is ascribed to the use of stick boundary conditions, because they ignore the amplitude variations associated with the roughness of the wall. Once that length scale is introduced (here, crudely, through a corrugated pipe), linear stability analyses lead to stable vortex formation at low Reynolds number above a finite amplitude of the corrugation and unsteady flow at a higher Reynolds number, where indications are that the vortex dislodges. Remarkably, extrapolation to infinite Reynolds number of both of these transitions leads to a finite and nearly identical value of the amplitude, implying that below this amplitude, the vortex cannot form because the wall is too smooth and, hence, stick boundary results prevail.

Fatty acid biosynthesis as a drug target in apicomplexan parasites.

Apicomplexan parasitic diseases impose devastating impacts on much of the world's population. The increasing prevalence of drug resistant parasites and the growing number of immuno-compromised individuals are exacerbating the problem to the point that the need for novel, inexpensive drugs is greater now than ever. Discovery of a prokaryotic, Type II fatty acid synthesis (FAS) pathway associated with the plastid-like organelle (apicoplast) of Plasmodium and Toxoplasma has provided a wealth of novel drug targets. Since this pathway is both essential and fundamentally different from the cytosolic Type I pathway of the human host, apicoplast FAS has tremendous potential for the development of parasite-specific inhibitors. Many components of this pathway are already the target for existing antibiotics and herbicides, which should significantly reduce the time and cost of drug development. Continuing interest--both in the pharmaceutical and herbicide industries--in fatty acid synthesis inhibitors proffers an ongoing stream of potential new anti-parasitic compounds. It has now emerged that not all apicomplexan parasites have retained the Type II fatty acid biosynthesis pathway. No fatty acid biosynthesis enzymes are encoded in the genome of Theileria annulata or T. parva, suggesting that fatty acid synthesis is lacking in these parasites. The human intestinal parasite Cryptosporidium parvum appears to have lost the apicoplast entirely; instead relying on an unusual cytosolic Type I FAS. Nevertheless, newly developed anti-cancer and anti-obesity drugs targeting human Type I FAS may yet prove efficacious against Cryptosporidium and other apicomplexans that rely on this Type I FAS pathway.

Convective Instabilities in Two Liquid Layers.

We perform linear stability calculations for horizontal fluid bilayers, taking into account both buoyancy effects and thermocapillary effects in the presence of a vertical temperature gradient. To help understand the mechanisms driving the instability, we have performed both long-wavelength and short-wavelength analyses. The mechanism for the large wavelength instability is complicated, and the detailed form of the expansion is found to depend on the Crispation and Bond numbers. The system also allows a conventional Rayleigh-Taylor instability if heavier fluid overlies lighter fluid, and the long-wavelength analysis describes this case as well. In addition to the asymptotic analyses for large and small wavelengths, we have performed numerical calculations using materials parameters for a benzene-water system.

Myxoma virus M-T5 protects infected cells from the stress of cell cycle arrest through its interaction with host cell cullin-1.

The myxoma virus (MV) M-T5 gene encodes an ankyrin repeat protein that is important for virus replication in cells from several species. Insight was gained into the molecular mechanisms underlying the role of M-T5 as a host range determinant when the cell cycle regulatory protein cullin-1 (cul-1) was identified as a cellular binding partner of M-T5 and found to colocalize with the protein in both nuclear and cytosolic compartments. Consistent with this interaction, infection with wild-type MV (vMyxlac) or a deletion mutant lacking M-T5 (vMyxT5KO) differentially altered cell cycle progression in a panel of permissive and nonpermissive cells. Cells infected with vMyxlac transitioned rapidly out of the G0/G1 phase and preferentially accumulated at the G2/M checkpoint, whereas infection with vMyxT5KO impeded progression through the cell cycle, resulting in a greater percentage of cells retained at G0/G1. Levels of the cul-1 substrate, p27/Kip-1, were selectively increased in cells infected with vMyxT5KO compared to vMyxlac, concurrent with decreased phosphorylation of p27/Kip-1 at Thr187 and decreased ubiquitination. Compared to cells infected with vMyxlac, cell death was increased in vMyxT5KO-infected cells following treatment with diverse stimuli known to induce cell cycle arrest, including infection itself, serum deprivation, and exposure to proteasome inhibitors or double-stranded RNA. Moreover, infection with vMyxlac, but not vMyxT5KO, was sufficient to overcome the G0/G1 arrest induced by these stimuli. These findings suggest that M-T5 regulates cell cycle progression at the G0/G1 checkpoint, thereby protecting infected cells from diverse innate host antiviral responses normally triggered by G0/G1 cell cycle arrest.

Phase field modeling of electrochemistry. I. Equilibrium.

A diffuse interface (phase field) model for an electrochemical system is developed. We describe the minimal set of components needed to model an electrochemical interface and present a variational derivation of the governing equations. With a simple set of assumptions: mass and volume constraints, Poisson's equation, ideal solution thermodynamics in the bulk, and a simple description of the competing energies in the interface, the model captures the charge separation associated with the equilibrium double layer at the electrochemical interface. The decay of the electrostatic potential in the electrolyte agrees with the classical Gouy-Chapman and Debye-Hückel theories. We calculate the surface free energy, surface charge, and differential capacitance as functions of potential and find qualitative agreement between the model and existing theories and experiments. In particular, the differential capacitance curves exhibit complex shapes with multiple extrema, as exhibited in many electrochemical systems.

Phase field modeling of electrochemistry. II. Kinetics.

The kinetic behavior of a phase field model of electrochemistry is explored for advancing (electrodeposition) and receding (electrodissolution) conditions in one dimension. We previously described the equilibrium behavior of this model [J. E. Guyer, W. J. Boettinger, J. A. Warren, and G. B. McFadden, Phys. Rev. E 69, 021603 (2004)]. We examine the relationship between the parameters of the phase field method and the more typical parameters of electrochemistry. We demonstrate ohmic conduction in the electrode and ionic conduction in the electrolyte. We find that, despite making simple, linear dynamic postulates, we obtain the nonlinear relationship between current and overpotential predicted by the classical "Butler-Volmer" equation and observed in electrochemical experiments. The charge distribution in the interfacial double layer changes with the passage of current and, at sufficiently high currents, we find that the diffusion limited deposition of a more noble cation leads to alloy deposition with less noble species.

Deciphering apicoplast targeting signals--feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins.

The malaria causing protozoan Plasmodium falciparum contains a vestigal, non-photosynthetic plastid, the apicoplast. Numerous proteins encoded by nuclear genes are targeted to the apicoplast courtesy of N-terminal extensions. With the impending sequence completion of an entire genome of the malaria parasite, it is important to have software tools in place for prediction of subcellular locations for all proteins. Apicoplast targeting signals are bipartite; containing a signal peptide and a transit peptide. Nuclear-encoded apicoplast protein precursors were analyzed for characteristic features by statistical methods, principal component analysis, self-organizing maps, and supervised neural networks. The transit peptide contains a net positive charge and is rich in asparagine, lysine, and isoleucine residues. A novel prediction system (PATS, predict apicoplast-targeted sequences) was developed based on various sequence features, yielding a Matthews correlation coefficient of 0.91 (97% correct predictions) in a 40-fold cross-validation study. This system predicted 22% apicoplast proteins of the 205 potential proteins on P. falciparum chromosome 2, and 21% of 243 chromosome 3 proteins. A combination of the PATS results with a signal peptide prediction yields 15% potentially nuclear-encoded apicoplast proteins on chromosomes 2 and 3. The prediction tool will advance P. falciparum genome analysis, and it might help to identify apicoplast proteins as drug targets for the development of novel anti-malaria agents.

Translocation of proteins across the multiple membranes of complex plastids.

Secondary endosymbiosis describes the origin of plastids in several major algal groups such as dinoflagellates, euglenoids, heterokonts, haptophytes, cryptomonads, chlorarachniophytes and parasites such as apicomplexa. An integral part of secondary endosymbiosis has been the transfer of genes for plastid proteins from the endosymbiont to the host nucleus. Targeting of the encoded proteins back to the plastid from their new site of synthesis in the host involves targeting across the multiple membranes surrounding these complex plastids. Although this process shows many overall similarities in the different algal groups, it is emerging that differences exist in the mechanisms adopted.

Poxvirus infection rapidly activates tyrosine kinase signal transduction.

Viruses have evolved a number of strategies to gain entry and replicate in host target cells that, for human immunodeficiency virus (HIV) and the poxvirus, myxoma virus, involve appropriating chemokine receptors. In this report we demonstrate that activation of multiple intracellular tyrosine phosphorylation events rapidly ensues following virus adsorption to NIH 3T3.CD4.CCR5 cells and affects the ultimate level of myxoma virus replication. UV-inactivated myxoma virus induces the rapid phosphorylation of CCR5 on tyrosine residues, the association of CCR5 with Jaks and p56(lck), and their phosphorylation-activation within minutes of virus adsorption. Additionally, we provide evidence for myxoma virus-inducible signal transducers and activators of transcription (Stat) and insulin receptor substrate (IRS) activation. In contrast to CCR5 activation effected by HIV Env protein, these myxoma virus-inducible phosphorylation events are not sensitive to pertussis toxin treatment. Moreover, in cells that are non-permissive for myxoma virus infection, we provide evidence that myxoma virus fails to invoke this tyrosine phosphorylation cascade. Consistent with the observation that infection of CCR5-expressing cells is blocked by herbimycin A and the Jak 2 inhibitor, tyrophostin AG490, we infer that viral infectivity may be dependent on non-G-protein-coupled signal transduction pathways triggered by the infecting myxoma virus particle. This provides a novel post-binding mechanism by which viruses can co-opt a cellular receptor to permit productive virus infection.

Trafficking and assembly of the cytoadherence complex in Plasmodium falciparum-infected human erythrocytes.

After invading human erythrocytes, the malarial parasite Plasmodium falciparum, initiates a remarkable process of secreting proteins into the surrounding erythrocyte cytoplasm and plasma membrane. One of these exported proteins, the knob-associated histidine-rich protein (KAHRP), is essential for microvascular sequestration, a strategy whereby infected red cells adhere via knob structures to capillary walls and thus avoid being eliminated by the spleen. This cytoadherence is an important factor in many of the deaths caused by malaria. Green fluorescent protein fusions and fluorescence recovery after photobleaching were used to follow the pathway of KAHRP deployment from the parasite endomembrane system into an intermediate depot between parasite and host, then onwards to the erythrocyte cytoplasm and eventually into knobs. Sequence elements essential to individual steps in the pathway are defined and we show that parasite-derived structures, known as Maurer's clefts, are an elaboration of the canonical secretory pathway that is transposed outside the parasite into the host cell, the first example of its kind in eukaryotic biology.