Equation of state of quark-nuclear matter

Quark-nuclear matter (QNM) is a many-body system containing hadrons and deconfined quarks. Starting from a microscopic quark-meson coupling (QMC) Hamiltonian with a density dependent quark-quark interaction, an effective quark-hadron Hamiltonian is constructed via a mapping procedure. The mapping is implemented with a unitary operator such that composites are redescribed by elementary-particle field operators that satisfy canonical commutation relations in an extended Fock space. Application of the unitary operator to the microscopic Hamiltonian leads to effective, hermitian operators that have a clear physical interpretation. At sufficiently high densities, the effective Hamiltonian contains interactions that lead to quark deconfinement. The equation of state of QNM is obtained using standard many-body techniques with the effective quark-hadron Hamiltonian. At low densities, the model is equivalent to a QMC model with confined quarks. Beyond a critical density, when quarks start to deconfine, the equation of state predicted for QNM is softer than the QMC equation of state with confined quarks.Comment: 10 pages, ws-procs9x6.cls (included), 2 eps figures, to appear in the Proceedings of the Joint CSSM/JHF Workshop, Adelaide, March 14-21, 200

Autoinhibition of the formin Cappuccino in the absence of canonical autoinhibitory domains.

Formins are a conserved family of proteins known to enhance actin polymerization. Most formins are regulated by an intramolecular interaction. The Drosophila formin, Cappuccino (Capu), was believed to be an exception. Capu does not contain conserved autoinhibitory domains and can be regulated by a second protein, Spire. We report here that Capu is, in fact, autoinhibited. The N-terminal half of Capu (Capu-NT) potently inhibits nucleation and binding to the barbed end of elongating filaments by the C-terminal half of Capu (Capu-CT). Hydrodynamic analysis indicates that Capu-NT is a dimer, similar to the N-termini of other formins. These data, combined with those from circular dichroism, suggest, however, that it is structurally distinct from previously described formin inhibitory domains. Finally, we find that Capu-NT binds to a site within Capu-CT that overlaps with the Spire-binding site, the Capu-tail. We propose models for the interaction between Spire and Capu in light of the fact that Capu can be regulated by autoinhibition

Spire stimulates nucleation by Cappuccino and binds both ends of actin filaments.

The actin nucleators Spire and Cappuccino synergize to promote actin assembly, but the mechanism of their synergy is controversial. Together these proteins promote the formation of actin meshes, which are conserved structures that regulate the establishment of oocyte polarity. Direct interaction between Spire and Cappuccino is required for oogenesis and for in vitro synergistic actin assembly. This synergy is proposed to be driven by elongation and the formation of a ternary complex at filament barbed ends, or by nucleation and interaction at filament pointed ends. To mimic the geometry of Spire and Cappuccino in vivo, we immobilized Spire on beads and added Cappuccino and actin. Barbed ends, protected by Cappuccino, grow away from the beads while pointed ends are retained, as expected for nucleation-driven synergy. We found that Spire is sufficient to bind barbed ends and retain pointed ends of actin filaments near beads and we identified Spire's barbed-end binding domain. Loss of barbed-end binding increases nucleation by Spire and synergy with Cappuccino in bulk pyrene assays and on beads. Importantly, genetic rescue by the loss-of-function mutant indicates that barbed-end binding is not necessary for oogenesis. Thus, increased nucleation is a critical element of synergy both in vitro and in vivo

Actin filament assembly by bacterial factors VopL/F: Which end is up?

Competing models have been proposed for actin filament nucleation by the bacterial proteins VopL/F. In this issue, Burke et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201608104) use direct observation to demonstrate that VopL/F bind the barbed and pointed ends of actin filaments but only nucleate new filaments from the pointed end

Equilibration of Concentrated Hard Sphere Fluids

We report a systematic molecular dynamics study of the isochoric equilibration of hard-sphere fluids in their metastable regime close to the glass transition. The thermalization process starts with the system prepared in a non-equilibrium state with the desired final volume fraction {\phi} but with a prescribed non-equilibrium static structure factor S_0(k; {\phi}). The evolution of the {\alpha}- relaxation time {\tau}{\alpha} (k) and long-time self-diffusion coefficient DL as a function of the evolution time tw is then monitored for an array of volume fractions. For a given waiting time the plot of {\tau}{\alpha} (k; {\phi}, tw) as a function of {\phi} exhibits two regimes corresponding to samples that have fully equilibrated within this waiting time ({\phi} \leq {\phi}(c) (tw)), and to samples for which equilibration is not yet complete ({\phi} \geq {\phi}(c) (tw)). The crossover volume fraction {\phi}(c) (tw) increases with tw but seems to saturate to a value {\phi}(a) \equiv {\phi}(c) (tw \rightarrow \infty) \approx 0.582. We also find that the waiting time t^(eq)_w({\phi}) required to equilibrate a system grows faster than the corresponding equilibrium relaxation time, t^(eq)({\phi}) \approx 0.27 \times [{\tau}{\alpha} (k; {\phi})]^1.43, and that both characteristic times increase strongly as {\phi} approaches {\phi}^(a), thus suggesting that the measurement of equilibrium properties at and above {\phi}(a) is experimentally impossible

Interaction between Microtubules and the Drosophila Formin Cappuccino and Its Effect on Actin Assembly

Formin family actin nucleators are potential coordinators of the actin and microtubule cytoskeletons, as they can both nucleate actin filaments and bind microtubules in vitro. To gain a more detailed mechanistic understanding of formin-microtubule interactions and formin-mediated actin-microtubule cross-talk, we studied microtubule binding by Cappuccino (Capu), a formin involved in regulating actin and microtubule organization during Drosophila oogenesis. We found that two distinct domains within Capu, FH2 and tail, work together to promote high-affinity microtubule binding. The tail domain appears to bind microtubules through nonspecific charge-based interactions. In contrast, distinct residues within the FH2 domain are important for microtubule binding. We also report the first visualization of a formin polymerizing actin filaments in the presence of microtubules. Interestingly, microtubules are potent inhibitors of the actin nucleation activity of Capu but appear to have little effect on Capu once it is bound to the barbed end of an elongating filament. Because Capu does not simultaneously bind microtubules and assemble actin filaments in vitro, its actin assembly and microtubule binding activities likely require spatial and/or temporal regulation within the Drosophila oocyte

DbarN interaction in a color-confining chiral quark model

We investigate the low-energy elastic DbarN interaction using a quark model that confines color and realizes dynamical chiral symmetry breaking. The model is defined by a microscopic Hamiltonian inspired in the QCD Hamiltonian in Coulomb gauge. Constituent quark masses are obtained by solving a gap equation and baryon and meson bound-state wave functions are obtained using a variational method. We derive a low energy meson-nucleon potential from a quark-interchange mechanism whose ingredients are the quark-quark and quark-antiquark interactions and baryon and meson wave functions, all derived from the same microscopic Hamiltonian. The model is supplemented with (sigma,rho,omega,a0) single-meson exchanges to describe the long-range part of the interaction. Cross-sections and phase shifts are obtained by iterating the quark-interchange plus meson-exchange potentials in a Lippmann-Schwinger equation. Once model parameters in meson exchange potential are fixed to describe the low-energy experimental phase shifts of the K+N and K0N reactions, predictions for Dbar0N and D-N reactions are obtained without introducing new parameters.Comment: 13 latex pages, 7 figure

Effects of experimental lightgaps and topography on enrichment plantings in a central Amazonian secondary forest

Enrichment plantings into secondary forest are an important option in restoring species diversity and ecosystem services. However, little attention has been given to environmental requirements for species performance. This study evaluated the effects of lightgaps and topographic position on the growth and survival of four native tree species (Pouteria caimito, Garcinia macrophylla, Dipteryx odorata and Cynometra bauhiniaefolia) planted into a 26-year old secondary forest originating from abandoned pastures in the central Amazon Basin. Artificial lightgaps and control plots under closed canopy were uniformly distributed on plateaus and bottomlands near water bodies. Seedlings were planted randomly into the plots and monitored for 28 months. Seedling survival rate was high (93%) and did not differ among species. Overall, lightgaps produced a 38% increase in seedling height relative to the controls. Although the four species naturally occur in mature forest, two of the four grew significantly more in lightgaps than in dosed canopy secondary forest. Overall, bottomlands facilitated greater seedling growth in height (38%) relative to plateaus, but only one species exhibited a significant increase. This study shows the importance of the environmental variability generated with canopy openings along the topographic gradient, suggesting that both the selection of species and microsite conditions of planting sites have to be considered important criteria in the recovery of degraded areas