Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms

Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The TRAPP complexes activate these GTPases via nucleotide exchange using a shared set of core subunits. The basal specificity of the TRAPP core is towards Rab1, yet the TRAPPII complex is specific for Rab11. A steric gating mechanism has been proposed to explain TRAPPII counterselection against Rab1. Here we present cryoEM structures of the 22-subunit TRAPPII complex from budding yeast, including a TRAPPII-Rab11 nucleotide exchange intermediate. The Trs130 subunit provides a ″leg″ that positions the active site distal to the membrane surface, and this leg is required for steric gating. The related TRAPPIII complex is unable to activate Rab11 due to a repulsive interaction, which TRAPPII surmounts using the Trs120 subunit as a ″lid″ to enclose the active site. TRAPPII also adopts an open conformation enabling Rab11 to access and exit from the active site chamber.

Interaction of Self-Sustained Pulses in Tunnel-Diode Oscillator Lattices

A one-dimensional lattice in tunnel-diode (TD) oscillators supports self-sustained solitary pulses resulting from the balance between gain and attenuation. By applying the reduction theory to the device’s model equation, it is found that two relatively distant pulses moving in the lattice are mutually affected by a repulsive interaction. This property can be efficiently utilized in equalizing pulse positions to achieve jitter elimination. In particular, when two pulses rotate in a small, closed lattice, they separate evenly at the asymptotic limit. As a result, the lattice loop can provide an efficient platform to obtain low-phase-noise multiphase oscillatory signals. In this work, the interaction between two self-sustained pulses in a TD-oscillator lattice is examined, and the properties of interpulse interaction are validated by conducting several measurements using a test breadboarded lattice.

Molecular dynamics simulation study of doxorubicin adsorption on functionalized carbon nanotubes with folic acid and tryptophan

In this work, molecular dynamics (MD) simulation is used to study the adsorption of the anticancer drug, doxorubicin (DOX), on the wall or surface of pristine and functionalized carbon nanotubes (FCNTs) in an aqueous solution. Initially, the CNTs were functionalized by tryptophan (Trp) and folic acid (FA), and then the DOX molecules were added to the system. The simulation results showed that the drug molecules can intensely interact with the FCNTs at physiological pH. Furthermore, it was found that as a result of functionalization, the solubility of FCNTs in an aqueous solution increases significantly. The effect of pH variation on drug release from both pristine and FCNTs was also investigated. The obtained results indicated that in acidic environments due to protonation of functional groups (Trp) and as a result of repulsive interaction between the DOX molecule and functional groups, the release of DOX molecules from FCNT’s surface is facilitated. The drug release is also strongly dependent on the pH and protonated state of DOX and FCNT.

Collective modes of type-II Weyl fermions with repulsive S-wave interaction

Three-dimensional type-II Weyl fermions possess overtilted conelike low-energy band dispersion. Unlike the closed ellipsoidal Fermi surface for type-I Weyl fermions, the Fermi surface is an open hyperboloid for type-II Weyl fermions. We evaluate the spin and density susceptibility of type-II Weyl fermions with repulsive S-wave interaction by means of Green’s functions. We obtain the particle-hole continuum along the tilted momentum direction and perpendicular to the tilted momentum direction, respectively. We find the zero sound mode in some repulsive interaction strengths by numerically solving the pole equations of the susceptibility within the random-phase approximation.

Aluminum depletion induced by co-segregation of carbon and boron in a bcc-iron grain boundary

The local variation of grain boundary atomic structure and chemistry caused by segregation of impurities influences the macroscopic properties of polycrystalline materials. Here, the effect of co-segregation of carbon and boron on the depletion of aluminum at a Σ5 (3 1 0 )[0 0 1] tilt grain boundary in a α − Fe-4 at%Al bicrystal is studied by combining atomic resolution scanning transmission electron microscopy, atom probe tomography and density functional theory calculations. The atomic grain boundary structural units mostly resemble kite-type motifs and the structure appears disrupted by atomic scale defects. Atom probe tomography reveals that carbon and boron impurities are co-segregating to the grain boundary reaching levels of >1.5 at%, whereas aluminum is locally depleted by approx. 2 at.%. First-principles calculations indicate that carbon and boron exhibit the strongest segregation tendency and their repulsive interaction with aluminum promotes its depletion from the grain boundary. It is also predicted that substitutional segregation of boron atoms may contribute to local distortions of the kite-type structural units. These results suggest that the co-segregation and interaction of interstitial impurities with substitutional solutes strongly influences grain boundary composition and with this the properties of the interface.

Convergence Towards the Vlasov–Poisson Equation from the N-Fermionic Schrödinger Equation

We consider the quantum dynamics of N interacting fermions in the large N limit. The particles in the system interact with each other via repulsive interaction that is regularized Coulomb potential with a polynomial cutoff with respect to N. From the quantum system, we derive the Vlasov–Poisson system by simultaneously estimating the semiclassical and mean-field residues in terms of the Husimi measure.

Detecting long-range interactions between migrating cells

Chemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories: For each movement step of a cell relative to the position of a potential target, we compute a p value that quantifies the likelihood of the movement direction under the null-hypothesis of blind migration. The resulting distribution of p values, pooled over all recorded cell trajectories, is then compared to an ensemble of reference distributions in which the positions of targets are randomized. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of our p value method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.

Ruppeiner geometry and thermodynamic phase transition of the black hole in massive gravity

The phase transition and thermodynamic geometry of a 4-dimensional AdS topological charged black hole in de Rham, Gabadadze and Tolley (dRGT) massive gravity have been studied. After introducing a normalized thermodynamic scalar curvature, it is speculated that its value is related to the interaction between the underlying black hole molecules if the black hole molecules exist. We show that there does exist a crucial parameter given in terms of the topology, charge, and massive parameters of the black hole, which characterizes the thermodynamic properties of the black hole. It is found that when the parameter is positive, the singlet large black hole phase does not exist for sufficient low temperature and there is a weak repulsive interaction dominating for the small black hole which is similar to the Reissner–Nordström AdS black hole; when the parameter is negative, an additional phase region describing large black holes also implies a dominant repulsive interaction. These constitute the distinguishable features of dRGT massive topological black hole from those of the Reissner–Nordström AdS black hole as well as the Van der Waals fluid system.