Solitary wave propagating over a bottom-mounted barrier is simulated using the Incompressible Smoothed Particle Hydrodynamics (ISPH) method in order to study generation and transport of turbulence associated with flow separation around submerged structures. For an accurate capture characteristics during propagation, rather than employing standard sub-particle scale (SPS) model, k - ε model coup...

‎The water wave generation by wave paddle and a freely falling rigid body are examined by using an Incompressible Smoothed Particle Hydrodynamics (ISPH)‎. ‎In the current ISPH method‎, ‎the pressure was evaluated by solving pressure Poisson equation using a semi-implicit algorithm based on the projection scheme and the source term of pressure Poisson equation contains both of divergence free ve...

Isoprenoid biosynthesis in plant plastids occurs via the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway. We used tobacco rattle virus (TRV) to posttranscriptionally silence the expression of the last two enzymes of this pathway, the IspG-encoded (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS) and the IspH-encoded isopentenyl/dimethylallyl diphosphate synthase (IDDS), as well as isopen...

(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate reductase (IspH) is a [Fe4S4] cluster-containing enzyme involved in isoprenoid biosynthesis in many bacteria as well as in malaria parasites and is an important drug target. Several inhibitors including amino and thiol substrate analogues, as well as acetylene and pyridine diphosphates, have been reported. Here, we investigate the mode of binding o...

This work aims at improving an incompressible SPH model (ISPH) by adapting to it the unified semi-analytical wall boundary conditions proposed by Ferrand et al. [1]. The ISPH algorithm considered is the one proposed by Lind et al. [2]. The new description of the wall boundaries allows to impose accurately a von Neumann boundary condition on the pressure that corresponds to the impermeability co...

We report the inhibition of the Aquifex aeolicus IspH enzyme (LytB, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, EC 1.17.1.2) by a series of diphosphates and bisphosphonates. The most active species was an alkynyl diphosphate having IC(50) = 0.45 microM (K(i) approximately 60 nM), which generated a very large change in the 9 GHz EPR spectrum of the reduced protein. On the basis of p...