Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Space-Time Directional Lyapunov Exponents for Cellular Automata

Space-time directional Lyapunov exponents are introduced. They describe the maximal velocity of propagation to the right or to the left of fronts of perturbations in a frame moving with a given velocity. The continuity of these exponents as function of the velocity and an inequality relating them to the directional entropy is proved.     

High-throughput screening of fuel cell electrocatalysts

The drawbacks of our earlier report of preparing fuel cell catalyst arrays by borohydride reduction of inkjet prepared arrays of metal salts are discussed along with the need for inclusion of state-of-the-art metrics in all array screening. An alternative method for screening of hydrogen/air cathode catalysts, direct methanol fuel cell (DMFC) anode catalysts, and catalyst loading studies is provided. State-of-the-art Johnson Matthey catalysts were used in control experiments to demonstrate the utility of the array fuel cell for high throughput screening of fuel cell catalysts in the 3-4 mg/cm² range. This report lays out hard learned rules for high throughput screening and demonstrates that the array fuel cell can be used for very precise screening of libraries of membrane electrode assembly (MEA) components without the pitfalls discussed in the introduction.     

Numerical approximation of generalized Newtonian fluids using Powell–Sabin–Heindl elements: I. theoretical estimates

In this paper we consider the numerical approximation of steady and unsteady generalized Newtonian fluid flows using divergence free finite elements generated by the Powell–Sabin–Heindl elements. We derive a priori and a posteriori finite element error estimates and prove convergence of the method of successive approximations for the steady flow case. A priori error estimates of unsteady flows are also considered. These results provide a theoretical foundation and supporting numerical studies are to be provided in Part II. Copyright © 2003 John Wiley & Sons, Ltd.     

A non‐linear and non‐local boundary condition for a diffusion equation in petroleum engineering

This article deals with a boundary value problem for Laplace equation with a non‐linear and non‐local boundary condition. This problem comes from petroleum engineering and is used to obtain an estimation of well productivity. The non‐linear and non‐local boundary condition is written on the well boundary. On the outer reservoir boundaries, we have both Dirichlet and Neumann conditions. In this paper, we prove the existence and uniqueness of a solution to this problem. The existence is proved by Schauder theorem and the uniqueness is obtained under more restricted conditions, when the involved operator is a contraction. Copyright © 2005 John Wiley & Sons, Ltd.     

Sufficient conditions of non‐uniqueness for the Coulomb friction problem

We consider the Signorini problem with Coulomb friction in elasticity. Sufficient conditions of non‐uniqueness are obtained for the continuous model. These conditions are linked to the existence of real eigenvalues of an operator in a Hilbert space. We prove that, under appropriate conditions, real eigenvalues exist for a non‐local Coulomb friction model. Finite element approximation of the eigenvalue problem is considered and numerical experiments are performed. Copyright © 2003 John Wiley & Sons, Ltd.     

Boundary position feedback control of Kirchhoff's non‐linear strings

This paper is concerned with global stabilization of an undamped non‐linear string in the case where any velocity feedback is not available. The linearized system has an infinite number of poles and zeros on the imaginary axis. In the case where any velocity feedback is not available, a parallel compensator is effective. The stabilizer is constructed for the augmented system which consists of the controlled system and a parallel compensator. It is proved that the string can be stabilized by linear boundary control. Copyright © 2003 John Wiley & Sons, Ltd.     

Hydromagnetic rotating flow of a fourth‐order fluid past a porous plate

The rotating flow in the presence of a magnetic field is a problem belonging to hydromagnetics and deserves to be more widely studied than it has been to date. In the non‐linear regime the literature is scarce. We develop the governing equations for the unsteady hydromagnetic rotating flow of a fourth‐order fluid past a porous plate. The steady flow is governed by a boundary value problem in which the order of differential equations is more than the number of available boundary conditions. It is shown that by augmenting the boundary conditions based on asymptotic structures at infinity it is possible to obtain numerical solutions of the nonlinear hydromagnetic equations. Effects of uniform suction or blowing past the porous plate, exerted magnetic field and rotation on the flow phenomena, especially on the boundary layer structure near the plate, are numerically analysed and discussed. The flow behaviours of the Newtonian fluid and second‐, third‐ and fourth‐order non‐Newtonian fluids are compared for the special flow problem, respectively. Copyright © 2004 John Wiley & Sons, Ltd.     

Pointwise stabilization of strings with non‐linear feedback

We consider an initial and boundary value problem for a homogenous string subject to an internal pointwise control. The solution resulting from a non‐linear feedback is studied. We give various explicit decay estimates depending on the control position and the feedback non‐linearity. Copyright © 2004 John Wiley & Sons, Ltd.     

Diffusion in poro‐plastic media

A model is developed for the flow of a slightly compressible fluid through a saturated inelastic porous medium. The initial‐boundary‐value problem is a system that consists of the diffusion equation for the fluid coupled to the momentum equation for the porous solid together with a constitutive law which includes a possibly hysteretic relation of elasto‐visco‐plastic type. The variational form of this problem in Hilbert space is a non‐linear evolution equation for which the existence and uniqueness of a global strong solution is proved by means of monotonicity methods. Various degenerate situations are permitted, such as incompressible fluid, negligible porosity, or a quasi‐static momentum equation. The essential sufficient conditions for the well‐posedness of the system consist of an ellipticity condition on the term for diffusion of fluid and either a viscous or a hardening assumption in the constitutive relation for the porous solid. Copyright © 2004 John Wiley & Sons, Ltd.