Nonlinear vibrations of buried landmines

The seismo-acoustic method is one of the most promising emerging techniques for the detection of landmines. Numerous field tests have demonstrated that buried landmines manifest themselves at the surface through linear and nonlinear responses to acoustic/seismic excitation. The present paper describes modeling of the nonlinear response in the framework of the mass-spring model of the soil-mine system. The perturbation method used in the model allows for the derivation of an analytical solution describing both quadratic and cubic acoustic interactions at the soil-mine interface. This solution has been compared with actual field measurements to obtain nonlinear parameters of the buried mines. These parameters have been analyzed with respect to mine types and burial depths. It was found that the cubic nonlinearity could be a significant contributor to the nonlinear response. This effect has led to the development of a new intermodulation detection algorithm based on dual-frequency excitation. Both quadratic and intermodulation nonlinear algorithms were evaluated at the U.S. Army outdoor testing facilities. The algorithms appear to complement each other in improving the overall detection performance.     

The indicatrix method in free boundary problems

Summary An approximate method for nonlinear problems with functional constraints is considered, in which the constraint in the whole domain is replaced by the constraint on a manifold of lower dimension. The stability criterion is introduced, and convergence theorems are proved for the onedimensional problem. Numerical results for the elastic-plastic torsion problem are given.     

Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study

Crystallographic studies of human purine nucleoside phosphorylase (hPNP) with several transition-state (TS) analogues in the immucillin family showed an unusual geometric arrangement of the atoms O-5', O-4', and O(P), the nucleophilic phosphate oxygen, lying in a close three-oxygen stack. These observations were corroborated by extensive experimental kinetic isotope effect analysis. We propose that protein-facilitated dynamic modes in hPNP cause this stack, centered on the ribosyl O-4' oxygen, to squeeze together and push electrons toward the purine ring, stabilizing the oxacarbenium character of the TS. As the N-ribosidic bond is cleaved during the reaction, the pK(a) values of N-7 and O-6 increase by the electron density expelled by the oxygen-stack compression toward the purine ring. Increased electron density in the purine ring improves electrostatic interactions with nearby residues and facilitates the abstraction of a proton from a solvent proton or an unidentified general acid, making the purine a better leaving group, and accelerating catalysis. Classical and mixed quantum/classical molecular dynamics (MD) simulations of the Michaelis complex of hPNP with the substrates guanosine and phosphate were performed to assess the existence of protein-promoting vibrations (PPVs). Analogous simulations were performed for the substrates in aqueous solution. In the catalytic site, the O-5', O-4', and O(P) oxygens vibrate at frequencies of ca. 125 and 465 cm(-1), as opposed to 285 cm(-1) in the absence of hPNP. The hybrid quantum mechanical/molecular mechanical method was used to assess whether this enzymatic vibration pushing the oxygens together is coupled to the reaction coordinate, and thus has a direct positive impact on catalysis. The potential energy surface for the phosphorolysis reaction for several snapshots taken from the classical MD simulation showed substantial differences in oxygen compression. Our calculations showed the existence of PPVs coupled to the reaction coordinate, which effect electronic alterations in the active site by pushing the three oxygen centers together in proximity, and accelerate substrate turnover in the phosphorolysis reaction catalyzed by hPNP.     

Multigrid algorithms for high-order discontinuous Galerkin discretizations of the compressible Navier–Stokes equations

Multigrid algorithms are developed for systems arising from high-order discontinuous Galerkin discretizations of the compressible Navier–Stokes equations on unstructured meshes. The algorithms are based on coupling both p- and h-multigrid (ph-multigrid) methods which are used in nonlinear or linear forms, and either directly as solvers or as preconditioners to a Newton–Krylov method.The performance of the algorithms are examined in solving the laminar flow over an airfoil configuration. It is shown that the choice of the cycling strategy is crucial in achieving efficient and scalable solvers. For the multigrid solvers, while the order-independent convergence rate is obtained with a proper cycle type, the mesh-independent performance is achieved only if the coarsest problem is solved to a sufficient accuracy. On the other hand, the multigrid preconditioned Newton–GMRES solver appears to be insensitive to this condition and mesh-independent convergence is achieved under the desirable condition that the coarsest problem is solved using a fixed number of multigrid cycles regardless of the size of the problem.It is concluded that the Newton–GMRES solver with the multigrid preconditioning yields the most efficient and robust algorithm among those studied.     

Exploring alternative approaches to computational fluid dynamics

This paper discusses advances in two areas which may have the potential to impact future simulation capabilities through advanced algorithms. This includes spectral multigrid (MG) solvers for high-order accurate spatial discretizations and efficient MG solvers for kinetic-based schemes. Preliminiary evidence is given illustrating the promise of these approaches for application to engineering simulations.     

Ab initio structure predictions using a hierarchical approach applied to 434 cro and the Drosophila homeodomain

A discrete-state ab initio protein structure prediction procedure is presented, based on the assumption that some proteins fold in an hierarchical way, where the early folding of independent units precedes and helps complete structure formation. It involves a first step predicting, by means of threading algorithms and local structure prediction methods, the location of autonomous protein subunits presenting favorable local and tertiary interactions. The second step consists of predicting the structure of these units by Monte Carlo simulated annealing using several database-derived potentials. In a last step, these predicted structures are used as starting conformations of additional simulations, keeping these structures frozen and including the complete protein sequence. This procedure is applied to two small DNA-binding proteins, 434 cro and the Drosophila melanogaster homeodomain that contain 65 and 47 residues, respectively, and is compared to the nonhierarchical procedure where the whole protein is predicted in a single run. The best predicted structures were found to present root-mean-square deviations relative to the native conformation of 2.7 ? in the case of the homeodomain and of 3.9 ? for 434 cro; these structures thus represent low-resolution models of the native structures. Strikingly, not only the helices were correctly predicted but also intervening turn motifs. Received: 6 July 2000 / Accepted: 8 September 2000 / Published online: 21 December 2000     

On the Petrials of thin rank 3 geometries

The aim of this paper is to extend the concept of a Petrial to thin (regular) rank three geometries. The main result is that if the Petrial of a thin regular residually connected geometry Γ is also a thin geometry, the geometry Γ has a linear diagram. Received 12 October 1999; revised 25 March 2000.     

Computational analysis of counter-based schemes for VLSI test pattern generation

The use of a binary counter as a mechanism for VLSI built-in test pattern generation is examined. Four different schemes are studied which are defined as partitioning problems on the rows of a binary matrix T. The goal in all problems is to minimize the maximum distance between the values of the binary patterns of any two rows of T, so that they can be generated by a counter in the minimum number of cycles. Although all schemes are NP-hard, an approximation algorithm is presented for the first scheme which guarantees solutions within 2·p from the optimal, where p is the prescribed number of partitions. The remaining problems are shown to be NP-complete even to be approximated within twice the optimal.