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At least 883 records · Page 49

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa

Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance. Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa. We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of antibacterial agents suitable for treatment of P. aeruginosa infections.

59 BASIC BIOLOGICAL SCIENCES↗

MULTISTEP AND CONTINUOUS PHYSICS-INFORMED NEURAL NETWORK METHODS FOR LEARNING GOVERNING EQUATIONS AND CONSTITUTIVE RELATIONS

In this work, we investigate the applicability and relative merit of discrete and continuous versions of physics-informed neural network (PINN) methods for learning unknown governing equations or constitutive relations in a nonlinear dynamical system. In the case of unknown dynamics, entire right-hand-side (RHS) equations of the ordinary differential equations are unknown. In the case of unknown constitutive relations, however, the RHS equations are known up to the specification of constitutive relations (that may depend on the state of the system). We use a deep neural network to model unknown governing equations or constitutive relations. The discrete PINN approach combines classical multistep discretization methods for dynamical systems with neural-network-based machine learning methods. On the other hand, the continuous versions utilize deep neural networks to minimize the residual function for the continuous governing equations. We use the case of a fedbatch bioreactor system to study the effectiveness of these approaches and discuss conditions for their applicability. Our results indicate that the accuracy of the trained neural network models is much higher for the cases where we only have to learn a constitutive relation instead of all dynamics. This finding corroborates the well-known fact from scientific computing that building as much structural information as is available into an algorithm can enhance its efficiency and/or accuracy.

97 MATHEMATICS AND COMPUTING↗

On the Response of a Herschel–Bulkley Fluid Due to a Moving Plate

In this paper, we study the boundary-layer flow of a Herschel–Bulkley fluid due to a moving plate; this problem has been experimentally investigated by others, where the fluid was assumed to be Carbopol, which has similar properties to cement. The computational fluid dynamics finite volume method from the open-source toolbox/library OpenFOAM is used on structured quad grids to solve the mass and the linear momentum conservation equations using the solver “overInterDyMFoam” customized with non-Newtonian viscosity libraries. The governing equations are solved numerically by using regularization methods in the context of the overset meshing technique. The results indicate that there is a good comparison between the experimental data and the simulations. The boundary layer thicknesses are predicted within the uncertainties of the measurements. The simulations indicate strong sensitivities to the rheological properties of the fluid.

36 MATERIALS SCIENCE↗

Integrating matrix solution of the hybrid state vector equations for beam vibration

A simple, versatile, and efficient computational technique has been developed for dynamic analysis of linear elastic beam and rod type of structures. Moreover, the method provides a rather general solution approach for two-point boundary value problems that are described by a single independent spatial variable. For structural problems, the method is implemented by a mixed state vector formulation of the differential equations, combined with an integrating matrix solution procedure. Highly accurate solutions are easily achieved with this approach. Example solutions are given for beam vibration problems including discontinuous stiffness and mass parameters, elastic restraint boundary conditions, concentrated inertia loading, and rigid body modes

Lehman, L. L.↗

Research study of space plasma boundary processes

Representation of the Earth's bow shock and magnetopause and their geometrically determined macrostructure was investigated. Computer graphic depictions of the global distributions of bow shock structures and elementary animation of the dynamics of those distributions in the changing solar wind were developed. The shock-foreshock boundary and subcritical bow shocks as observed by ISEE 1 and 2 are discussed.

Greenstadt, E. W.↗

Some recent advances in computational aerodynamics for helicopter applications

The growing application of computational aerodynamics to nonlinear helicopter problems is outlined, with particular emphasis on several recent quasi-two-dimensional examples that used the thin-layer Navier-Stokes equations and an eddy-viscosity model to approximate turbulence. Rotor blade section characteristics can now be calculated accurately over a wide range of transonic flow conditions. However, a finite-difference simulation of the complete flow field about a helicopter in forward flight is not currently feasible, despite the impressive progress that is being made in both two and three dimensions. The principal limitations are today's computer speeds and memories, algorithm and solution methods, grid generation, vortex modeling, structural and aerodynamic coupling, and a shortage of engineers who are skilled in both computational fluid dynamics and helicopter aerodynamics and dynamics.

Mccroskey, W. J.↗

Analyzing Control/Structure Interactions

CO-ST-IN computer program developed to facilitate study of control/structure interactions; dynamic coupling between control systems and flexible structures. Works in conjunction with other programs to enhance analysis of vibrations. Designed to complement and enhance rather than replace software tools for analysis of control systems and dynamics of structures. FORTRAN 77 program.

Carney, K.↗

Numerical simulation of jet noise

Jet noise and jet-induced structural loads have become key issues in the design of commercial and military aircraft. Computational Fluid Dynamics (CFD) can be of use in predicting the underlying jet shear-layer instabilities and, in conjunction with classical acoustic theory, jet noise. The computational issues involved in the resolution of high Reynolds number unsteady jet flows are addressed in this paper. Once these jet flows can be accurately resolved, it should be possible to use acoustic theory to extract, for example, the far-field jet noise. An assessment of future work and computational resources required for directly computing far-field jet noise is also presented.

Van Dalsem, W. R.↗

Summary of the Third AIAA CFD Drag Prediction Workshop

The workshop focused on the prediction of both absolute and differential drag levels for wing-body and wing-al;one configurations of that are representative of transonic transport aircraft. The baseline DLR-F6 wing-body geometry, previously utilized in DPW-II, is also augmented with a side-body fairing to help reduce the complexity of the flow physics in the wing-body juncture region. In addition, two new wing-alone geometries have been developed for the DPW-II. Numerical calculations are performed using industry-relevant test cases that include lift-specific and fixed-alpha flight conditions, as well as full drag polars. Drag, lift, and pitching moment predictions from previous Reynolds-Averaged Navier-Stokes computational fluid Dynamics Methods are presented, focused on fully-turbulent flows. Solutions are performed on structured, unstructured, and hybrid grid systems. The structured grid sets include point-matched multi-block meshes and over-set grid systems. The unstructured and hybrid grid sets are comprised of tetrahedral, pyramid, and prismatic elements. Effort was made to provide a high-quality and parametrically consistent family of grids for each grid type about each configuration under study. The wing-body families are comprised of a coarse, medium, and fine grid, while the wing-alone families also include an extra-fine mesh. These mesh sequences are utilized to help determine how the provided flow solutions fair with respect to asymptotic grid convergence, and are used to estimate an absolute drag of each configuration.

Vassberg, John C.↗

Computational Fluid Dynamics-Based Aeroservoelastic Analysis with Hyper-X Applications

A finite element computational fluids dynamics-based aeroservoelastic analysis methodology is presented in this paper, in which both structural and fluids discretization are achieved by the finite element method, and their interaction is modeled by the transpiration boundary condition technique. In the fluids discipline either inviscid or viscous flow may be accounted for, usually employing unstructured grids.Adescription of a novel viscous flow solver employing unstructured grids is given in detail. Provisions are made for digital as well as analog controllers. These new aeroservoelastic analysis techniques are next applied for the solution of a number of example problems including the novel Hyper-X launch vehicle. Experimental and actual flight test data are also compared with analysis results that signify to the efficacy and accuracy of the newly developed solution procedures.

Gupta, K. K.↗

Fiber Bragg Grating Sensor System for Monitoring Smart Composite Aerospace Structures

Lightweight, electromagnetic interference (EMI) immune, fiber-optic, sensor- based structural health monitoring (SHM) will play an increasing role in aerospace structures ranging from aircraft wings to jet engine vanes. Fiber Bragg Grating (FBG) sensors for SHM include advanced signal processing, system and damage identification, and location and quantification algorithms. Potentially, the solution could be developed into an autonomous onboard system to inspect and perform non-destructive evaluation and SHM. A novel method has been developed to massively multiplex FBG sensors, supported by a parallel processing interrogator, which enables high sampling rates combined with highly distributed sensing (up to 96 sensors per system). The interrogation system comprises several subsystems. A broadband optical source subsystem (BOSS) and routing and interface module (RIM) send light from the interrogation system to a composite embedded FBG sensor matrix, which returns measurand-dependent wavelengths back to the interrogation system for measurement with subpicometer resolution. In particular, the returned wavelengths are channeled by the RIM to a photonic signal processing subsystem based on powerful optical chips, then passed through an optoelectronic interface to an analog post-detection electronics subsystem, digital post-detection electronics subsystem, and finally via a data interface to a computer. A range of composite structures has been fabricated with FBGs embedded. Stress tensile, bending, and dynamic strain tests were performed. The experimental work proved that the FBG sensors have a good level of accuracy in measuring the static response of the tested composite coupons (down to submicrostrain levels), the capability to detect and monitor dynamic loads, and the ability to detect defects in composites by a variety of methods including monitoring the decay time under different dynamic loading conditions. In addition to quasi-static and dynamic load monitoring, the system can capture acoustic emission events that can be a prelude to structural failure, as well as piezoactuator-induced ultrasonic Lamb-waves-based techniques as a basis for damage detection.

Moslehi, Behzad↗

Data‐Driven Engineering of Thermostable Collagen‐Mimetic Peptoid Triple Helices

Collagen-mimetic peptides (CMPs) are engineered molecules designed to replicate the triple-helical structure of natural collagen. A repeating x–y-Gly sequence is the defining motif of CMPs and is critical to their triple-helical structure and stability. Substitutions to the residues occupying the x and y positions present a means to modulate the CMP structure and properties. Peptoid residues—N-substituted glycine derivatives—present an attractive potential substitution due to their thermal stability, proteolytic resistance, biocompatibility, and diverse palette of non-natural side chains, but also tend to introduce a high degree of backbone flexibility that can diminish the stability of the triple helix. In this work, we report a computational active learning cycle comprising molecular dynamics simulation, Gaussian process regression, and Bayesian optimization to computationally identify a number of promising peptoid substitutions predicted to stabilize the desired quaternary structure through side chain interactions and produce stable peptoid-based collagen-like triple helices. To experimentally test the computational predictions, a top candidate identified by the screen was synthesized and imaged using scanning electron microscopy to resolve fibril-like bundles consistent with collagen-like triple helices. This work predicts a number of CMP peptoid substitutions capable of forming stable triple-helical structures, presents a generalizable design strategy for engineering desired peptoid structures, and opens new avenues for the design of peptoid-based biomimetic materials.

active learning↗

Results of NASTRAN modal analyses and ground vibration tests on the YF-12A airplane

The YF-12A aircraft, a delta-winged vehicle powered by two jet engines, was utilized in an investigation of the structural dynamic characteristics of a large, flexible, supersonic research vehicle. A large NASA structural analysis (NASTRAN) finite-element model was used to compute the ten lowest frequency symmetric and ten lowest frequency antisymmetric modes for the YF-12A aircraft. The results of the analysis were compared with experimental data obtained in a ground vibration test conducted with the completed aircraft. It was found that the finite-element structural model employed provides an adequate prediction of the dynamic behavior of the aircraft structure in the case of basic wing and body modes.

Kordes, E. E.↗

Efficient eigensolution reanalysis of nonclassically damped structures

Effective methods of approximate eigensolution reanalysis of modified nonclassically damped structures are developed. For structures with passive or active discrete damping devices or with damping treatment, the system becomes nonproportionally damped and the computation of its dynamic responses may require the use of complex modes. For larger systems, the computation of complex modes is very expensive. Thus it is desirable to have approximate reanalysis techniques for the efficient evaluation of the effect of design changes. In recent years, the assumed mode reanalysis method was successfully applied to minimum weight design of undamped structures with natural frequency constraints. The accuracy of the assumed mode reanalysis method can be improved dramatically if the global approximation function includes the normal modes of the original system and their derivatives. This approach was demonstrated to be effective even for a system with shape changes. The approach used by Noor et al. for eigensolution reanalysis of undamped structures is extended to treat a nonclassically damped system.

Wang, Bo Ping↗

Linear and nonlinear dynamic instability of rotating polytropes

A three-dimensional hydrodynamic computer program is used to study the growth of nonaxisymmetric structures in rapidly rotating, self-gravitating polytropes. Models with polytropic index n = 0.8, 1.0, 1.3, 1.5, and 1.8 are studied. The initially axisymmetric equilibria are constructed by the Ostriker-Mark self-consistent-field method. The nonaxisymmetric pattern that develops out of low-amplitude random noise is a two-armed spiral with a well-defined pattern speed and growth rate which closely match properties of the toroidal mode predicted from the linear, second-order tensor-virial equation. A Fourier analysis of each polytrope's azimuthal density distribution shows that, even in the linear amplitude regime, higher-order angular patterns also develop exponentially in time. The higher-order patterns ultimately move in synchronization with the broad two-armed spiral, creating a narrow two-armed spiral. As the polytropic index is decreased, a more open and centrally more barlike pattern develops.

Williams, Harold A.↗

Robustness in the presence of mixed parametric uncertainty and unmodeled dynamics

Continuing the development of the structured singular value approach to robust control design, the authors investigate the problem of computing the structured singular value (mu) in the case of mixed real parametric and complex uncertainty. The problem is shown to be equivalent to a smooth constrained finite-dimensional optimization problem. In view of the fact that the functional to be maximized may have several local extrema, an upper bound on mu whose computation is numerically tractable is established; this leads to a sufficient condition of robust stability and performance. A historical perspective on the development of the mu theory is included.

Fan, Michael K. H.↗