Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

Time-resolved volumetric measurement of fine-scale coherent structures in turbulence.

We present full volumetric (three-dimensional) time-resolved (+one-dimensional) measurements of the velocity field in a large water mixing tank, allowing us to assess spatial and temporal rotational energy (enstrophy) and turbulent energy dissipation intermittency. In agreement with previous studies, highly intermittent behavior is observed, with intense coherent flow structures clustering in the periphery of larger vortices. However, further to previous work the full volumetric measurements allow us to separate out the effects of advection from other effects, elucidating not only their topology but also the evolution of these intense events, through the local balance of stretching and diffusion. These findings contribute toward a better understanding of the intermittency phenomenon, which should pave the way for more accurate models of the small-scale motions based on an understanding of the underlying flow physics.

A comparison of methods for assessing the lifetime reliability of a moored FPSO

Current design codes for floating offshore structures are based on measures of short-term reliability. That is, a design storm is selected via an extreme value analysis of the environmental conditions and the reliability of the vessel in that design storm is computed. Although this approach yields valuable information on the vessel motions, it does not produce a statistically rigorous assessment of the lifetime probability of failure. An alternative approach is to perform a long-term reliability analysis in which consideration is taken of all sea states potentially encountered by the vessel during the design life. Although permitted as a design approach in current design codes, the associated computational expense generally prevents its use in practice. A new efficient approach to long-term reliability analysis is presented here, the results of which are compared with a traditional short-term analysis for the surge motion of a representative moored FPSO in head seas. This serves to illustrate the failure probabilities actually embedded within current design code methods, and the way in which design methods might be adapted to achieve a specified target safety level.

Secondary flow near an undulatory surface induced by wall blocking effect

Prandtl's secondary mean motions of the second kind near an undulating surface were explained in terms of turbulent blocking effect and kinematic boundary conditions at the surface, and its order of magnitude was estimated. Isotropic turbulence is distorted by the undulating surface of wavelength λ and amplitude h with a low slope, so that h « λ. The prime mechanism for generating the mean flow is that the far-field Isotropic turbulence is distorted by the non-local blocking effect of the surface to become anisotropic axisymmetric turbulence near the surface with principal axis that is not aligned with the local curvature of the undulation. Then the local analysis can be applied and the mechanism is similar to the mean flow generation mechanism for homogeneous axisymmetric turbulence over a planer surface, i.e. gradients of the Reynolds stress caused by the turbulent blocking effect generate the mean motions. The results from this simple analysis are consistent with previous exact analysis in which the effects of curvature are strictly taken into account. The results also qualitatively agree with flow visualization over an undulating surface in a mixing-box.

A comparison of methods for the coupled analysis of floating structures

The dynamic analysis of a deepwater floating platform and the associated mooring/riser system should ideally be fully coupled to ensure a reliable response prediction. It is generally held that a time domain analysis is the only means of capturing the various coupling and nonlinear effects accurately. However, in recent work it has been found that for an ultra-deepwater floating system (2000m water depth), the highly efficient frequency domain approach can provide highly accurate response predictions. One reason for this is the accuracy of the drag linearization procedure over both first and second order motions, another reason is the minimal geometric nonlinearity displayed by the mooring lines in deepwater. In this paper, the aim is to develop an efficient analysis method for intermediate water depths, where both mooring/vessel coupling and geometric nonlinearity are of importance. It is found that the standard frequency domain approach is not so accurate for this case and two alternative methods are investigated. In the first, an enhanced frequency domain approach is adopted, in which line nonlinearities are linearized in a systematic way. In the second, a hybrid approach is adopted in which the low frequency motion is solved in the time domain while the high frequency motion is solved in the frequency domain; the two analyses are coupled by the fact that (i) the low frequency motion affects the mooring line geometry for the high frequency motion, and (ii) the high frequency motion affects the drag forces which damp the low frequency motion. The accuracy and efficiency of each of the methods are systematically compared. Copyright © 2007 by ASME.

Dynamics of in-plane arch rocking: An energy approach

This study employs an analytical model to describe the rocking response of a masonry arch to in-plane seismic loading. Through evaluation of the rate of energy input to the system, the model reveals the ground motions that cause maximum rocking amplification. An experimental investigation of small-scale masonry arches subjected to past earthquake time histories is used to evaluate the analytical model and to explore arch rocking behaviour. The results demonstrate that rocking amplification can occur, but is highly sensitive to slight variations in the ground motion. Thus, the accuracy to which the arch response can be predicted is brought into perspective. The concept that the primary impulse of an expected ground motion is fundamentally important in predicting arch collapse is evaluated in light of the developed energy approach. Finally, a statistical method is proposed for predicting the probability of arch collapse during seismic loading.

On the use of combined compact scheme for numerical solution of the two-layer oceanic shallow water equations

Many types of oceanic physical phenomena have a wide range in both space and time. In general, simplified models, such as shallow water model, are used to describe these oceanic motions. The shallow water equations are widely applied in various oceanic and atmospheric extents. By using the two-layer shallow water equations, the stratification effects can be considered too. In this research, the sixth-order combined compact method is investigated and numerically implemented as a high-order method to solve the two-layer shallow water equations. The second-order centered, fourth-order compact and sixth-order super compact finite difference methods are also used to spatial differencing of the equations. The first part of the present work is devoted to accuracy assessment of the sixth-order super compact finite difference method (SCFDM) and the sixth-order combined compact finite difference method (CCFDM) for spatial differencing of the linearized two-layer shallow water equations on the Arakawa's A-E and Randall's Z numerical grids. Two general discrete dispersion relations on different numerical grids, for inertia-gravity and Rossby waves, are derived. These general relations can be used for evaluation of the performance of any desired numerical scheme. For both inertia-gravity and Rossby waves, minimum error generally occurs on Z grid using either the sixth-order SCFDM or CCFDM methods. For the Randall's Z grid, the sixth-order CCFDM exhibits a substantial improvement , for the frequency of the barotropic and baroclinic modes of the linear inertia-gravity waves of the two layer shallow water model, over the sixth-order SCFDM. For the Rossby waves, the sixth-order SCFDM shows improvement, for the barotropic and baroclinic modes, over the sixth-order CCFDM method except on Arakawa's C grid. In the second part of the present work, the sixth-order CCFDM method is used to solve the one-layer and two-layer shallow water equations in their nonlinear form. In one-layer model with periodic boundaries, the performance of the methods for mass conservation is compared. The results show high accuracy of the sixth-order CCFDM method to simulate a complex flow field. Furthermore, to evaluate the performance of the method in a non-periodic domain the sixth-order CCFDM is applied to spatial differencing of vorticity-divergence-mass representation of one-layer shallow water equations to solve a wind-driven current problem with no-slip boundary conditions. The results show good agreement with published works. Finally, the performance of different schemes for spatial differencing of two-layer shallow water equations on Z grid with periodic boundaries is investigated. Results illustrate the high accuracy of combined compact method.

Effect of previous cyclic axial loads on pile groups

Numerous piles are often subjected to the combination of cyclic axial and cyclic lateral loads in service, such as piled foundations for offshore platforms which may suffer swaying and rocking motions owing to wind and wave actions. In this research, centrifuge tests were conducted to investigate the effect of previous cyclic axial loads on the performance of pile groups subjected to subsequent cyclic lateral loads. Different pile installation methods were also applied to study the different behaviour of bored and jacked pile groups subjected to cyclic loads. During lateral load cycling, it is seen that cyclic axial loads to which pile groups were previously subjected could reduce the pile cap permanent lateral displacement in the first lateral load cycle but do not influence the incremental rate of permanent displacement in the following lateral load cycles. Moreover, it is found that previous cyclic axial loads could improve the pile cap cyclic lateral secant stiffness, especially for the pre-jacked pile group. When rocking motions were induced by cyclic lateral loads, pile groups subjected to cyclic axial loads before have smaller permanent settlement than those without the cyclic axial loading effect. The designers of piles that are intended to resist significant lateral loads without excessive deformations in service may wish to deploy cyclic axial preloading, accordingly.

Silhouette-based object phenotype recognition using 3D shape priors

This paper tackles the novel challenging problem of 3D object phenotype recognition from a single 2D silhouette. To bridge the large pose (articulation or deformation) and camera viewpoint changes between the gallery images and query image, we propose a novel probabilistic inference algorithm based on 3D shape priors. Our approach combines both generative and discriminative learning. We use latent probabilistic generative models to capture 3D shape and pose variations from a set of 3D mesh models. Based on these 3D shape priors, we generate a large number of projections for different phenotype classes, poses, and camera viewpoints, and implement Random Forests to efficiently solve the shape and pose inference problems. By model selection in terms of the silhouette coherency between the query and the projections of 3D shapes synthesized using the galleries, we achieve the phenotype recognition result as well as a fast approximate 3D reconstruction of the query. To verify the efficacy of the proposed approach, we present new datasets which contain over 500 images of various human and shark phenotypes and motions. The experimental results clearly show the benefits of using the 3D priors in the proposed method over previous 2D-based methods. © 2011 IEEE.

Development of a servo-hydraulic earthquake actuator for the Cambridge Turner beam centrifuge

Dynamic centrifuge modelling has been carried out at Cambridge since the late 1970s. Over this period, three different mechanical earthquake actuators were developed. In this paper the development of a new servo-hydraulic earthquake actuator is described. The basic design principles are explained along with the need to carry out these designs to match the existing services and systems of the 35 year old Turner beam centrifuge at Cambridge. In addition, some of the features of the Turner beam centrifuge are exploited in the design of this new earthquake actuator. The paper also explains the mechanical fabrication of the actuator and the control systems that were developed in order to generate real earthquake motions. Finally, the performance of this new servo-hydraulic earthquake actuator is presented and assessed based on a wide range of earthquake input motions.

Comparison of Camera Motion Estimation Methods for 3D Reconstruction of Infrastructure

Camera motion estimation is one of the most significant steps for structure-from-motion (SFM) with a monocular camera. The normalized 8-point, the 7-point, and the 5-point algorithms are normally adopted to perform the estimation, each of which has distinct performance characteristics. Given unique needs and challenges associated to civil infrastructure SFM scenarios, selection of the proper algorithm directly impacts the structure reconstruction results. In this paper, a comparison study of the aforementioned algorithms is conducted to identify the most suitable algorithm, in terms of accuracy and reliability, for reconstructing civil infrastructure. The free variables tested are baseline, depth, and motion. A concrete girder bridge was selected as the "test-bed" to reconstruct using an off-the-shelf camera capturing imagery from all possible positions that maximally the bridge's features and geometry. The feature points in the images were extracted and matched via the SURF descriptor. Finally, camera motions are estimated based on the corresponding image points by applying the aforementioned algorithms, and the results evaluated.

Machine Vision Enhanced Post-earthquake Inspection

Camera motion estimation is one of the most significant steps for structure-from-motion (SFM) with a monocular camera. The normalized 8-point, the 7-point, and the 5-point algorithms are normally adopted to perform the estimation, each of which has distinct performance characteristics. Given unique needs and challenges associated to civil infrastructure SFM scenarios, selection of the proper algorithm directly impacts the structure reconstruction results. In this paper, a comparison study of the aforementioned algorithms is conducted to identify the most suitable algorithm, in terms of accuracy and reliability, for reconstructing civil infrastructure. The free variables tested are baseline, depth, and motion. A concrete girder bridge was selected as the "test-bed" to reconstruct using an off-the-shelf camera capturing imagery from all possible positions that maximally the bridge's features and geometry. The feature points in the images were extracted and matched via the SURF descriptor. Finally, camera motions are estimated based on the corresponding image points by applying the aforementioned algorithms, and the results evaluated.

Optimized selection of key frames for monocular videogrammetric surveying of civil infrastructure

Videogrammetry is an inexpensive and easy-to-use technology for spatial 3D scene recovery. When applied to large scale civil infrastructure scenes, only a small percentage of the collected video frames are required to achieve robust results. However, choosing the right frames requires careful consideration. Videotaping a built infrastructure scene results in large video files filled with blurry, noisy, or redundant frames. This is due to frame rate to camera speed ratios that are often higher than necessary; camera and lens imperfections and limitations that result in imaging noise; and occasional jerky motions of the camera that result in motion blur; all of which can significantly affect the performance of the videogrammetric pipeline. To tackle these issues, this paper proposes a novel method for automating the selection of an optimized number of informative, high quality frames. According to this method, as the first step, blurred frames are removed using the thresholds determined based on a minimum level of frame quality required to obtain robust results. Then, an optimum number of key frames are selected from the remaining frames using the selection criteria devised by the authors. Experimental results show that the proposed method outperforms existing methods in terms of improved 3D reconstruction results, while maintaining the optimum number of extracted frames needed to generate high quality 3D point clouds.© 2012 Elsevier Ltd. All rights reserved.

Efficient truncation scheme for modeling deepwater mooring lines

This paper is aimed at enabling the confident use of existing model test facilities for ultra deepwater application without having to compromise on the widely accepted range of scales currently used by the floating production industry. Passive line truncation has traditionally been the preferred method of creating an equivalent numerical model at reduced depth; however, these techniques tend to suffer in capturing accurately line dynamic response and so reproducing peak tensions. In an attempt to improve credibility of model test data the proposed truncation procedure sets up the truncated model, based on line dynamic response rather than quasi-static system stiffness. The upper sections of each line are modeled in detail, capturing the wave action zone and all coupling effects with the vessel. These terminate to an approximate analytical model that aims to simulate the remainder of the line. Stages 1 & 2 are used to derive a water depth truncation ratio. Here vibration decay of transverse elastic waves is assessed and it is found that below a certain length criterion, the transverse vibrational characteristics for each line are inertia driven, hence with respect to these motions the truncated model can assume a linear damper whose coefficient depends on the local line properties and vibration frequency. Stage 3 endeavors to match the individual line stiffness between the full depth and truncated models. In deepwater it is likely that taut polyester moorings will be used which are predominantly straight and have high axial stiffness that provides the principal restoring force to static and low frequency vessel motions. Consequently, it means that the natural frequencies of axial vibrations are above the typical wave frequency range allowing for a quasi-static solution. In cases of exceptionally large wave frequency vessel motions, localized curvature at the chain seabed segment and tangential skin drag on the polyester rope can increase dynamic peak tensions considerably. The focus of this paper is to develop an efficient scheme based on analytic formulation, for replicating these forces at the truncation. The paper will close with an example case study of a single mooring under extreme conditions that replicates exactly the static and dynamic characteristics of the full depth line. Copyright © 2012 by the International Society of Offshore and Polar Engineers (ISOPE).

Thermal stratification produced by plumes and jets in enclosed spaces

The airflow and thermal stratification produced by a localised heat source located at floor level in a closed room is of considerable practical interest and is commonly referred to as a 'filling box'. In rooms with low aspect ratios H/R ≲ 1 (room height H to characteristic horizontal dimension R) the thermal plume spreads laterally on reaching the ceiling and a descending horizontal 'front' forms separating a stably stratified, warm upper region from cooler air below. The stratification is well predicted for H/R ≲ 1 by the original filling box model of Baines and Turner (J. Fluid. Mech. 37 (1968) 51). This model represents a somewhat idealised situation of a plume rising from a point source of buoyancy alone-in particular the momentum flux at the source is zero. In practical situations, real sources of heating and cooling in a ventilation system often include initial fluxes of both buoyancy and momentum, e.g. where a heating system vents warm air into a space. This paper describes laboratory experiments to determine the dependence of the 'front' formation and stratification on the source momentum and buoyancy fluxes of a single source, and on the location and relative strengths of two sources from which momentum and buoyancy fluxes were supplied separately. For a single source with a non-zero input of momentum, the rate of descent of the front is more rapid than for the case of zero source momentum flux and increases with increasing momentum input. Increasing the source momentum flux effectively increases the height of the enclosure, and leads to enhanced overturning motions and finally to complete mixing for highly momentum-driven flows. Stratified flows may be maintained by reducing the aspect ratio of the enclosure. At these low aspect ratios different long-time behaviour is observed depending on the nature of the heat input. A constant heat flux always produces a stratified interior at large times. On the other hand, a constant temperature supply ultimately produces a well-mixed space at the supply temperature. For separate sources of momentum and buoyancy, the developing stratification is shown to be strongly dependent on the separation of the sources and their relative strengths. Even at small separation distances the stratification initially exhibits horizontal inhomogeneity with localised regions of warm fluid (from the buoyancy source) and cool fluid. This inhomogeneity is less pronounced as the strength of one source is increased relative to the other. Regardless of the strengths of the sources, a constant buoyancy flux source dominates after sufficiently large times, although the strength of the momentum source determines whether the enclosure is initially well mixed (strong momentum source) or stably stratified (weak momentum source). © 2001 Elsevier Science Ltd. All rights reserved.