Simulation of masonry out-of-plane failure modes by multi-body dynamics

The seismic assessment of the local failure modes in existing masonry buildings is currently based on the identification of the so-called local mechanisms, often associated with the out-of-plane wall behavior, whose stability is evaluated by static force-based approaches and, more recently, by some displacement-based proposals. Local mechanisms consist of kinematic chains of masonry portions, often regarded as rigid bodies, with geometric nonlinearity and concentrated nonlinearity in predefined contact regions (unilateral no-tension behavior, possible sliding with friction). In this work, the dynamic behavior of local mechanisms is simulated through multi-body dynamics, to obtain the nonlinear response with efficient time history analyses that directly take into account the characteristics of the ground motion. The amplification/filtering effects of the structure are considered within the input motion. The proposed approach is validated with experimental results of two full-scale shaking-table tests on stone masonry buildings: a sacco-stone masonry façade tested at Laboratório Nacional de Engenharia Civil and a two-storey double-leaf masonry building tested at European Centre for Training and Research in Earthquake Engineering (EUCENTRE).

Analysis and modeling of ants’ behavior from single to multi-body

In order to shed light on the collective behavior of social insects, we analyzed the behavior of ants from single to multi-body. In an experimental set-up, ants are placed in hemisphere without a nest and food. Trajectory of ants is recorded. From this bottom-up approach, we found that collective behavior of ants as follows: 1. Activity of single ant increases and decreases periodically. 2. Spontaneous meeting process is observed between two ants and meeting spot of two ants is localized in hemisphere. 3. Result on division of labor is obtained between two ants.

Multi-body simulation of a canine hind limb: model development, experimental validation and calculation of ground reaction forces

Background: Among other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS-) model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces. Methods: The anatomical geometries of the MBS-model have been established using computer tomography- (CT-) and magnetic resonance imaging- (MRI-) data. The CT-data were collected from the pelvis, femora, tibiae and pads of a mixed-breed adult dog. Geometric information about 22 muscles of the pelvic extremity of 4 mixed-breed adult dogs was determined using MRI. Kinematic and kinetic data obtained by motion analysis of a clinically healthy dog during a gait cycle (1 m/s) on an instrumented treadmill were used to drive the model in the multi-body simulation. Results and Discussion: As a result the vertical ground reaction forces (z-direction) calculated by the MBS-system show a maximum deviation of 1.75%BW for the left and 4.65%BW for the right hind limb from the treadmill measurements. The calculated peak ground reaction forces in z- and y-direction were found to be comparable to the treadmill measurements, whereas the curve characteristics of the forces in y-direction were not in complete alignment. Conclusion: In conclusion, it could be demonstrated that the developed MBS-model is suitable for simulating ground reaction forces of dogs during walking. In forthcoming investigations the model will be developed further for the calculation of forces and moments acting on the hip joint during different movements, which can be of help in context with the in silico development and testing of hip prostheses.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Multi-finger grasps in a dynamic environment

Most current state-of-the-art haptic devices render only a single force, however almost all human grasps are characterised by multiple forces and torques applied by the fingers and palms of the hand to the object. In this chapter we will begin by considering the different types of grasp and then consider the physics of rigid objects that will be needed for correct haptic rendering. We then describe an algorithm to represent the forces associated with grasp in a natural manner. The power of the algorithm is that it considers only the capabilities of the haptic device and requires no model of the hand, thus applies to most practical grasp types. The technique is sufficiently general that it would also apply to multi-hand interactions, and hence to collaborative interactions where several people interact with the same rigid object. Key concepts in friction and rigid body dynamics are discussed and applied to the problem of rendering multiple forces to allow the person to choose their grasp on a virtual object and perceive the resulting movement via the forces in a natural way. The algorithm also generalises well to support computation of multi-body physics

Modelling inter-body contacts in a multiphysics framework

Abstract not available.

Multi-physics modelling for design optimization and manufacturing on high-performance parallel systems

Abstract not available

Modellbildung und Untersuchung eines magnetisch gelagerten Rundtisches

Active magnetic bearing, round table, multi-body system, state-control

Puunkäsittelykoneen simulointi ja mekaaniset häviöt

Diplomityö on osa Savonia-amk:n koneosaston TOVI-projektia, jossa metsä-konevalmistaja Ponsse Oyj on mukana. Työssä tutkittiin Ponsse Oyj:n metsäkoneen harvesteripäätä. Tavoitteena oli harvesteripään puun syöttöliikkeessä syntyvien mekaanisten häviöiden selvittäminen. Mekaanisilla häviöillä tarkoitamme karsintaterien kitkavoimia ja syöttörullien vierintävastusta.Edellisten lisäksi tavoitteena oli tutkia puun syöttöliikkeen simuloitavuutta monikappaledynamiikkaan perustuvalla simu-lointiohjelmistolla. Työ toteutettiin mittaamalla harvesteripään hydraulisten toimilaitteiden paineita, puun syötön aikana. Mittasimme myös puun ja harvesteripään välistä liikematkaa, nopeutta, kiihtyvyyttä, sekä puun paksuutta. Mittausten lisäksi harvesteripäästä rakennettiin simulointimalli. Mitattujen paineiden avulla laskettiin vastaavien toimilaitteiden synnyttämät voimat ja momentit. Simulointimallilla toistettiin mittaustapahtumat, käyttäen mittausten avulla laskettuja voimia ja momentteja. Mallin kitkakertoimien ja vierintävastusten avulla simuloidut ja mitatut liikematkat haettiin yhteneviksi. Toisin sanoen, simulointimalli verifioitiin todellisuutta vastaavaksi, jolloin simulointimallista voitiin lukea syntyneet häviöt.

Kiinnirullaimen dynamiikan ja värähtelyjen simulointi

Diplomityössä tutkittiin kaupallisen monikappaledynamiikkaohjelmiston soveltuvuutta kiinnirullaimen dynamiikan ja värähtelyjen tutkimiseen. Erityisen kiinnostuneita oltiin nipin kuvauksesta sekä nipissä tapahtuvista värähtelyistä. Tässä diplomityössä mallinnettiin kiinnirullaimen ensiö- ja toisiokäytöt sekä tampuuritela. Malli yhdistettiin myöhemmin Metso Paper Järvenpäässä rinnakkaisena diplomityönä tehtyyn malliin, joista muodostui kahteen ratkaisijaan perustuva simulointimalli. Simulointimalli rakennettiin käyttämään kahta erillistä ratkaisijaa, joista toinen on mekaniikkamallin rakentamisessa käytetty ADAMS-ohjelmisto ja toinen säätöjärjestelmää ja hydraulipiirejä kuvaava Simulink-malli. Nipin mallintamiseksi tampuuritela ja rullaussylinteri mallinnettiin joustaviksi käyttäen keskitettyjen massojen menetelmää. Siirtolaitteissa sekä runkorakenteissa tapahtuvat joustot kuvattiin yhden vapausasteen jousi-vaimennin voimilla kuvattuina järjestelminä. Tässä diplomityössä on myös keskitytty esittelemään ADAMS-ohjelmiston toimintaa ohjeistavasti sekä käsittelemään parametrisen mallintamisen etuja. Työssä havaittiin monikappaledynamiikan soveltuvuus kiinnirullaimen dynamiikan sekä dynaamisten voimien aiheuttamien värähtelyjen tutkimiseen. Suoritetuista värähtelymittauksista voitiin tehdä vain arvioita. Mallin havaittiin vaativan lisätutkimusta ja kehitystyötä

Mekatronisten koneiden reaaliaikainen simulointi Linux-ympäristössä

Työn tavoitteena oli selvittää mahdollisuuksia käyttää Linux-ympäristöä mekatronisten koneiden reaaliaikaisessa simuloinnissa. Työssä tutkittiin C-kielellä tehdyn reaaliaikaisen simulointimallin ratkaisua Linux-käyttöjärjestelmässä RTLinux-reaaliaikalaajennuksen avulla. Reaaliaikainen simulointi onnistui RTLinuxin avulla tehokkaasti ja mallinnusmenetelmien rajoissa tarkasti. I/O-toimintojen lisäämistä erillisten I/O-korttien avulla ei tarkasteltu tässä työssä. Reaaliaikaista Linuxia ei ole aikaisemmin käytetty mekatronisten koneiden simulointiin. Tämän vuoksi valmiita työkaluja ei ole olemassa. Linux-ympäristö ei näin ollen sovellu kovin hyvin yleiseen koneensuunnitteluun mallintamisen työläyden vuoksi.

Monikappalesysteemin esikäsittelijä kaupallisessa ympäristössä

Työn tavoitteena oli tehdä monikappalesysteemin esikäsittelijä, joka toimii CAD-ohjelmiston yhteydessä. CAD-ohjelmistoksi valittiin SolidWorks-ohjelmisto. Esikäsittelijästä tehtiin yhteensopiva monikappaledynamiikan simulointi ohjelmiston kanssa, joka on kehitetty Lappeenrannan teknillisessä yliopistossa. Aikaansaadun esikäsittelijän avulla pystytään tuottamaan monikappaledynamiikan simuloinnissa tarvittavat lähtötiedot. Lähtötiedot esikäsittelijä laskee käyttäjän tekemästä kokoonpanokuvasta ja käyttäjän antamista tiedoista. Esikäsittelijän toiminta verifioitiin kaupallisin simulointiohjelmisto ADAMS:n avulla. Esikäsittelijän todettiin toimivan luotettavasti ja täyttävän sille asetetut vaatimukset. Lisäksi esikäsittelijän todettiin nopeuttavan huomattavasti simulointimallien tekoa.