Deriving Protein Structures Efficiently by Integrating Experimental Data into Biomolecular Simulations

Proteine sind molekulare Nanomaschinen in biologischen Zellen. Sie sind wesentliche Bausteine aller bekannten Lebensformen, von Einzellern bis hin zu Menschen, und erfüllen vielfältige Funktionen, wie beispielsweise den Sauerstofftransport im Blut oder als Bestandteil von Haaren. Störungen ihrer physiologischen Funktion können jedoch schwere degenerative Krankheiten wie Alzheimer und Parkinson verursachen. Die Entwicklung wirksamer Therapien für solche Proteinfehlfaltungserkrankungen erfordert ein tiefgreifendes Verständnis der molekularen Struktur und Dynamik von Proteinen. Da Proteine aufgrund ihrer lichtmikroskopisch nicht mehr auflösbaren Größe nur indirekt beobachtet werden können, sind experimentelle Strukturdaten meist uneindeutig. Dieses Problem lässt sich in silico mittels physikalischer Modellierung biomolekularer Dynamik lösen. In diesem Feld haben sich datengestützte Molekulardynamiksimulationen als neues Paradigma für das Zusammenfügen der einzelnen Datenbausteine zu einem schlüssigen Gesamtbild der enkodierten Proteinstruktur etabliert. Die Strukturdaten werden dabei als integraler Bestandteil in ein physikbasiertes Modell eingebunden. In dieser Arbeit untersuche ich, wie sogenannte strukturbasierte Modelle verwendet werden können, um mehrdeutige Strukturdaten zu komplementieren und die enthaltenen Informationen zu extrahieren. Diese Modelle liefern eine effiziente Beschreibung der aus der evolutionär optimierten nativen Struktur eines Proteins resultierenden Dynamik. Mithilfe meiner systematischen Simulationsmethode XSBM können biologische Kleinwinkelröntgenstreudaten mit möglichst geringem Rechenaufwand als physikalische Proteinstrukturen interpretiert werden. Die Funktionalität solcher datengestützten Methoden hängt stark von den verwendeten Simulationsparametern ab. Eine große Herausforderung besteht darin, experimentelle Informationen und theoretisches Wissen in geeigneter Weise relativ zueinander zu gewichten. In dieser Arbeit zeige ich, wie die entsprechenden Simulationsparameterräume mit Computational-Intelligence-Verfahren effizient erkundet und funktionale Parameter ausgewählt werden können, um die Leistungsfähigkeit komplexer physikbasierter Simulationstechniken zu optimieren. Ich präsentiere FLAPS, eine datengetriebene metaheuristische Optimierungsmethode zur vollautomatischen, reproduzierbaren Parametersuche für biomolekulare Simulationen. FLAPS ist ein adaptiver partikelschwarmbasierter Algorithmus inspiriert vom Verhalten natürlicher Vogel- und Fischschwärme, der das Problem der relativen Gewichtung verschiedener Kriterien in der multivariaten Optimierung generell lösen kann. Neben massiven Fortschritten in der Verwendung von künstlichen Intelligenzen zur Proteinstrukturvorhersage ermöglichen leistungsoptimierte datengestützte Simulationen detaillierte Einblicke in die komplexe Beziehung von biomolekularer Struktur, Dynamik und Funktion. Solche computergestützten Methoden können Zusammenhänge zwischen den einzelnen Puzzleteilen experimenteller Strukturinformationen herstellen und so unser Verständnis von Proteinen als den Grundbausteinen des Lebens vertiefen

Non-Invasive Electrocardiographic Imaging of Ventricular Activities: Data-Driven and Model-Based Approaches

Die vorliegende Arbeit beleuchtet ausgewählte Aspekte der Vorwärtsmodellierung, so zum Beispiel die Simulation von Elektro- und Magnetokardiogrammen im Falle einer elektrisch stillen Ischämie sowie die Anpassung der elektrischen Potentiale unter Variation der Leitfähigkeiten. Besonderer Fokus liegt auf der Entwicklung neuer Regularisierungsalgorithmen sowie der Anwendung und Bewertung aktuell verwendeter Methoden in realistischen in silico bzw. klinischen Studien

Assessment of the equivalent dipole layer source model in the reconstruction of cardiac activation times on the basis of BSPMs produced by an anisotropic model of the heart

Contains fulltext : 191955.pdf (Publisher’s version ) (Open Access

Solving the Inverse Problem of Electrocardiography on the Endocardium Using a Single Layer Source

The inverse problem of electrocardiography consists in reconstructing cardiac electrical activity from given body surface electrocardiographic measurements. Despite tremendous progress in the field over the last decades, the solution of this problem in terms of electrical potentials on both epi- and the endocardial heart surfaces with acceptable accuracy remains challenging. This paper presents a novel numerical approach aimed at improving the solution quality on the endocardium. Our method exploits the solution representation in the form of electrical single layer densities on the myocardial surface. We demonstrate that this representation brings twofold benefits: first, the inverse problem can be solved for the physiologically meaningful single layer densities. Secondly, a conventional transfer matrix for electrical potentials can be split into two parts, one of which turned out to posess regularizing properties leading to improved endocardial reconstructions. The method was tested in-silico for ventricular pacings utilizing realistic CT-based heart and torso geometries. The proposed approach provided more accurate solution on the ventricular endocardium compared to the conventional potential-based solutions with Tikhonov regularization of the 0th, 1st, and 2nd orders. Furthermore, we show a uniform spatio-temporal behavior of the single layer densities over the heart surface, which could be conveniently employed in the regularization procedure

Non-invasive Localization of the Ventricular Excitation Origin Without Patient-specific Geometries Using Deep Learning

Ventricular tachycardia (VT) can be one cause of sudden cardiac death affecting 4.25 million persons per year worldwide. A curative treatment is catheter ablation in order to inactivate the abnormally triggering regions. To facilitate and expedite the localization during the ablation procedure, we present two novel localization techniques based on convolutional neural networks (CNNs). In contrast to existing methods, e.g. using ECG imaging, our approaches were designed to be independent of the patient-specific geometries and directly applicable to surface ECG signals, while also delivering a binary transmural position. One method outputs ranked alternative solutions. Results can be visualized either on a generic or patient geometry. The CNNs were trained on a data set containing only simulated data and evaluated both on simulated and clinical test data. On simulated data, the median test error was below 3mm. The median localization error on the clinical data was as low as 32mm. The transmural position was correctly detected in up to 82% of all clinical cases. Using the ranked alternative solutions, the top-3 median error dropped to 20mm on clinical data. These results demonstrate a proof of principle to utilize CNNs to localize the activation source without the intrinsic need of patient-specific geometrical information. Furthermore, delivering multiple solutions can help the physician to find the real activation source amongst more than one possible locations. With further optimization, these methods have a high potential to speed up clinical interventions. Consequently they could decrease procedural risk and improve VT patients' outcomes.Comment: 14 pages, 9 figures. Abstract was shortened for arXi

Validation and Opportunities of Electrocardiographic Imaging: From Technical chievements to Clinical Applications

[EN] Electrocardiographic imaging (ECGI) reconstructs the electrical activity of the heart from a dense array of body-surface electrocardiograms and a patient-specific heart-torso geometry. Depending on how it is formulated, ECGI allows the reconstruction of the activation and recovery sequence of the heart, the origin of premature beats or tachycardia, the anchors/hotspots of re-entrant arrhythmias and other electrophysiological quantities of interest. Importantly, these quantities are directly and non-invasively reconstructed in a digitized model of the patient's three-dimensional heart, which has led to clinical interest in ECGI's ability to personalize diagnosis and guide therapy. Despite considerable development over the last decades, validation of ECGI is challenging. Firstly, results depend considerably on implementation choices, which are necessary to deal with ECGI's ill-posed character. Secondly, it is challenging to obtain (invasive) ground truth data of high quality. In this review, we discuss the current status of ECGI validation as well as the major challenges remaining for complete adoption of ECGI in clinical practice. Specifically, showing clinical benefit is essential for the adoption of ECGI. Such benefit may lie in patient outcome improvement, workflow improvement, or cost reduction. Future studies should focus on these aspects to achieve broad adoption of ECGI, but only after the technical challenges have been solved for that specific application/pathology. We propose 'best' practices for technical validation and highlight collaborative efforts recently organized in this field. Continued interaction between engineers, basic scientists, and physicians remains essential to find a hybrid between technical achievements, pathological mechanisms insights, and clinical benefit, to evolve this powerful technique toward a useful role in clinical practice.This study received financial support from the Hein Wellens Fonds, the Cardiovascular Research and Training Institute (CVRTI), the Nora Eccles Treadwell Foundation, the National Institute of General Medical Sciences of the National Institutes of Health (P41GM103545), the National Institutes of Health (NIH HL080093), the French government as part of the Investments of the Future program managed by the National Research Agency (ANR-10-IAHU-04), from the VEGA Grant Agency in Slovakia (2/0071/16), from the Slovak Research and Development Agency (APVV-14-0875), the Fondo Europeo de Desarrollo Regional (FEDER), the Instituto de Salud Carlos III (PI17/01106) and from Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana (AICO/2018/267) and NIH grant (HL125998) and National Science Foundation (ACI-1350374).Cluitmans, M.; Brooks, D.; Macleod, RS.; Dossel, O.; Guillem Sánchez, MS.; Van Dam, P.; Svehlikova, J.... 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Online adaptive geometry predictor of aquaculture fish-nets

This paper proposes an online adaptive geometry predictor for aquaculture fish-nets. The 3D fish-net model is based on a lumped-mass method according to which the net meshes are represented by four interconnected cylindrical elements. The external forces are applied at the center of each element, while the internal forces are calculated as tension forces between two neighboring mass points. The model is validated through several simulations for a small-scale open cylinder exposed to steady uniform current. The preliminary simulation results of the full aquaculture net system are provided as well. The proposed predictor will be used as an information source in the control architecture of an underwater vehicle