Efficient algorithms for simulation and analysis of many-body systems

This thesis introduces methods to efficiently generate and analyze time series data of many-body systems. While we have a strong focus on biomolecular processes, the presented methods can also be applied more generally. Due to limitations of microscope resolution in both space and time, biomolecular processes are especially hard to observe experimentally. Computer models offer an opportunity to work around these limitations. However, as these models are bound by computational effort, careful selection of the model as well as its efficient implementation play a fundamental role in their successful sampling and/or estimation. Especially for high levels of resolution, computer simulations can produce vast amounts of high-dimensional data and in general it is not straightforward to visualize, let alone to identify the relevant features and processes. To this end, we cover tools for projecting time series data onto important processes, finding over time geometrically stable features in observable space, and identifying governing dynamics. We introduce the novel software library deeptime with two main goals: (1) making methods which were developed in different communities (such as molecular dynamics and fluid dynamics) accessible to a broad user base by implementing them in a general-purpose way, and (2) providing an easy to install, extend, and maintain library by employing a high degree of modularity and introducing as few hard dependencies as possible. We demonstrate and compare the capabilities of the provided methods based on numerical examples. Subsequently, the particle-based reaction-diffusion simulation software package ReaDDy2 is introduced. It can simulate dynamics which are more complicated than what is usually analyzed with the methods available in deeptime. It is a significantly more efficient, feature-rich, flexible, and user-friendly version of its predecessor ReaDDy. As such, it enables---at the simulation model's resolution---the possibility to study larger systems and to cover longer timescales. In particular, ReaDDy2 is capable of modeling complex processes featuring particle crowding, space exclusion, association and dissociation events, dynamic formation and dissolution of particle geometries on a mesoscopic scale. The validity of the ReaDDy2 model is asserted by several numerical studies which are compared to analytically obtained results, simulations from other packages, or literature data. Finally, we present reactive SINDy, a method that can detect reaction networks from concentration curves of chemical species. It extends the SINDy method---contained in deeptime---by introducing coupling terms over a system of ordinary differential equations in an ansatz reaction space. As such, it transforms an ordinary linear regression problem to a linear tensor regression. The method employs a sparsity-promoting regularization which leads to especially simple and interpretable models. We show in biologically motivated example systems that the method is indeed capable of detecting the correct underlying reaction dynamics and that the sparsity regularization plays a key role in pruning otherwise spuriously detected reactions

Foreign direct investment and the equity home bias puzzle

La extensa literatura macroeconómica que pretende explicar el ampliamente observado equity home bias ignora a las empresas internacionalmente activas. En un modelo DSGE que presenta la elección endógena de las empresas de ser activas internacionalmente —ya sea a través de las exportaciones o por medio de la inversión extranjera directa (IED)—, encontramos que las tenencias de capital óptimas de los agentes están sesgadas hacia las empresas nacionales. Nuestro hallazgo indica que la diversificación internacional no es tan negativa como sugieren las medidas empíricas del equity home bias.The vast macroeconomic literature trying to explain the widely observed equity home bias disregards internationally active firms. In a DSGE model that features the endogenous choice of firms to become internationally active through either exports or foreign direct investment (FDI), we find that the optimal equity holdings of agents are biased towards domestic firms. Our finding indicates that international diversification is not as bad as empirical measures of the equity home bias suggest

Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution

Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done efficiently using coarse-grained simulations, from which meaningful physicochemical information can be inferred if the corresponding all-atom configurations are reconstructed. However, this procedure of backmapping to reintroduce the lost atomistic detail into coarse-grain structures has proven a challenging task due to the many feasible atomistic configurations that can be associated with one coarse-grain structure. Existing backmapping methods are strictly frame-based, relying on either heuristics to replace coarse-grain particles with atomic fragments and subsequent relaxation or parametrized models to propose atomic coordinates separately and independently for each coarse-grain structure. These approaches neglect information from previous trajectory frames that is critical to ensuring temporal coherence of the backmapped trajectory, while also offering information potentially helpful to producing higher-fidelity atomic reconstructions. In this work, we present a deep learning-enabled data-driven approach for temporally coherent backmapping that explicitly incorporates information from preceding trajectory structures. Our method trains a conditional variational autoencoder to nondeterministically reconstruct atomistic detail conditioned on both the target coarse-grain configuration and the previously reconstructed atomistic configuration. We demonstrate our backmapping approach on two exemplar biomolecular systems: alanine dipeptide and the miniprotein chignolin. We show that our backmapped trajectories accurately recover the structural, thermodynamic, and kinetic properties of the atomistic trajectory data

Estudio sobre la influencia del cloruro sódico e hidróxido cálcico en la corrosión de acero corrugado

Los objetivos de este PFC son: 1. Inicialmente se trata de desarrollar un método de ensayo que permita identificar y cuantificar los efectos que determinadas variables del entorno tienen en la corrosión del acero. 2. Establecer un método de cuantificación de la corrosión que permita comparar numéricamente los resultados obtenidos por el método de ensayo desarrollado. 3. Aplicar los métodos desarrollados para cuantificar la influencia del cloruro sódico sobre la corrosión del acero. 4. Comprobar el efecto inhibidor que un ambiente básico tiene sobre la corrosión del acero corrugado. 5. Comprobar el efecto que determinadas variables (tiempo, reactivos y potencial eléctrico) tienen sobre la corrosión del acero corrugado. 6. Contrastar la degradación del acero corrugado en ensayos de corrosión forzada y ensayos a largo plazo bajo condiciones controladas.Escuela de Arquitectura e Ingeniería de EdificaciónUniversidad Politécnica de Cartagen

Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments

Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios

Material systems for FM-/AFM-coupled skyrmions in Co/Pt-based multilayers

By means of systematic first-principles calculations based on density functional theory we search for suitable materials that can host antiferromagnetically coupled skyrmions. We concentrate on fcc-stacked (111)-oriented metallic $Z$/Co/Pt ($Z=4d$ series: Y$-$Pd, the noble metals: Cu, Ag, Au, post noble metals: Zn and Cd) magnetic multilayers of films of monatomic thickness. We present quantitative trends of magnetic properties: Magnetic moments, interlayer exchange coupling, spin-stiffness, Dzyaloshinskii-Moriya interaction, magnetic anisotropy, and the critical temperature. We show that some of the $Z$ elements (Zn, Y, Zr, Nb, Tc, Ru, Rh, and Cd) can induce antiferromagnetic interlayer coupling between the magnetic Co layers, and that they influence the easy magnetization axis. Employing a multiscale approach, we transfer the micromagnetic parameters determined from $ab$ $initio$ to a micromagnetic energy functional and search for one-dimensional spin-spiral solutions and two-dimensional skyrmions. We determine the skyrmion radius by numerically solving the equation of the skyrmion profile. We found an analytical expression for the skyrmion radius that covers our numerical results and is valid for a large regime of micromagnetic parameters. Based on this expression we have proposed a model that allows to extrapolate from the $ab$ $initio$ results of monatomic films to multilayers with Co films consisting of several atomic layers containing $10\,$nm skyrmions. We found thickness regimes where tiny changes of the film thickness may alter the skyrmion radius by orders of magnitude. We estimated the skyrmion size as function of temperature and found that the size can easily double going from cryogenic to room temperature. We suggest promising material systems for ferromagnetically and antiferromagnetically coupled spin-spiral and skyrmion systems.Comment: 18 pages, 7 figure

Weed populations in the main cultures of Luxembourg: control options and monitoring in a complex environmental and political framework

Chemische Unkrautbekämpfung wird aufgrund von ökotoxikologischen Bedenken diskutiert. Um Landwirten zu helfen, die Ausbreitung von Unkräutern auch bei sinkender Verfügbarkeit von Herbiziden begrenzen zu können, wurden Projekte zu modifizierten Fruchtfolgen zur Reduzierung des Unkrautdruckes, digitale Ansätze für bessere Entscheidungen zum Herbizideinsatz und zur besseren Integration von nicht-chemischen Unkrautbekämpfungsmaßnahmen begonnen. In einem ersten Monitoring in den Rapsbeständen Luxemburgs wurden relativ weit verbreitete Arten wie Stellaria media, Viola arvensis, Polygonum aviculare sowie Poa annua, Elymus repens, und Apera spica-venti gefunden. Chenopodium album wurde neben den im Frühjahr keimenden Polygonum-Arten in moderater bis hoher Individuenzahl im Mais gefunden. Polygonum convolvulus wurde nach chemischer Bekämpfung in hoher Dichte am Standort Kuborn gefunden, wohingegen C. album schlecht von mechanischen Methoden bekämpft wurde. Alopecurus myosuroides-Pflanzen mit reifen Samen wurden nahezu ausschließlich im Süden Luxemburgs gefunden. Alle 35 bislang getesteten A. myosuroides Sämlingsproben waren resistent gegen Stomp® Aqua (mit dem K1 Hemmstoff Pendimethalin). Im Fall von Sigma® Maxx (mit den ALS-Inhibitoren Iodosulfuron+Mesosulfuron), waren jeweils 2 von 35 Proben sensitiv bzw. moderat resistent. 31 Proben waren resistent gegenüber Sigma® Maxx. 17 von 35 Proben waren sensitiv gegenüber Axial® (mit dem ACC-ase Inhibitor Pinoxaden), während 18 Proben resistent gegenüber Axial® waren.Due to ecotoxicological and environmental reasons, chemical treatments for weed control are under discussion. To help farmers in coping with challenges imposed by restricted herbicide availability, projects on using modified crop rotations for reducing weed pressure, digital approaches for better decision support, and a better integration of non-chemical weeding were initiated. First monitoring programs in winter oilseed rape in Luxembourg offered a preliminary overview about mainly widespread weed species like Stellaria media, Viola arvensis, Polygonum aviculare as well as Poa annua, Elymus repens and Apera spica-venti. Chenopodium album was found in moderate and high numbers in maize, as well as the spring-germinating Polygonum species. Polygonum convolvulus escaped from or re-emerged after the chemical control at location Kuborn, while C. album was poorly controlled by the mechanical treatments. Alopecurus myosuroides plants with mature seeds were almost exclusively found in the South of Luxembourg. All 35 A. myosuroides seedling samples tested so far were resistant towards Stomp® Aqua (containing the microtubule assembly inhibitor pendimethalin). In case of Sigma® Maxx (containing the ALS inhibitors iodosulfuron+mesosulfuron), 2 out of 35 samples were sensitive and moderately resistant, respectively. 31 samples were resistant to Sigma® Maxx. 17 out of 35 samples were sensitive to Axial® (containing the ACC-ase inhibitor pinoxaden), while 18 samples were resistant to Axial®