Complex extreme nonlinear waves: classical and quantum theory for new computing models

The historical role of nonlinear waves in developing the science of complexity, and also their physical feature of being a widespread paradigm in optics, establishes a bridge between two diverse and fundamental fields that can open an immeasurable number of new routes. In what follows, we present our most important results on nonlinear waves in classical and quantum nonlinear optics. About classical phenomenology, we lay the groundwork for establishing one uniform theory of dispersive shock waves, and for controlling complex nonlinear regimes through simple integer topological invariants. The second quantized field theory of optical propagation in nonlinear dispersive media allows us to perform numerical simulations of quantum solitons and the quantum nonlinear box problem. The complexity of light propagation in nonlinear media is here examined from all the main points of view: extreme phenomena, recurrence, control, modulation instability, and so forth. Such an analysis has a major, significant goal: answering the question can nonlinear waves do computation? For this purpose, our study towards the realization of an all-optical computer, able to do computation by implementing machine learning algorithms, is illustrated. The first all-optical realization of the Ising machine and the theoretical foundations of the random optical machine are here reported. We believe that this treatise is a fundamental study for the application of nonlinear waves to new computational techniques, disclosing new procedures to the control of extreme waves, and to the design of new quantum sources and non-classical state generators for future quantum technologies, also giving incredible insights about all-optical reservoir computing. Can nonlinear waves do computation? Our random optical machine draws the route for a positive answer to this question, substituting the randomness either with the uncertainty of quantum noise effects on light propagation or with the arbitrariness of classical, extremely nonlinear regimes, as similarly done by random projection methods and extreme learning machines

First-principles modeling of chemistry in mixed solvents: Where to go from here?

Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents

Understanding fluorescent amyloid biomarkers by computational chemistry

Protein misfolding diseases, including neurodegenerative disorders like Alzheimer’s disease, are characterized by the involvement of amyloid aggregation, which emphasizes the need for molecular biomarkers for effective disease diagnosis. The thesis addresses two aspects of biomarker development: firstly, the computation of vibrationally resolved spectra of small fluorescent dyes to detect amyloid aggregation, and secondly, the binding and unbinding processes of a novel ligand to the target protein. In relation to the first aspect, a hybrid model for vibrational line shapes of optical spectra, called VCI-in-IMDHO, is introduced. This model enables the treatment of selected modes using highly accurate and anharmonic vibrational wave function methods while treating the remaining modes using the approximate IMDHO model. This model reduces the computational cost and allows for the calculation of emission line shapes of organic dyes with anharmonicity in both involved electronic states. The interaction between the dyes and their environment is also explored to predict the photophysical properties of the oxazine molecules in the condensed phase. The position and the choice of the solvent molecule have a significant impact on the spectra of the studied systems as they altered the spectral band shape. However, further studies are necessary to confirm the findings. In addition to neurodegenerative diseases, the systemic amyloidoses represent another group of disorders caused by misfolded or misassembled proteins. In the cardiac domain, the accumulation of amyloid fibrils formed by the transthyretin (TTR) protein leads to cardiac dysfunction and restrictive cardiomyopathy. The investigation of binding and unbinding pathways between the TTR protein and its ligands is crucial for gaining a comprehensive understanding and enabling early detection of systemic amyloidoses and related disorders. Hence, exploring the different binding modes and the dissociation pathways of TTR-ligand complex is the primary objective of the second aspect of this thesis. The experimental study provides evidence of binding and X-ray crystallographic structure data on TTR complex formation with the fluorescent salicylic acid-based pyrene amyloid ligand (Py1SA). However, the electron density from X-ray diffraction did not allow confident placement of Py1SA, possibly due to partial ligand occupancy. Molecular dynamics and umbrella sampling approaches were used to determine the preferred orientation of the Py1SA ligand in the binding pocket, with a distinct preference for the binding modes with the salicylic acid group pointing into the pocket.Deutsche Forschungs-gemeinschaft (DFG)/Emmy Noether/KO 5423/1- 1/E

Vision 2040: A Roadmap for Integrated, Multiscale Modeling and Simulation of Materials and Systems

Over the last few decades, advances in high-performance computing, new materials characterization methods, and, more recently, an emphasis on integrated computational materials engineering (ICME) and additive manufacturing have been a catalyst for multiscale modeling and simulation-based design of materials and structures in the aerospace industry. While these advances have driven significant progress in the development of aerospace components and systems, that progress has been limited by persistent technology and infrastructure challenges that must be overcome to realize the full potential of integrated materials and systems design and simulation modeling throughout the supply chain. As a result, NASA's Transformational Tools and Technology (TTT) Project sponsored a study (performed by a diverse team led by Pratt & Whitney) to define the potential 25-year future state required for integrated multiscale modeling of materials and systems (e.g., load-bearing structures) to accelerate the pace and reduce the expense of innovation in future aerospace and aeronautical systems. This report describes the findings of this 2040 Vision study (e.g., the 2040 vision state; the required interdependent core technical work areas, Key Element (KE); identified gaps and actions to close those gaps; and major recommendations) which constitutes a community consensus document as it is a result of over 450 professionals input obtain via: 1) four society workshops (AIAA, NAFEMS, and two TMS), 2) community-wide survey, and 3) the establishment of 9 expert panels (one per KE) consisting on average of 10 non-team members from academia, government and industry to review, update content, and prioritize gaps and actions. The study envisions the development of a cyber-physical-social ecosystem comprised of experimentally verified and validated computational models, tools, and techniques, along with the associated digital tapestry, that impacts the entire supply chain to enable cost-effective, rapid, and revolutionary design of fit-for-purpose materials, components, and systems. Although the vision focused on aeronautics and space applications, it is believed that other engineering communities (e.g., automotive, biomedical, etc.) can benefit as well from the proposed framework with only minor modifications. Finally, it is TTT's hope and desire that this vision provides the strategic guidance to both public and private research and development decision makers to make the proposed 2040 vision state a reality and thereby provide a significant advancement in the United States global competitiveness

Biomechanical analysis of Ascending Thoracic Aortic Aneurysm (ATAA)

According to the reports of the World Health Organisation (WHO), cardiovascular diseases are the number one cause of death worldwide. Specifically, arterial disease and degeneration are the major reasons for cardiovascular death and disability. Because these diseases are dependent on the changes of the mechanical properties of the arterial wall, it is very important to know as much as possible about the structural composition of arteries. The human aorta is the biggest artery in the body and consists of three main parts, ascending aorta, aortic arch and descending aorta. The walls of the arteries consist of three layers, the intima, media and adventitia, where each of the layers has different physiological functions and therefore distinct mechanical properties. These were investigated using, i.e., uniaxial tensile, inflation or planar biaxial-testing. Purpose of this thesis was to apply the biomechanical approach by mean of numerical and experimental test referring to patient-specific aortic geometries with ascending thoracic aortic aneurysms. However, despite the ample literature and the related scientific and industrial activity in this field, many different phenomena are not yet consolidated. The PhD Thesis is then divided into two main sections: the first is composed by a brief introduction on ATAA, with some background about mechanical properties of soft tissues, the evolution of the constitutive model, some remarks of the continuum. The second section of the thesis is based on the different research activities developed during the PhD

Adsorption Dynamics and Bonding Analysis of Organic Molecules on Silicon(001) Surfaces

In this thesis, the adsorption of ethylene, tetrahydrofuran (THF), cyclooctyne and 5-Ethoxymethyl-5-methylcyclooctyne (EMC) on Si(001) surfaces is studied using computational methods. While ethylene and THF act as model systems that allow to understand how unsaturated carbon-carbon bonds and ether groups interact with these surfaces, cyclooctyne and EMC are potential candidates for the formation of organic/semiconductor interfaces and therefore more application-oriented. The thesis is focusing on two aspects of adsorption: Bonding analysis and adsorption dynamics. In bonding analysis, periodic Energy Decomposition Analysis (pEDA), which allows to understand the formation of chemical bonds betwen molecule and surface, was applied. The reaction dynamics was simulated using two approaches: Statistical thermodynamics, which can be applied if thermodynamic equilibrium is achieved, and explicitly calculating the evolution of the system over time using ab initio molecular dynamics (AIMD). For ethylene, the results show that a dative bond between the carbon-carbon double bond and an empty orbital at a surface atom forms in the weakly bound intermediate state. In contrast to physisorbed intermediates on metal surfaces, this state is not mobile. Additionally, the influence of surface pre-coverage by atoms and molecules on the reactivity of ethylene is investigated in a second study. The study of THF reveals that the adsorption mirrors the acid-catalyzed cleavage of ethers in solution and that the mechanism is equivalent to a concerted nucleophilic substitution. For cyclooctyne, it is explained why the formation of two molecule-surface bonds stabilizes the system far more than the formation of four such bonds. Ring strain and enhanced dispersion interactions due to the size of the molecule lead to additional stabilization in comparison to linear alkynes like acetylene. In contrast to alkenes, cyclooctyne can adsorb either directly into the final state or via a short lived transient state. However, the lifetime of this transient state is so low that isolation at usual experimental conditions is not possible. The conclusive study of EMC shows that the molecule bonds selectively via the strained triple bond and therefore confirms its suitability as a building block for organic/semiconductor interfaces. The ether group does not affect the reactivity and adsorption dynamics of the triple bond and cyclooctyne results can be transferred to this part of the molecule. The reactivity of the ether group is influenced by the sterically demanding residue, however, adsorption of this group is highly unlikely. Overall, the studies in this thesis show that the application of chemical concepts and methods can bring in valuable contributions to the field of surface science. The pEDA in particular allows to describe the bonding between molecule and surface both qualitatively and quantitatively, and therefore enables an understanding of the relative energies between different adsorption structures. Furthermore, the investigation of the dynamics allows to predict how the system evolves on different time scales and which structures form preferably. The approaches presented in this thesis can most likely be transferred to other systems as well (e.g. adsorption on metal surfaces) and allow to deliver new insight into different fields of research in surface science and material science

Computation of optical properties of chromophores in different environments using QM/MM methods

Die theoretische Beschreibung der Wechselwirkung zwischen Molekülen und Licht kann herausfordernd sein, insbesondere dann, wenn es sich um flexible Farbstoffe in einer komplexen und dynamischen Umgebung handelt. Obgleich quantenmechanische (QM) Methoden den angeregten Zustand eines Moleküls beschreiben können, sind sie zu rechenaufwändig, um strukturelle Fluktuationen simulieren zu können. Darüber hinaus ist die mögliche Systemgröße, die beschrieben werden kann, durch die Rechenkosten begrenzt. Aus diesem Grund kommen für die Untersuchung von Farbstoffen in Proteinumgebung semiempirische und Multiskalenansätze ins Spiel. Die semiempirische Time-Dependent Long-range Corrected Density Functional Tight Binding (TD-LC-DFTB2) Methode wurde als effiziente Alternative zu ab initio Methoden oder der Dichtefunktionaltheorie in Bezug auf Geometrien im angeregten Zustand und Anregungsenergien getestet. Sie wurde in QM/MM Simulationen angewandt, in denen sie einen angeregten Fluorophor beschrieb, dessen Umgebung von einem klassischen Kraftfeld beschrieben wurde. Diese neue Strategie für die Untersuchung von Fluoreszenz wurde sorgfältig anhand von Literaturergebnissen bewertet, indem die Ergebnisse sowohl mit experimentellen als auch mit theoretischen Studien, die auf anderen Ansätzen basieren, verglichen wurden. Es wurde herausgefunden, dass TD-LC-DFTB2 im Allgemeinen Geometrien und Anregungsenergien von ausreichender Qualität liefert, aber es wurden auch einige Schwächen entdeckt. Außerdem wurde ein optischer Glukosesensor untersucht, der aus dem Glukosebindeprotein und einem angefügten Fluorophor besteht. Mit Hilfe von klassischen Molekulardynamiksimulationen (MD Simulationen) konnten Zusammenhänge zwischen der Anwesenheit von Glukose, den Proteinkonformationen und dem Aufenthaltsort des Farbstoffs gefunden werden. Daraus ergab sich ein starker Hinweis auf die Funktionsweise des Sensors. Schließlich wurde der Energietransfer in einem Pigment-Protein-Komplex untersucht. Der Fenna-Matthews-Olson-Komplex von Photosynthese betreibenden grünen Schwefelbakterien beinhaltet mehrere Bakteriochlorophyll a -- Pigmente in seinem Proteingerüst. Diese leiten die im Chlorosome gesammelte Anregungsenergie mit erstaunlicher Effizienz zum Reaktionszentrum weiter. Es wird Vorarbeit für eine Simulation der Exzitonenpropagation durch den Komplex gezeigt. Anregungsenergien und die Kopplungen zwischen den Pigmenten, das heißt die Elemente des exzitonischen Hamiltonoperators, wurden mit TD-LC-DFTB2 für Strukturen aus klassischen MD Simulationen berechnet. Dadurch wurde ein Eindruck zu deren Entwicklung über die Zeit und den Einfluss der Proteinumgebung gewonnen. Weiterhin wurden diese Daten genutzt, um neuronale Netze zu trainieren, die Anregungsenergien und Kopplungen noch schneller als TD-LC-DFTB2 vorhersagen können

Geometric integrators and the Hamiltonian Monte Carlo method

This paper surveys in detail the relations between numerical integration and the Hamiltonian (or hybrid) Monte Carlo method (HMC). Since the computational cost of HMC mainly lies in the numerical integrations, these should be performed as efficiently as possible. However, HMC requires methods that have the geometric properties of being volume-preserving and reversible, and this limits the number of integrators that may be used. On the other hand, these geometric properties have important quantitative implications for the integration error, which in turn have an impact on the acceptance rate of the proposal. While at present the velocity Verlet algorithm is the method of choice for good reasons, we argue that Verlet can be improved upon. We also discuss in detail the behaviour of HMC as the dimensionality of the target distribution increases.This work was supported in part by a Catalyst Grant to N. B-R. from the Provost’s Fund for Research at Rutgers University–Camden under project no. 205536, and also in part by the NSF Research Network in Mathematical Sciences: ‘Kinetic description of emerging challenges in multiscale problems of natural sciences’ (PI, Eitan Tadmor; NSF grant no. 11-07444). J.M.S. has been supported by project MTM2016-77660-P(AEI/FEDER, UE) funded by MINECO (Spain)

Ultrafast Laser Control of Molecular Quantum Dynamics from a Core-Electron Perspective

This work introduces two experimental approaches to control quantum dynamics in molecules, employing core electrons as messengers. A laser source providing ultrashort pulses has been developed to access the timescale of electronic and structural dynamics inside molecules. Pulses of few-cycle durations in the 1 µm to 2 µm short-wavelength infrared (SWIR) spectral region provide intensities up to 1015 W/cm2 . In combination with a vacuum beamline, this experimental setup allows for ultrafast laser control of molecular dynamics probed by core-electron transitions via x-ray absorption spectroscopy (XAS). The first experiment investigates the manipulation of molecular electronic structure. Here, a soft x-ray (SXR) pulse probes simultaneously to an SWIR pulse of variable intensity. The measured intensityvii dependent absorbance changes in SF6 reveal an increased effective electronic-exchange energy. This demonstrates the alteration of this purely quantum-mechanical component of the electron-electron interaction for the first time. In a second experiment, an SWIR pulse induces coherent molecular vibrations with amplitudes of ten times the diameter of the nucleus. Subsequently, a time-delayed SXR pulse probes the bond-length changes via core-level transitions. This enables an unprecedented 14 femtometer precision which paves the way for site-specific vibrational metrology in gas-phase molecules. Overall, these results enable ultrafast chemical control on a quantum level