Computational studies have become an essential tool in biochemistry, providing detailed insight into biological systems alongside experimental studies. Molecular simulation can predict protein conformational dynamics and the impact of mutations, enabling rapid and low-cost investigation of potential therapeutic targets and better understanding of biological systems. Molecular dynamics (MD) is a computational method able to model ensembles of biomolecular conformations in solution by simulating atomic motion at high temporal resolution. The principle limitation of MD is the ability to collect sufficient data for equilibrium sampling. However, with the progression of high-performance computing (HPC) clusters and distributed computing platforms, timescales previously inaccessible to MD can be reached and relevant protein parameters can be extracted using modeling. From these simulations, Markov state models (MSMs) are used extract system-relevant kinetic and thermodynamic information. An MSM represents a series of memoryless, probabilistic transitions between discrete states in a kinetically meaningful way. The obtained information is used to understand the relationships between relevant protein conformations, thus enabling a comprehensive understanding of the modelled system in a human-readable format. Recent advancements in model scoring and hyper-parameterization moved MSM construction away from anecdotal, case-by-case basis to a highly systematic approach that focuses on optimization and validity. Thus, modern MSMs are employed to investigate protein properties, and predict experimental observables using system-representative ensembles of conformations. Additionally, a comprehensive MSM can be combined with sparse experimental data to generate an improved interpretation of the system. My work focuses on performing all-atom massively-parallel MD simulation using the Folding@home distributed computing platform in order to build comprehensive MSMs that are used in improving simulation accuracy and protein design. This work results in the development of an unbiased framework for MSM building that is used to lend insight into simulation parameters, extract novel system behavior and enable clear comprehension of a target function, such as impact of mutations or emphasis of rare events. / Chemistry

In the search for molecular species in the interstellar medium and extraterrestrial planetary atmospheres, theoretical methods continue to be an invaluable tool to astronomically minded chemists. Using state-of-the art methods, this doctoral work characterizes the electronically excited states of interstellar radicals, cations, and even rare anions and also predicts the gas phase fundamental vibrational frequencies of the cis and trans-HOCO radicals, as well as the cis-HOCO anion. First, open-shell coupled cluster methods of singles and doubles (CCSD) and singles and doubles with triples-inclusion (CC3) are tested on the C₂H and C₄H radicals. The significant double-excitation character, as well as the quartet multiplicity of some states yields inaccurate excitation energies and large spin contamination with CCSD. CC3 somewhat improves this for select states, but discrepancies between CC and multireference results for certain states exist and likely arise from the lack of spin adaptation in conventional spin-orbital CC. Next, coupled-cluster methods predict the presence of an excited state of the closed-shell allyl cation and its related H₂CCCHCH₂⁺ cousin at 443 nm near an unidentified laboratory peak at 442.9 nm which is also close to one of the largest unattributed interstellar absorption features. Additionally, the dipole moments, electron binding energies, and excited states of neutral radicals and corresponding closed-shell anions of interstellar interest are also computed. These are calibrated against experimental data for CH₂CN⁻ and CH₂CHO⁻. Since coupled cluster theory closely reproduces the known experimental data, dipole-bound excited states for eight previously unknown anions are predicted: CH2SiN⁻ , SiH₂CN⁻, CH₂SiHO⁻, SiN⁻, CCOH⁻, HCCO⁻, SiCCN⁻, and SiNC⁻. In addition, we predict the existence of one rare valence-bound excited state of CH₂SiN⁻ and also SiCCN⁻ as well as even rarer two valence-bound states of CCSiN⁻. Lastly, the reaction of CO + OH and its transient potential intermediate, the HOCO radical, may be responsible for the regeneration of CO₂ in the Martian atmosphere, but past spectroscopic observations have not produced a full gas-phase set of the fundamental vibrational frequencies of the HOCO radical. Using established, highly-accurate quantum chemical coupled cluster tech- niques and quartic force fields, all six fundamental vibrational frequencies for 1 ²A′ cis and trans-HOCO and 1 ¹A′ cis-HOCO⁻ are computed in the gas phase. / Ph. D.

G-quadruplexes (GQs) are highly stable noncanonical nucleic acid structures that form in the DNA of human cells and play fundamental roles in maintaining genomic stability and regulating gene expression. These unique structures exert broad influence over biologically important processes and can modulate cell survival and human health. In fact, mutations, hyper-stability, and dissociation of GQs are implicated in neurodegenerative disease, mental retardation, premature-aging conditions, and various cancers. As such, GQs are novel drug targets. GQ-targeting therapeutics are developed to influence the folding and genetic interactions of GQs that are implicated in diseased states. To do so requires a greater understanding of GQ structure and dynamics and molecular dynamics (MD) simulations are well suited to provide these fundamental insights. Previous MD simulations of GQs have provided limited information due to inaccuracies in their models, namely the nonpolarizable nature of their force fields (FFs). The cutting-edge Drude polarizable FF models electronic degrees of freedom, allowing charge distribution to change in response to its environment. This is an important component for modeling ion-ion and ion-DNA interactions and can influence the overall stability of GQ structures. The work herein employs the Drude polarizable FF to 1) describe the role of electronic structure on the dynamics and folded stability of GQs, 2) determine the impact of ion interaction on GQ stability, and 3) characterize the role of G-hairpin motifs in GQ intermediates. Such fundamental investigations will help clarify GQs role in healthy and diseased states and transform our understanding of noncanonical DNA, improving human health, therapeutic design, and fundamental science. / Doctor of Philosophy / Human health and disease are influenced by unique nucleic acid structures called G-quadruplexes (GQs). GQs form when DNA or RNA fold into a square-shaped structure that is stabilized by ion interactions and special hydrogen bonding patterns. These GQ structures exert broad influence over normal biological processes, but also play a role in neurodegeneration, intellectual disabilities, premature-aging conditions, and various cancers, many of which are chemotherapeutic resistant. As such, modulating GQ structures, or their interactions with proteins, is a promising therapeutic approach. However, a greater understanding of GQ folding, folded structure, and interactions with other biomolecules is needed to do so. Computational techniques such as molecular dynamics (MD) simulations use experimental data and fundamental biophysics to gain new insights on these properties and inform novel drug design. In this project, we explored the dynamics of several distinct GQ structures and folding intermediates with state-of-the-art MD simulation methods. In doing so, we provided new insight on their structural features as well as their interactions with extended DNA sequences and different ion types, which serve as fundamental information for future structural or computer-aided drug design studies.

Yes / A new type of model, FFLUX, to describe the interaction between atoms has been developed as an alternative to traditional force fields. FFLUX models are constructed from applying the kriging machine learning method to the topological energy partitioning method, Interacting Quantum Atoms (IQA). The effect of varying parameters in the construction of the FFLUX models is analyzed, with the most dominant effects found to be the structure of the molecule and the number of conformations used to build the model. Using these models the optimization of a variety of small organic molecules is performed, with sub kJ mol-1 accuracy in the energy of the optimized molecules. The FFLUX models are also evaluated in terms of their performance in describing the potential energy surfaces (PESs) associated with specific degrees of freedoms within molecules. While the accurate description of PESs presents greater challenges than individual minima, FFLUX models are able to achieve errors of <2.5 kJ mol-1 across the full C-C-C-C dihedral PES of n-butane, indicating the future possibilities of the technique.

Os príons são proteínas que causam um grupo de doenças neurodegenerativas invariavelmente fatais, sendo uma das mais conhecidas a encefalopatia espongiforme bovina (ou doença da vaca louca). A proteína príon celular (PrPc), rica em estrutura α-helicoidal, sofre uma mudança na sua estrutura secundária produzindo a proteína patológica (PrPSc; o príon) na qual prevalecem folhas-β. Devido a falta de dados de estruturais de alta resolução dos príons, simulações de DM podem ser particularmente úteis para estudar o redobramento de PrP. Estudos experimentais e computacionais, descritos na literatura, indicam que a utilização de pH ácido é capaz de criar alguma instabilidade estrutural, produzindo um ganho de estrutura-β na região N-terminal antes desestruturada. Este trabalho se propõe a investigar computacionalmente as mudanças estruturais na proteína príon celular do hamster Sírio induzidas por alteração de pH. Para isso, foi avaliada a influência do uso de diferentes campos de força (GROMOS, AMBER e OPLS), diferentes estados de protonação dos resíduos de histidina, diferentes condições iniciais e diferentes métodos de cálculo de interações eletrostáticas de longo alcance (GRF e SPME). A partir da evolução temporal das estruturas secundárias, foi observada uma forte dependência dos resultados com o uso de diferentes parâmetros de simulação. De fato, a tendência de pH descrita na literatura não foi claramente observada neste trabalho. Isso pode estar associado com a necessidade de se investir mais em múltiplas simulações de dinâmica molecular para quantificar com maior precisão o comportamento estrutural dos fragmentos protéicos em cada pH de estudo. / Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy (or mad cow disease). The cellular prion protein (PrPc), rich in α-helical structure, undergoes a change in its secondary structure producing the pathological protein (PrPSc, the prion) in which β-sheet structure prevails. Because of the lack of high-resolution prion structural data, MD simulations can be particularly useful to study PrP misfolding. Experimental and computational studies, described in literature, indicate that the use of low pH is capable to create some structural instability, producing a gain of β-structure content in the otherwise unstructured N-terminal region. This work aims to investigate computationally structural changes in the cellular prion protein of Syrian hamster induced by pH change. For this, we evaluated the influence of different force fields (GROMOS, AMBER and OPLS), different protonation states of histidine residues, different initial conditions and different methods for calculating long-range electrostatic interactions (GRF and SPME). From the time evolution of the secondary structures, we observed a strong dependence on the simulation parameters. In fact, the pH tendency described in literature was not clearly observed in this work. It may be associated with the need to invest more in multiple molecular dynamics simulations to quantify more accurately the structural behavior of the protein fragments in each pH study.

The concept of tailored force fields is seen as an enabler for the construction of large scale space structures. Manufacturing would take place in space using in-situ resources thereby eliminating the size and weight restriction commonly placed on space vehicles and structures. This thesis serves as the first investigation of opening the way to a generalized fabrication technology by means of force fields. Such a technology would be non-contact, flexible, and automated. The idea is based on the principle that waves carry momentum and energy with no mass transport. Scattering and gradient forces are generated from various types of wave motion. Starting from experiments on shaping walls using acoustic force fields, this thesis extends the technology to electromagnetic fields. The interaction physics of electromagnetic waves with dielectric material is studied. Electromagnetic forces on neutral dielectric material are shown to be analogous to acoustic forces on sound-scattering material. By analogy to the acoustic experiments, force fields obtained by optical tweezers are extended to longer wavelength electromagnetic waves while remaining in the Rayleigh scattering regime. Curing of the surface formed takes place by use of a higher frequency beam that scans the surface and melts a subsurface layer enabling a sintering effect to take place between the particles. The resulting capability is explored at its extremes in the context of building massive structures in Space. A unification of these areas is sought through a generalization of the various theories provided in the literature applicable for each field.

Στις τελευταίες δεκαετίες η σμίκρυνση (miniaturization) έχει αποτελέσει ένα σημαντικό παράγοντα στην ανάπτυξη της τεχνολογίας. Ένας από τους κύριους στόχους της μέσω της μικρομηχανικής (micro-engineering) είναι η παραγωγή ολοκληρωμένων Μικρο-Ηλεκτρο-Μηχανικών Συστημάτων (MEMS), τα οποία χρηςιμοποιούνται σήμερα ως υποσυστήματα σε πάρα πολλές εφαρμογές. Αντικείμενο της παρούσας διατριβής είναι ο παράλληλος χειρισμός καθώς και η ανοιχτού βρόχου/άνευ αισθητήρων συναρμολόγηση μικροαντικειμένων χωρίς τη χρήση μικροβραχιόνων. Για το σκοπό αυτό η έρευνα επικεντρώθηκε σε τέσσερις διαφορετικές διαδικασίες/προσεγγίσεις: α) το μικροχειρισμό με τρισδιάστατα πεδία δυνάμεων, β) το μικροχειρισμό με προγραμματιζόμενα πεδία δυνάμεων στο επίπεδο, γ) το χειρισμό μικροαντικειμένων έγκλειστων σε σταγόνες υγρού και δ) την αυτοσυναρμολόγηση μικροαντικειμένων με ηλεκτροστατικές δυνάμεις. / In the last decades, miniaturization has become an important factor in the development of technology. One of its main objectives through the discipline of micro-engineering is the production of integrated Micro-Electro-Mechanical Systems (MEMS), which are currently used as sub-systems in many applications. The target of this thesis is the parallel manipulation and the open-loop/sensorless assembly of microparts without the use of microrobots. For this purpose, the research was focused on four different procedures: a) micromanipulation with 3D force fields, b) micromanipulation with programmable force fields on a plane, c) manipulation of microparts enclosed in a droplet of liquid and d)self-assembly of microparts with electrostatic forces.

Os príons são proteínas que causam um grupo de doenças neurodegenerativas invariavelmente fatais, sendo uma das mais conhecidas a encefalopatia espongiforme bovina (ou doença da vaca louca). A proteína príon celular (PrPc), rica em estrutura α-helicoidal, sofre uma mudança na sua estrutura secundária produzindo a proteína patológica (PrPSc; o príon) na qual prevalecem folhas-β. Devido a falta de dados de estruturais de alta resolução dos príons, simulações de DM podem ser particularmente úteis para estudar o redobramento de PrP. Estudos experimentais e computacionais, descritos na literatura, indicam que a utilização de pH ácido é capaz de criar alguma instabilidade estrutural, produzindo um ganho de estrutura-β na região N-terminal antes desestruturada. Este trabalho se propõe a investigar computacionalmente as mudanças estruturais na proteína príon celular do hamster Sírio induzidas por alteração de pH. Para isso, foi avaliada a influência do uso de diferentes campos de força (GROMOS, AMBER e OPLS), diferentes estados de protonação dos resíduos de histidina, diferentes condições iniciais e diferentes métodos de cálculo de interações eletrostáticas de longo alcance (GRF e SPME). A partir da evolução temporal das estruturas secundárias, foi observada uma forte dependência dos resultados com o uso de diferentes parâmetros de simulação. De fato, a tendência de pH descrita na literatura não foi claramente observada neste trabalho. Isso pode estar associado com a necessidade de se investir mais em múltiplas simulações de dinâmica molecular para quantificar com maior precisão o comportamento estrutural dos fragmentos protéicos em cada pH de estudo. / Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy (or mad cow disease). The cellular prion protein (PrPc), rich in α-helical structure, undergoes a change in its secondary structure producing the pathological protein (PrPSc, the prion) in which β-sheet structure prevails. Because of the lack of high-resolution prion structural data, MD simulations can be particularly useful to study PrP misfolding. Experimental and computational studies, described in literature, indicate that the use of low pH is capable to create some structural instability, producing a gain of β-structure content in the otherwise unstructured N-terminal region. This work aims to investigate computationally structural changes in the cellular prion protein of Syrian hamster induced by pH change. For this, we evaluated the influence of different force fields (GROMOS, AMBER and OPLS), different protonation states of histidine residues, different initial conditions and different methods for calculating long-range electrostatic interactions (GRF and SPME). From the time evolution of the secondary structures, we observed a strong dependence on the simulation parameters. In fact, the pH tendency described in literature was not clearly observed in this work. It may be associated with the need to invest more in multiple molecular dynamics simulations to quantify more accurately the structural behavior of the protein fragments in each pH study.

Os príons são proteínas que causam um grupo de doenças neurodegenerativas invariavelmente fatais, sendo uma das mais conhecidas a encefalopatia espongiforme bovina (ou doença da vaca louca). A proteína príon celular (PrPc), rica em estrutura α-helicoidal, sofre uma mudança na sua estrutura secundária produzindo a proteína patológica (PrPSc; o príon) na qual prevalecem folhas-β. Devido a falta de dados de estruturais de alta resolução dos príons, simulações de DM podem ser particularmente úteis para estudar o redobramento de PrP. Estudos experimentais e computacionais, descritos na literatura, indicam que a utilização de pH ácido é capaz de criar alguma instabilidade estrutural, produzindo um ganho de estrutura-β na região N-terminal antes desestruturada. Este trabalho se propõe a investigar computacionalmente as mudanças estruturais na proteína príon celular do hamster Sírio induzidas por alteração de pH. Para isso, foi avaliada a influência do uso de diferentes campos de força (GROMOS, AMBER e OPLS), diferentes estados de protonação dos resíduos de histidina, diferentes condições iniciais e diferentes métodos de cálculo de interações eletrostáticas de longo alcance (GRF e SPME). A partir da evolução temporal das estruturas secundárias, foi observada uma forte dependência dos resultados com o uso de diferentes parâmetros de simulação. De fato, a tendência de pH descrita na literatura não foi claramente observada neste trabalho. Isso pode estar associado com a necessidade de se investir mais em múltiplas simulações de dinâmica molecular para quantificar com maior precisão o comportamento estrutural dos fragmentos protéicos em cada pH de estudo. / Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy (or mad cow disease). The cellular prion protein (PrPc), rich in α-helical structure, undergoes a change in its secondary structure producing the pathological protein (PrPSc, the prion) in which β-sheet structure prevails. Because of the lack of high-resolution prion structural data, MD simulations can be particularly useful to study PrP misfolding. Experimental and computational studies, described in literature, indicate that the use of low pH is capable to create some structural instability, producing a gain of β-structure content in the otherwise unstructured N-terminal region. This work aims to investigate computationally structural changes in the cellular prion protein of Syrian hamster induced by pH change. For this, we evaluated the influence of different force fields (GROMOS, AMBER and OPLS), different protonation states of histidine residues, different initial conditions and different methods for calculating long-range electrostatic interactions (GRF and SPME). From the time evolution of the secondary structures, we observed a strong dependence on the simulation parameters. In fact, the pH tendency described in literature was not clearly observed in this work. It may be associated with the need to invest more in multiple molecular dynamics simulations to quantify more accurately the structural behavior of the protein fragments in each pH study.

Le but de cette thèse est une revisite du potentiel SIBFA. Ceci inclut un travail et une réflexion sur la méthodologie de cette approche avec une implémentation proposant une utilisation plus large. De plus, une nouvelle calibration de champ de forces raffiné est permise aujourd’hui. En effet, la décomposition d’énergie intermoléculaire SAPT donne accès à toutes les composantes avec rigueur. La reproduction des résultats ab-initio par un potentiel analytique laisse entrevoir des applications prometteuses. Au-delà du coup de calcul considérablement réduit par rapport aux méthodes de chimie quantique, son intégration dans un code de dynamique moléculaire ouvre les portes à de nombreuses études encore plus prometteuses hors de portée de la chimie quantique. Enfin l’optimisation de ce code, avec une parallélisation bien étudiée, en feront un outil majeur de la biochimie. Dans une première partie, nous introduirons les notions et principes essentiels à la dynamique moléculaire. Un premier chapitre exposera la mécanique classique utilisé dans les programmes les plus distribués et utilisés. Un second chapitre introduira les méthodes permettant un meilleur traitement des interactions non-covalentes essentielles dans les études de complexes ligand-récepteur. Une seconde partie abordera de manière plus concrète la stratégie d’implémentation de SIBFA dans Tinker. Celle-ci s’organisera autour de trois chapitres, traitant chaque composante énergétique intermoléculaire. L’objectif de cette thèse est de proposer un socle solide autour du traitement des interactions non covalentes dans le cadre des champs de forces polarisables de dernières générations et de présenter le modèle d’eau hybride AMOEBA/SIBFA. / The purpose of this thesis is to revisit the potential of SIBFA (Sum of Interactions Between Fragments Ab initio computed) [...]