In recent years, several interesting biological roles played by RNA have come to light. Apart from their known role in translation of genetic information from DNA to protein, they have been shown to act as enzymes as well as regulators of gene expression. Protein-RNA complexes are involved in regulating cellular processes like cell division, differentiation, growth, cell aging and death. A number of clinically important viruses have RNA as their genetic material. Defective RNA molecules have been linked to a number of human diseases. The ability of RNA to adopt stunningly complex three-dimensional structures aids in diverse functions like catalysis, metabolite sensing and transcriptional control. Several secondary structure motifs are observed in RNA, of which the double-helical RNA motif is ubiquitous and well characterized. Though DNA duplexes have been shown to be present in many polymorphic states, RNA duplexes are believed to exhibit conservatism. Early fibre diffraction analysis on molecular structures of natural and synthetically available oligo- and polynucleotides suggested that the double-helical structures of RNA might exist in two forms: A-form and A′-form. New improved crystallographic methods have contributed to the increased availability of atomic resolution structures of many biologically significant RNA molecules. With the available structural information, it is feasible to try and understand the contribution of the variations at the base pair, base-pair step and backbone torsion angle level to the overall structure of the RNA duplex. Further, the effect of protein binding on RNA structure has not been extensively analysed. These studies have not been investigated in greater detail due to the focus of the research community on understanding conformational changes in proteins when bound to RNA, and due to the lack of a significant number of solved RNA structures in both free and protein-bound state. While studies on the conformation of the DNA double-helical stem have moved beyond the dinucleotide step into tri-, tetra-, hexa- and octanucleotide levels, similar knowledge for RNA even at the dinucleotide step level is lacking. In this thesis, the results of detailed analyses to understand the contribution of the base sequence towards RNA conformational variability as well as the structural changes incurred upon protein binding are reported. Objectives The primary objective of this thesis is to understand the following through detailed analyses of all available high-resolution crystal structures of RNA. 1 Exploring sequence-dependent variations exhibited by dinucleotide steps formed by Watson-Crick (WC) base pairs in RNA duplexes. 2 Identifying sequence-dependent variations exhibited by dinucleotide steps containing non-Watson-Crick (NWC) base pairs in RNA duplexes. 3 Developing a web application for the generation of sequence-dependent non-uniform nucleic acid structures. 4 Investigating the relationship between base sequence and backbone torsion-angle preferences in RNA double helices followed by molecular dynamics simulation using various force fields, to check their ability to reproduce the above experimental findings. Chapter 1 gives an overview of the structural features and polymorphic states of RNA duplexes and the present understanding of the structural architecture of RNA, thereby laying the background to the studies carried out subsequently. The chapter also gives a brief description on the methodologies applied. Relevant methodologies and protocols are dealt with in detail in the respective chapters. Sequence-dependent base-pair step geometries in RNA duplexes A complete understanding of the conformational variability seen in duplex RNA molecules at the dinucleotide step level can aid in the understanding of their function. This work was carried out to derive geometric information using a non-redundant RNA crystal structure dataset and to understand the conformational features (base pair and base-pair step parameters) involving all Watson-Crick (WC) (Chapter 2) and non-Watson-Crick (NWC) base pairs (Chapter 3). The sequence-dependent variations exhibited by the base-pair steps in RNA duplexes are elaborated. Further, potential non-canonical hydrogen bond interactions in the steps are identified and their relationship with dinucleotide step geometry is discussed. Comparison of the features of dinucleotide steps between free and protein-bound RNA datasets suggest variations at the base-pair step level on protein binding, which are more pronounced in non-Watson-Crick base pair containing steps. Chapter 4 describes a web-server NUCGEN-Plus, developed for building and regeneration of curved and non-uniform DNA and RNA duplexes. The main algorithm is a modification of our earlier program NUCGEN that worked mainly for DNA. The WC step parameters and intra-base parameters for RNA were obtained from the work detailed in Chapter 2. The FORTRAN code and input sequence file format was modified. The program has two modules: a) Using the model-building module, the program can build duplex structures for a given input DNA/RNA sequence. Options are available for selecting various derived or user specified base-pair step parameters, and fibre diffraction parameters that can be used in the building process. The program can generate double-helical structures up to 2000 nucleotides in length. In addition, the program can calculate the curvature of the generated duplex at defined length scale. b) Using the regeneration module, double-helical structures of nucleic acids can be rebuilt from the existing solved structures. Further, variants of an existing structure can be generated by varying the input geometric parameters. The web-server has a user-friendly interface and is freely available in the public domain at: http://nucleix.mbu.iisc.ernet.in/nucgenplus/index.html Sequence dependence of backbone torsion angle conformers in RNA duplexes RNA molecules consist of covalently linked nucleotide units. Each of these units has six rigid torsional degrees of freedom (α, β, γ, δ, ε, and ζ) for the backbone and one (χ) around the glycosidic bond connecting the base to the ribose, thereby providing conformational flexibility. An understanding of the relationship between base sequence and structural variations along the backbone can help deduce the rationale for sequence conservation and also their functional importance. Chapter 5 describes in detail the torsion angle-dependent variations seen in dinucleotide steps of RNA duplex. A non-redundant, high resolution (≤2.5Å) crystal structure dataset was created. Base-specific preferences for the backbone and glycosidic torsion angles were observed. Non-A-form torsion angle conformers were found to have a greater prevalence in protein-bound duplexes. Further validation of the above observation was performed by analysing the RNA backbone conformers and the effect of protein binding, in the crystal structure of E. coli 70S ribosome. Chapter 5 further describes the molecular dynamics simulation studies carried out to understand the effect of force fields on the RNA backbone conformer preferences. A 33mer long duplex was simulated using seven different force fields available in AMBER and CHARMM program, each for 100 ns. Trajectory analyses suggest the presence of sequence-dependent torsion angle preferences. Torsion angle conformer distribution closer to that of crystal structures was observed in the system simulated using parmbsc0 force field. Molecular dynamics simulation studies of AU/AU base-pair step A unique geometric feature, unlike that in other purine-pyrimidine (RY) steps in the crystal dataset analysis, was reported for AU/AU step (see Chapter 2). Appendix 1 describes the work carried out to validate these features observed in the crystal structures using simulation studies. Additionally, the effect of nearest-neighbor base pairs on the AU/AU step geometry were examined. General Conclusion Overall, the findings of this thesis work suggest that RNA duplexes exhibit sequence-dependent structural variations and sample a large volume of the double-helical conformational space. Further, protein binding affects the local base-pair step geometry and backbone conformation.

The discovery of carbon nanotubes (CNTs) in 1991 by Iijima revealed the possibility of ultra-strong materials exploiting the properties of materials at smaller length scales. The superior strength, stiffness, and ability to perform under extreme conditions motivated researchers to investigate further on CNTs and similar materials at nanoscale. This resulted in discovery of various nanostructures such boron nitride nanotubes (BNNTs), graphene, hexagonal boron nitride sheets etc. Many of such nanostructures exhibited superior strength and stiffness comparable to that of CNTs. Out of these nanotubes, BNNTs have recently attracted attention from researchers due to their excellent mechanical properties similar to that of CNTs along with better chemical and thermal stability. Thus, BNNTs can be used for varieties of applications such as protective shield for nanomaterials, optoelectronics, bio-medical, nano spintronics, field-emission tips in scanning tunneling and atomic force microscope, and as reinforcement in composites. BNNTs are also used in other applications such as water cleansing, hydrogen storage, and gas accumulators. To exploit these ultra-strong materials, the mechanics of materials under different conditions of loading and failure need to be studied and understood. Also, to make use of the material in a nanocomposite or other applications, the material properties should be evaluated. The present work is focused on the computational study of the mechanics of nanotubes with special reference to BNNTs and CNTs. Note that the attention is not given to the material but to the nanostructure and mechanics. Hence depending on the state-of-the-art, BNNTs and CNTs are used wherever it is appropriate along with justifications. The chapter-wise outline of the present work is given below. The first chapter is an introduction along with a state-of-the-art literature review. The second chapter introduces the molecular simulation methodology in brief. The chapters from the third to the seventh present the work in detail and describe the major contributions. The final chapter summarizes the work along with a few possible directions to extend the present work. Chapter 1 In this chapter, the importance of computational techniques to study the mechanics at the nanoscale is outlined. A brief introduction to various nanostructures and nanotubes are also given. A detailed literature review on the mechanics of nanotubes with special attention to elastic properties, buckling, tensile failure, and as reinforcement in nanocomposites is presented. Chapter 2 In this chapter, the molecular simulation technique is outlined. The molecular dynamics (MD) simulation is one of the most common simulation techniques used to study materials at the nanoscale. A few interatomic potentials that are used in an MD simulation are explained. Theories linking continuum mechanics with the molecular dynamics are also explained here. Chapter 3 In this chapter, the elastic behavior of single-walled BNNTs under axial and torsional loading is studied. Molecular dynamics (MD) simulation is carried out with a tersoff potential for modeling the interatomic interactions. Different chiral configurations with similar diameter are considered to study the effect of chirality on the elastic and shear moduli. Furthermore, the effects of tube length on elastic modulus are also studied by considering different aspects ratios. It is observed that both elastic and shear moduli depend on the chirality of a nanotube. For aspect ratios less than 15, the elastic modulus reduces monotonically with an increase in the chiral angle. For chiral nanotubes the torsional response shows a dependence on the direction of loading. The difference between the shear moduli against and along the chiral twist directions is maximum for a chiral angle of 15◦, and zero for zigzag (0◦) and armchair (30◦) configurations. Chapter 4 Buckling of nanotubes have been studied using many methods such as MD, molecular mechanics, and continuum based shell theories. In MD, motion of the individual atoms are tracked under an applied temperature and pressure, ensuring a reliable estimate of the material response. The response thus simulated varies for individual nanotubes and is only as accurate as the force field used to model the atomic interactions. On the other hand, there exists a rich literature on the understanding of continuum mechanics based shell theories. Based on the observations on the behavior of nanotubes, there have been a number of shell-theory-based approaches to study the buckling of nanotubes. Although some of these methods yield a reasonable estimate of the buckling stress, investigation and comparison of buckled mode shapes obtained from continuum analysis and MD are sparse. Previous studies show that a direct application of shell theories to study nanotube buckling often leads to erroneous results. In this chapter, the nonlocal effect on the mechanics of nanostructures is studied using Eringen’s nonlocal elasticity. The buckling of carbon nanotubes is considered as an example to demonstrate and understand the nonlocal effect in the nanotubes. Single-walled armchair nanotubes with the radius varying from 3.4nm to 17.7nm are considered and their critical buckling stresses are predicted based on multiscale modeling techniques including classical and nonlocal continuum mechanics theories and MD simulation. Fitting nonlocal mechanics models to MD simulation yields a radius-dependent length-scale parameter, which increases approximately linearly with the radius of carbon nanotube. In addition, the nonlocal shell model is found to be a better continuum model than the nonlocal beam model due to its ability to include the circumferential nonlocal effect. Chapter 5 In this chapter, the effects of geometrical imperfections on the buckling of nanotubes are studied. The present study reveals that a major source of the error in continuum shell theories in calculating the buckling stress can be attributed to the geometrical imperfections. Here, geometrical imperfections refer to the departure of the shape of the nanotube from a perfect cylindrical shell. Analogous to the shell buckling in the macro-scale, in this work the nanotube is modeled as a thin-shell with initial imperfection. Then a nonlinear buckling analysis is carried out using the Riks method. It is observed that this proposed approach yields significantly improved estimate of the buckling stress and mode shapes. It is also shown that the present method can account for the variation of buckling stress as a function of the temperature considered. Hence, this turn out to be a robust method for a continuum analysis of nanotubes taking in the effect of variation of temperature as well. Chapter 6 In this chapter, the effects of Stone-Wales (SW) and vacancy defects on the failure behavior of BNNTs under tension are investigated using MD simulations. The Tersoff-Brenner potential is used to model the atomic interaction and the temperature is maintained close to 300 K. The effect of a SW defect is studied by determining the failure strength and failure mechanism of nanotubes with different radii. In the case of a vacancy defect, the effect of an N-vacancy and a B-vacancy is studied separately. Nanotubes with different chirality but similar diameter are considered first to evaluate the chirality dependence. The variation of failure strength with the radius is then studied by considering nanotubes of different diameter but same chirality. It is observed that the armchair BNNTs are extremely sensitive to defects, whereas the zigzag configurations are the least sensitive. In the case of pristine BNNTs, both armchair and zigzag nanotubes undergo brittle failure, whereas in the case of defective BNNTs only the zigzag ones undergo brittle failure. An interesting defect-induced plastic behavior is observed in defective armchair BNNTs. For this nanotube, the presence of a defect triggers mechanical relaxation by bond breaking along the closest zigzag helical path, with the defect as the nucleus. This mechanism results in a plastic failure. Chapter 7 In this chapter, the utility of BNNTs as reinforcement for nanocomposites with metal matrix is studied using MD simulation. Due to the light weight, aluminium is used as the matrix. The influence of number of walls on the strength and stiffness of the nanocomposite is studied using single-and double-walled BNNTs. The three body tersoff potential is used to model the atomic interactions in BNNTs, while the embedded atom method (EAM) potential is used to model the aluminium matrix. The van der Waals interaction between different groups — the aluminium matrix with the nanotube or the between the concentric tubes in double walled BNNT — is modeled using a Lennard Jones potential. A representative volume element approach is used to model the nanocomposite. The constitutive relations for the nanocomposite is also proposed wherein the elastic constants are obtained using the MD simulation. The nanocomposite with reinforcement shows improved axial stiffness and strength. The double-walled BNNT provides more strength to the nanocomposite than the single-walled BNNT. The BNNT reinforcement can be used to design nanocomposites with varying strength depending on the direction of the applied stress. Chapter 8 The summary of the work with a broad outlook is presented in this chapter. The major conclusions of the work are reiterated and possible directions for taking the work further ahead are mentioned.

À l'approche de la transition vitreuse les fondus de polymères montrent une augmentation importante de la viscosité de plusieurs ordres de grandeur. Le but de cette étude est d'acquérir une compréhension plus profonde des propriétés viscoélastiques des fondus de polymères vitrifiables. Les polymères sont modélisés comme des chaînes flexibles en utilisant un modèle de bille-ressort. Les propriétés dynamiques sont analysées dans le cadre de la théorie de couplage de mode idéale. Nous constatons que la température critique de couplage de mode varie avec l'inverse de la longueur de chaîne. En étudiant la fonction de relaxation de cisaillement, nous constatons que les processus de relaxation polymériques, ne sont pas modifiés, mais décalés vers des temps plus importants en approchant la transition vitreuse. / Polymer melts show a remarkable increase of their viscosity by many orders of magnitude on approaching the glass transition. The aim of this study is to gain a deeper insight into the viscoelastic properties of glass forming polymer melts. The polymers are modeled as flexible chains using a bead-spring model. The dynamic properties are analyzed in the framework of the ideal mode-coupling theory. We find that the critical temperature of the ideal mode-coupling theory scales with the reciprocal chain length. By studying the shear relaxation function we find that the polymer relaxation processes are not altered but shifted to later times in the approach of the glass transition.

Fundamental understanding of the behaviour of nuclear fuel has been of great importance. Enhancing this knowledge not only by means of experimental observations, but also via multi-scale modelling is of current interest. The overall goal of this thesis is to understand the impact of atomic interactions on the nuclear fuel material properties. Two major topics are tackled in this thesis. The first topic deals with non-stoichiometry in uranium dioxide (UO2) to be addressed by empirical potential (EP) studies. The second fundamental question to be answered is the effect of the atomic fraction of americium (Am), neptunium (Np) containing uranium (U) and plutonium (Pu) mixed oxide (MOX) on the material properties.UO2 has been the reference fuel for the current fleet of nuclear reactors (Gen-II and Gen-III); it is also considered today by the Gen-IV International Forum for the first cores of the future generation of nuclear reactors on the roadmap towards minor actinide (MA) based fuel technology. The physical properties of UO2 highly depend on material stoichiometry. In particular, oxidation towards hyper stoichiometric UO2 – UO2+x – might be encountered at various stages of the nuclear fuel cycle if oxidative conditions are met; the impact of physical property changes upon stoichiometry should therefore be properly assessed to ensure safe and reliable operations. These physical properties are intimately linked to the arrangement of atomic defects in the crystalline structure. The first paper evaluates the evolution of defect concentration with environment parameters – oxygen partial pressure and temperature by means of a point defect model, with reaction energies being derived from EP based atomic scale simulations. Ultimately, results from the point defect model are discussed, and compared to experimental measurements of stoichiometry dependence on oxygen partial pressure and temperature. Such investigations will allow for future discussions about the solubility of different fission products and dopants in the UO2 matrix at EP level.While the first paper answers the central question regarding the dominating defects in non-stoichiometry in UO2, the focus of the second paper was on the EP prediction of the material properties, notably the lattice parameter of Am, Np containing U and Pu MOX as a function of atomic fractions.The configurational space of a complex U1-y-y’-y’’PuyAmy’Npy’’O2 system, was assessed via Metropolis-Monte Carlo techniques. From the predicted configuration, the relaxed lattice parameter of Am, Np bearing MOX fuel was investigated and compared with available literature data. As a result, a linear behaviour of the lattice parameter as a function of Am, Np content was observed, as expected for an ideal solid solution. These results will allow to support and increase current knowledge on Gen-IV fuel properties, such as melting temperature, for which preliminary results are presented in this thesis, and possibly thermal conductivity in the future. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Atomlagenabscheidung (ALD, Atomic Layer Deposition) ist als präzise Technik zur Abscheidung dünner Schichten bekannt. Mittels wechselweisen Einleitens von Precursorgasen in einen Reaktor erzeugt der Prozess auch auf strukturierten Substraten gleichmäßige dünne Schichten. Durch die selbstsättigende Natur der zu Grunde liegenden Reaktionen sind sowohl die Wachstumsrate als auch die Zusammensetzung wohldefiniert, weshalb sich Atomlagenabscheidung beispielsweise zur Herstellung nanoskopischer Bauelemente im Bereich der Mikroelektronik eignet. Obwohl Aluminiumoxid vermehrt Aufmerksamkeit für seine hohe Bandlücke (~9 eV) sowie die relativ hohe Dielektrizitätskonstante (k ~ 9) geerntet hat, ist oftmals trotz vielseitiger Untersuchungen der anwendbaren Precursorpaare nur wenig über die strukturellen Eigenschaften sowie die Wachstumskriterien der resultierenden Schichten bekannt. In dieser Arbeit wurde eine kombinierte Simulationsmethode entwickelt, mit der sich Atomlagenabscheidung mittels elementarer Reaktionen auf beliebig strukturierten Substraten simulieren lässt. Molekulardynamische Berechnungen ermöglichen dabei atomare Genauigkeit, wohingegen die Ankunft der individuellen Precursoratome durch Kinetic Monte Carlo-Methoden dargestellt werden. Diese Aufteilung erlaubt die Kopplung der molekulardynamischen Präzision mit den Größenordnungen einer KMC-Simulation, welche prinzipiell die Betrachtung von Milliarden von Atomen zulässt. Durch asynchrone Parallelisierung mit bis zu tausenden Arbeiterprozessen wird zudem die Effizienz gegenüber einer herkömmlichen Molekulardynamiksimulation ausreichend erhöht, um binnen weniger Stunden mehrere Abscheidungszyklen nahezu unabhängig von der Größe des betrachteten Raumes, welche im Bereich von Quadratmikrometern liegen kann, zu simulieren. Zur abschließenden Validierung des Modells und seiner Implementierung werden einerseits Versuche einfacher Schichtwachstumsprozesse unternommen, andererseits wird die Atomlagenabscheidung des wohluntersuchten Precursorpaares Trimethylaluminium (TMA, Al(CH3)3) und Wasser simuliert und die resultierende Schicht auf Übereinstimmung mit bestehenden Daten geprüft.:1 Einführung 1.1 Anwendungen von Atomlagenabscheidung 1.2 Aktueller Stand 1.2.1 Experimentelle Untersuchungen 1.2.2 Kinetic Monte Carlo-Simulationen von Dwivedi 1.2.3 Kinetic Monte Carlo-Simulationen von Mazaleyrat 1.2.4 Molekulardynamik-Simulationen 1.2.5 Dichtefunktionaltheoretische Rechnungen von Musgrave 1.3 Motivation 2 Grundlagen 2.1 Atomlagenabscheidung 2.1.1 Einführung zur Atomlagenabscheidung 2.1.2 ALD von Metalloxiden 2.1.3 ALD von Al2O3 2.2 Kinetic Monte Carlo Methoden 2.2.1 KMC-Formalismus 2.2.2 KMC-Algorithmen 2.3 Molekulardynamik 2.3.1 Grundlagen 2.3.2 Methoden zur Ensembledarstellung 2.3.3 Potentialarten 2.3.4 Numerische Optimierungen 3 Kombiniertes Modell 3.1 Verwendetes Kinetic Monte Carlo-Modell 3.2 Kombiniertes Modell 3.2.1 Abscheidungszyklus 3.2.2 Simulationsraum 3.2.3 Ereignisse 3.2.4 Parallelisierungsmethode 3.2.5 Abhängigkeitsgraph 4 Implementierung 4.1 Existierende Software 4.1.1 LAMMPS 4.1.2 SPPARKS 4.1.3 Sonstige Software 4.2 LibKMC 4.2.1 Modularisierung 4.2.2 Abhängigkeiten 4.3 Implementierung des kombinierten Modells 4.3.1 Vorstellung der Software 4.3.2 Einbindung von LibKMC 4.3.3 Einbindung von LAMMPS 4.3.4 Host-Worker-System 4.3.5 Substratgenerierung 5 Validierung 5.1 Validierung des kombinierten Modelles 5.1.1 Wachstumskriterium 5.1.2 Sättigungskriterium 5.1.3 Parallelisierungseffizienz 5.2 Untersuchungen von Al2O3 5.2.1 Potentialuntersuchungen 5.2.2 Schichtwachstumseigenschaften 5.2.3 Strukturanalyse 6 Zusammenfassung und Ausblick Literaturverzeichnis Danksagung

Diese Arbeit widmet sich der Untersuchung der dynamischen und strukturellen Eigenschaften sowie des Phasenverhaltens konzentrierter flüssiger Elektrolyte und ihrer Anwendung in Energiespeichern mittels Methoden der statistischen Mechanik und mithilfe atomistischer Molekulardynamik (MD) Simulationen. Zuerst untersuchen wir die Struktur-Eigenschafts-Beziehungen in konzentrierten Elektrolytlösungen wie sie in Lithium-Schwefel (Li/S), durch wir ein MD Simulationsmodell repräsentativer state-of-the-art Elektrolyt-Systeme für Li/S-Batterien bestehend aus Polysulfiden, lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) und LiNO 3 Elektrolyten mit jeweils unterschiedlichen Kettenlängen gemischt in organischen Lösungsmitteln aus 1,2-dimethoxyethane and 1,3-dioxolane erstellen. Als Zweites befassen wir uns mit der Phasenseparation, die auftritt, wenn sich die physikalisch-chemischen Eigenschaften flüssiger Gemische voneinander unterscheiden. Diese Systeme bestehen üblicherweise aus einem konzentrierten anorganischen Salz und einer ionischen Flüssigkeit. In dieser Arbeit untersuchen wir eine Vielfalt von hochkonzentrierten wässrigen Elektrolytlösungen, die aus unterschiedlichen Zusammensetzungen von LiCl und LiTFSI bestehen. Daraufhin beantworten wir die Frage, wie unterschiedlich die Komponenten in der wässrigen Lösung gemischt sein sollten, damit eine solche flüssig-flüssig-Phasentrennung stattfinden kann. Als letztes untersuchen wir die Ladungsabschirmung, die ein grundlegendes Phänomen ist, das die Struktur von Elektrolyten im Bulk und an Grenzflächen bestimmt. Wir haben in dieser Arbeit die Abschirmlängen für verschiedene Elektrolyte von niedrigen bis zu hohen Konzentrationen untersucht. / Electrolytes can be found in numerous applications in daily life as well as in scientific research. The increases in demand for energy-storage systems, such as fuel cells, supercapacitors and batteries in which liquid electrolyte properties are critical for optimal function, draw critical attention to the physical and chemical properties of electrolytes. Those energy-storage devices contain intermediate or highly concentrated electrolytes where established theories, like the Debye-Hückel (DH) theory, are not applicable. Despite the efforts to describe the physical properties of intermediate or highly concentrated electrolytes, theoretical atomistic-level studies are still lacking. This thesis is devoted to critically investigate the transport/structural properties and a phase behavior of concentrated liquid electrolytes and their application in energy-storage devices, using statistical mechanics and atomistic molecular dynamics (MD) simulations. Firstly, we investigate the structure-property relationship in concentrated electrolyte solutions in next-generation lithium-sulfur (Li/S) batteries. Secondly, phase separation may exist if the physio-chemical properties of liquid mixtures are very different. Recently, the coexistence phase of two aqueous solutions of different salts at high concentrations was found, called aqueous biphasic systems. We explore a wide range of compositions at room temperature for highly concentrated aqueous electrolytes solutions that consist of LiCl and LiTFSI. Lastly, charge screening is a fundamental phenomenon that governs the structure of liquid electrolytes in the bulk and at interfaces. From the DH theory, the screening length is expected to be extremely small in highly concentrated electrolytes. Yet, recent experiments show unexpectedly high screening lengths in those. This intriguing phenomenon has prompted a new set of theoretical works. We investigate the screening lengths for various electrolytes from low to high concentrations.

No description available.

Antiviral drug resistance is a major problem in the treatment of viral infections, including influenza and hepatitis C virus (HCV). Influenza neuraminidase (NA) is a viral sialidase on the surface of the influenza virion and a primary antiviral target in influenza. Two subtypes of NA predominate in humans, N1 and N2, but different patterns of drug resistance have emerged in each subtype. To provide a framework for understanding the structural basis of subtype specific drug resistance mutations in NA, we used molecular dynamics simulations to define dynamic substrate envelopes for NA to determine how different patterns of drug resistance have emerged in N1 and N2 NA. Furthermore, we used the substrate envelope to analyze HCV NS3/4A protease inhibitors in clinical development. In addition, influenza hemagglutinin (HA) is a primary target of neutralizing antibodies against influenza. Novel broadly neutralizing antibodies (BnAbs) against the stem region of HA have been described and inhibit several influenza viral subtypes, but antibody neutralization escape mutations have emerged. We identified potential escape mutations in broadly neutralizing antibody F10 that may impact protein dynamics in HA that are critical for function. We also solved crystal structures of antibody fragments that are important for understanding the structural basis of antibody binding for influenza BnAbs. These studies can inform the design of improved therapeutic strategies against viruses by incorporating an understanding of structural elements that are critical for function, such as substrate processing and protein dynamics, into the development of novel therapeutics that are robust against resistance.

No description available.

No description available.