The mechanisms of thermal transport in defect-free silicon nanostructures are examined using a combination of lattice dynamics (LD) calculations and the Boltzmann transport equation (BTE). To begin, the thermal conductivity reduction in thin films is examined using a hierarchical method that first predicts phonon transport properties using LD calculations, and then solves the phonon BTE using the lattice Boltzmann method. This approach, which considers all of the phonons in the first Brillouin-zone, is used to assess the suitability of common assumptions used to reduce the computational effort. Specifically, we assess the validity of: (i) neglecting the contributions of optical modes, (ii) the isotropic approximation, (iii) assuming an averaged bulk mean-free path (i.e., the Gray approximation), and (iv) using the Matthiessen rule to combine the effect of different scattering mechanisms. Because the frequency-dependent contributions to thermal conductivity change as the film thickness is reduced, assumptions that are valid for bulk are not necessarily valid for thin films. Using knowledge gained from this study, an analytical model for the length-dependence of thin film thermal conductivity is presented and compared to the predictions of the LD-based calculations. The model contains no fitting parameters and only requires the bulk lattice constant, bulk thermal conductivity, and an acoustic phonon speed as inputs. By including the mode-dependence of the phonon lifetimes resulting from phonon-phonon and phonon-boundary scattering, the model predictions capture the approach to the bulk thermal conductivity better than predictions made using Gray models based on a single lifetime. Both the model and the LD-based method are used to assess a procedure commonly used to extract bulk thermal conductivities from length-dependent molecular dynamics simulation data. Because the mode-dependence of thermal conductivity is not included in the derivation of this extrapolation procedure, using it can result in significant error. Finally, phonon transport across a silicon/vacuum-gap/silicon structure is modelled using lattice dynamics and Landauer theory. The phonons transmit thermal energy across the vacuum gap via atomic interactions between the leads. Because the incident phonons do not encounter a classically impenetrable potential barrier, this mechanism is not a tunneling phenomenon. The heat flux due to phonon transport can be 4 orders of magnitude larger than that due to photon transport predicted from near-field radiation theory.

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To unravel the mysteries of complex biological processes carried out by biomolecules it is necessary to adopt a multifaceted approach, which involves employing a wide variety of tools both computational and experimental. In order to gain a clear understanding of the function of biomolecules their three dimensional structure is required. X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy are the only two methods capable of providing high-resolution three-dimensional structure of biomolecules. NMR has the advantage of allowing the study of structure of biomolecules in solution and is better equipped to characterize the dynamics of the protein. Protein structure determination by NMR spectroscopy consists of recombinant expression of isotopically labeled proteins, purification, data collection, data processing, resonance assignment, distance restraint and angular restraint generation, structure calculation and structure validation. Apart from 3D structure determination of biomolecules NMR has become the method of choice for studying transient protein-protein interactions, which are notoriously difficult to study at higher resolution by other methods. Mass spectrometry plays an important role in enabling rapid identification of biomolecules and their modifications. The high sensitivity and resolution mass spectrometry offers makes it the method of choice for studying post-transitional modification of proteins. Use of computers in biology has played an essential role in elucidating those structure function relationships in biomolecules that are not possible to study by experimental techniques. The first chapter of this thesis deals with the introduction of methods used in this study. A brief introduction about the theory of Nuclear Magnetic Resonance (NMR) spectroscopy is given. Protein NMR methods used for structure determination of medium sized proteins are discussed. A part of this chapter discusses about the application of mass spectrometry in biochemistry and the use of tandem MS/MS experiments in identification of proteins and peptide fragments. Finally, the last part of this chapter gives an introduction about the theory of molecular dynamics and techniques used in the post processing of MD trajectories to elucidate the dynamics of proteins. The second chapter of this thesis is concerned with NMR characterization of a novel protein-protein interaction between the glycolytic enzyme Triosephosphate isomerase and the redox protein Thioredoxin. Chemical shift perturbation studies have been done to map the binding interfaces of these proteins. The structure of the complex was then modeled using NMR restraints based docking using the known 3D structure of these proteins. The docked complex reveals crucial insights into the glutathione mediated redox regulation of Triosephosphate isomerase and the role of thioredoxin as a deglutathionylating agent. Enzyme activity assays of Triosephosphate isomerase were done to show the inhibitory effects of s-glutathionylation of Cys217 and the role of thioredoxin as a deglutathionylating agent. The third chapter of the thesis is aimed to address some important issues related to the inhibition of Plasmodium falciparum Triosephosphate isomerase by S-glutathionylation. Oxidative stress induces protein glutathionylation which is a reversible post translational modification consisting of the formation of a mixed disulfide between protein cysteines and glutathione. Mass spectrometric analysis of the kilnetics of glutathionylation along with enzyme activity assays clearly show that gluthionylation of either Cys-13 (situated in the dimmer interface) or Cys-217 (situated in Helix G) can render the enzyme inactive. Molecular dynamics simulations provide a mechanistic basis of inhibition and predict that glutathionylation at Cys217 allosterically induces loop 6 disorder. The fourth chapter of this thesis addresses the stabilizing effect of introduction of a cross-strand disulfide bond across a non-hydrogen bonded position of an antiparallel beta sheet. Multidimensional heteronuclear NMR experiments have been used to get the backbone and side-chain resonance assignments, distance and angular restraints. In addition RDC based restraints have been used to calculate the structure of oxidixed form of L79C, T89C thiroedoxin. The observation of predominantly –RH staple conformation among the NMR ensemble in typical of cross-strand disulfides. The fifth chapter of this thesis deals with the dynamics of thioredoxin using computational methods.In this chapter analysis of known complexes of thiroedoxin was done to determine binding hot spot residues using free energy calculations. The physicochemical basis for the multispecificity of thioredoxin is probed using molecular dynamics simulations. In this chapter it has been shown that conformational selection plays a very important role in thioredoxin target recognition.

Diblock-Copolymers (DBCs), created by covalently joining two chemically distinct polymer blocks, spontaneously form various nanoscale morphologies such as lamellae, cylinders, spheres, etc. due to the chemical incompatibility of its constituent blocks. This effect is called microphase separation in the literature. Because of this self-organizing property DBCs find applications in many areas e.g. in creating selective membranes, and in polymer based modern electronic devices like organic photovoltaics where the internal morphology plays an important role in determining the performance of the device. Many such modern devices are based on thin film technologies and uses copolymer nanocomposites as it exhibits advantageous electrical, optical, and mechanical properties. Also, DBC can direct the spatial distribution of nanoparticles (NPs) in the polymer matrix via microphase separation. Generally, two types of NPs are distinguished with respect to their monomer affinity: selective NPs which prefer one component of DBC, and non-selective NPs which interact equally with both components of DBC. In this work, using molecular dynamics simulations and analytical calculations, we explore the effect of adding both types of NP in the copolymer matrix considering a thin film (or confined) geometry. We consider a cylinder forming DBC melt confined by purely repulsive walls in slit geometry and study the behavior of the system upon adding non-selective NPs. Two models of non-selective interactions between the monomers and NPs are applied, i.e repulsive and weakly attractive interactions (athermal and thermal cases respectively). Spatial distribution of NPs in the copolymer matrix is sensitive to the NP-monomer interaction behavior. We focus on the thermal case and discuss, in particular, the following points: (1) role of diblock and polymer-wall interfaces, (2) spatial distribution of NPs, and (3) NP segregation and uptake behavior by the copolymer film. The uptake of NPs by the copolymer film in the thermal case displays a non-monotonic dependence on temperature which can be explained qualitatively using a mean-field model. In general, addition of non-selective NPs do not affect the copolymer morphology and the NPs are preferentially localized at the interface between microphase domains. Morphological transitions are observed when adding selective NPs to the copolymer matrix. By varying the amount of selective NPs and diblock composition we systematically explore the various structures formed by the nanocomposites under confinement and constructed the corresponding phase diagram in diblock composition and NP concentration. We also discuss the NP induced orientation transition of lamellar structure and study the stability of lamellar phases formed by the nanocomposites. To study the commensurability and wetting transition of horizontally oriented lamellar phase formed by the nanocomposites we have developed a mean field model based on the strong segregation theory. Our model predicts that it is possible to reduce the frustration in a film of fixed thickness by properly tuning the NP-monomer interaction strength. Furthermore, the model predicts a discontinuous transition between the non-wetted phase (where a dense NP layer is present in the polymer-substrate interface) and wetted phase (where the substrate is covered by polymers). Finally, we extend our study to non-equilibrium where we apply a shear flow field to copolymer thin films. Here, we study the flow behavior, lamellae deformation and change of pair-wise interaction energy, and macroscopic response like kinetic friction coefficient and viscosity of the copolymer thin film with and without NPs. / Lösungen von Diblock-Copolymeren (DBC), welche durch die kovalente Bindung zweier chemisch unterschiedlicher linearer Polymerblöcke entstehen, können spontan mikroskopische Strukturen ausbilden, welche je nach dem Grad der chemischen Kompatibiliät der Blöcke beispielsweise lamellen-, zylinder- oder kugelartige Formen zeigen. Dieses Phänomen wird meist als Mikrophasenseparation bezeichnet. Aufgrund dieser selbstorganisierenden Eigenschaft finden DBCs Anwendungen in vielen Bereichen der Forschung und der Industrie. Beispielsweise zur Erzeugung selektiver Membranen oder in moderner polymerbasierter Elektronik, wie organischen Solarzellen, wo die innere Struktur eine wichtige Rolle spielt um die Leistungsfähigkeit zu erhöhen. Viele moderne Geräte basieren auf der Technologie dünner Schichten und nutzen Copolymer-Nanokomposite um elektrische, optische oder mechanische Eigenschaften zu verbessern. In Folge der Mikrophasenseparation kann man mit Hilfe von DBC die räumliche Verteilung von Nanopartikeln (NP) in der Polymermatrix kontrollieren. Man unterscheidet im Allgemeinen zwischen zwei Arten von NP: selektive NP, welche eine der beiden Komponenten der DBC bevorzugen und nicht-selektive NP, welche mit beiden Komponenten gleichartig wechselwirken. In der vorliegenden Arbeit nutzen wir molekulardynamische Simulationen und analytische Rechnungen um den Eigenschaften zu studieren, welche eine Zugabe von selektiven und nicht-selektiven NP auf eine dünnschichtige Copolymermatrix hat. Wir betrachten eine zylinderformende Schmelze aus DBC, welche in einem dünnen Film, zwischen zwei harten Wänden eingeschränkt ist, und untersuchen das Verhalten des Systems unter Zugabe nicht-selektiver NP. Zwei Modelle nicht-selektiver Wechselwirkungen werden angenommen: ausschließlich repulsive (athermische) Wechselwirkungen und schwach anziehende (thermische) Wechselwirkungen. Die räumliche Verteilung der NP ist abhängig von dem jeweiligen Wechselwirkungsverhalten. Wir konzentrieren uns hierbei auf den thermischen Fall und diskutieren speziell folgende Schwerpunkte: (1.) die Rolle der sich ausbildenden Grenzschichten, (2.) die räumliche Verteilung der NP und (3.) die Abscheidung der NP, sowie die Aufnahmefähigkeit derselben durch die Polymermatrix. Im thermische Fall zeigt die Aufnahme der NP durch die Copolymerschicht eine nicht-monotone Abhängigkeit von der Temperatur, was mit Hilfe eines Mean-Field Modells erklärt werden kann. Die Zugabe nicht-selektiver NP hat keinen Einfluss auf die Struktur der Copolymermatrix und die NP werden vorzugsweise an der Grenzschicht der jeweiligen Mikrophasen gefunden. Im Gegensatz dazu kann man durch die Zugabe selektiver NP eine Strukturveränderung in der Copolymermatrix feststellen. Durch Veränderung der Menge der NP und der Zusammensetzung der DBC können wir systematisch unterschiedliche Strukturen des räumlich eingeschränkten Nanokomposits erzeugen und ein entsprechendes Phasendiagram bezüglich der NP Konzentration und der DBC Zusammensetzung erstellen. Wir untersuchen auch die durch NP induzierte Orientierung der Lamellenstruktur und analysieren ihre Stabilität. Um den sogenannten Kommensurabilitäts- und Benetzungsübergang in horizontal orientierten Lamellenstrukturen zu untersuchen haben wir ein Mean-Field Modell entwickelt, welches auf der Annahme der 'starken Segregation' basiert. Unser Modell macht die Vorhersage, dass es möglich ist die Frustration in einem Kompositfilm zu reduzieren, indem man die NP-Monomer-Wechselwirkung entsprechend anpasst. Zusätzlich sagt das Modell einen diskontinuierlichen Übergang zwischen der unbenetzten Phase (Ausbildung einer dichten NP Konzentration an der Polymer-Substrat Grenzschicht) und der benetzten Phase (das Substrat ist ausschließlich vom Polymerkomposit bedeckt) voraus. Abschließend weiten wir unsere Untersuchungen auf Nicht-Gleichgewichtszustände aus und induzieren durch Scherung der Substratwände einen Strömungprofil im Kompositfilm. Dabei analysieren wir das Strömungsverhalten, die Lamellendeformation und die Änderung der paarweisen Wechselwirkungsenergie. Wir untersuchen auch makroskopische Größen, wie den kinetischen Reibungskoeffizienten und die Viskosität, je in An- und Abwesenheit von Nanopartikeln.

The mechanisms of thermal transport in defect-free silicon nanostructures are examined using a combination of lattice dynamics (LD) calculations and the Boltzmann transport equation (BTE). To begin, the thermal conductivity reduction in thin films is examined using a hierarchical method that first predicts phonon transport properties using LD calculations, and then solves the phonon BTE using the lattice Boltzmann method. This approach, which considers all of the phonons in the first Brillouin-zone, is used to assess the suitability of common assumptions used to reduce the computational effort. Specifically, we assess the validity of: (i) neglecting the contributions of optical modes, (ii) the isotropic approximation, (iii) assuming an averaged bulk mean-free path (i.e., the Gray approximation), and (iv) using the Matthiessen rule to combine the effect of different scattering mechanisms. Because the frequency-dependent contributions to thermal conductivity change as the film thickness is reduced, assumptions that are valid for bulk are not necessarily valid for thin films. Using knowledge gained from this study, an analytical model for the length-dependence of thin film thermal conductivity is presented and compared to the predictions of the LD-based calculations. The model contains no fitting parameters and only requires the bulk lattice constant, bulk thermal conductivity, and an acoustic phonon speed as inputs. By including the mode-dependence of the phonon lifetimes resulting from phonon-phonon and phonon-boundary scattering, the model predictions capture the approach to the bulk thermal conductivity better than predictions made using Gray models based on a single lifetime. Both the model and the LD-based method are used to assess a procedure commonly used to extract bulk thermal conductivities from length-dependent molecular dynamics simulation data. Because the mode-dependence of thermal conductivity is not included in the derivation of this extrapolation procedure, using it can result in significant error. Finally, phonon transport across a silicon/vacuum-gap/silicon structure is modelled using lattice dynamics and Landauer theory. The phonons transmit thermal energy across the vacuum gap via atomic interactions between the leads. Because the incident phonons do not encounter a classically impenetrable potential barrier, this mechanism is not a tunneling phenomenon. The heat flux due to phonon transport can be 4 orders of magnitude larger than that due to photon transport predicted from near-field radiation theory.

The (001) surface of silicon has been the topic of our study in this thesis. The clean surface, an-adatom or submonolayer adsorption on the surface, the monolayer adsorption and its stability conditions as well as growth simulation on the surface were investigated using the state of the art techniques. We have used ab initio density functional calculations based on norm-conserving pseudopotentials to investigate the Mg adsorption on the Si(001) surface for 1/4, 1/2 and 1 monolayer (ML) coverages. For both 1/4 and 1/2 ML coverages it has been found that the most favorable site for the Mg adsorption is the cave site between two dimer rows consistent with recent experiments. For the 1 ML coverage (2 Mg atoms per 2X1 unit cell) we have found that the most preferable configuration is when both Mg atoms on 2X1 reconstruction occupy the two shallow sites. We have found that the minimum energy configurations for 1/4 ML coverage is a 2X2 reconstruction while for the 1/2 and 1 ML coverages they are 2X1. Same method was also used to investigate the surface stress and energetics of the clean-, Sb-adsorbed-, and Sb-interdiffused-Si(001) surface. It is found that interdiffusion of Sb into deeper layers of Si(001) leads to a more isotropic surface stress but corresponds to a higher total energy configuration. As a result of competition between stress relief and energy gain, the surface with all the Sb atoms adsorbed on top of Si(001) surface layer is predicted to have a less ordered geometry and roughness in z-direction. We have repeated the similar calculations on the Ge(001) surface for comparison. Finally using empirical molecular dynamics method, we have investigated the crystalline growth of silicon on Si(001) as a function of substrate temperature and incident particle energy. Our results show that the increase of substrate temperature enhances the crystallinity in the film grown on the Si(001) surface, on the other hand, the crystalline growth can be enhanced at low temperature by using higher incidence energy.

The Sutton Chen and quantum Sutton Chen potentials are used in molecular dynamics simulations to describe the structural, thermodynamical, and transport properties of Pd, Ni and their binary alloys in solid, liquid, and glass phases. Static properties including elastic constants, pair distribution function, static structure factor, and dynamical properties consisting of phonon dispersion relation, diffusion coefficient, and viscosity are computed at various temperatures. The melting temperatures for Pd-Ni system are obtained. The transferability of the potentials is tested by simulating the solid and liquid states. The eutectic concentration Pd0.45Ni0.55 is quenched at four different cooling rates. The system goes into glass formation at fast cooling rates, while it evolves to crystal at slow cooling rate. Comparison of calculated structural and dynamical properties with the available experiments and other calculations shows satisfactory consistency.

The very fundamental properties of biological membranes can be understood by studying their formation. This sets a good foundation for research related to how the membranes interact with organic molecules and ions; something of great value in the quest of explaining transport phenomena through cell membranes. It is furthermore of growing interest within the pharmacological research and contributes to the apprehension of life at the molecular level. In this thesis Molecular Dynamics has been used to simulate how evenly distributed phospholipids solvated in water leads to the formation of monolayers. An automation program has been written in Python for performing these simulations and is to be used as the foundation for performing simulations in further studies. The program was used to simulate model systems of high- and low concentrations of DPPC lipids. The DPPC lipid, like most other lipids, consist of a hydrophilic "head" part and two lipophilic "tails", which is the main cause of the lipids interacting in such a manner that forms membranes. The low concentration system was simulated for a total of 3 ns with all lipids having reached the surface at 1.5 ns, and the all lipids in the high concentration system had risen at 41 ns with a total simulation time of 43 ns. / De mest grundläggande egenskaperna hos cellmembran kan förstås genom att studera hur dessa bildas. Detta skapar en bra grund för forskning relaterad till hur membranen interagerar med organiska molekyler och joner; något av stort värde i bemödandet att förklara transportfenomen genom cellmembran. Dessutom är det av växande intresse inom den farmakologiska forskningen och bidrar till kunskapen om liv på den molekylära nivån. I denna avhandling har Molekylär Dynamik använts för att simulera hur jämnt fördelade fosfolipider lösta i vatten leder till bildandet av monoskiktade membran. Ett automatiseringsprogram har skrivits i Python för att utföra dessa simuleringar och ska komma att användas som grund för genomförandet av simuleringar i vidare studier. Programmet användes för att simulera modellsystem med höga och låga koncentrationer av DPPC lipider. DPPC lipiden, liksom de flesta andra lipider, består av en hydrofil ''huvud'' -del och två lipofila ''svansar'', vilket är den huvudsakliga orsaken till att lipiderna interagerar på ett sådant sätt som driver bildandet av ett membran. Lågkoncentrationssystemet simulerades i totalt 3 ns, varav 1,5 ns behövdes för att alla lipider skulle nå vattenytan. Alla lipider i högkoncentrationssystemet hade kommit upp till ytan efter 41 ns och för detta system utfördes simuleringen under en total tid på 43 ns.

I have set for a challenging study that combined experimental and theoretical approaches in an attempt to resolve a role of small aminoacids in intermolecular interactions. First, I have proposed a hypothesis that described the interaction among individual aminoacids forming D helices of D1 and D2 proteins based on molecular dynamic simulations of a simplified model representing the reaction centre of photosystem II. Stability of the putative interhelical hydrogen bond network connecting D1 and D2 proteins was investigated experimentally with dynamic force spectroscopy using atomic force microscope. The results of both methods are in a full agreement with each other and reveal the key role of D1-Gly208 aminoacid in stability and functionality of photosystem II by providing milieu for weak interactions among three contact points at the cross of D helices: D1-Gly208 (O) and D2-Cys211 (O?), D1-Ser209 (O?) and D2-Ile204 (O), D1-Ser212 (O?) and D2-Gly207 (O). Mutation of the D1-Gly208 led to the increase in probability of the binding among the aforementioned aminoacids, undesirably strengthening the overall interactions among the proteins compromising photosynthetic capacity (D1-Ser208) or disabling of autotrophic growth (D1-Val208).