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Molecular simulation is an indispensable tool in many different disciplines such as physics, biology, chemical engineering, materials science, drug design, and others. Performing large-scale molecular simulation is of great interest to biologists and chemists, because many important biological and pharmaceutical phenomena can only be observed in very large molecule systems and after sufficiently long time dynamics. On the other hand, molecular simulation methods usually have very steep computational costs, which limits current molecular simulation studies to relatively small systems. The gap between the scale of molecular simulation that existing techniques can handle and the scale of interest has become a major barrier for applying molecular simulation to study real-world problems. In order to study large-scale molecular systems using molecular simulation, it requires developing highly parallel simulation algorithms and constantly adapting the algorithms to rapidly changing high performance computing architectures. However, many existing algorithms and codes for molecular simulation are from more than a decade ago, which were designed for sequential computers or early parallel architectures. They may not scale efficiently and do not fully exploit features of today's hardware. Given the rapid evolution in computer architectures, the time has come to revisit these molecular simulation algorithms and codes. In this thesis, we demonstrate our approach to addressing the computational challenges of large-scale molecular simulation by presenting both the high-performance algorithms and software for two important molecular simulation applications: Hartree-Fock (HF) calculations and hydrodynamics simulations, on highly parallel computer architectures. The algorithms and software presented in this thesis have been used by biologists and chemists to study some problems that were unable to solve using existing codes. The parallel techniques and methods developed in this work can be also applied to other molecular simulation applications.

The physical understanding of biological processes such as transcription requires the knowledge of double-stranded DNA (dsDNA) physics. A notable thermo- dynamic property of dsDNA is its denaturation, at the melting temperature, in which it unwinds into two single-stranded DNAs via the formation of denat- uration bubbles (segment of consecutive unpaired base-pairs). The dynamics of denaturation has been studied so far at the base-pair (bp) scale, ignoring conformational chain degrees of freedom. These studies do not explain the very long closure times of 20 to 100 s, measured by Altan-Bonnet et al., of 18 bps long bubbles at room temperature. In this thesis, we study the closure of pre-equilibrated large bubbles, by using Brownian dynamics simulations of two simple DNA coarse- grained models. We show that the closure occurs via two steps: rst, a fast zipping of the initial bubble occurs until a meta-stable state is reached, due to the large bending and twisting energies stored in the bubble. Then, the meta-stable bubble closes either via rotational di usion of the sti side arms until their alignment, or bubble di usion until it reaches the chain end, or locally by thermal activation, depending on the DNA length and elastic moduli. We show that the physical mechanism behind these long timescales is therefore the dynamical coupling between base-pair and chain degrees of freedom.

L'enjeu principal de cette thèse est de comprendre et prédire les propriétés structurales et rhéologiques de suspensions colloïdales en tenant compte d'éléments complexes tels que (1) les interactions hydrodynamiques (IHs) et/ou (2) des forces extérieures. Nous employons dans cette thèse deux des techniques numériques les plus rapides de la littérature: la dynamique brownienne standard (BD), pour les systèmes où les IHs peuvent être ignorées; et la technique hybride "stochastic rotation dynamics - molecular dynamics" (SRD-MD), pour les systèmes où les IHs doivent être incorporées.Trois systèmes colloïdaux différents ont été étudiés. Le premier est un système de sphères dures soumis à un cisaillement, où le but a été de vérifier que l'introduction des IHs dans la SRD-MD peut correctement reproduire la relation entre la viscosité et la fraction volumique. Les résultats de viscosité sont en accord avec les résultats connus, qu'ils soient analytiques, numériques et expérimentaux. Le second système consiste en une suspension d'alumine, pour laquelle les interactions sont décrites par la théorie DLVO (Derjaguin-Landau-Verwey-Overbeek). Les simulations montrent que le seuil de percolation (phi_c) diminue lorsque la profondeur du puits de potentiel augmente. De plus, nous observons que la prise en compte des IHs tend à former des structures plus allongées également, par rapport aux structures obtenues sans les IHs. Les valeurs de phi_c obtenues dans les simulations sont en bon accord avec celles estimées par le modèle de la contrainte seuil (YODEL) établi par Flatt et Bowen. Le troisième système comporte deux types de colloïdes qui interagissent par un potentiel de Yukawa. Ce système binaire est soumis à l'influence d'un mur attractif. Nous montrons que la présence d'un mur attractif peut altérer la structure cristalline des agrégats à la surface telle qu'une structure de type CsCl qui se forme au lieu de la structure métastable de type NaCl. Finalement, nous avons réalisé une étude préliminaire par SRD-MD de suspensions soumises à un cisaillement oscillant. Nous montrons que lorsque la suspension est soumise au cisaillement oscillant en même temps que l'agrégation se produit, des structures plus compactes se forment. / The main objective of this thesis is to predict and understand the structural and rheological properties of colloidal suspensions when (1) hydrodynamic interactions (HIs) and/or (2) external forces are present. We employ two of the fastest techniques in literature: Brownian dynamics (BD), for systems without HIs; and the hybrid "stochastic rotation dynamics - molecular dynamics" (SRD-MD) for systems with HIs. Three different systems were studied. The first is a system of hard spheres subjected to shear, where the goal was to ensure that SRD-MD can correctly reproduce the viscosity vs. volume fraction relationship. The results are consistent with known analytical, numerical and experimental data. The second system is an alumina suspension described by the DLVO theory (Derjaguin-Landau-Verwey-Overbeek). The simulations show that the percolation threshold (phi_c) decreases as the depth of the potential well increases. Moreover, we note that HIs tend to form more elongated structures compared to the systems without HIs. The phi_c values ​​obtained are in good agreement with those estimated by Flatt and Bowen's yield stress model (YODEL). The third system consists of binary colloids that interact by Yukawa potential and subjected to the influence of an attractive wall. We show that the presence of an attractive wall may alter the crystalline structures such that CsCl crystals are formed instead of the metastable NaCl crystals. Finally, we conducted a preliminary study of suspensions under an oscillating shear. We show that when the aggregation process suspension coincides with the oscillatory motion, more compact structures are formed.

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Diploma thesis was aimed to deal with evaluation of microrheology method in the research of biopolymer-protein. Used biopolymer was sodium hyaluronate and proteins were trypsin and chymotrypsin. For measuring of microrheology were used particles with different radius (0,5 m and 1 m). It was found, that both substances have viscous charakter. Passive microrheology is suitable for measuring the viscoelastic properties of biopolymers.

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In this workshop we will discuss some fundamentals of equilibrium and non-equilibrium thermodynamics, in particular how concentration gradients are formed due to the Soret effect. At first we will pay attention to the analysis of fluctuations at macroscopic thermodynamic equilibrium for the determination of the Fick diffusion coefficient and the thermal diffusivity. Then, starting with the extended diffusion equation, we will derive solutions for the concentration field under common experimental geometries and introduce modern optical techniques for the measurement of the Fick diffusion, thermodiffusion and Soret coefficients.

Colloidal particles provide the ideal building blocks for the next generation of microdevices, such as advanced sensors and precision drug delivery systems. However, many such applications require the use of top-down (i.e. humanly controllable) forces to manipulate colloidal particles with single-particle precision, and current methods can only achieve such precision for small numbers of particles at a time. To address this challenge, we propose using chemical forces in combination with existing top-down techniques to enable the control of larger numbers of particles simultaneously. Controlling colloids using chemical reactions is a novel technique not typically utilized. Due to its distinct difference from other control methods, it provides new degrees of freedom to work with which offer new opportunities for designing colloidal devices. In this dissertation, we show how modern control theory can be used to implement the control of colloidal particles using chemical forces. We use Brownian dynamics simulations to test control strategies for three different situations: directly controlling chemical reactions to produce a desired concentration gradient, controlling a reactive colloidal particle that interacts chemically with other colloids to move them to desired locations, and controlling the dynamics of active colloidal particles to manipulate their collective behavior. The results obtained in this work will demonstrate the plausibility of each of these three control strategies and provide insights into the choices of physical parameters that can be used in future experiments.

<p>This thesis describes water proton and deuterium relaxation processes, as seen by Nuclear Magnetic Resonance (NMR) spectroscopy, using Brownian Dynamics (BD) or Molecular Dynamics (MD) simulations. The MD simulations reveal new detailed information about the dynamics and order of water molecules outside of a lipid bilayer. This is very important information in order to fully understand deuterium NMR measurements in lipid bilayer systems, which require an advanced analysis, because of the complicated water motion (such as tumbling and self-diffusion). The BD simulation methods are combined with the powerful Stochastic Liouville Equation (SLE) in its Langevin form (SLEL) to give new insight into both ¹H₂O and ²H₂O relaxation. The new simulation techniques which combine BD and SLEL can give important new information in cases where other methods do not apply. The deuterium relaxation is described in the context of a water/lipid interface and is in a very elegant way combined with the simulation of diffusion on curved surfaces developed by our research group. ¹H₂O spin-lattice relaxation is described for paramagneticsystems. With this we mean systems with paramagnetic transition metal ions or complexes, that are dissolved into a water solvent. The theoretical description of such systems are quite well investigated but such systems are not yet fully understood. An important consequence of the Paramagnetic Relaxation Enhancement (PRE) calculations when using the SLEL approach combined with BD simulations is that we obtain the electron correlation functions, which describe the relaxation of the paramagnetic electron spins. This means for example that it is also straight forward to generate Electron Spin Resonance (ESR) lineshapes.</p>