This thesis studies strong, completely charged polyelectrolyte brushes. Extensive molecular dynamics simulations are performed on different polyelectrolyte brush systems using local compute servers and massively parallel supercomputers. The full Coulomb interaction of charged monomers, counterions, and salt ions is treated explicitly. The polymer chains are anchored by one of their ends to a uncharged planar surface. The chains are treated under good solvent conditions. Monovalent salt ions (1:1 type) are modelled same as counterions. The studies concentrate on three different brush systems at constant temperature and moderate Coulomb interaction strength (Bjerrum length equal to bond length): <br><br> The first system consists of a single polyelectrolyte brush anchored with varying grafting density to a plane. Results show that chains are extended up to about 2/3 of their contour length. The brush thickness slightly grows with increasing anchoring density. This slight dependence of the brush height on grafting density is in contrast to the well known scaling result for the osmotic brush regime. That is why the result obtained by simulations has stimulated further development of theory as well as new experimental investigations on polyelectrolyte brushes. This observation can be understood on a semi-quantitative level using a simple scaling model that incorporates excluded volume effects in a free-volume formulation where an effective cross section is assigned to the polymer chain from where couterions are excluded. The resulting regime is called nonlinear osmotic brush regime. Recently this regime was also obtained in experiments. <br><br> The second system studied consists of polyelectrolyte brushes with added salt in the nonlinear osmotic regime. Varying salt is an important parameter to tune the structure and properties of polyelectrolytes. Further motivation is due to a theoretical scaling prediction by Pincus for the salt dependence of brush thickness. In the high salt limit (salt concentration much larger than counterion concentration) the brush height is predicted to decrease with increasing external salt, but with a relatively weak power law showing an exponent -1/3. There is some experimental and theoretical work that confirms this prediction, but there are other results that are in contradiction. In such a situation simulations are performed to validate the theoretical prediction. The simulation result shows that brush thickness decreases with added salt, and indeed is in quite good agreement with the scaling prediction by Pincus.<br><br> The relation between buffer concentration and the effective ion strength inside the brush at varying salt concentration is of interest both from theoretical as well as experimental point of view. The simulation result shows that mobile ions (counterions as well as salt) distribute nonhomogeneously inside and outside of the brush. To explain the relation between the internal ion concentration with the buffer concentration a Donnan equilibrium approach is employed. Modifying the Donnan approach by taking into account the self-volume of polyelectrolyte chains as indicated above, the simulation result can be explained using the same effective cross section for the polymer chains. The extended Donnan equilibrium relation represents a interesting theoretical prediction that should be checked by experimental data.<br><br> The third system consist of two interacting polyelectrolyte brushes that are grafted to two parallel surfaces. The interactions between brushes are important, for instance, in stabilization of dispersions against flocculation. In the simulations pressure is evaluated as a function of separation D between the two grafting planes. The pressure behavior shows different regimes for decreasing separation. This behavior is in qualitative agreement with experimental data. At relatively weak compression the pressure behavior obtained in the simulation agrees with a 1/D power law predicted by scaling theory. Beyond that the present study could supply new insight for understanding the interaction between polyelectrolyte brushes. / In dieser Arbeit werden vollständig geladene, starke Polyelektrolytbürsten untersucht. Unter Verwendung lokaler Computeserver und massiv paralleler Supercomputer wurden umfangreiche Molekulardynamik Simulationen von verschiedenen Polyelektrolytbürsten Systemen ausgeführt. Die vollständige Coulomb Wechselwirkung zwischen geladenen Monomeren, Gegen- und Salzionen wird explizit berücksichtigt. Die Polymerketten – in gutem Lösungsmittel simuliert – sind mit einem Ende an einer ungeladenen, planaren Grenzfläche verankert. Monovalente Salzionen (1:1) werden identisch wie Gegenionen modelliert. Simulationen bei konstanter Temperatur und moderater Stärke der Coulomb Wechselwirkung (Bjerrum Länge etwa gleich der Bindungslänge) konzentrieren sich auf drei Systeme:<br><br> 1. Polyelektrolytbürsten ohne Salzionen mit variabler Ankerdichte der Ketten<br> Die Simulationsergebnisse zeigen, dass die Polyelektrolytketten bis zu 2/3 ihrer Konturlänge gestreckt sind, wobei die Bürstenhöhe mit zunehmender Ankerdichte leicht wächst. Diese schwache Abhängigkeit steht im Widerspruch zu theoretischen Ergebnissen, die Unabhängigkeit von der Ankerdichte im so genannten osmotischen Regime vorhersagen. In der Folge haben die Simulationen sowohl weitergehende theoretische Überlegungen als auch neue experimentelle Untersuchungen an Polyelektrolytbürsten stimuliert. Zwischenzeitlich konnte die Beobachtung auf semi-quantitativer Ebene auf der Basis eines einfachen Skalenmodells verstanden werden, welches das Eigenvolumen der Polymerketten im Rahmen einer freien Volumen Näherung berücksichtigt. Dabei wird der Kette ein effektiver Querschnitt zugeordnet, von dem Gegenionen ausgeschlossen sind. Das resultierende Regime, in dem nichtlineare Entropie und Elastizität berücksichtigt sind, wird als nichtlinear osmotisches Regime bezeichnet. In der Zwischenzeit konnte dieses Regime auch experimentell verifiziert werden.<br><br> 2. Polyelektrolytbürsten im nichtlinear osmotischen Regime mit variabler Salzkonzentration <br> Struktur und Eigenschaften von Polyelektrolyten können in einfacher Weise durch Veränderung der Salzkonzentration beeinflusst werden. Nach Pincus sollte für starke Salzkonzentration (groß gegenüber der Konzentration der Gegenionen) die Bürstenhöhe mit wachsender Konzentration abnehmen, jedoch nur als relativ schwaches Potenzgesetz mit einem Exponenten -1/3. In der Literatur sind experimentelle und theoretische Ergebnisse bekannt, die diese theoretische Vorhersage bestätigen – allerdings auch solche, die dazu im Widerspruch stehen. In einer solchen Situation sind Simulationen ein geeignetes Mittel, um theoretische Vorhersagen zu überprüfen: In der Tat bestätigen die vorliegenden Simulationsergebnisse in eindeutiger Weise die theoretische Vorhersage von Pincus.<br><br> Das Verhältnis zwischen Buffer Konzentration und effektiver Ionenstärke in der Polymerschicht ist nicht nur von theoretischem Interesse, sondern hat ebenso experimentelle Relevanz. Die Simulationen zeigen, dass die mobilen Ionen innerhalb und außerhalb der Polyelektrolytbürste inhomogen verteilt sind. Ein Erklärungsversuch mit Hilfe des Donnan Gleichgewichts liefert nur für sehr kleine Salzkon-zentrationen befriedigende Übereinstimmung, ansonst ein qualitativ unterschiedliches Verhalten. Wird jedoch das Eigenvolumen der Ketten in ähnlicher Weise wie oben skizziert berücksichtigt, können die Simulationsdaten bei identischer Parameterwahl in nahezu perfekter Übereinstimmung reproduziert werden. Der erweiterte Ansatz für das Donnan Gleichgewicht in konzentrierten Systemen stellt eine interessante theoretische Vorhersage dar, die auch experimentell überprüft werden sollte.<br><br> 3. Wechselwirkung zwischen zwei Polyelektrolytbürsten ohne Salz <br> Repulsive Wechselwirkungen zwischen Polymerbürsten haben in unterschiedlichen Zusammenhängen eine große Bedeutung, so z.B. bei der Stabilisierung von Dispersionen oder bei der Reduzierung von Reibungswiderständen in biologischen Systemen. In den vorgestellten Simulationen von zwei Polyelektrolytbürsten, die an gegenüberliegende Grenzflächen verankert sind, wird der osmotische Druck in Abhängigkeit vom Abstand D der Ankerflächen untersucht. Mit abnehmendem Abstand werden unterschiedliche Regime im Verhalten des Druckes beobachtet. Dieses Verhalten stimmt qualitativ mit experimentellen Ergebnissen überein. Für relativ schwache Überlappung folgt das Verhalten des Drucks dem theoretisch vorhergesagten 1/D Skalengesetz. Darüber hinaus liefert die Simulationsuntersuchung neue Daten zum Verständnis der Wechselwirkung zwischen Polyelektrolyt Bürsten.

Cellulose is a linear polysaccharide, serving as reinforcement in plant cell walls.Understanding its structure and properties is of importance in the developmentof nanostructured cellulose materials. The aim of this thesis is to address thisquestion by applying the computer simulation technique Molecular Dynamics(MD) onto an atomistic model of a native crystal form of cellulose.A molecular model of crystalline cellulose Iβ was developed and simulatedwith the GROMACS simulation software package.Temperature dependence of the crystal bulk model was investigated. A gradualtransition was observed between 350 K and 500 K in concordance with experimentalresults. The high temperature structure differed from the originalstructure in terms of crystal cell parameters, hydrogen bonding network andelastic modulus.Spin-lattice relaxation times, T1, from solid-state Nuclear Magnetic Resonancespectroscopy were compared with values calculated from the dynamics ofthe C4-H4 vector in MD simulations. Calculated T1 compared well with experimentallyobtained, suggesting well reproduced dynamics. Moreover, a differencein T1 of about a factor 2 was found for C4 atoms at surfaces parallel to differentcrystallographic planes. This supports a proposed explanation regarding anobserved doublet for C4 atoms in the NMR spectrum.Interaction energies between crystalline cellulose and water and 6− hydroxyhexanal(CL) were determined from simulations. Water was found to interactstronger with cellulose than CL. Moreover, the effect of grafting CL onto surfacecellulose chains was examined. For both water and CL interfaces, grafting ledto increased interaction. Electrostatic interactions were dominating in all cases,however grafting increased the importance of van der Waals interactions.The experimental approach to investigate polymer desorption by pulling itfrom a surface by the use of Atomic Force Microscopy (AFM) was enlightenedwith a modelling study. A single cellulose octamer was pulled from a cellulosecrystal into water and cyclohexane. Resulting pull-off energies proved a clearsolvent effect, 300 − 400 [kJ/mole] in cyclohexane and 100 − 200 [kJ/mole] inwater.In general, MD was shown to be useful when applied in combination withfeasible experimental techniques such as NMR and AFM to increase the fundamentalunderstanding of cellulose structure and properties. / Cellulosa förstärker cellväggen i växter i form av nanostrukturerade och mycketstarka fibriller. För utvecklingen av nya cellulosamaterial från dessa fibriller ären förståelse för cellulosans struktur och egenskaper viktig. Syftet med dennaavhandling är att med hjälp av en atomistisk modell och molekyldynamiskadatorsimuleringar (MD) öka kunskapen om cellulosa på atomär nivå.En atomistisk modell av kristallin cellulosa Iβ utvecklades och simuleradesmed simuleringsprogrampaketet GROMACS.Temperaturberoendet hos kristallin cellulosa i bulk undersöktes. Mellan350 K och 500 K skedde en gradvis kristallin strukturomvandling. Vid högre temperaturhade cellulosan annorlunda kristall-enhetscellsparametrar, vätebindingsmönsteroch elastisk modul jämfört med orginalstrukturen.Systemet cellulosa-vatten har stor praktisk betydelse. Spinn-gitter-relaxationstiderT1 beräknades därför från dynamiken hos C4-H4-vektorn i MD-simuleringaroch jämfördes med värden uppmätta med fastfas-NMR. De beräknadevärdena stämde väl överens med de experimentella och dynamiken vid ytan kanantas vara välreproducerad i modellen. Dessutom kunde en skillnad i T1 meden faktor 2 för C4-atomer på ytkedjor vid olika kristallografiska plan påvisas.Simuleringsresultaten stödjer därmed en tidigare föreslagen förklaring till endubblett för C4-atomer i cellulosans NMR-spektrum.Växelverkansenergier mellan cellulosa och polymeren PCL är intressant förnanokompositmaterial. Därför bestämdes växelverkansenergier mellan kristallincellulosa och vatten och cellulosa och 6-hydroxyhexanal (CL). Växelverkan mellancellulosa med vatten visade sig vara större än mellan cellulosa och CL.Ympning av CL-molekyler på cellulosaytan ledde till ökad växelverkan för såvälgränsytor mot vatten som mot CL. Elektrostatisk växelverkan dominerade vidsamtliga gränsytor, även om CL-ympning orsakade ökad andel av van der Waalskrafter.Polymerdesorption kan undersökas med hjälp av atomkraftmikroskopi (AFM).Ett simulerat experiment med MD utfördes därför genom att en cellulosaoktamerdrogs från en cellulosayta in i vatten eller cyklohexan. Det krävdes avsevärtmindre energi att dra loss oktameren i cyklohexan (300−400 kJ/mol) jämförtmed vatten (100 − 200 kJ/mol). Resultaten analyserades i termer av specifikväxelverkan mellan cellulosaoktameren och identifierbara kemiska grupper påcellulosaytan.MD har stor potential att öka förståelsen för cellulosa på molekylär nivå.MD-simuleringar kan inspirera experimentella mätningar genom upptäckter avnya fenomen. MD kan dessutom tillföra nya aspekter vid analys av experimentellaresultat. Det har i avhandlingen demonstrerats för metoder som NMR,AFM, mekanisk provning och mätning av termisk utvidgning / QC 20100621

The dynamical behaviors of tricarboxylic acid derivative, 1,3,5-tris(carbox- ymethoxy) benzene[TCMB, C6H3(OCH2COOH)3] on an Au surface is investigated by molecular dynamics. A TCMB molecule adsorbed on the Au(111) substrate is first probed into the structure arrangement. It founds that there are four possible conformations of the TCMB molecule that is adsorbed on the Au(111) substrate. The main difference on its conformation is the orientation of its functional group, which lead the molecule that forms the lock-and-key (LAK) behavior and prompts the molecule that become more stable on the substrate. As this result, the LAK behavior directly affects the trajectories of movement and dynamical behaviors. Another topic is to observe the behavior of TCMB molecule on Au(110) and Au(100) surface, respectively. As well as the result of the TCMB molecule adsorbed on the Au(111) substrate, it also shows a different behavior on dynamical behaviors when the TCMB molecule adsorbed on the Au(110) and Au(100) substrate. Moreover, we found that the diffusion direction of TCMB molecule is dependent on the arrangement of the adsorbed surface. From the observation of the trajectory of the TCMB molecule, we found that diffusion range is most wide on Au(100) plane. The translational direction of TCMB molecule tend to move on the <110> direction as the molecule is migrate on the Au(100) plane, whereas that tend to move on the [1ī0] direction as the molecule is migrate on the Au(110) plane. From the description above, we know that TCMB molecule with different conformations on different plane of surface arrangement displays different trajectories of movement and dynamical behaviors. Therefore, in order to understand the dynamical behaviors of TCMB monolayer on gold surface. In this work, the temperature effect on the adsorption behavior and the dynamic behavior of TCMB monolayer structure on the Au(111) substrate are investigated. From the calculation of the cohesive energy between molecules and the interaction energy between the molecule and the Au(111) substrate, we found that there are significant changes in cohesive energy and interaction energy at specific temperatures, which can be attributed to the deformation of the monolayer structure. Finally, the mean square displacement (MSD), diffusion coefficient(D) and distance between the molecule and the Au(111) substrate are calculated to investigate the diffusion property and motion behavior of TCMB monolayer at specific temperatures.

Molecular dynamic simulation is utilized to investigate the adsorption mechanism of water molecules surrounding Au nanoparticle of different sizes. We selected 13, 55, 147 atoms icosahedral gold nanopartilce in our model and their diameter are 7.92&#x00C5;, 13.2&#x00C5;, 18.5&#x00C5;, respectively. We calculated density profile of water molecules and found that there were two adsorption layers out of the surface of gold nanoparticles. We also calculated average number of hydrogen bonds per water . It is higer in the adsorption layer than in bulk water region and we found that the direction of hydrogen bonds are numerously parallel with gold surface in the adsorption layer. We also claculated orientational order parameter for water molecules and explore the difference of the tetrahedral structure of the water molecules between the adsorption layer and bulk water region. Besides, we compared of cases of different gold sizes.

ATP Binding Cassette (ABC) transporters are trans-membrane proteins that exist in all phyla. Mutations in this family of proteins can cause inherited diseases like Cystic Fibrosis. ABC transporters consist of dimers of nucleotide binding domains (NBDs) and transmembrane domains (TMDs). NBDs regulate ABC transporters by binding to and hydrolyzing ATP. Although NBD-ATP interactions, NBD-TMD interactions and NBD-water interactions are known to be crucial to the function of these proteins, it is still not clear what structural and energetic factors are involved in the NBD-NTP interactions, how NBD and TMD interact with each other, how water is involved in the functions of ABC transporters and what are the structures and energetics of protein bound water. Molecular modeling and molecular dynamics (MD) simulations were conducted to interpret and predict the structural and energetic factors in control and action of two ABC transporters, CvaB and SUR2B. Water is essential for ABC transporters to carry out their functions, to increase the accuracy of simulations. Therefore, water potentials in molecular modeling and dynamics simulations were improved based on the calculation of water structures from protein surface. Previous study showed the NBDs of ABC transporter CvaB bind tighter to GTP than to ATP at lower temperature but not at high temperature. The MD simulations in this study suggested the velocity of water molecules initiates the temperature dependent functional change of proteins. Previous study found that Ser1387 in the NBD of SUR2B, an ABC transporter in vascular smooth muscles, is critical to Kir6.1/SUR2B channel. The molecular modeling and dynamics simulation conducted on SUR2B showed that Ser1387 is located at a region that contacts a TMD. Upon the phosphorylation, the interaction between the NBD and TMD was enhanced which led to an inter domain movement. Water is essential for ABC transporters to carry out their functions, to increase the accuracy of simulations, and, therefore, the structures and energetics of protein bound water were studied. The water radial distribution function for protein bound water was calculated from 105 atomic resolution protein crystal structures and was found to be sharper than that observed for bulk water.

This dissertation focuses on the behavior of homogeneous FCC metallic interfaces on the nanoscale. Specifically, atomistic calculations (molecular statics and molecular dynamics) with embedded-atom method potentials are used to study the fundamental failure processes that occur at a bicrystal interface in Cu and Al as a result of a mechanical deformation. There are four primary objectives to this dissertation. First, molecular statics calculations are used to determine the most appropriate (minimum energy) structure of homogeneous bicrystal interfaces in Cu and Al. Interface structures and energies are reported in this work, with comparison to both theoretical and experimental characterizations of interface configuration. Second, molecular dynamics simulations are performed to provide a characterization of atomic scale inelastic behavior, including both dislocation and void nucleation activities which lead to interfacial failure. Specifically, two types of interfaces are highlighted in this work: a mirror symmetric interface in aluminum and an asymmetrically dissociated interface in copper. Distorted interface structures (after the dislocation nucleation event) are discussed in terms of partial dislocations or disclinations. Third, molecular dynamics simulations are used to investigate potential relationships between interface structure and interface properties or morphology. The orientation of the primary slip planes with respect to the loading direction and the porosity within the interface region are found to be critical factors in defining the strength of the bicrystal interface, for example. Finally, results of the atomistic calculations are utilized to motivate improved forms for continuum interface separation potentials, ultimately increasing the applicability of these relationships to include cohesive failure in ductile crystalline materials.

Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules. MD has now been widely used in materials, biochemical and pharmaceutical research. In recent years, zirconium phosphate (ZrP) compounds developed a new type of multi-function mediated porous materials, which the crystalline £\-zirconium phosphate (£\-ZrP) is a cationic layered compounds, with a neat layer structure and easy to design. Cetyl trimethyl ammonium bromide (CTAB) is a cationic surfactant, it¡¦s one kind of ammonium salt of a long carbon chain as hydrophobic groups. Ion exchange can occur with other exchangeable cations. In this study, we first use CTAB inserted into £\-ZrP interlayer to prepare £\-ZrP-CTAB material. Second, we add phenol solution in the system, and use molecular dynamics simulations to observe the solution¡¦s penetration and adsorption. The result shows that pure water can permeate through £\-ZrP CTAB membrane, and pure phenol will be adsorbed by the £\-ZrP-CTAB membrane. If we add phenol solution, the water molecules can pass through the £\-ZrP-CTAB membrane but phenol molecule can¡¦t. It can achieve the effect of separation of the mixed solution. Last we simulate phenolate solution system. The result shows that the number of phenolate molecule enter the membrane is less than phenol molecule in phenol solution. This result is also consistent with the experiments mentioned in the literature.

The surface phenemona in polishing process induced by nano-particle was studied in this thesis. The properties of particle, rigidity and geometry, are forced. A perfect polished surface includes lower roughness and thinner damage layer. Besides a perfect surface, how we get higher rate of remove is also an important thing. The goal is to get the relation between induced surface phenomena and properities of nano-particle. The M.D. (Molecular Dynamic) simulation is uesed in this thesis. The specicaly lowered integral timestep is second for simulating the rigidity of nano-particle with saving simulation time and geting accurate in simulation results. In order to simuate the nano-particle rigidity and adhesive effects between nanoparticle and work surface, the modified potential function is used. Considering the types of nano-particle motion which are pure rolling and sliding, the different geometric shapes are used . In the results of simulation about the rigidity of particles, the phenomena induced by rolling particles and rigidity don¡¦t have apparent correlation. For sliding particles, the lower rigidity and lower thick damage layer was. However, if the rigidity is too weak to hold the particle geometric shape, the damage layer thickness is larger. In the results of simulation about particle shapes, the sliding particle with larger front angle will indcue deeper damager layer. It¡¦s because the more workpiece atoms could move to the bottom or rear of the particles to make more damaged atoms. If the length of particle bottom be increased, the interactive behavior between particle and work surface would become more violently to make deeper damaged layer. The rolling particle with scraggy surface can cohere more atoms than the ball particle even in the lower adhesive coefficient, but induced roughness will be higher .

In recent years, the characteristic of Nano fluid channel has important contribute in bio-technology and nano-machine. Gold atoms in all materials have significant effects on human bodies, which have attracted considerable academic interests when applied to biotechnology. Especially the Au nanotubes has combine an excellent bio-compatible not only using in chemical analyzed and chemical inspect, but also has function on transport fluid molecule in micro channel. This study utilizes molecular dynamics to the behavior of water molecules inside Au nanotubes. We used the potential of Spohr, F3C and Tight-binding in different water density and temperature to investigate the adsorption mechanism and dynamic behavior of water molecules inside Au nanotubes. We discuss the numbers of absorbed water molecule near the inner tube wall all achieve to saturation at three different densities, temperature and size of Au nanotubes. This work we compared water density, the percentage profiles of hydrogen bond, orientational order and flux for water molecules inside the Au nanotubes.

By means of molecular dynamics simulation the effect of external direct current electric field on the polyethylene-like (PE-like) polymer and methyl chloride solvent system is investigated. Three systems include normal solution, dilute solution, and lower-density solution are simulated. For each system, four conditions include non-charged polymers in nonpolar solvents, non-charged polymers in polar solvents, charged polymers in nonpolar solvents, and charged polymer in polar solvents are simulated. The diffusion behavior of polymer in solvent is as functions of electric field, polarity of solvent molecules, and polarity of polymer. When an electric field is applied to the system include dielectric molecules, our calculation shows that the center of mass diffusion constant of polymer depends on the alignment of charged polymer or polar solvent molecules, the mobility of charged polymer or solvent molecules and the density of the system. The mobility of polar molecules results in the increase of the center of mass diffusion constant of polymer. The alignment of polar molecules results in the increase of fluid viscosity. This decreases the center of mass diffusion constant of polymer.