An aqueous solution of electrolytes can be modelled simplistically as charged hard spheresdispersed in a dielectric continuum. We review various classical theories for hard sphere systems including the Percus-Yevick theory, the mean spherical approximation, the Debye-Hückel theory and the hyper-netted chain theory, and we compare the predictions of the theories with simulation results. The statistical associating fluid theory (SAFT) has proved to be accurate for neutral polymers. It is modified to cope with charged polyelectrolyte systems. A chain term for the charged reference fluid is introduced into the theory. Some well-established results are reproduced in this study and we also introduce new terms and discuss their effects. The results show that the SAFT is semi-quantitatively correct in predicting the phase behaviour of polyelectrolytes. The electrostatic attraction between unlike charged particles at low temperature is very strong. The short-range attractions between unlike pairs are treated via an association theory while the remaining interactions are handled by hypernetted chain theory. This method works quite well with multiple associating sites. The phase prediction for the size and charge symmetric restricted primitive model is quantitatively correct as compared with simulation results. Furthermore, it also gives semi-quantitatively correct predictions for the phase behaviour of size- and charge-asymmetric cases. Dissipative particle dynamics (DPD) is a powerful simulation technique for mesoscopic systems. Molecules with specific shapes (rods and spheres) are simulated using this technique.By tuning the density of the system, some liquid crystal phase transitions can be observed.The properties of spider silk fibroin are also modelled by DPD, indicating a possible route offorming spider silk.

Isoporous membranes manufactured from diblock copolymer are successfully produced at laboratory scale under controlled conditions. Because of the complex phenomena involved, membrane preparation requires trial and error methodologies to find the optimal conditions, leading to a considerable demand of resources. Experimental insights demonstrate that the self-assembly of the block copolymers in solution has an effect on the final membrane structure. Nevertheless, the complete understanding of these multi-scale phenomena is elusive. Herein we use the coarse-grained method Dissipative Particle Dynamics to study the self-assembly of block copolymers that are used for the preparation of the membranes. To simulate representative time and length scales, we introduce a framework for model reduction of polymer chain representations for dissipative particle dynamics, which preserves the properties governing the phase equilibria. We reduce the number of degrees of freedom by accounting for the correlation between beads in fine-grained models via power laws and the consistent scaling of the simulation parameters. The coarse-graining models are consistent with the experimental evidence, showing a morphological transition of the aggregates as the polymer concentration and solvent affinity change. We show that hexagonal packing of the micelles can occur in solution within different windows of polymer concentration depending on the solvent affinity. However, the shape and size dispersion of the micelles determine the characteristic arrangement. We describe the order of crew-cut micelles using a rigid-sphere approximation and propose different phase parameters that characterize the emergence of monodisperse-spherical micelles in solution. Additionally, we investigate the effect of blending asymmetric diblock copolymers (AB/AC) over the properties of the membranes. We observe that the co-assembly mechanism localizes the AC molecules at the interface of A and B domains, and induces the swelling of the B-rich domains. The B-C interactions control the curvature of the assemblies in these blends. Finally, we study the self-assembly triblock copolymers used for membranes fabrication. We show that the polymer concentration, the block-copolymer composition, and the swelling of the micelle are responsible for the formation of elongated micelles in the casting solution. The formation of nanoporous membranes arises from the network-like packing of those micelles.

No description available.

No description available.

Lipid molecules are amphiphilic in nature consisting of a hydrophilic head group and hydrophobic hydrocarbon tails. The lipid bilayer consists of two layers of lipid molecules arranged with their hydrophobic tails facing each other and their hydrophilic head groups solvated by water. Lipid bilayers with hydrophilic polymer chains grafted onto the head groups have applications in various fields, such as stabilization of liposomes designed for targeted drug delivery, synthesis of supported bilayers for biomaterial applications, surface modification of implanted medical devices to prevent biological fouling and design of in vitro biosensors. The focus of this thesis lies in understanding the effects of polymer grafting on the thermodynamics and mechanical properties of lipid bilayers. Dissipative particle dynamics (DPD) has evolved as a promising method to study complex soft matter systems. The basic DPD algorithm, and its implementation are discussed in Chapter 2 of this thesis. It is important to achieve a tensionless state while studying phase transitions and deducing the mechanical properties of the bilayer. We proposed a modification of the Andersen barostat which can be incorporated in a DPD simulation to achieve the tensionless state as well as carry out simulations at a prescribed tension. In Chapter 3 of this thesis the effect of polymer grafting on single tailed lipid bilayers is studied. Simulations are carried out by varying the grafting fraction, Gf, defined as the ratio of the number of polymer molecules to the number of lipid molecules. At lowGf, the bilayer shows a sharp transition from the gel (Lβ) to the liquid crystalline (Lα) phase. This main melting transition temperature is lowered as Gf is increased. Corresponding to this, an increase in the area per head group is also observed. Above a critical value of Gf the interdigitated, LβI phase is observed prior to the main transition for the longer lipid tails. The analysis for two tailed lipids as a function of polymer chain length is extensively studied in Chapter 5. For the case of two tailed lipids, an intermediate interdigitated phase was not observed and the decrease in the melting temperature is more pronounced as the length of the polymer chain is increased. The scaling for fractional change in the area per head group, as well as the decrease in transition temperature as a function of polymer grafting are in good agreement with mean field theory predictions. The bending modulus (k) and area stretch modulus (kA) are essential for determining the shape and the mechanical stability of biological cells or lipid based vesicles. In simulations, the bending modulus k is evaluated from the Fourier transform of the out-of-plane fluctuations of the bilayer mid-plane. In Chapter 4 of this thesis, we illustrate that a surface representation based on Delanuay triangulation provides a robust parameter free representation of the bilayer surface. By evaluating the bending modulus for single tail lipids of different tail lengths, the continuum scaling relation d2 is verified. To our knowledge this is the first systematic investigation and verification of this scaling relationship using computer simulations. Using the continuum relation, =kAd2/ we find that α depends weakly on the tail lengths of the bilayer. Nevertheless we illustrate that a value of α=130 can be used to reliably estimate the bending modulus from the area stretch modulus for polymer free bilayers. Using our method, we are also able to capture the low q scalings and obtain the bending modulus of the gel (Lβ) phase. Grafted polymer was found to increase the value of the bending modulus for single tail lipids. Although the presence of polymer directly increases the area per head group, the suppressed height fluctuations dominate and the bending modulus increases for the single tail lipids. For two tail lipids a small decrease in the bending modulus was observed at low grafting fractions and short polymer chains. For large polymer lengths the bending modulus was found to increase monotonically.

O estudo de redes complexas tem alavancado um tremendo interesse em anos recentes. Uma das características salientes de redes complexas é a presença de comunidades, ou grupos de nós densamente conectados. A detecção de comunidades pode não apenas ajudar a entender as estruturas topológicas de redes complexas, mas também pode fornecer novas técnicas para aplicações reais, como mineração de dados. Neste trabalho, propomos um novo modelo para detecção de comunidades em redes complexas, no qual várias partículas caminham na rede e competem umas com as outras para marcar seu próprio território e rejeitar partículas intrusas. O processo atinge o equilíbrio dinâmico quando cada comunidade tem apenas uma partícula. Nossa abordagem não apenas pode obter bons resultados na detecção de comunidades, como também apresenta diversas características interessantes: 1) O processo de competição de partículas é similar a muitos processos naturais e sociais, tais como competição de animais por recursos, exploração territorial por humanos (animais), campanhas eleitorais, etc.. Portanto, o modelo proposto neste trabalho pode ser útil para simular a dinâmica evolutiva de tais processos. 2) Neste modelo, nós introduzimos uma regra para controlar o nível de aleatoriedade do passeio da partícula. Descobrimos que uma pequena porção de aleatoriedade pode aumentar bastante a taxa de detecção de comunidades. Nossa descoberta é análoga ao notável fenômeno chamado ressonância estocástica onde o desempenho de um sistema determinístico não-linear pode ser bastante melhorado através da introdução de um certo nível de ruído. É interessante notar que tal fenômeno é observado em uma situação diferente aos sistemas clássicos de ressonância estocástica. 3) Nossa descoberta indica que a aleatoriedade tem um papel importante em sistemas evolutivos. Ela serve para automaticamente escapar de armadilhas não desejáveis e explorar novos espaços, isto é, ela é um descobridor de novidades. 4) Uma análise quantitativa para processo de competição entre duas particulas e duas comunidades foi conduzida, a qual é um passo de avanço para desenvolvimento de teoria fundamental de aprendizado competitivo / Study of complex networks has triggered tremendous interests in recent years. One of the salient features of complex networks is the presence of communities, or groups of densely connected nodes. Community detection can not only help to understand the topological structure of complex networks, but also provide new techniques for real applications, such as data mining. In this work, a new model for complex network community detection is proposed, in which several particles walk in the network and compete with each other to mark their own territory and reject particle intruders. The process reaches dynamics equilibrium when each community has only one particle. This approach not only can get good community detection results, but also presents several interesting features: 1) The particle competition process is rather similar to many natural and social processes, such as resource competition by animals, territory exploration by humans (animal), election campaigns, etc.. Thus, the model proposed in this work may be useful to simulate dynamical evolution of such processes. 2) In this model, a rule to control the level of randomness of particle walking is introduced. We found a small portion of randomness can largely improve the community detection rate. Such a finding is analogous to a remarkable phenomenon called stochastic resonance (SR) where the performance of a nonlinear deterministic system can be largely enhanced by introducing a certain level of noise. Interestingly, such a SR-type phenomenon is observed in quite a different situation from classical SR systems. 3) Our finding indicates that randomness has an important role in evolutionary systems and in machine learning. It serves to automatically escape some undesirable traps and explore new spaces, i.e., it is a novelty finder. 4) A quantitative analysis for two particle competition in two communities is provided. This is a step toward the development of fundamental theory of competitive learning

Articular cartilage has a limited ability to heal due to its avascular, aneural, and alymphatic nature. Currently, there is a need for alternative therapies for diseases that affect articular cartilage such as osteoarthritis. Recently, it has been shown that tissue constructs, which resemble cartilage in structure and function, can be cultured in vitro in a cell-polymer bioreactor system. Bioreactors provide a three dimensional environment that promotes cell proliferation and matrix production. The primary objective of this study is to accurately simulate fluid mechanics using the lattice Boltzmann method for application to a cell-polymer bioreactor system. Lattice Boltzmann (LB) is a flexible computation technique that will allow for the simulation of a moving construct under various bioreactor conditions. The method predicts macroscopic hydrodynamics by considering virtual particle interactions. Derived from the Lattice Gas Automata, lattice Boltzmann allows for mass transfer, complex geometries, and particle dynamics. A primary goal is to characterize the accuracy of the LB implementation and eventually the shear stresses felt by a tissue construct in this dynamic environment. This information is important since recent studies show that chondrocytic function may depend on the mechanical stimuli produced by fluid flow. Hence, shear stress may affect the final mechanical properties of tissue constructs. In this study, numerical simulations are done first in 2D and then extended to 3D to test the LB implementation. Simulations of the rotating wall vessel (RWV) bioreactor are then undertaken. The results are benchmarked against computations done with a commercial CFD package, FLUENT, and compared with analytic solutions and experimental data.

The purpose of this research is to understand the sinking particle dynamics in the Gaoping Submarine Canyon (GPSC), the change of their geochemical character, and their causal relationship with dynamic parameters. Also this research inquires into the significance of sedimentary environment, transport process, and the influence of non-tidal actions (turbidity current) in the sedimentary environment. The field experiments including LADCP moorings, T6KP(1/10/-3/20), and T7KP (7/7-9/11) sediment traps moorings were deployed in the GPSC to collect the time-series data of sinking particle and related dynamic parameters. Parameters of discrete sediment analysis were used to build continuous time-series data by interpolation, and time series analysis applied to understand the change of physical and geochemical character and their correlation with dynamic parameters. The results showed that sinking particles of different grain-size classes confront different forces in the canyon and their grain-size distribution structures are influenced accordingly. Vertical component of the flow has more influences on coarse particles, while the along canyon flow component has more influences on fine particles. The influence of semidiurnal tide on sinking particle is not clearly resoloved, but spring tide and neap tide affect them significantly. GPSC is normally a stable deposition environment dominated by tidal currents. Particle-reactive materials vary upon with clay concentration, coarse paericles vary upon with the flow field, and the change of benthic nepheloid layer thickness during spring and neap tide cycle affects the vertical distribution of particle size-groups near the bottom of canyon. The particle in the upper (rim) and lower (near the bottom) canyon belong to different transport and dynamic regimes. The upper part was affected by upwelling and shelf processes, while the lower part was affected by tidal currents. In case of episodic event, if surge-like turbidity flows pass near the canyon floor, in the waxing phase, the sinking particle would be affected by the strong momentum of resuspension and mixing which leads to a dramatic change of geochemical character of these particles. In turbidity current event, coarse sand and silt are the major particle sizes with low clay content, suspended sediment concentration about 4.41 g / l. The fluctuation of time series analysis by HHT found a frequency between 2.1~9.8 clcle per day. In the waning phase, dynamics and geochemical character of sinking particle will gradually return to those variations in tidal dominance. In winter, most sinking particles in GPSC are the source material (particles of biological origin) coming from the off-sea with the upcanyon flow during spring tide period. In summer, most sinking particles in GPSC are the terrigenous material (higher organic matter) output from the Gaoping River during typhoons, and flowing to the South China Sea along the canyon with turbidity flow.

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The nano/micro particles have been widely used as a carrier of therapeutic and contrast imaging agents. The nano/micro particles have many advantages, such as, specificity, controlled release, multifunctionality and engineerability. By tuning the chemical, physical and geometrical properties, the efficacy of delivery of nano/micro particle can be improved. In this study, by analyzing the effect of physical and geometrical properties of particle, such as, size, shape, material property and flow condition, the optimal condition for particle delivery will be explored. The objectives of this study are (1) to develop predictive mathematical models and (2) experimental models for particle margination and adhesion, and (3) to find optimal particle geometry in terms of size and shape to enhance the efficiency of its delivery. The effect of particle size expressed in terms of Stokes number and shape, namely, spherical, ellipsoidal, hemispherical, discoidal and cylindrical particle on the particle trajectory is investigated. For discoidal and cylindrical particles, the effect of aspect ratio is also considered. To calculate particle trajectory in the linear shear flow near the substrate, Newton's law of motion is decomposed into hydrodynamic drag and resistance induced by particle motion. The drag and resistance is estimated through finite volume formulation using Fluent v6.3. Particle behavior in the linear shear flow does strongly depend on Stokes number. Spherical particle is transported following the streamline in the absence of external body force. However, non-spherical particles could across the streamline and marginate to the substrate. For non-spherical particles, the optimal [Stokes number] in terms of particle margination is observed; [Stokes number almost equal to] 20 for ellipsoidal, hemispherical and discoidal particle; [Stokes number almost equal to] 10 for cylindrical particle. For discoidal particle with [gamma subscript d]=0.2 shows fastest margination to the substrate. The effect of gravitational force is also considered with respect to the fluid direction. When the gravitational force is applied, mostly, gravitational force plays a dominant role for particle margination. However, using small particle aspect ratio ([gamma subscript d]=0.2 and 0.33), spontaneous drift induced by particle-fluid-substrate interaction could overcome gravitational effect in some cases ([Stokes number]=10, G=0.1). In addition the adhesion characteristic of spherical particle has been studied using in vitro micro fluidic chamber system with different particle size and flow condition. The experimental results are compared to the mathematical model developed by Decuzzi and Ferrari (Decuzzi and Ferrari, 2006) and in vivo test (Decuzzi et al., 2010). The optimal particle size for S=75 and 90 is found to be 4-5 [micrometer] through the in vitro non-specific interaction of spherical particle on the biological substrate. The suggested mathematical model has proven to be valid for current experimental condition. At the end, the mathematical model, in vitro flow chamber results and in vivo test have been compared and the scaling law for particle adhesion on the vessel wall has been confirmed. / text