Sharif Digital Repository

Stretching dynamics of polymers in microfluidics is of particular interest for polymer scientists. As a charged polymer, a polyelectrolyte (PE) can be deformed from its coiled equilibrium configuration to an extended chain by applying uniform or nonuniform electric fields. By means of hybrid lattice Boltzmann (LB)-molecular dynamics (MD) simulations, we investigate how the condensed counterions (CIs) around the PE contribute to the polymer stretching in inhomogeneous fields. As an application, we discuss the translocation phenomena and entropic traps, when the driving force is an applied external electric field  

Deformation of single stranded DNA in a translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside a narrow pore is obtained. With an analysis based on the "electrohydrodynamic equivalence" we determine the possibility of the extension of a charged polymer due to the presence of an electric field gradient in the vicinity of the pore entrance. With a multi-scale hybrid simulation (LB-MD), it is shown that an effective deformation before reaching the pore occurs, which facilitates the process of finding the entrance for... 

In certain types of biomimetic surgery systems, micro robots inspired by Paramecium are designed to swim in a capillary tube for gaining access to internal organs with minimal invasion. Gaining insight into the mechanics of Paramecium swimming in a capillary tube is vital for optimizing the design of such systems. There are two approaches to modeling the physics of micro swimming. In the envelope approach, which is widely accepted by researchers, Paramecium is approximated as a sphere, self-propelled by tangential and normal surface distortions. However, not only is this approach incapable of considering the specific geometry of Paramecium, but it also neglects short range hydrodynamic... 

Swarm motion is an amazing collective behavior in nature for energy saving. Inspiring this natural phenomenon in microorganisms’ swimming, we have proposed a motion strategy for a swarm of microrobots to reduce their energy consumption during path tracking. The investigated microrobot is an artificial Self-Propelled Microswimmer (SPM) with high maneuverability at low Reynolds number flow (Re ≪ 1). In this study, we have demonstrated that forming a swarm behavior with minimum energy consumption requires the microswimmers to be close enough to each other, since at small distances the hydrodynamic interactions of microswimmers reduce their energy consumption. Moreover, we also showed that... 

Swarm motion is an amazing collective behavior in nature for energy saving. Inspiring this natural phenomenon in microorganisms’ swimming, we have proposed a motion strategy for a swarm of microrobots to reduce their energy consumption during path tracking. The investigated microrobot is an artificial Self-Propelled Microswimmer (SPM) with high maneuverability at low Reynolds number flow (Re ≪ 1). In this study, we have demonstrated that forming a swarm behavior with minimum energy consumption requires the microswimmers to be close enough to each other, since at small distances the hydrodynamic interactions of microswimmers reduce their energy consumption. Moreover, we also showed that... 

A weakly compressible smoothed particle hydrodynamics (WCSPH) method is used along with a new no-slip boundary condition to simulate movement of rigid bodies in incompressible Newtonian fluid flows. It is shown that the new boundary treatment method helps to efficiently calculate the hydrodynamic interaction forces acting on moving bodies. To compensate the effect of truncated compact support near solid boundaries, the method needs specific consistent renormalized schemes for the first and second-order spatial derivatives. In order to resolve the problem of spurious pressure oscillations in the WCSPH method, a modification to the continuity equation is used which improves the stability of... 

von Willebrand factor (VWF) is a naturally collapsed protein that participates in primary haemostasis and coagulation events. The clotting process is triggered by the adsorption and conformational changes of the plasma VWFs localized to the collagen fibres found near the site of injury. We develop coarse-grained models to simulate the adsorption dynamics of VWF flowing near the adhesive collagen fibres at different shear rates and investigate the effect of factors such as interaction and cooperativity of VWFs on the success of adsorption events. The adsorption probability of a flowing VWF confined to the receptor field is enhanced when it encounters an adhered VWF in proximity to the... 

Emulsion flooding is a promising method for enhanced oil recovery (EOR). The static and dynamic behavior of the emulsions is greatly influenced by the nature of the applied surfactant. In this work, the effect of fatty acids, as natural surface-active agents, and their chain length on the emulsion behavior was investigated in both bulk and porous media. A panel of the fatty acids with different chain lengths (6 < C < 18) was applied at constant concentration and pH. Upon the static stability tests, emulsion stability at the optimum value of chain length (C14) was increased by two orders of magnitude. Under the optimal condition, the hydrogen bonding between dissociated and undissociated...