Sharif Digital Repository

We study the formation of a vortex with fourfold symmetry in a minimal model of self-propelled particles, confined inside a squared box, using computer simulations and also theoretical analysis. In addition to the vortex pattern, we observe five other regimes in the system: a homogeneous gaseous phase, band structures, moving clumps, moving clusters, and vibrating rings. All six regimes emerge from controlling the strength of noise and from the contribution of repulsion and alignment interactions. We study the shape of the vortex and its symmetry in detail. The pattern shows exponential defect lines where incoming and outgoing flows of particles collide. We show that alignment and repulsion... 

Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's... 

This research regards to a two-dimensional lateral pushing nanomanipulation using Atomic Force Microscope (AFM). Yet a reliable control of the AFM tip position during the AFM-based manipulation process is a chief issue since the tip can jump over the target nanoparticle and then the process can fail. However, a detailed Modeling and understanding of the interaction forces on the AFM tip is important for prosperous manipulation control and a nanometer resolution tip positioning. In the proposed model, Lund-Grenoble (LuGre) dynamic friction model is used as friction force on the contact surface between the nanoparticle and the substrate. This model leads to a stick-slip behavior of the... 

This research presents two-dimensional controlled pushing-based nanomanipulation using an Atomic Force Microscope (AFM). A reliable control of the AFM tip position is crucial to AFM-based manipulation since the tip can jump over the target nanoparticle causing the process to fail. However, detailed modeling and an understanding of the interaction forces on the AFM tip have a central role in this process. In the proposed model, the Lund-Grenoble (LuGre) method is used to model the dynamic friction force between the nanoparticle and the substrate. This model leads to the stick-slip behavior of the nanoparticle, which is in agreement with the experimental behavior at nanoscale. Derjaguin... 

Distributed-parameters vibration model of microcantilevers in tapping-mode Atomic Force Microscopy (AFM) is developed and is shown to be highly nonlinear. The question of why these nonlinearities are important and how they influence the predicted frequency response behavior of the cantilevers is addressed by comparing the results of developed model with a simple lumpedparameters model that has been extensively studied in the literature so far. The interaction forces between the microcantilever tip and the sample is supposed to be the same in both models and consist of attractive and repulsive interaction force regimes. In addition, experimental measurements are provided for a typical... 

This research regards to a two-dimensional lateral pushing nanomanipulation using Atomic Force Microscope (AFM). Yet a reliable control of the AFM tip position during the AFM-based manipulation process is a chief issue since the tip can jump over the target nanoparticle and then the process can fail. However, a detailed Modeling and understanding of the interaction forces on the AFM tip is important for prosperous manipulation control and a nanometer resolution tip positioning. In the proposed model, Lund-Grenoble (LuGre) dynamic friction model is used as friction force on the contact surface between the nanoparticle and the substrate. This model leads to a stick-slip behavior of the... 

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the... 

Engineered water (EW) flooding is one of the enhanced oil recovery (EOR) techniques in carbonate reservoirs. In this method, the wettability of reservoir rock is altered by controlling the amount of various ions in the injected brine. The thermodynamics of wettability is related to the surface interactions and stability of water film on a rock surface. It can be identified by calculating disjoining pressure isotherms. In this study, core flooding tests, contact angle and zeta potential measurements along with the disjoining pressure isotherm calculation by the DLVO theory were used to investigate the wettability alteration of dolomite rock. Four brines include reservoir formation water...