Sharif Digital Repository

DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method... 

We provide the simulation of electroosmotic phenomenon in nanochannels using the Dissipative Particle Dynamics (DPD) method. We study the electroosmotic phenomenon for both newtonian and non-newtonian fluids. Literature shows that most of past electroosmotic studies have been concentrated on continuum newtonian fluids. However, there are many nano/microfluidic applications, which need to be treated as either non-newtonian fluids or non-continuum fluids. In this paper, we simulate the electroosmotic flow in nanochannel considering no limit if it is neither continuum nor non-nonewtonian. As is known, the DPD method has several important advantages compared with the classical molecular dynamics... 

In this study, the mechanisms of passing water and salt ions through nanoporous single-layer graphene membrane are simulated using classical molecular dynamics. The effects of functional groups placed in nanopores and feed water's salt concentration on water desalination are investigated. In order to understand the role of functional groups in desalination process, Methyl, Ethyl and a combination of Fluorine and Hydrogen molecules are distributed around the nanopores. In all cases, different number of functional molecules is employed in order to find an optimum distribution of the groups at hand. The results show that an appropriate distribution of Alkyl groups can properly stop the salt... 

Spin lattice relaxation rate is investigated for 3D tilted cone Weyl semimetals (TCWSMs). The nuclear spin relaxation rate is presented as a function of temperature and tilt parameter. We find that the relaxation rate behaves as (1-ζ2)-α with α ≈ 9 where 0 ζ < 1 is the tilt parameter. We demonstrate that such a strong enhancement for ζ ≲ 1 that gives rise to very fast relaxation rates, is contributed by a new hyperfine interactions arising from the tilt itself. This can be attributed to the combination of anisotropy of the Fermi surface and an additional part related to the structure of the spacetime: extracting an effective density of states (DOS) ρ from the Korringa relation, we show that... 

Models for chatter prediction in machining often use a mechanistic force model that calculate the force as the product of a material dependent cutting constant and chip area. However, in reality, the forces are the result of complex interaction between the tool and the chip, and are affected by many factors. The effects of these complex, and often nonlinear, factors on the machining dynamics may only be included in chatter prediction if the chip formation process is simulated concurrently with simulation of the machining dynamics. In this paper, finite element simulation of the chip formation process is combined with simulation of chatter dynamics and the inter-relationship between the chip... 

Carbon nanotubes (CNTs) are excellent candidates for torsional elements used in nanoelectro-mechanical systems (NEMS). Simulations show that after being twisted to a certain angle, they buckle and lose their mechanical strength. In this paper, classical molecular dynamics simulations are performed on single-walled carbon nanotubes (CNTs) to investigate the effects of torsion speed and temperature on CNT torsional properties. The AIREBO potential is employed to describe the bonded interactions between carbon atoms. The MD simulations clearly show that the buckling of CNTs in torsion is a reversible process, in which by unloading the buckled CNT in opposite direction, it returns to its... 

This paper is focused on presenting an accurate framework to describe frequency-dependent energy harvesting via magnetic shape memory alloys (MSMAs). Modeling strategy incorporates the phenomenological constitutive model developed formerly together with the magnetic diffusion equation. A hyperbolic hardening function is employed to define reorientation-induced strain hardening in the material, and the diffusion equation is used to add dynamic effects to the model. The MSMA prismatic specimen is surrounded by a pickup coil, and the induced voltage during martensite-variant reorientation is investigated with the help of Faraday's law of magnetic field induction. It has been shown that, in... 

Bridge behavior under passing traffic loads has been studied for the past 50 years. This paper presents how to model congestion on bridges and how the maximum dynamic stress of bridges change during the passing of moving vehicles. Most current research is based on mid-span dynamic effects due to traffic load and most bridge codes define a factor called the dynamic load allowance (DLA), which is applied to the maximum static moment under static loading. This paper presents an algorithm to solve the governing equation of the bridge as well as the equations of motions of two real European trucks with different speeds, simultaneously. It will be shown, considering congestion in eight case... 

The secondary suspension of most new EMU and DMU rail vehicles is equipped with air springs, to offer a good ride comfort to passengers. Air springs are a very important isolating component, which guarantees good ride comfort during the trip. In most rail-vehicle models developed by researchers, the thermo-dynamical effects of air springs in the rail-vehicle dynamics are not considered and secondary suspension is modeled by simple springs and dampers. As the performance of suspension components, especially for air springs, have significant effects on railvehicle dynamics and the ride comfort of passengers, a complete nonlinear thermo-dynamical air spring model, which is a combination of two... 

In this paper, formulation and implementation of finite element analysis within an Arbitrary Lagrangian Eulerian (ALE) description is presented for large deformation analysis of elasto-viscoplastic materials. The rate effects are included using a consistent procedure. An implicit algorithm with backward Euler integration scheme is used to integrate the elasto-viscoplastic constitutive equations. Also, the closed form of the consistent tangent operator is derived using the momentum balance equation to reduce the computation time. A fully coupled ALE procedure is used which includes dynamic effects. The proposed algorithm is implemented in an ALE code and its effectiveness and efficiency is...