Sharif Digital Repository

Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic... 

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... 

2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent adsorption properties, zeolites have found application in diverse chemical processes, e.g., gas adsorption, water purification, and wastewater treatment. Prediction of zeolite performance for a targeted application saves time and expense as such projection... 

Nonequilibrium molecular dynamics simulations are used to study the motion of a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60 molecule is actuated and moves along the system while it just randomly dances along the perpendicular direction. Increasing the temperature gradient increases the directed velocity of C60. It is found that the free energy decreases as the C60 molecule moves toward the cold end. The driving mechanism based on the temperature gradient suggests the construction of nanoscale graphene-based motors  

Often, during fabrication of thin films on substrates, different types of defects may be introduced into the films. Recently, the determination of the elastic fields due to the self-assembly of quantum dots or strained islands in thin films has been of major concern. In the micromechanical studies, such strained islands are modeled by inclusions. This paper aims to develop a theory pertaining to the presence of nano-inclusions of various geometries within thin films having face centered cubic (fcc) structure. To this end, the notion of eigenstrain is combined with a many body inter-atomic potential suitable for fcc crystals. The interaction between atoms is modeled via Sutton-Chen (SC)... 

We have investigated the water permeation through carbon nanotube (CNT) membranes as a model of peptide nanotube channels (PNCs). The effect of different charge configured CNTs which tailored based on some artificial ion channels on the water permeation through the channels have been studied. In addition, the temperature dependence of the permeation has been investigated. We have found that there is a jump in the permeation which is somehow related to the characteristics of each channel and the temperature of this permeation jump changes according to the channel configuration. Our investigation on the channels shows that the temperature at which the permeation jump occurs is related to the... 

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of... 

An accurate molecular dynamics simulation of the nanocavity flow cannot be achieved without considering correct thermal treatments for the molecules both distributed in the flow and located at the cavity walls and without including their interactions correctly. In this study, we specify constant temperature at the nanocavity vertical walls; however, we examine three different thermal wall models, including a rigid wall, a controlled-temperature flexible wall, and a noncontrolled-temperature flexible wall, to model the horizontal wall behaviors. Comparing the results of these three models with each other, it is possible to evaluate the effect of wall model on the resulting temperature and... 

We use three-dimensional molecular dynamics simulation to investigate the driven flow between two parallel plates separated by argon atoms. Our simulations show that fluids in such channels can be continuously driven. Difference in surface wettability can cause a difference in fluid density along the nano channel. To control the nanochannel temperature walls, we use the thermal wall idea, which models the walls using atoms connected to their original positions by enforcing linear spring forces. In this study, we propose a nanochannel system in which, half of the channel has a low surface wettability, while the other half has a higher surface wettability and that the middle part of channel... 

Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25... 

In this paper we report the results of classical molecular dynamics (MD) simulation of hexanoic acid adsorption on calcite (101-4) surface plane using Pavese and AMBER force fields for calcite and hexanoic acid, respectively. Pair correlation function, strictly suggests a well-structured adsorption. Density profile indicates the adsorption occurs through double-bonded O atom of the acid head group by direct interaction with Ca atom at calcite surface. Adsorption orientation of H and double-bonded O atoms was found to be as lock and key with respect to calcite surface Ca and O atoms, facilitating an effective adsorption. Adsorption time evolution indicates that O atom adsorption is... 

Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in submicron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less... 

In this paper the classical molecular structural mechanics model of graphene is modified to improve its accuracy for the analysis of transverse deformations. To this aim, a sample graphene sheet under a uniform pressure is modeled by both molecular dynamics and molecular structural mechanics methods. The sectional properties of the beam element, by which the covalent bonds are modeled, are modified such that the difference between the results of the molecular mechanics model and molecular dynamics simulation is minimized. Using this modified model, the buckling behavior of graphene under a uniform edge pressure is investigated subjected to different boundary conditions for both zigzag and... 

We have conducted Molecular Dynamics (MD) simulations with the Environment-Dependent Interatomic Potential (EDIP) to obtain the natural frequency of ultra-thin Silicon Nanowires (SiNWs) with various crystallographic structures, boundary conditions and dimensions. As expected, results show that the mechanical properties of SiNWs are size-/orientation-dependent. The observed phenomena are ascribed to the surface effects which become dominant due to the large surface-to-volume number of atoms at the investigated range of dimensions. Due to their accuracy, atomistic simulations are widely accepted for the investigations of such nano-scaled systems; however, they suffer from high computational... 

In the present work, the mechanical properties, in particular, the Poisson's ratio of four two-dimensional silica structures, called here α,β,γ and δ are studied by means of molecular dynamics simulations. The α structure has been synthesized experimentally and the others have been reported as the most stable low-energy structures that reveal in-plane negative Poisson's ratio based on the first principles calculations. Among these structures, β-silica exhibits the largest in-plane negative Poisson's ratio which is 2–4 times higher than penta-graphene. Our results illustrate that the classical molecular dynamics simulation reproduces results in agreement with those of the first principles... 

The efficiency of water flooding methods is known to improve by applying ion-tuned water injection. Although there is a consensus that such improvement happens through reversing reservoir wettability characteristics to more water-wet state, the true impact of ions is still ambiguous among contradictory debates. The well-known molecular dynamics (MD) simulation techniques would shed light on such ambiguities to gain deep atomic-scale understanding of the process. Results from MD simulations show that the presence of Na+ and Cl¯ ions leads to the formation of an electrical double layer in adjacency of calcite surface while Mg2+ ions dominantly make complexes with hydrocarbons throughout the... 

Molecular dynamics simulation was applied in this study to scrutinize the interfacial properties of water nano-film confined between calcite mineral and hydrocarbon layer, as two intrinsically different media. Such system resembles the environment experienced by water molecules in the pore spaces of underground carbonate reservoirs. The interplay between water film and confining phases, oil and mineral, strongly influences hydrocarbon production process; however, there is a lack of detailed understanding of the involved interactions. MD simulations indicate development of several layers with different water densities in the confined brine. Water molecules form well-ordered structure in three... 

Carbon nanoropes (CNRs) are of interest for a wide variety of nanotechnological applications. Since little attention has been paid to mechanical properties of CNRs, their axial elastic modulus is explored herein. Molecular dynamics (MDs) simulations are adopted for analysis of Young's modulus of CNRs. It is also shown that increase in the initial helical angle decreases Young's modulus; however, by increase in the number of CNTs and strands, different influence on Young's modulus emerges. Therefore, the highest value of Young's modulus obtained at the lower value of initial helical angle and consequently, Young's modulus of bundle of straight CNTs is higher than CNRs with hierarchical... 

Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...