Sharif Digital Repository

In recent years, nanocars with p-carborane wheels have been a subject of interest as an artificial molecular machine. Researchers aim to discover compositions that are easier to fabricate, efficient and are more stable on the surface. The p-carborane molecule has all these key elements, making it a viable choice as a nanocar wheel, and the mobility of a nanocar is heavily influenced by the motion of its wheels. In this research, we use classical Molecular Dynamics (MD) in isothermal conditions to specify the regime of motion of p-carborane at different temperatures. We find that by raising the temperature, three different regimes of motion may be observed: jumps to adjacent cells, long... 

We studied the mobility of p-carborane on a gold surface by analyzing the potential energy surfaces (PES) and simulating the motion of p-carborane using the classical molecular dynamics (MD) method. In the first section, we calculated the PES of p-carborane molecules on a gold surface during pure translation (sliding) and pure rotation independently and then employed this PES to predict the probable motion of p-carborane. These calculations were performed in several major orientations during sliding as well as different fixed positions during rotational movements to enable us to find the p-carborane motion threshold on a gold surface. In the second section, we use classical MD in isothermal... 

Once in biological fluids, the surface of nanoparticles (NPs) is rapidly covered with a layer of biomolecules (i.e., the "protein corona") whose composition strongly determines their biological identity, regulates interactions with biological entities including cells and the immune system, and consequently directs the biological fate and pharmacokinetics of nanoparticles. We recently introduced the concept of a "personalized protein corona" which refers to the formation of different biological identities of the exact same type of NP after being exposed to extract plasmas from individuals who have various types of diseases. As different diseases have distinct metabolomic profiles and... 

Structural and dynamic properties of ions confined in nanoslits are crucial to understand the fundamental mechanism underlying a wide range of chemical and biological phenomena. K + and Cl - show similar ion mobilities in a bulk aqueous solution, whereas they exhibit a remarkable difference when transporting through an angstrom-scale channel. Our molecular dynamics simulations uncover that such discrepancy originates from the subtle differences in their hydration structures and preferable locations across the channel. Opposite charge causes different water dipolar orientations around ions, mediating the distance and tribological interactions between hydrated ions and channel's walls.... 

We investigate the effects of topological constraints in catenanes composed of interlinked ring polymers on their size in a good solvent as well as on the location of their θ-point when the solvent quality is worsened. We mainly focus on poly[n]catenanes consisting of n ring polymers each of length m interlocked in a linear fashion. Using molecular dynamics simulations, we study the scaling of the poly[n]catenane's radius of gyration in a good solvent, assuming in general that Rg ∼ mμnν and we find that μ = 0.65 ± 0.02 and ν = 0.60 ± 0.01 for the range of n and m considered. These findings are further rationalized with the help of a mean-field Flory-like theory yielding the values of μ =... 

The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose. In this study, we carry out molecular dynamics simulations to investigate the relation between the concentration of cholesterol and the thermal conductivity of a model membrane. Our results suggest an increase in the membrane thermal conductivity upon increasing the... 

Owing to the local/heterogeneous structures in supercooled liquids, after several decades of research, it is now clear that supercooled liquids are structurally different from their conventional liquid counterparts. Accordingly, an approach based on a local probe should provide a better understanding about the local mechanical properties as well as heterogeneous structures. Recently, the superiority of active microrheology over global rheology has been demonstrated [Yu et al., Sci. Adv., 2020, 6, 8766]. Here, we elaborate this new avenue of research and provide more evidence for such superiority. We report on the results of an extensive molecular dynamics simulation of active microrheology... 

Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have... 

Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviours. Performing the planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is reduced extremely in comparison to 3D simulations. To perform this study, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behaviour of the aforementioned system. Pushing of...