| 1. |
- Fadaei Naeini, Vahid, Postdoctoral Researcher, 1988-, et al.
(author)
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Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation
- 2022
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In: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 12:28, s. 17803-17816
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Journal article (peer-reviewed)abstract
- In this paper, a series of equilibrium molecular dynamics simulations (EMD), steered molecular dynamics (SMD), and computational electrophysiology methods are carried out to explore water and ion permeation through mechanosensitive channels of large conductance (MscL). This research aims to identify the pore-lining side chains of the channel in different conformations of MscL homologs by analyzing the pore size. The distribution of permeating water dipole angles through the pore domains enclosed by VAL21 and GLU104 demonstrated that water molecules are oriented toward the charged oxygen headgroups of GLU104 from their hydrogen atoms to retain this interaction in a stabilized fashion. Although, this behavior was not perceived for VAL21. Numerical assessments of the secondary structure clarified that, during the ion permeation, in addition to the secondary structure alterations, the structure of Tb-MscL would also undergo significant conformational changes. It was elucidated that VAL21, GLU104, and water molecules accomplish a fundamental task in ion permeation. The mentioned residues hinder ion permeation so that the pulling SMD force is increased remarkably when the ions permeate through the domains enclosed by VAL21 and GLU102. The hydration level and potassium diffusivity in the hydrophobic gate of the transmembrane domain were promoted by applying the external electric field. Furthermore, the implementation of an external electric field altered the distribution pattern for potassium ions in the system while intensifying the accumulation of Cl− in the vicinity of ARG11 and ARG98.
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| 2. |
- Fadaei Naeini, Vahid, Postdoctoral Researcher, 1988-, et al.
(author)
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Unraveling the pressure-viscosity behavior and shear thinning in glycerol using atomic scale molecular dynamics simulations
- 2023
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In: Journal of Molecular Liquids. - : Elsevier. - 0167-7322 .- 1873-3166. ; 390:part A
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Journal article (peer-reviewed)abstract
- In order to increase the usage and explore new applications of glycerol as a replacement for fossil-based lubricants its properties needs to be known at the fundamental level. In this study, the viscosity of pure glycerol at high pressures and strain rates has been investigated using of molecular dynamics (MD) simulations, utilizing both the Green-Kubo (GK) formalism and the SLLOD algorithm. Although the viscosity acquired by the GK method is in agreement with the corresponding experimental values at low pressure, a significant distinction was identified between the viscosity obtained by the GK method and the experimental values at higher pressures (P > 0.5 GPa). This results in a clear difference between the viscosity-pressure coefficient attained by the GK method and the corresponding experimental value. The SLLOD method using a non-equilibrium MD (NEMD) platform was exploited to take into account the simultaneous effects of strain rate and pressure on viscosity. As a result, the pressure-viscosity coefficient acquired by the SLLOD algorithm approaches the experimental value. By combining the experimental outputs for viscosity at low strain rates ( < 104 s−1) with the SLLOD outputs at higher rates ( > 105 s−1), the evolutions of glycerol viscosity with pressure and strain rate were ultimately achieved. Implementing this computational platform depicts the shear thinning process in pure glycerol in a wide range of pressures and strain rates.
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| 3. |
- Foroutan, Masumeh, et al.
(author)
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Unraveling Flow Separation at the Water–Carbon Nanotube Interface: An Atomic-Scale Overview by Molecular Dynamics Simulation
- 2022
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In: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 38:14, s. 4256-4265
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Journal article (peer-reviewed)abstract
- Flow separation near the fluid–solid surface has attracted attention for decades. It is critical to understand the behavior of separated flow adjacent to the solid walls to broaden its range of potential applications. Therefore, we conducted molecular dynamics investigations to consider water flow separation at the water–carbon nanotube (CNT) interface for different diameters of CNTs between 13 and 50 Å and different pressures of 0.1–1.254 GPa. Density heat maps indicated that water flow separation is observed for all CNTs under high pressures, and an empty space of water molecules or evacuation is formed behind the CNTs. It is shown that in CNTs with small diameters, (10, 10) and (20, 20), the structure of the first layer (FL) of water molecules or hydrated layer adjacent to the CNT wall is completely preserved, indicating that evacuation occurs from behind the CNTs. In (30, 30) and (40, 40) CNTs, flow separation occurred from the FL of water molecules near the solid surface, and the layered structure of water around CNTs is completely destroyed. Our findings of fluid–solid and fluid–fluid interaction energies suggested that the flow separation can be due to an attraction between the FL of water molecules and CNT and a repulsion between the water molecules in the hydrated layer and the outer layers. Moreover, analyzing the relationship between the CNT size and flow separation revealed that in the case of small CNTs, there are extra water molecules that contribute to the structural stability of the hydrated layer by strengthening the repulsive interaction in the liquid–liquid surface.
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| 4. |
- Johansson, Pontus, et al.
(author)
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Insights of the Ultralow Wear and Low Friction of Carbon Fiber Reinforced PTFE in Inert Trace Moisture Environment
- 2023
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In: Tribology letters. - : Springer. - 1023-8883 .- 1573-2711. ; 71:3
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Journal article (peer-reviewed)abstract
- Ultralow wear rates and low friction have been observed for carbon fiber reinforced PTFE (CF/PTFE) when sliding against steel or cast iron in dry gas environments. Although the strong environmental sensitivity of this tribosystem is well known, the origin of the outstanding tribological performance in dry gas remains unanswered. Some researchers attribute the low friction and wear to the formation of carbon-rich surfaces in the absence of oxygen and moisture in the environment. However, low friction between carbon surfaces is generally dependent on moisture. In this paper, extensive analyzes are conducted on the tribofilms formed on the CF/PTFE surface and the steel counterface after sliding in a high-purity nitrogen environment. TEM analysis of a cross-section of the tribofilm on the steel surface reveals that the sliding surface consists mainly of iron (II) fluoride and not carbon, even though a significant amount of carbon was observed near the surface. XPS and TEM analysis further revealed that the tribofilm formed on the worn composite surface consisted of nanoparticle agglomerates, anchored to the PTFE matrix and to each other by carbon with turbostratic structure. Turbostratic carbon also formed an ultrathin and surface-oriented superficial layer on top of the agglomerates. Governing mechanisms of the low friction and wear of the CF/PTFE—steel tribosystem were investigated by complementary tribotests with pure graphite samples and MD simulations of the identified surfaces. These indicated that the low friction between the carbon and iron fluoride in the tribofilms is due to poor adhesion between the distinctly different surfaces.
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| 5. |
- Khayamian, Mohammad Ali, et al.
(author)
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A label-free graphene-based impedimetric biosensor for real-time tracing of the cytokine storm in blood serum; suitable for screening COVID-19 patients
- 2021
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In: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 11:55, s. 34503-34515
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Journal article (peer-reviewed)abstract
- Concurrent with the pandemic announcement of SARS-CoV-2 infection by the WHO, a variety of reports were published confirming the cytokine storm as the most mortal effect of the virus on the infected patients. Hence, cytokine storm as an evidenced consequence in most of the COVID-19 patients could offer a promising opportunity to use blood as a disease progression marker. Here, we have developed a rapid electrochemical impedance spectroscopy (EIS) sensor for quantifying the overall immune activity of the patients. Since during the cytokine storm many types of cytokines are elevated in the blood, there is no need for specific detection of a single type of cytokine and the collective behavior is just measured without any electrode functionalization. The sensor includes a monolayer graphene on a copper substrate as the working electrode (WE) which is able to distinguish between the early and severe stage of the infected patients. The charge transfer resistance (RCT) in the moderate and severe cases varies about 65% and 138% compared to the normal groups, respectively and a specificity of 77% and sensitivity of 100% based on ELISA results were achieved. The outcomes demonstrate a significant correlation between the total mass of the three main hypercytokinemia associated cytokines including IL-6, TNF-α and IFN-γ in patients and the RCT values. As an extra application, the biosensor's capability for diagnosis of COVID-19 patients was tested and a sensitivity of 92% and specificity of 50% were obtained compared to the RT-PCR results.
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| 6. |
- Rajabali, M., et al.
(author)
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Experimental and molecular dynamics studies of an ultra-fast sequential hydrogen plasma process for fabricating phosphorene-based sensors
- 2021
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11
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Journal article (peer-reviewed)abstract
- Low concentration phosphorene-based sensors have been fabricated using a facile and ultra-fast process which is based on an exfoliation-free sequential hydrogen plasma treatment to convert the amorphous phosphorus thin film into mono- or few-layered phosphorene sheets. These sheets have been realized directly on silicon substrates followed by the fabrication of field-effect transistors showing the low leakage current and reasonable mobility for the nano-sensors. Being capable of covering the whole surface of the silicon substrate, red phosphorus (RP) coated substrate has been employed to achieve large area phosphorene sheets. Unlike the available techniques including mechanical exfoliation, there is no need for any exfoliation and/or transfer step which is significant progress in shortening the device fabrication procedure. These phosphorene sheets have been examined using transmission electron microscopy (TEM), Scanning electron microscopy (SEM), Raman spectroscopy and atomic-force microscopy (AFM). Electrical output in different states of the crystallization as well as its correlation with the test parameters have been also extensively used to examine the evolution of the phosphorene sheets. By utilizing the fabricated devices, the sensitivity of the phosphorene based-field effect transistors to the soluble L-Cysteine in low concentrations has been studied by measuring the FET response to the different concentrations. At a gate voltage of − 2.5 V, the range of 0.07 to 0.60 mg/ml of the L-Cysteine has been distinguishably detected presenting a gate-controlled sensor for a low-concentration solution. A reactive molecular dynamics simulation has been also performed to track the details of this plasma-based crystallization. The obtained results showed that the imparted energy from hydrogen plasma resulted in a phase transition from a system containing red phosphorus atoms to the crystal one. Interestingly and according to the simulation results, there is a directional preference of crystal growth as the crystalline domains are being formed and RP atoms are more likely to re-locate in armchair than in zigzag direction.
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| 7. |
- Sedghiniya, Sima, et al.
(author)
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A V(iii)-induced metallogel with solvent stimuli-responsive properties: structural proof-of-concept with MD simulations
- 2021
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In: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 11:58, s. 36801-36813
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Journal article (peer-reviewed)abstract
- A new solvent stimuli-responsive metallogel (VGel) was synthesized through the introduction of vanadium ions into an adenine (Ade) and 1,3,5-benzene tricarboxylic acid (BTC) organogel, and its supramolecular self-assembly was investigated from a computational viewpoint. A relationship between the synthesized VGel integrity and the self-assembly of its components is demonstrated by a broad range of molecular dynamics (MD) simulations, an aspect that has not yet been explored for such a complex metallogel in particular. MD simulations and Voronoi tessellation assessments, both in agreement with experimental data, confirm the gel formation. Based on excellent water stability and the ethanol/methanol stimuli-responsive feature of the VGel an easy-to-use visualization assay for the detection of counterfeit liquor with a 6% (v/v) methanol limit of detection in 40% (v/v) ethanol is reported. These observations provide a cheap and technically simple method and are a step towards the immersible screening of similar molecules in methanol-spiked beverages.
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