Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation.

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.

A V(iii)-induced metallogel with solvent stimuli-responsive properties: structural proof-of-concept with MD simulations.

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.

A label-free graphene-based impedimetric biosensor for real-time tracing of the cytokine storm in blood serum; suitable for screening COVID-19 patients.

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 (R CT) 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 R CT 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.

Enhanced wettability of long narrow carbon nanotubes in a double-walled hetero-structure: unraveling the effects of a boron nitride nanotube as the exterior.

Studying the structure and dynamics of nano-confined water inside carbon nanotubes has consistently attracted the wide-spread interest of researchers. In the present work, molecular dynamics simulations indicated internal nonwetting behavior for the central region of the long and narrow single-wall carbon nanotube (5,5) (SWNT) and showed that continuous single-file water molecules are not formed through it. Unlike the SWNT, by adding boron nitride nanotubes (6,6) as an outer wall to the SWNT, a continuously long single-file water chain is formed through the double-walled carbon and boron nitride hetero-nanotube (DWHNT) and thorough internal wetting of the DWHNT is observed. The position and the number of water molecules, electrostatic potential heatmap of the nanotube's wall, free energy profile of nano-confined water, and number of hydrogen bonds between them confirmed the aforementioned results and complete internal wetting of the DWHNT. After using the boron nitride nanotube (6,6) as the outer wall, an homogeneous electrostatic potential distribution in the DWHNT and increase in the hydrophilic characteristics of the nano-channel wall are observed, bringing about gradual trapping of more water molecules through it. Finally, water molecules occupied the central region of the DWHNT and a thorough single-file water chain is formed inside the nano-channel. Water dipole orientation inside the DWHNT and their radial distribution function asserted the occurrence of the liquid-solid quasi-phase transition of single-file water molecules confined inside the long and narrow carbon nanotube (5,5) under ambient conditions.

Evaporation of Water on Suspended Graphene: Suppressing the Effect of Physically Heterogeneous Surfaces.

Evaporation of water nanodroplets on a hydrophilically adjusted graphene sheet was studied based on a molecular dynamics approach. Suspended graphene was used as a physically heterogeneous surface, and fixed graphene was considered as an ideally flat surface. State of the triple-phase contact line (TPCL) and shape evolution were addressed at four different temperatures on both substrates. Additionally, contact angle (CA) was studied during 3 and 22.5 ns simulations in both closed and opened conditions. The observed constant contact angle regime was predictable for the fixed graphene. However, it was not expected for the suspended system and was attributed to the oscillations of the substrate atoms. The size of the nanodroplet also affects the constant-contact-angle mode in both systems, when the number of water molecules decreases to less than 500. The oscillations created a surface on which physical heterogeneities were varying through time. Examination of the evaporation and condensation processes revealed higher rates for the fixed systems. Local mass fluxes were calculated to reveal the contribution of TPCL and meridian surface (MS) of the nanodroplet to evaporation and condensation. The obtained results indicate similar values for the mass flux ratio at the TPCL, which remains twice as large as the MS for both suspended and fixed graphene. The results confirm the assumption that a surface with varying heterogeneities can overwhelm the droplet and act as an ideally flat surface.