Molecular dynamics simulation channel

Molecular dynamics simulations were performed to tune the transport of water molecules in nanostructured membrane in a desalination process. Four armchair-type (7,7), (8,8), (9,9) and (10,10) carbon nanotubes (CNTs) with pore diameters around 1 nm were chosen, their interior surfaces were modified with -OH, -CH3 and -F groups. Simulation results show that water transport in nanochannel depends on confined water structures which could be regulated by precisely controlled channel diameter and chemical functionalization...

The assembly of long-range aligned structures of two-dimensional nanosheets (2DNSs) in polymer nanocomposites (PNCs) is in urgent need for the design of nanoelectronics and lightweight energy-storage materials of high conductivity for electricity or heat. These 2DNS are thin and exhibit thermal fluctuations, leading to an intricate interplay with polymers in which entropic effects can be exploited to facilitate a range of different assemblies. In molecular dynamics simulations of experimentally studied 2DNSs, we show that the layer-forming crystallization of 2DNSs is programmable by regulating the strengths and ranges of polymer-induced entropic depletion attractions between pairs of 2DNSs, as well as between single 2DNSs and a substrate surface, by exclusively tuning the temperature and size of the 2DNS...

Soybean phytophthora blight is a severe menace to global agriculture, causing annual losses surpassing USD 1 billion. Present crop loss mitigation strategies primarily rely on chemical pesticides and disease-resistant breeding, frequently surpassed by the pathogens' quick adaptive evolution. In this urgent scenario, our research delves into innovative antimicrobial peptides characterized by low drug resistance and environmental friendliness. Inhibiting chitin synthase gene activity in Phytophthora sojae impairs vital functions such as growth and sporulation, presenting an effective method to reduce its pathogenic impact...

Claudins are one of the major components of tight junctions (TJs) that polymerize within the cell membrane and form interactions between cells. Some claudins seal the paracellular space, limiting paracellular flux, while others form selectively permeable ion channels that control the paracellular permeability of small ions. Claudin strands are known to be dynamic and reshape within TJs to accommodate large-scale movements and rearrangements of epithelial tissues. Here, we summarize the recent computational and modeling studies on claudin assembly into tetrameric ion channels and their polymerization into μm long strands within the membrane...

Claudin polymers constitute the tight junction (TJ) backbone that forms paracellular barriers, at least for bigger solutes. While some claudins also seal the barrier for small electrolytes, others form ion channels. For cation-selective claudin-15 and claudin-10b, structural models of channels embedded in homo-polymeric strands have been suggested. Here, we generated a model for the prototypic anion-selective claudin-10a channel. Based on previously established claudin-10b models, dodecamer homology models of claudin-10a embedded in two membranes were analyzed by molecular dynamics simulations...

In recent years, hydrogen (H2 ) has become the most sought-after sustainable energy carrier by virtue of its high energy content and carbon-free emission. The practical implementation of hydrogen as an alternative fuel calls for an efficient and secure storage medium. Within this framework, we have investigated Li-grafted Si-doped γ-graphyne for H2 storage applications by implementing the cutting-edge density functional theory (DFT). A dynamically and thermally stable Si-doped γ-graphyne (SiG) monolayer is functionalized with Li metal atoms that augmented the hydrogen binding strength of the nanolayer by almost three times, owing to the polarization effect of the Li atoms...

Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap...

Voltage-gated sodium channels (NaV ) are pivotal proteins responsible for initiating and transmitting action potentials. Emerging evidence suggests that proteolytic cleavage of sodium channels by calpains is pivotal in diverse physiological scenarios, including ischemia, brain injury, and neuropathic pain associated with diabetes. Despite this significance, the precise mechanism by which calpains recognize sodium channels, especially given the multiple calpain isoforms expressed in neurons, remains elusive...

This study introduces a novel approach for synthesizing Benzoxazine-Centered Polychiral Polyheterocycles (BPCPHCs) via an innovative asymmetric carbene-alkyne metathesis-triggered cascade. Overcoming challenges associated with intricate stereochemistry and multiple chiral centers, the catalytic asymmetric Carbene Alkyne Metathesis-mediated Cascade (CAMC) is employed using dirhodium catalyst/Brønsted acid co-catalysis, ensuring precise stereo control as validated by X-ray crystallography. Systematic substrate scope evaluation establishes exceptional diastereo- and enantioselectivities, creating a unique library of BPCPHCs...

BACKGROUND: Andersen-Tawil syndrome type 1 is a rare heritable disease caused by mutations in the gene coding the strong inwardly rectifying K+ channel Kir2.1. The extracellular Cys (cysteine)122 -to-Cys154 disulfide bond in the channel structure is crucial for proper folding but has not been associated with correct channel function at the membrane. We evaluated whether a human mutation at the Cys122 -to-Cys154 disulfide bridge leads to Kir2.1 channel dysfunction and arrhythmias by reorganizing the overall Kir2...

We use molecular dynamics (MD) simulation and nanofluidic experiments to probe the non-equilibrium transient physics of two nanochannel-confined polymers driven against a permeable barrier in a flow field. For chains with a persistence length P smaller than the channel diameter D, both simulation and experiment with dsDNA reveal nonuniform mixing of the two chains, with one chain dominating locally in what we term "aggregates." Aggregates undergo stochastic dynamics, persisting for a limited time, then disappearing and reforming...

Environmental water contamination, particularly by heavy metal ions, has emerged as a worldwide concern due to their non-biodegradable nature and propensity to accumulate in soil and living organisms, posing a significant risk to human health. Therefore, the effective removal of heavy metal ions from wastewater is of utmost importance for both public health and environmental sustainability. In this study, we propose and design a membrane consisting of fluorographene (F-GRA) nanochannels to investigate its heavy metal ion removal capacity through molecular dynamics simulation...

Rare earth elements (REEs), critical to modern industry, are difficult to separate and purify, given their similar physicochemical properties originating from the lanthanide contraction. Here, we systematically study the transport of lanthanide ions (Ln3+ ) in artificially confined angstrom-scale two-dimensional channels using MoS2 -based building blocks in an aqueous environment. The results show that the uptake and permeability of Ln3+ assume a well-defined volcano shape peaked at Sm3+ . This transport behavior is rooted from the tradeoff between the barrier for dehydration and the strength of interactions of lanthanide ions in the confinement channels, reminiscent of the Sabatier principle...

Improving interfacial thermal transport is crucial for heat dissipation in devices with interfaces, such as electronics, buildings, and solar panels. Here, we design a strategy by utilizing the water adsorption-desorption process in porous metal-organic frameworks (MOFs) to tune the interfacial heat transfer, which could benefit their potential in cooling or heat dissipation applications. We observe a changeable thermal conductance across the solid/porous MOF interfaces owing to the dense water channel formed by the adsorbed water molecules in MOFs...

Surfactant flooding has been considered as a promising approach for chemically enhanced oil recovery (EOR). However, this technique encounters several limitations, such as high costs, environmental concerns, and reduced efficiency under high-temperature and high-salinity reservoir conditions. Recently, nanoparticles have also been proposed as an alternative for EOR due to their superior properties compared with surfactants. This research employs molecular dynamics simulations to explore the impact of modified SiO2 nanoparticles on oil-water interfacial behaviors and the detachment of oil droplets from an oil-wet surface...

Stroke is the second cause of mortality among adult males and the first cause of death in adult females all around the world. It is also recognized as one of the most important causes of morbidity and dementia in adults. Stenosis or rupture of the only channels of the blood supply from the heart to the brain (carotid arteries) is among the main causes of stroke. In this regard, treatment of the lesions of carotid arteries, including atherosclerosis and aneurysm, could be a huge step in preventing stroke and improving brain performance...

High-Harmonic Generation (HHG) spectra of randomly aligned bromoform (CHBr3 ) molecules have been experimentally measured and theoretically simulated at various laser pulse intensities. From the experiments, we obtained a significant number of harmonics that goes beyond the cutoff limit predicted by the three-step model (3SM) with ionization from HOMO. To interpret the experiment, we resorted to real-time time-dependent configuration interaction with single excitations. We found that electronic bound states provide an appreciable contribution to the harmonics...

Voltage-gated sodium channels (Naᵥ) are membrane proteins which open to facilitate the inward flux of sodium ions into excitable cells. In response to stimuli, Naᵥ channels transition from the resting, closed state to an open, conductive state, before rapidly inactivating. Dysregulation of this functional cycle due to mutations causes diseases including epilepsy, pain conditions, and cardiac disorders, making Naᵥ channels a significant pharmacological target. Phosphoinositides are important lipid cofactors for ion channel function...

Magnesium (Mg 2+ ) uptake systems are present in all domains of life given the vital role of this ion. Bacteria acquire Mg 2+ via conserved Mg 2+ channels and transporters. The transporters are required for growth when Mg 2+ is limiting or during bacterial pathogenesis, but, despite their significance, there are no known structures for these transporters. Here we report the first structure of the Mg 2+ transporter MgtA solved by single particle cryo-electron microscopy (cryo-EM). Using mild membrane extraction, we obtained high resolution structures of both a homodimeric form (2...

Developing synthetic molecular devices for controlling ion transmembrane transport is a promising research field in supramolecular chemistry. These artificial ion channels provide models to study ion channel diseases and have huge potential for therapeutic applications. Compared with self-assembled ion channels constructed by intermolecular weak interactions between smaller molecules or cyclic compounds, metallacage-based ion channels have well-defined structures and can exist as single components in the phospholipid bilayer...