Development of Semiempirical Models for Proton Transfer Reactions in Water

This letter presents a method for the parametrization of semiempirical models for proton transfer reactions in water clusters. Two new models are developed: AM1-W, which is a reparameterization of the classic AM1 model, and AM1PG-W, which is a modified AM1-like model including a pairwise correction to the core repulsion function. Both models show good performance on hydrogen-bonding energies and on proton transfer energy profiles, which are of great importance for proton transfer reactions in large water clusters and in proteins. The parametrization method introduced is general and can be used to develop any other system-specific semiempirical models

Enhanced Recovery of Oil Mixtures from Calcite Nanopores Facilitated by CO₂ Injection

Slow production, preferential recovery of light hydrocarbons, and low recovery factors are common challenges in oil production from unconventional reservoirs dominated by nanopores. Gas injection-based techniques such as CO2 Huff-n-Puff have shown promise in addressing these challenges. However, a limited understanding of the recovery of oil mixtures on the nanopore scale hinders their effective optimization. Here, we use molecular dynamics simulations to study the recovery of an oil mixture (C10 + C19) from a single 4 nm-wide calcite dead-end pore, both with and without CO2 injection. Without CO2 injection, oil recovery is much faster than expected from oil vaporization and features an undesired selectivity, i.e., the preferential recovery of lighter C10. With CO2 injection, oil recovery is accelerated and its selectivity toward C10 is greatly mitigated. These recovery behaviors are understood by analyzing the spatiotemporal evolution of C10, C19, and CO2 distributions in the calcite pore. In particular, we show that interfacial phenomena (e.g., the strong adsorption of oil and CO2 on pore walls, their competition, and their modulation of transport behavior) and bulk phenomena (e.g., solubilization of oil by CO2 in the middle portion of the pore) play crucial roles in determining the oil recovery rate and selectivity

Towards a maximally-robust self-balancing robotic bicycle without reaction-moment gyroscopes nor reaction wheels

A presentation from BMD 2016.<br

Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH₃, while others, notably in plants, transport the positively charged NH₄⁺. On the basis of the structural data for AmtB from Escherichia coli, we illustrate the mechanism by which proteins from the Amt family can sustain electrogenic transport. Free energy calculations show that NH₄⁺ is stable in the AmtB pore, reaching a binding site from which it can spontaneously transfer a proton to a pore-lining histidine residue (His168). The substrate diffuses down the pore in the form of NH₃, while the excess proton is cotransported through a highly conserved hydrogen-bonded His168–His318 pair. This constitutes a novel permeation mechanism that confers to the histidine dyad an essential mechanistic role that was so far unknown

Table2_Mechanistic studies of MALAT1 in respiratory diseases.DOCX

Background: The incidence of respiratory diseases and the respiratory disease mortality rate have increased in recent years. Recent studies have shown that long non-coding RNA (lncRNA) MALAT1 is involved in various respiratory diseases. In vascular endothelial and cancer cells, MALAT1 expression triggers various changes such as proinflammatory cytokine expression, cancer cell proliferation and metastasis, and increased endothelial cell permeability.Methods: In this review, we performed a relative concentration index (RCI) analysis of the lncRNA database to assess differences in MALAT1 expression in different cell lines and at different locations in the same cell, and summarize the molecular mechanisms of MALAT1 in the pathophysiology of respiratory diseases and its potential therapeutic application in these conditions.Results: MALAT1 plays an important regulatory role in lncRNA with a wide range of effects in respiratory diseases. The available evidence shows that MALAT1 plays an important role in the regulation of multiple respiratory diseases.Conclusion: MALAT1 is an important regulatory biomarker for respiratory disease. Targeting the regulation MALAT1 could have important applications for the future treatment of respiratory diseases.</p