Unravelling the mechanism of glucose binding in a protein-based fluorescence probe: molecular dynamics simulation with a tailor-made charge model

Fluorophores linked to the glucose/galactose-binding protein (GGBP) are a promising class of glucose sensors with potential application in medical devices for diabetes patients. Several different fluorophores at different positions in...

Challenges of Track Access Charges Model Redesign

It has been exactly 20 years since the common grounds for the design of track access charges (TAC) were laid for the European railways by the publication of Directive 2001/14/EC. However, these grounds were defined broadly, thus resulting in significant divergence both in the models applied by countries and during the model redesign within one country over the course of time. The participants in the process of charge system redesign includes all stakeholders from a country’s railway sector (infrastructure manager, train operating companies, the ministries responsible for transport, finance and economy, government, and regulatory bodies). Their opinions and requirements are often opposed, and they all need to be acknowledged simultaneously. This paper aims to solve the issue of ensuring continuity in the charge model redesign while achieving a balance between the requirements of all stakeholders. Moreover, it tackles the issue of producing a sustainable long-term TAC model by using survey methods and statistical analysis. The proposed approach was tested in practice during the access charge model redesign for the railways of Montenegro. The results show the importance of continual enhancement in TAC model development as one of the challenges and key precursors for the harmonization of all stakeholders’ requirements.

Bridging the 12-6-4 Model and the Fluctuating Charge Model

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r4 based on theory. Hence, we developed the 12-6-4 model and showed it could solve this deficiency in a physically meaningful way. However, our previous research also found that the 12-6-4 model overestimated the coordination numbers (CNs) for some highly charged metal ions. And we attributed this artifact to that the current 12-6-4 scheme lacks a correction for the interactions among the first solvation shell water molecules. In the present study, we considered the ion-included dipole interaction by using the 12-6 model with adjusting the atomic charges of the first solvation shell water molecules. This strategy not only considers the ion-induced dipole interaction between ion and the first solvation shell water molecules but also well accounts for the increased repulsion among these water molecules compared to the bulk water molecules. We showed this strategy could well reproduce the experimental HFE and IOD values for Mg2+, Zn2+, Al3+, Fe3+, and In3+ and solve the CN overestimation issue of the 12-6-4 model for Fe3+ and In3+. Moreover, our simulation results showed good agreement with previous ab initio MD simulations. In addition, we derived the physical relationship between the C4 parameter and induced dipole moment, which agreed well with our simulation results. Finally, we discussed the implications of the present work for simulating metalloproteins. Due to the fluctuating charge model uses a similar concept to the 12-6 model with adjusting atomic charges, we believe the present study builds a bridge between the 12-6-4 model and the fluctuating charge model.

A new theoretical approach to the strain dependence of magnetic crystal-field anisotropy

We report on the derivation of analytical equations for ab-initio calculations of the strain dependence of crystal-electric-field (CEF) parameters for arbitrary deformations. The calculation is based on the fundamental assumption that the charge distribution deforms in the same way as the crystal. Based on this deformed-charge model, simple formulas for the practical usage are given for various site symmetries of cubic lattices under uniform strain. These formulas can be used to predict the change of the magnetic crystal-field anisotropy under strain, which is important for the design of magnetic materials and devices. As an example for the power of the method, we present a calculation of the magnetic contribution to the thermal expansion in some rare-earth-based materials.

Quantitative Study on MFL Signal of Pipeline Composite Defect Based on Improved Magnetic Charge Model

Pipeline magnetic flux leakage (MFL) internal detection technology is the most widely used and effective method in the field of long-distance oil and gas pipeline online detection. With the improvement of data quantization precision, the influence of stress on MFL signal has been paid more and more attention. In this paper, the relationship between stress and saturation magnetization is introduced based on J-A theory. The analytical model of MFL detection signal for pipeline composite defects is established. The MFL signal characteristics of composite defects are quantitatively calculated. The effect of stress on MFL signal is studied. The theoretical analysis is verified by experimental data and excavation results. The researches show that the saturation magnetization of ferromagnets decreases exponentially with the increase of stress in strong magnetic field. The MFL signal of composite defect is weaker than that of volumetric defects of the same dimension. The axial amplitude and radial peak-to-peak value of MFL signal decrease with the increase of stress around the defect. The axial amplitude and radial peak-to-peak value of MFL signal increase non-linearly with the increase of width and depth of defects. When using MFL signal to judge the defect depth, it is necessary to make clear whether there is stress concentration phenomenon around the defect because the stress will lead to underestimation of the defect depth.