Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice

Molecular dynamics and experimental analysis of energy behavior during stress relaxation in magnetorheological elastomers

The diverse applications of magnetorheological elastomer (MRE) drive efforts to understand consistent performance and resistance to failure. Stress relaxation can lead to molecular chain deterioration, degradation in stiffness and rheological properties, and ultimately affect the life cycle of MRE. However, quantifying the energy and molecular dynamics during stress relaxation is challenging due to the difficulty of obtaining atomic-level insights experimentally. This study employs molecular dynamics (MD) simulation to elucidate the stress relaxation in MRE during constant strain. Magnetorheological elastomer models incorporating silicone rubber filled with varying magnetic iron particles (50-80 wt%) were constructed. Experimental results from an oscillatory shear rheometer showed the linear viscoelastic region of MRE to be within 0.001-0.01% strain. The simulation results indicated that stress relaxation has occurred, with stored energies decreased by 8.63-52.7% in all MRE models. Monitoring changes in energy components, the highest final stored energy (12,045 kJ) of the MRE model with 80 wt% Fe particles was primarily attributed to stronger intramolecular and intermolecular interactions, revealed by higher potential energy (3262 kJ) and van der Waals energy (- 2717.29 kJ). Stress relaxation also altered the molecular dynamics of this MRE model as evidenced by a decrease in kinetic energy (9362 kJ) and mean square displacement value (20,318 Å2). The MD simulation provides a promising quantitative tool for elucidating stress relaxation, preventing material failure and offering insights for the design of MRE in the nanotechnology industry.

Molecular structure, vibrational spectral, electron density analysis on linaloe oil and molecular docking efficacy against the therapeutic target on human immunodeficiency virus-1 organism (VIRAL protein)

Natural traditional medicine extensively uses certain terpenes and gives plants their flavor, aroma, and color. Treatments for bacterial infections, malaria, and cardiovascular disorders, anti-inflammatory, promote circulation, and heal wounds. 3,7-Dimethyl-1,6-octadien-3-ol (Linalool) is a naturally occurring monoterpene alcohol with no cycle and is a colorless liquid. Spectral analysis such as UV absorption spectra, NMR for structure determination, and IR and Raman for vibrational analysis. The Quantum mechanical approach uses DFT, ELF, and LOL-promolecular electron density, non-relaxed, and atomic density analysis. The biomolecular studies such as molecular dynamics using protein-ligand complex with HIV-1 organism (energy minimization). ADMET for the usage of linalool in different metabolism studies and Molecular docking for binding affinity, its reactive site estimation, and macromolecules that come into contact with protein receptors and conclude ligand binding affinity with protein.

Identification of novel umami peptides from yeast extract and the mechanism against T1R1/T1R3

Yeast extract was separated by using ultrafiltration, gel filtration chromatography, and preparative high-performance liquid chromatography for analyzing the umami mechanism. 13 kinds of umami peptides were screened out from 73 kinds of peptides which were identified in yeast extract using nanoscale ultra-performance liquid chromatography-tandem mass spectrometry and virtual screening. The umami peptides were found to have a threshold range of 0.07-0.61 mM. DWTDDVEAR exhibited a strong umami taste with a pronounced enhancement effect for monosodium glutamate. Molecular docking studies revealed that specific amino acid residues in the T1R1 subunit, including Arg316, Ser401, and Asp315, played a critical role in the umami perception with these peptides. Overall, the study highlights the potential of natural flavor enhancers and provides insights into the mechanism of umami taste perception.