Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis.

A comprehensive understanding of molecular interactions and functions is imperative for unraveling the intricacies of viral protein behavior and conformational dynamics during cellular entry. Focusing on the SARS-CoV-2 spike protein (SARS-CoV-2 sp), a Principal Component Analysis (PCA) on a subset comprising 131 A-chain structures in presence of various inhibitors was conducted. Our analyses unveiled a compelling correlation between PCA modes and Anisotropic Network Model (ANM) modes, underscoring the reliability and functional significance of low-frequency modes in adapting to diverse inhibitor binding scenarios. The role of HR1 in viral processing, both linear Normal Mode Analysis (NMA) and Nonlinear NMA were implemented. Linear NMA exhibited substantial inter-structure variability, as evident from a higher Root Mean Square Deviation (RMSD) range (7.30 Å), nonlinear NMA show stability throughout the simulations (RMSD 4.85 Å). Frequency analysis further emphasized that the energy requirements for conformational changes in nonlinear modes are notably lower compared to their linear counterparts. Using simulations of molecular dynamics at constant pH (cpH-MD), we successfully predicted the pKa order of the interconnected residues within the HR1 mutations at lower pH values, suggesting a transition to a post-fusion structure. The pKa determination study illustrates the profound effects of pH variations on protein structure. Key results include pKa values of 9.5179 for lys-921 in the D936H mutant, 9.50 for the D950N mutant, and a slightly higher value of 10.49 for the D936Y variant. To further understand the behavior and physicochemical characteristics of the protein in a biologically relevant setting, we also examine hydrophobic regions in the prefused states of the HR1 protein mutants D950N, D936Y, and D936H in our study. This analysis was conducted to ascertain the hydrophobic moment of the protein within a lipid environment, shedding light on its behavior and physicochemical properties in a biologically relevant context.

Structural and Electromagnetic Signatures of Anatase and Rutile NTs and Sheets in Three Different Water Models under Different Temperature Conditions.

Experimental studies of TiO2 nanotubes have been conducted for nearly three decades and have revealed the remarkable advantages of this material. Research based on computer simulations is much rarer, with research using density functional theory (DFT) being the most significant in this field. It should be noted, however, that this approach has significant limitations when studying the macroscopic properties of nanostructures such as nanosheets and nanotubes. An alternative with great potential has emerged: classical molecular dynamics simulations (MD). MD Simulations offer the possibility to study macroscopic properties such as the density of phonon states (PDOS), power spectra, infrared spectrum, water absorption and others. From this point of view, the present study focuses on the distinction between the phases of anatase and rutile TiO2. The LAMMPS package is used to study both the structural properties by applying the radial distribution function (RDF) and the electromagnetic properties of these phases. Our efforts are focused on exploring the effect of temperature on the vibrational properties of TiO2 anatase nanotubes and an in-depth analysis of how the phononic softening phenomenon affects TiO2 nanostructures to improve the fundamental understanding in different dimensions and morphological configurations. A careful evaluation of the stability of TiO2 nanolamines and nanotubes at different temperatures is performed, as well as the adsorption of water on the nanosurface of TiO2, using three different water models.

Ontological Model in the Identification of Emotional Aspects in Alzheimer Patients.

The present work describes the development of a conceptual representation model of the domain of the theory of formal grammars and abstract machines through ontological modeling. The main goal is to develop an ontology capable of deriving new knowledge about the mood of an Alzheimer's patient in the categories of wandering, nervous, depressed, disoriented or bored. The patients are from elderly care centers in Ambato Canton-Ecuador. The population consists of 147 individuals of both sexes, diagnosed with Alzheimer's disease, with ages ranging from 75 to 89 years. The methods used are the taxonomic levels, the semantic categories and the ontological primitives. All these aspects allow the computational generation of an ontological structure, in addition to the use of the proprietary tool Pellet Reasoner as well as Apache NetBeans from Java for process completion. As a result, an ontological model is generated using its instances and Pellet Reasoner to identify the expected effect. It is noted that the ontologies come from the artificial intelligence domain. In this case, they are represented by aspects of real-world context that relate to common vocabularies for humans and applications working in a domain or area of interest.

Experimental Studies on TiO2 NT with Metal Dopants through Co-Precipitation, Sol-Gel, Hydrothermal Scheme and Corresponding Computational Molecular Evaluations.

In the last decade, TiO2 nanotubes have attracted the attention of the scientific community and industry due to their exceptional photocatalytic properties, opening a wide range of additional applications in the fields of renewable energy, sensors, supercapacitors, and the pharmaceutical industry. However, their use is limited because their band gap is tied to the visible light spectrum. Therefore, it is essential to dope them with metals to extend their physicochemical advantages. In this review, we provide a brief overview of the preparation of metal-doped TiO2 nanotubes. We address hydrothermal and alteration methods that have been used to study the effects of different metal dopants on the structural, morphological, and optoelectrical properties of anatase and rutile nanotubes. The progress of DFT studies on the metal doping of TiO2 nanoparticles is discussed. In addition, the traditional models and their confirmation of the results of the experiment with TiO2 nanotubes are reviewed, as well as the use of TNT in various applications and the future prospects for its development in other fields. We focus on the comprehensive analysis and practical significance of the development of TiO2 hybrid materials and the need for a better understanding of the structural-chemical properties of anatase TiO2 nanotubes with metal doping for ion storage devices such as batteries.

Ab Initio Calculations of Chitosan Effects on the Electronic Properties of Unpassivated Triangular ZnO Nanowires Oriented along [0001] Directions.

In recent years, both chitosan and ZnO nanostructures have been identified as potential antibacterial substances; however, the potential applications of chitosan adsorbed on ZnO nanowires have not been explored and could offer exciting new perspectives for both materials, for example, in biocompatible electronic circuits. In this work, we investigate the effect of chitosan on the electronic properties of triangular ZnO nanowires (ZnO NWs) from a theoretical perspective. All calculations were performed using density functional theory within the generalized gradient approximation. We considered six different positions of the chitosan molecule (CS) on the nanowire surface. We varied the amine position of CS, viewing it parallel, perpendicular, and at a 45° angle with respect to the NW axis. Our results show that all configurations are chemically stable; moreover, the interaction of the NW surface with the OH radical of CS creates flat states within the band gap energy of the ZnO NWs that might resemble p-doping. In addition, these states induce changes in the band gap energy of the ZnO NWs. All NWs show high chemical stability regardless of the CS position; hence, the adsorption results of all NW assemblies appear to be chemically favorable.

Density Gradients, Cellular Structure and Thermal Conductivity of High-Density Polyethylene Foams by Different Amounts of Chemical Blowing Agent.

LDPE (low-density polyethylene) foams were prepared using the improved compression moulding technique (ICM) with relative densities ranging from 0.3 to 0.7 and with different levels of chemical blowing agents (from 1% to 20%). The density gradients, cellular structure and thermal conductivity of the foams were characterized. The density and amount of CBA used were found to have a significant effect on the cellular structure both at the mesoscale (density gradients) and at the microscale (different cell sizes and cell densities). In addition, the thermal conductivity of the samples is very sensitive to the local structure where the heat flux is located. The technique used to measure this property, the Transient Plane Source method (TPS), makes it possible to detect the presence of density gradients. A simple method for determining these gradients based on thermal conductivity data was developed.

Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study.

Infrared (IR) and Terahertz (THz) spectroscopy simulations were carried out using CHARMM35b2 to determine protein stability. The stabilities of three bacterial cold shock proteins (Csps) originating from mesophiles, thermophiles and hyper- thermophiles respectively were investigated in this study. The three different Csps were investigated by Normal-Mode analysis and Molecular Dynamics simulation of THz spectra using the Hessian matrix for solvated systems, interpreted in the harmonic approximation at optimum near-melting temperatures of each homologue, by incorporating differences in the hydrous and anhydrous states of the Csps. The results show slight variations in the large scale protein motion. However, the IR spectra of Csps observed at the low frequency saddle surface region, clearly distinguishes the thermophilic and mesophilic proteins based on their stability. Further studies on protein stability employing low-frequency collective modes have the potential to reveal functionally important conformational changes that are biologically significant.

Water evaporation and conformational changes from partially solvated ubiquitin.

Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes are monitored by studying a variety of intermediate partially solvated ubiquitin structures. We find that ubiquitin shrinks with decreasing hydration shell and exposes more of its hydrophilic surface area to the surrounding.

Evaporation of solvent molecules by ultrafast heating: effect on conformation of solvated protein.

Using molecular dynamics simulation, we compare two cases of ultrafast heating of a small water droplet containing a solvated protein (echistatin). If the water temperature after irradiation is above the critical temperature, explosive boiling liberates the protein within some 10 ps of its hydration shell, while its temperature remains relatively low. By comparing with the case where the water shell is heated to the same final temperature, but without complete evaporation, we demonstrate that the protein conformation is governed by the hydration shell rather than by the protein temperature.

Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.

Vibrational excitations of low-frequency collective modes are essential for functionally important conformational transitions in proteins. We carried out an analysis of the low-frequency modes in the G protein coupled receptors (GPCR) family of cone opsins based on both normal-mode analysis and molecular dynamics (MD) simulations. Power spectra obtained by MD can be compared directly with normal modes. In agreement with existing experimental evidence related to transmembrane proteins, cone opsins have functionally important transitions that correspond to approximately 950 modes and are found below 80 cm(-1). This is in contrast to bacteriorhodopsin and rhodopsin, where the important low-frequency transition modes are below 50 cm(-1). We find that the density of states (DOS) profile of blue opsin in a solvent (e.g. water) has increased populations in the very lowest frequency modes (<15 cm(-1)); this is indicative of the increased thermostability of blue opsin. From our work we found that, although light absorption behaves differently in blue, green and red opsins, their low-frequency vibrational motions are similar. The similarities and differences in the domain motions of blue, red and green opsins are discussed for several representative modes. In addition, the influence of the presence of a solvent is reported and compared with vacuum spectra. We thus demonstrate that terahertz spectroscopy of low-frequency modes might be relevant for identifying those vibrational degrees of freedom that correlate to known conformational changes in opsins.