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

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

[Abstract] 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.Financial support from the seed grant “Computational modeling of biomaterials and applications to bioengineering and classical and quantum machine learning for predicting social engineering (2022–2026, code: INV-0014-03-011)”, Universidad Indoamérica, Ecuador, awarded to S.P.T.Ecuador. Universidad Indoamérica; INV-0014-03-01

Validation of previous computer models and MD simulations of discoidal HDL by a recent crystal structure of apoA-I.

HDL is a population of apoA-I-containing particles inversely correlated with heart disease. Because HDL is a soft form of matter deformable by thermal fluctuations, structure determination has been difficult. Here, we compare the recently published crystal structure of lipid-free (Δ185-243)apoA-I with apoA-I structure from models and molecular dynamics (MD) simulations of discoidal HDL. These analyses validate four of our previous structural findings for apoA-I: i) a baseline double belt diameter of 105 Å ii) central α helixes with an 11/3 pitch; iii) a "presentation tunnel" gap between pairwise helix 5 repeats hypothesized to move acyl chains and unesterified cholesterol from the lipid bilayer to the active sites of LCAT; and iv) interchain salt bridges hypothesized to stabilize the LL5/5 chain registry. These analyses are also consistent with our finding that multiple salt bridge-forming residues in the N-terminus of apoA-I render that conserved domain "sticky." Additionally, our crystal MD comparisons led to two new hypotheses: i) the interchain leucine-zippers previously reported between the pair-wise helix 5 repeats drive lipid-free apoA-I registration; ii) lipidation induces rotations of helix 5 to allow formation of interchain salt bridges, creating the LCAT presentation tunnel and "zip-locking" apoA-I into its full LL5/5 registration

Band-Gap Engineering: Lithium Effect on the Electronic Properties of Hydrogenated 3C-SiC (1 1 0) Surfaces

Silicon carbide has structural strength, high electronic conductivity, low diffusion barrier and high storage capacity, which are suitable for engineering applications such as lithium-ion batteries, electric vehicles, uninterruptible power supplies and SiC diodes. In particular, 3C-SiC monolayers oriented along the (1 1 0) crystallographic direction that could have symmetric surfaces have been poorly studied, as have the effects of surface passivation on their physical and electronic properties. In this work, we investigate the influence of lithium on the electronic properties of hydrogenated surfaces in 3C-SiC monolayers using density functional theory. We examine the electronic properties of surfaces fully passivated with hydrogen with those of surfaces fully passivated with lithium and those with mixed passivation. Our results show that only fully hydrogenated surfaces exhibit a direct band-gap, while the full Li, CH+SiLi, and H+Li (Formula presented.) passivations exhibit metallic behavior. The CLi+SiH, H+1LiC, and H+1LiSi passivation systems decrease the band-gap compared to the hydrogenated case and show an indirect band-gap. The formation energy of the system shows that the most stable arrangement is full-H, followed by H+1LiC, and the most unstable system is full-Li, which has a positive formation energy

Hydrogen Economy and Its Production Impact on Automobile Industry Forecasting in Ecuador Using Principal Component Analysis

Hydrogen vehicles are operating in many parts of the world. However, in South America these cars are not on the streets. Even there are merchant hydrogen plants in the continent, hydrogen stations are not available yet. Doing a PCA analysis with H2 Vehicle Simulator Framework, Principal component 1 is related with amount of storage of hydrogen. Second principal component is related with autonomy and the last principal component with raw distance. Nowadays hydrogen price is around 12 USD per kilo in Europe and it is expensive for South America. The goal is to achieve a price of 2.15 USD in future with different renewable energies like: nuclear energy, hydro electrical, biomass and photo voltaic. Other goal is to reduce the vehicle price because the cost of a hydrogen car is 2.62 more expensive on average than a combustion car in Ecuador. One alternative to incentive the introduction of hydrogen vehicles is with hydrogen taxis vehicles like Paris is doing. Photo voltaic energy available in Tungurahua province is enough to produce hydrogen for all the taxis of Ambato city

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

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

Perturbation theory for open quantum systems at the steady state

We propose a theoretical method for studying open quantum systems at the steady state within the framework of the perturbation theory. This approach allow us to compute the density operator of the system perturbatively and, in principle, to obtain an expression for its density matrix elements explicitly. To illustrate our methodology, we provide a case study of a nonlinear two-level system coupled to a thermal reservoir and special attention is given to the relationship between nonlinearity and nonclassicality. In particular, this relation is quantified by considering the quantum measures as the nonclassical depth, nonclassical distance and the quantum fidelity. We find that the nonclassicality is originated at least by second order contribution of nonlinear terms in quantum dynamics. 2000 MSC: 46N50, 37N20, 46N5

Band-Gap Engineering: Lithium Effect on the Electronic Properties of Hydrogenated 3C-SiC (1 1 0) Surfaces

Silicon carbide has structural strength, high electronic conductivity, low diffusion barrier and high storage capacity, which are suitable for engineering applications such as lithium-ion batteries, electric vehicles, uninterruptible power supplies and SiC diodes. In particular, 3C-SiC monolayers oriented along the (1 1 0) crystallographic direction that could have symmetric surfaces have been poorly studied, as have the effects of surface passivation on their physical and electronic properties. In this work, we investigate the influence of lithium on the electronic properties of hydrogenated surfaces in 3C-SiC monolayers using density functional theory. We examine the electronic properties of surfaces fully passivated with hydrogen with those of surfaces fully passivated with lithium and those with mixed passivation. Our results show that only fully hydrogenated surfaces exhibit a direct band-gap, while the full Li, CH+SiLi, and H+Lic passivations exhibit metallic behavior. The CLi+SiH, H+1LiC, and H+1LiSi passivation systems decrease the band-gap compared to the hydrogenated case and show an indirect band-gap. The formation energy of the system shows that the most stable arrangement is full-H, followed by H+1LiC, and the most unstable system is full-Li, which has a positive formation energy