Water Box Research Articles

Behavior of Trapped Molecules in Lantern-Like Carcerand Superphanes.

Superphanes are a group of organic molecules from the cyclophane family. They are characterized by the presence of two parallel benzene rings joined together by six bridges. If these bridges are sufficiently long, the superphane cavity can be large enough to trap small molecules or ions. Using ab initio (time scale of 80 ps) and classical (up to 200 ns) molecular dynamics (MD) methods, we study the behavior of five fundamental molecules (M = H2O, NH3, HF, HCN, MeOH) encapsulated inside the experimentally reported lantern-like superphane and its two derivatives featuring slightly modified side bridges. The main focus is studying the dynamics of hydrogen bonds between the trapped M molecule and the imino nitrogen atoms of the side chains of the host superphane. The length of the N···H hydrogen bond increases in the following order: HF < HCN < H2O < MeOH < NH3. The mobility of the trapped molecule and its preferred position inside the superphane cage depend not only on the type of this molecule but also largely on the in/out conformational arrangement of the imino nitrogens in the side chains of the superphane. Their inward-pointing positions allow the formation of strong N···H hydrogen bonds. For this reason, these nitrogens are the preferred sites of interaction. The mobility of the molecules and their residence times on each side of the superphane have been explained by referring to the symmetry and conformation of the given superphane cage. All force field MD simulations have shown that the encapsulated molecule remained inside the superphane cage for 200 ns without any escape event to the outside. Moreover, our simulations based on some endohedral complexes in the water box also showed no exchange event. Thus, the superphanes we study are true carcerand molecules. We attribute this property to the hydrophobic side chains and their pinwheel arrangement, which makes the side walls of the studied superphanes fairly impenetrable to small molecules.

Stability and cavitation of nanobubble: Insights from large-scale atomistic molecular dynamics simulations.

We perform large-scale atomistic simulations of a system containing 12 × 106 atoms, comprising an oxygen gas-filled bubble immersed in water, to understand the stability and cavitation induced by ultrasound. First, we propose a method to construct a bubble/water system. For a given bubble radius, the pressure inside the bubble is estimated using the Young-Laplace equation. Then, this pressure is used as a reference for a constant temperature, constant pressure simulation of an oxygen system, enabling us to extract a sphere of oxygen gas and place it into a cavity within an equilibrated water box. This ensures that the Young-Laplace equation is satisfied and the bubble is stable in water. Second, this stable bubble is used for ultrasound-induced cavitation simulations. We demonstrate that under weak ultrasound excitation, the bubble undergoes stable cavitation, revealing various fluid velocity patterns, including the first-order velocity field and microstreaming. These fluid patterns emerge around the bubble on a nanometer scale within a few nanoseconds, a phenomenon challenging to observe experimentally. With stronger ultrasound intensities, the bubble expands significantly and then collapses violently. The gas core of the collapsed bubble, measuring 3-4nm, exhibits starfish shapes with temperatures around 1500K and pressures around 6000bar. The simulation results are compared with those from Rayleigh-Plesset equation modeling, showing good agreement. Our simulations provide insights into the stability and cavitation of nanosized bubbles.

Electrochemical oxidation of UV filters: A first-principles molecular dynamics study.

A theoretical model is proposed to study the oxidation mechanisms of the organic UV filters BP3 and BP4 during electrochemical water treatment utilizing Car-Parrinello molecular dynamics. Factors such as the amount of solvent to be included and how to design the system with the least possible intervention are discussed. The stages of the proposed model consist of the optimization of the geometries by density functional theory methods, the equilibration of the structure immersed in a water box, the inclusion of the reactive species, and the analysis of the reaction energies of each reaction pathway. The ab-initio molecular dynamics simulations lead to several products, and some trends can be identified, in accordance with the well-known reactivity rules of organic chemistry. The products proposed in this work are intermediates in longer oxidative pathways.

Performance Evaluation of a Condenser at a Combined Cycle Power Plant Using the LMTD Method

This study evaluates the performance of the condenser at the Cilegon Combined Cycle Power Plant (CCPP) using the Logarithmic Mean Temperature Difference (LMTD) method to measure the heat transfer rate. Routine maintenance carried out on the condenser in the form of cleaning the condenser water box and condenser tube from garbage and crust on the condenser tube wall. Currently, condenser maintenance follows a routine schedule that is tied to steam turbine maintenance, without taking actual condenser performance into account. This can lead to inefficiencies and unnecessary downtime. The goal of this research is to assess the heat transfer rate of the condenser before and after maintenance to judge its effectiveness. Data on temperature changes were gathered in June 2023, before maintenance, and again in July 2023, after an overhaul. The analysis shows that the heat transfer rate increased from 51,362,294.48 kcal/h to 127,246,219.7 kcal/h, while the LMTD value rose from 0.76°C to 1.86°C. Based on these results, the study suggests a new approach to maintenance that focuses on performance. Specifically, maintenance should be done when the heat transfer rate drops below 110,000,000 kcal/h. This approach will help ensure the condenser works at its best, improve the plant's overall efficiency, and prevent the need for unnecessary maintenance. By aligning maintenance with performance data, the plant can boost output while lowering costs and downtime.

“In Silico” prediction of antibiotics biodegradation by Ganoderma lucidum GILCC 1 laccase

Antibiotics present a pressing environmental challenge as emerging pollutants due to their persistence and role in promoting antibiotic-resistant bacteria. To model the utilization of Ganoderma lucidum GlLCC1 laccase in degrading antibiotics, a 3D homology model of GILCC1, based on Lentinus tigrinus mushroom laccase, was utilized. Five broad-spectrum WHO-designated antibiotics with molecular weights between 100 and 500 Da were selected. Molecular dynamics simulations were conducted at pH 3.0 and 7.0 to evaluate the interactions between GILCC1 and antibiotics in a TIP3P water box, with system behaviour assessed at 300 °K using an NPT assembly. ABTS (2,2ʹ-Azino-bis (3-ethylbenzthiazoline-6-sulfonic Acid)) served as the comparison molecule. The binding free energy indicated a strong affinity between 3D GILCC1 and various ligands. At pH 3.0, GILCC1 exhibited significant Gibbs free energy (ΔG), indicating a high affinity for Levofloxacin (LVX; −8.2 kcal mol−1), Sulfisoxazole (SFX; −7.8 kcal mol−1), Cefuroxime (CXM; −7.5 kcal mol−1), Cephradine (CFD; −7. 5 kcal mol−1), ABTS (−7.6 kcal mol−1), and Tetracycline (TE; −7.5 kcal mol−1), attributed to pocket topology and interactions such as hydrogen bonds and van der Waals forces. Electron transfer in GILCC1 involved a chain of residues, including His395 and Phe239. Although the affinity decreased at pH 7.0, the potential of GILCC1 to degrade antibiotics remained plausible. This study accurately predicted the behaviour of the laccase-antibiotic system, providing atomic-level insights into molecular interactions and emphasizing the importance of experimental assays and assessments of antibiotic degradation in wastewater, considering various chemical compounds. The use of ABTS as a mediator was suggested to enhance molecule affinity.Graphical abstract

Radiation-induced DNA damage by proton, helium and carbon ions in human fibroblast cell: Geant4-DNA and MCDS-based study

Background. Radiation-induced DNA damages such as Single Strand Break (SSB), Double Strand Break (DSB) and Complex DSB (cDSB) are critical aspects of radiobiology with implications in radiotherapy and radiation protection applications. Materials and Methods. This study presents a thorough investigation into the effects of protons (0.1–100 MeV/u), helium ions (0.13–100 MeV/u) and carbon ions (0.5–480 MeV/u) on DNA of human fibroblast cells using Geant4-DNA track structure code coupled with DBSCAN algorithm and Monte Carlo Damage Simulations (MCDS) code. Geant4-DNA-based simulations consider 1 μm × 1 μm × 0.5 μm water box as the target to calculate energy deposition on event-by-event basis and the three-dimensional coordinates of the interaction location, and then DBSCAN algorithm is used to calculate yields of SSB, DSB and cDSB in human fibroblast cell. The study investigated the influence of Linear Energy Transfer (LET) of protons, helium ions and carbon ions on the yields of DNA damages. Influence of cellular oxygenation on DNA damage patterns is investigated using MCDS code. Results. The study shows that DSB and SSB yields are influenced by the LET of the particles, with distinct trends observed for different particles. The cellular oxygenation is a key factor, with anoxic cells exhibiting reduced SSB and DSB yields, underscoring the intricate relationship between cellular oxygen levels and DNA damage. The study introduced DSB/SSB ratio as an informative metric for evaluating the severity of radiation-induced DNA damage, particularly in higher LET regions. Conclusions. The study highlights the importance of considering particle type, LET, and cellular oxygenation in assessing the biological effects of ionizing radiation.

Environmental and behavioral variables associated with lower urinary tract diseases in domestic cats

Objectives: Feline lower urinary tract disease (LUTD) is a frequently seen disease with multiple etiologies. Since it is a complex condition, the aim of this study is to evaluate the factors that may affect the development of the disease.&#x0D; Materials and Methods: Demographic, clinical, behavioral and environmental parameters of 30 cats diagnosed with lower urinary tract disease and 15 aged-matched healthy cats presented to Ankara University Small Animal Hospital were evaluated. &#x0D; Results: In the diseased group, the male population was higher and the cats were overweight. The number of food, water and litter boxes and litter material were found to differ significantly between groups. Daily habits such as playing with a scratching board and self-grooming differed between the groups. Inappropriate behaviors observed by the owners of the cats in the first group were listed as urinating/defecating outside the litter box and showing aggression towards the owner, guests, and/or other animals. &#x0D; Conclusions: The results of this study show that the detailed evaluation and regulation of the daily needs of cats is important for the emergence or recurrence of the disease and therefore may contribute to the correct management of the treatment process in cats with lower urinary tract disease.

A Novel In-Line Measurement and Analysis Method of Bubble Growth-Dependent Strain and Deformation Rates during Foaming.

Bubble growth processes are highly influenced by the elongational viscosity of the blowing agent-loaded polymer melt. Therefore, the elongational viscosity is an important parameter for the development of new polymers for foaming applications, as well as for the prediction of bubble growth processes. Thus, knowledge of the initial expansion and deformation behavior in dependency on the polymer, the blowing agent concentration, and the process conditions is necessary. This study presents a novel method for the in-line observation and analysis of the initial expansion and deformation behavior within the bead foam extrusion process. For this purpose, nitrogen as the blowing agent was injected into the polymer melt (PS and PLA) during the extrusion process. The in-line observation system consists of a borescope equipped with a camera, which was integrated into the water box of an underwater pelletizer. The camera is controlled by a developed trigger by means of angular step signal analysis of a rotary encoder on the cutter shaft of the underwater pelletizer. Thus, images can be taken at any time during the foaming process depending on the cutter position to the die outlet. It is shown that the developed method provides reliable results and that the differences of the initial expansion and deformation behavior during bubble growth can be analyzed in-line in dependency on real foaming process conditions and the type of polymer used.

Self-association as a solubility limiting factor of riboflavin in aqueous media.

Single crystal X-ray diffraction analysis of needle shaped riboflavin (RF) crystals revealed π-stacking of RF's isoalloxazine units (distance: 3.643-3.313 Å) with syn-orientated ribityl chains. In line with this, classical molecular dynamics (MD) (400 ns) using an isobaric-isothermal (NPT) ensemble of eight RF in a water box (〈V〉 ∼ 508.62 nm3, 〈p〉 = 1.11 bar) revealed anti-aligned aggregation of RF in water (COM-distance: 4 Å). Comparing umbrella sampling for the separation of two RF molecules to the separation of two lumichrome molecules, the similar mean potential force for the separation of RF and lumichrome (22.8 kJ mol-1; 24.4 kJ mol-1) proved dispersive interactions as the origin of RF's aggregation. Though stacking of RF is the major water-solubility limiting factor, the conformation of RF's ribityl chain may alter the solubility in water. Both, MD (in water) and COSMO-RS (in water continuum) predicted that conformations of RF with an extended ribityl chain are thermodynamically preferred over any conformations with internal hydrogen bonds between hydroxyl groups and nitrogen/oxygen atoms of the pyrimidine moiety of the flavin ring. Interestingly, COSMO-RS predicted the solubility of the extended conformation to be significantly lower than the latter leading to the very low average solubility of RF. Nuclear Overhauser effect measurements (NOESY) of the structurally related sodium riboflavin 5'-monophosphate (RF-PO4) in deuterium oxide confirmed π-stacking of the isoalloxazine rings. In conformity with the 350 times higher water-solubility of RF-PO4, NOESY also indicated a contorted conformation of the ribityl phosphate chain, whereas, for RF, indications for a contorted chain were not observed.

Structural Effect of Gγ and Aγ Globin Chains in Fetal Hemoglobin Tetramer

Introduction. Hemoglobin (Hb) is a tetrameric oxigen and carbon dioxide transportation protein; it is composed of four polypeptide chains, two of alpha type, which can be ζ, α 2 or α 1; and two beta chains, which include ε, Gγ, Aγ, δ or β (Antonini and Brunori, 1970).The synthesis of these globin chains depends on the stage of human development; in embryonic stages the hemoglobins Gower I (ζ 2ε 2), Gower II (α 2ε 2) and Portland (ζ 2γ 2) are synthesized; subsequently, from the third week of gestation begins the synthesis of fetal hemoglobin (HbF) formed by two alpha chains and two gamma chains (α 2γ 2); finally during the last trimester the second hemoglobin switching takes place consisting on decreased synthesis of gamma globin chains and the beginning of beta and delta globin chain synthesis that will be forming adult hemoglobin (α 2β 2) and hemoglobin A 2 (α 2δ 2), which will remain constant throughout extrauterine life (Wilber, 2011). One of the molecular mechanisms that has allowed the evolutionary success of humans has been gene duplication, although it results from a random process it favors DNA variation that increases the adaptive capacity of a population (Magadum, 2013). The high homology between duplicated genes is clear, however, it allows differences to arise because of genetic conversion, globin genes HBG2, HBG1, for instance ,which can be observed in their functional products; Gγ and Aγ globin chains (Chen, 2007), both formed by 146 residues, with their distinct difference a position 136 where there is a change of glycine in Gγ by alanine in Aγ and maintain a ratio of 3:1 ( Gγ: Aγ) during fetal stages; while in extra uterine life this ratio is reversed to 2:3 ( Gγ: Aγ), the heterogeneity of γ globins available for HbF synthesis allows the formation of three variants of the same molecule α 2Gγ 2; 2α A/Gγ and 2α Aγ 2; these γ globin chainsdifferences potential implication on HbF interaction with oxygen has not been elucidated as well as whether the presence of a specific type occurs to a greater or lesser extent in different pathologies(Alter 1979). Objective . To evaluate the structural effect of the type of γ globin chain in three models of Fetal Hemoglobin. Methodology . Modeling of the three HbF possible structures: α 2Gγ 2; 2α A/Gγ and 2α Aγ 2 was performed on UCSF Chimera using the crystallography structures of a HbA (1a3n) and Hb Bart (1i3d) hemoglobins as atomic position templates of α and Aγglobin chains. HbF models as well as HbA and Bart hemoglobin (as reference) where then uploaded to CHARMM-GUIplatform to establish system conditions for molecular dynamic simulation such as force field (c36m), water box size (90 Å) and temperature (310 K), molecular dynamics simulation was run for 100 ns on GROMCS (by triplicate), results were analyzed by Root Mean Square Deviation (RMDS) and Root Mean Square Fluctuation (RMSF) of γ globin chains. Results.Three different HbF tetrameric structures where created based on γ globin chains available α 2Gγ 2; 2α A/Gγ and 2α Aγ 2, RMSD shows fluctuation in atomic positions through time among the three HbF models (figure 1: a, b, c), it is shown that the HbF behavior most similar to HbA (figure 1d) is the 2α A/Gγ (figure 1b)which could indicate that this particular type of HbF would be the more abundant during healthy extrauterine life since HbA responds to a normoxic environment that can become hypoxic at medular level when some disease are present, leukemia for instance. By comparing Bart hemoglobin to HbF models is clear that Aγreduces residues movement, limiting tetramer flexibility thus restraining allosteric changes needed for gases exchange, which can be seen when analyzing HbF γ globin chains at 100-146 residues region where there is no fluctuation in the Aγ 2chains opposite to what is shown by Gγ 2 (Figure 2a, b and c). To evaluate these RMSD results, cluster analysis was performed for each replica in the three HbF structures, resulting in values of α 2Gγ 2: 0.13, 2α A/Gγ and 2α Aγ 2: 0.12 with differences below 0.20 among replicates showing the validity of the results. Conclusion and perspectives . There are structural changes in HbF depending on the presence of Gγ or Aγ globin chains. Further studies are required to identify the type of tetramer present in healthy individuals as in patients with different blood malignancies where HbF has been reported as a therapeutic target or risk factor to understand its effect and association with opposite outcomes.

Impact of ozonation on the formation of particulate nitrosodi-methylamine (NDMA) in atmosphere

The contribution of ozonation to the formation of particulate nitrosodi-methylamine (NDMA) in the aqueous aerosol phase was investigated using measurement data from 2018 in Seoul, Republic of Korea and a box model. The correlation between the NDMA concentration and aerosol liquid water content and box model results showed that aqueous aerosol phase reactions, including nitrosation and ozonation, might contribute to the formation of NDMA. The concentration of NDMA and the ratio of O3/dimethylamine exhibited a negative correlation, suggesting that the contribution of ozonation to NDMA formation may not be significant. Furthermore, when the daily concentration of NDMA exceeded 10 ng/m3, the pH was 3.96 ± 0.48, indicating that the impact of ozonation on NDMA concentration might not be significant. To quantitatively investigate the contribution of ozonation, the ozonation mechanism that forms NDMA was included in the box model developed in our previous study. The model results showed that the ozonation contributed to the ambient concentration of NDMA (7.9 ± 3.8% (winter); 1.9 ± 3.0% (spring); 10.0 ± 0.77% (summer); 3.6 ± 7.3% (autumn)). It is estimated that the relatively higher O3/NOx ratio in summer (1.63 ± 0.69; 0.64 ± 0.52 (winter); 1.14 ± 0.92 (spring); 0.52 ± 0.54 (autumn)) could enhance ozonation and that relatively lower pH in summer (2.2 ± 0.4; 5.3 ± 1.2 (winter); 3.9 ± 1.2 (spring); 3.9 ± 0.7 (autumn)) could hinder nitrosation compared to that in other seasons.

Genesis of the Yi’nan Tongjing Gold–Copper Skarn Deposit, Luxi District, North China Craton: Evidence from Fluid Inclusions and H–O Isotopes

The Luxi district presents an exceptional research area for the investigation of the significant role played by magma exsolution fluids in the mineralization process of Au–Cu deposits. A particularly noteworthy occurrence within this region is the Yi’nan Tongjing Au–Cu skarn deposit, situated in the central-southern part of the Luxi district. This deposit primarily occurs in the contact zone between the early Cretaceous Tongjing complex and the Proterozoic to Cambrian sequences. The ore formation process observed in this deposit can be categorized into three distinct stages: (I) thermal metamorphism, (II) prograde alteration, and (III) retrograde alteration. The retrograde alteration stage is further divided into four sub-stages: late skarn (III-1), oxide (III-2), sulfide (III-3), and late quartz-calcite (III-4). It is primarily during the III-3 sub-stage that gold mineralization occurs. Petrographic analysis has identified three types of fluid inclusions (FIs) within garnet, quartz, and calcite grains. These include liquid-rich two-phase aqueous FIs, vapor-rich two-phase aqueous FIs, and halite-bearing multi-phase FIs. The homogenization temperatures of fluid inclusions from stages II, III-3, and III-4 range between 430–457 °C, 341–406 °C, and 166–215 °C (first to third quartiles), respectively. The garnet samples from stage II exhibit hydrogen and oxygen isotope compositions (δ18OH2O = 6.8‰ and δD = −73‰) that are indicative of a typical magma source. However, the hydrogen and oxygen isotopes of sub-stages III-1, III-2, and III-3 (δ18OH2O = 7.32‰ to 9.74‰; δD = −107‰ to −81.9‰) fall below the magma water box while the hydrogen and oxygen isotope values of III-4 (δ18OH2O = −5.3‰ to −0.9‰ and δD = −103.8‰ to −67‰) tend to move towards the meteoric water line. Furthermore, the ore-forming fluid displays characteristics of a mixture between the crustal and mantle fluids. The Tongjing complex occurred along a weakened fault zone, initiating a process of thermal metamorphism upon contact with the wall rock. This thermal metamorphism resulted in the formation of diverse assemblages, including hornfels, reaction skarns, and skarnoids. Subsequently, the upward movement of ore-forming fluids triggered exsolution which led to the establishment of a high-temperature, medium-salinity NaCl–H2O system with a single phase at depths ranging from 1–3 km. This marked the formation of the prograde alteration stage. Afterward, the ore-forming fluid underwent water–rock interactions and the admixture of meteoric water at a depth of 1–2 km. These processes facilitated phase separation, commonly referred to as boiling, resulting in the transformation of the ore-forming fluid into higher salinity fluids and lower-density gases. This evolutionary transition ultimately induced the precipitation and liberation of gold and copper from the fluid.

In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non-native interactions.

We examine the influence of cellular interactions in all-atom models of a section of the Homo sapiens cytoplasm on the early folding events of the three-helix bundle protein B (PB). While genetically engineered PB is known to fold in dilute water box simulations in three microseconds, the three initially unfolded PB copies in our two cytoplasm models using a similar force field did not reach the native state during 30-microsecond simulations. We did however capture the formation of all three helices in a compact native-like topology. Folding in vivo is delayed because intramolecular contact formation within PB is in direct competition with intermolecular contacts between PB and surrounding macromolecules. In extreme cases, intermolecular beta-sheets are formed. Interactions with other macromolecules are also observed to promote structure formation, for example when a PB helix in our simulations is shielded from solvent by macromolecular crowding. Sticking and crowding in our models initiate sampling of helix/sheet structural plasticity of PB. Relatedly, in past in vitro experiments, similar GA domains were shown to switch between two different folds. Finally, we also observed that stickiness between PB and the cellular environment can be modulated in our simulations through the reduction in protein hydrophobicity when we reversed PB back to the wild-type sequence. This study demonstrates that even fast-folding proteins can get stuck in non-native states in the cell, making them useful models for protein-chaperone interactions and early stages of aggregate formation relevant to cellular disease.

Hysteroscopic suture of levonorgestrel-releasing intrauterine system: learning curve for in vitro simulation training.

To simulate hysteroscopic suturing in vitro and analyze the learning curve of gynecologists with different experience levels. Three gynecologists were trained on uterine models in a circulating water box. The posterior uterine wall was sutured 10 times under hysteroscopy for 5 consecutive days, and the time of each suture procedure was recorded. Doctors A, B, and C completed 50 posterior uterine sutures. After Dr. C completed 50 sutures on the posterior wall, he added 50 sutures on the anterior wall (Group D). The mean suturing time was 71.54 ± 68.158 s in Group A, 50.10 ± 28.060 s in Group B, 34.04 ± 10.457 s in Group C, and 30.38 ± 8.734 s in Group D. The difference between Groups C and B and between Groups B and A was statistically significant. There was no statistically significant difference between Groups C and D. Simulation curves were created using the number of features as the abscissa and cumulative sum as the coordinate, with peak curves of 19, 27, and 18 cases for Group A, B, and C, respectively. Doctors with experience in single-hole laparoscopic surgery or hysteroscopic suture surgery can significantly shorten the hysteroscopic suturing time.

Fabrication of a flexible stretchable hydrogel-based antenna using a femtosecond laser for miniaturization.

We demonstrated a new method of fabricating a stretchable antenna by injecting liquid metal (LM) into a femtosecond-laser-ablated embedded hydrogel microchannel, and realized miniaturization of a stretchable dipole antenna based on hydrogel substrate. Firstly, symmetrical microchannels with two equal and linear branches were formed by a femtosecond laser in the middle of a hydrogel substrate, and then were filled with LM by use of a syringe needle. Using this method, a stretchable LM-dipole antenna with each dimension of 24 mm × 0.6 mm × 0.2 mm separated by a 2-mm gap, was formed in the middle of a 70 mm × 12 mm × 7 mm hydrogel slab. Since the polyacrylamide (PAAm) hydrogel contained ∼ 95 wt % deionized water with a high permittivity of 79 in the 0.5 GHz - 1.5 GHz range, the hydrogel used to prepare the flexible antenna can be considered as distilled water boxes. Experiments and simulations showed that a 5-cm-long LM-dipole embedded in hydrogel resonated at approximately 927.5 MHz with an S11 value of about - 12.6 dB and omnidirectional radiation direction. Benefiting from the high permittivity of the hydrogel, the dipole length was downsized by about half compared with conventional polymer substrates at the same resonant frequency. By varying the applied strain from 0 to 48%, the resonant frequency of the hydrogel/LM dipole antenna can be tuned from 770.3 MHz to 927.0 MHz. This method provides a simple and scalable technique for the design and preparation of LM-pattern microstructures in hydrogels, and has potential applications in hydrogel-based soft electronic device.

Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation.

Previously, it was shown that the telescoping box scheme, in combination with adaptive steered molecule dynamics (ASMD), can be used to estimate the potential of mean force (PMF) with a decrease in computational cost associated with large solvation boxes. Since ASMD reduces to umbrella sampling (US) in the limit of infinitely slow pulling velocity, a hypothesis was made that the telescoping box scheme can be extended to include the US method. The hypothesis was tested using the unfolding pathway of a polyalanine peptide in a water box and translocation of α-tocopherol through the human membrane. Two different approaches were tried: telescoping US (TELUS), in which the number of solvent molecules was linearly coupled to the reaction coordinate, and Block-TELUS, which was a compromise between the fixed solvation box of the US and the window-wise variable solvation box of TELUS. In the case of polyalanine peptide in a water box, both approaches gave overlapping potential of mean force (PMF) concerning the benchmark US-PMF. Window-wise comparison of properties like root-mean-square inner product, Ramachandran plot, α-helix content, and hydrogen bond formation was used to verify that both approaches captured the same dynamics as the US method. Applying the Block-TELUS protocol in the system with diffusing α-tocopherol through the bilayer resulted in overlapping PMF to its US benchmark. A comparison between the window-wise orientation of the chromanol headgroup also produced almost identical results. This study concluded that with the careful application of telescoping solvation boxes, a less computationally expensive US could be performed for systems where the effect of distant solvent molecules on the configurational space sampled in the window depends on the value of the reaction coordinate.

Microscopic Mechanism of Proton Transfer in Pure Water under Ambient Conditions.

Water molecules and the associated proton transfer (PT) are prevalent in chemical and biological systems and have been a hot research topic. Spectroscopic characterization and ab initio molecular dynamics (AIMD) simulations have previously revealed insights into acidic and basic liquids. Presumably, the situation in the acidic/basic solution is not necessarily the same as in pure water; in addition, the autoionization constant for water is only 10-14 under ambient conditions, making the study of PT in pure water challenging. To overcome this issue, we modeled periodic water box systems containing 1000 molecules for tens of nanoseconds based on a neural network potential (NNP) with quantum mechanical accuracy. The NNP was generated by training a dataset containing the energies and atomic forces of 17 075 configurations of periodic water box systems, and these data points were calculated at the MP2 level that considers electron correlation effects. We found that the size of the system and the duration of the simulation have a significant impact on the convergence of the results. With these factors considered, our simulations showed that hydronium (H3O+) and hydroxide (OH-) ions in water have distinct hydration structures, thermodynamic and kinetic properties, e.g., the longer-lasting and more stable hydrated structure of OH- ions than that of H3O+, as well as a significantly higher free energy barrier for the OH--associated PT than that of H3O+, leading the two to exhibit completely different PT behaviors. Given these characteristics, we further found that PT via OH- ions tends not to occur multiple times or between many molecules. In contrast, PT via H3O+ can synergistically occur among multiple molecules and prefers to adopt a cyclic pattern among three water molecules, while it occurs mostly in a chain pattern when more water molecules are involved. Therefore, our studies provide a detailed and solid microscopic explanation for the PT process in pure water.

Enhancing Middle School Learning about Geography and Topographic Maps Using Hands-on Play and Geospatial Technologies

The objective of this research was to determine if and to what extent students’ learning of geographic concepts can be improved through incorporation of hands-on play with Play-Doh® and LEGO® and geospatial technologies, specifically drones. The project team conducted six months of biweekly, collaborative instruction at Comstock Middle School in Michigan incorporating in-class activities such as drawing mental maps, creating contour lines of model landscapes in water boxes, constructing 3D landscapes from 2D topographic maps, building and operating small drones, and more. Compared pre- and post-tests reveal a 14% increase in overall scores, a statistically significant improvement in student performance.

Vitamin A and vitamin D3 protect the visual apparatus during the development of dopamine-2 receptor knockout mouse model of Parkinsonism.

Dopamine-related movement disorders are associated with a loss of visual acuity. Studies have shown that chemical stimulation of the vitamin D3 receptor (VDR) ameliorates movement disorders; however, the chemical stimulation is not effective when there is a deficiency of vitamin A in the cells. In the study, we examine the role of VDR and its interplay with vitamin A in impaired visual function in the dopamine deficit model. Thirty (30) male mice with an average weight of 26 g ± (2) were divided into six group (NS,-D2,-D2 + VD D2 + VD,-D2 + VA,-D2 + (VD + VA) and-D2 + D2 groups). Dopamine deficit models of movement disorders were created using 15 mg/kg of haloperidol (-D2) injected intraperitoneally daily for 21days. In the-D2 + (VD + VA) group, 800 IU/day of vitamin D3 (VD) and 1000 IU/day of vitamin A were concurrently used, while in the-D2 + D2 group, bromocriptine (+D2) was used as the standard treatment of the model. At the end of the treatment phase, the animals were subjected to visual water box test for visual acuity. The level of oxidative stress was measured using Superoxide dismutase (SOD) and malondialdehyde (MDA) in the retina and visual cortex. The level of cytotoxicity in these tissues was measured using Lactate dehydrogenase (LDH) assay, while the structural integrity of these tissues was assessed using a light microscope by assessing slide mounted sections that were stained with haematoxylin and eosin. A significant decline in time taken to reach the escape platform in the visual water box test was observed in the-D2 (p<0.005) and-D2 + D2 (p<0.05) group. In the retina and the visual cortex, a significant increase in LDH, MDA and the density of degenerating neurons was observed in the-D2 and-D2 + D2 groups. LDH level in the retina was also found to be significantly increased in (-D2 + VD,-D2 + VA,-D2 + (VD + VA). A Significant decrease in SOD was found in the retina and visual cortex of-D2 and-D2 + D2 group. In the histology of the retina, thinning of the retina, retinal fold, distortion and retinal detachment were all seen in the-D2 group. These structural alterations were not seen in other groups. Histological hallmarks of degeneration were observed in the visual cortex of the mice from the-D2 (p<0.001),-D2 + D2 (p<0.005) and-D2 + VD (p<0.05) groups only. Dopamine-deficient models of movement disorders are associated with loss of visual functions, especially due to thinning of the retina, retinal fold, retinal detachment, and neurodegeneration in the visual cortex. Supplementation during the development of the model with vitamin D3 and vitamin A prevented the deterioration of the retina and visual cortex by reducing the degree of oxidative stress and cytotoxicity.

The effect of changing the molecular structure of the surfactant on the dissolution of lamellar phases

Dissolution processes of surfactants, especially when in the lamellar phase, into water are important for product formulation. Understanding this process at a molecular level will help to enhance product design and control surfactant processes. The main goal of this study is to examine the effect of different lengths of surfactants and the hydrophobic to hydrophilic ratio on the dissolution process of surfactants. To achieve this goal dissipative particle dynamic (DPD) simulations were used. Lamellar equilibrium simulations were carried out for different surfactant chain lengths at 80 vol% with water. The surfactant chains were each run in a simulation box of dimensions 20 × 20 × 20 until equilibrium was reached. The lamellar phase formed for all different surfactant chain lengths and, after the initial equilibrium the surfactant systems were then simulated with a water box for dissolution. The dissolution process was tracked by visual analysis, local concentration analysis, micelle size, and a zonal model to calculate the diffusion parameter.Results show that as the surfactant chain length increased by adding more of the hydrophobic beads, the dissolution process slowed down. Increasing the hydrophilic part of the surfactant speeds up the dissolution process, but the effect of adding more of the hydrophobic part is greater than the effect of adding more of the hydrophilic part on the dissolution process.