Search Results (18)

The relationship between protein structure and function is intrinsically interconnected, as the structure of a protein directly determines its functional properties. To investigate the effects of temperature and pressure on protein function, this study employed ethyl carbamate (EC) hydrolase as a model food enzyme and conducted molecular dynamics (MD) simulations under varying temperature and pressure levels to elucidate its structure–function relationship. By systematically analyzing the dynamic changes in root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), hydrogen bonding, catalytic pocket conformation, and packing density under different temperature and pressure conditions, we revealed the structural adaptability of EC hydrolase. Furthermore, we analyzed the characteristics of EC hydrolase using molecular dynamics simulations with temperature and pressure levels, as well as conformational bias-based computer-aided engineering, providing both theoretical and experimental foundation for the adaptability mechanisms of enzymes under extreme conditions. Full article

A batch mixer is an important piece of equipment for polymer filling modification, and the kinematics of agglomerate breakup and distribution are necessary for the structure design and mixing process optimization of the rotor, particularly in light of the cohesive forces that exist within the agglomerate. In this paper, computational fluid dynamics (CFD) was coupled with discrete element method (DEM) to simulate the mixing process, including breakup and distribution, which was further quantitatively evaluated by the post-processing involving numerical method. To study the mixing process of an agglomerate composed of massive spherical particles (individual particle ratio was r), the coordinates of the particles were exported from the CFD-DEM simulation results. Then, the coordinate data were automatically processed with an automate custom-built post-processing program to obtain the average radius of gyration (R_gy) and the particle distribution density (ε). The kinematics analyzation of breakup and distribution was represented by curve of R_gy/r versus mixing time (t) and curve of ε versus t, respectively. The value of R_gy/r and ε decreased over time until they reached an equilibrium and vibrated around a certain value. In particular, a notable decline in the value of R_gy/r was observed following an increase prior to critical time. The increase in R_gy/r stated that the agglomerate or aggregates undergo stretching deformation. Additionally, mixing processes of rotors with different pressurization coefficients (S) and rotation speeds could be facilitated and intensified by large S and high rotation speed. Finally, a “breakup-line” was developed by considering the influence of cohesive force and rotation speed on the agglomerate breakup process. The agglomerate could be broken if the combination of rotation speed and bonding strength was above the “breakup line”, otherwise the agglomerate was not broken. Furthermore, rotors with larger slopes exhibited stronger breakup ability. Full article

Bombyx mori silk fibroin is a promising biopolymer with notable mechanical strength, biocompatibility, and potential for diverse biomedical applications, such as tissue engineering scaffolds, and drug delivery. These properties are intrinsically linked to the structural characteristics of silk fibroin, making it essential to understand its molecular stability under varying environmental conditions. This study employed molecular dynamics simulations to examine the structural stability of silk I and silk II conformations of silk fibroin under changes in temperature (298 K to 378 K) and pressure (0.1 MPa to 700 MPa). Key parameters, including Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of Gyration (R_g) were analyzed, along with non-bonded interactions such as van der Waals and electrostatic potential energy. Our findings demonstrate that both temperature and pressure exert a destabilizing effect on silk fibroin, with silk I exhibiting a higher susceptibility to destabilization compared to silk II. Additionally, pressure elevated the van der Waals energy in silk I, while temperature led to a reduction. In contrast, electrostatic potential energy remained unaffected by these environmental conditions, highlighting stable long-range interactions throughout the study. Silk II’s tightly packed β-sheet structure offers greater resilience to environmental changes, while the more flexible α-helices in silk I make it more susceptible to structural perturbations. These findings provide valuable insights into the atomic-level behavior of silk fibroin, contributing to a deeper understanding of its potential for applications in environments where mechanical or thermal stress is a factor. The study underscores the importance of computational approaches in exploring protein stability and supports the continued development of silk fibroin for biomedical and engineering applications. Full article

Fibres in the micro- and nanometre scale are suited to a broad range of applications, including drug delivery and tissue engineering. Electrospinning is the manufacturing method of choice, but it has some limitations. Novel pressure-driven fibre-forming techniques, like pressurised gyration (PG), overcome these limitations; however, the compatibility of PG with biological materials has not yet been evaluated in detail. For the first time, this limitation of PG was investigated by optimising PG for microbial cell processing and incorporating bacterial cultures into fibrous polymeric scaffolds for sustained release. Multiple polymer–solvent systems were trialled, including polyvinylpyrrolidone (PVP)/phosphate-buffered saline (PBS) 25% w/v, polyethylene oxide (PEO)/PBS 20% w/v, and PVP/ethanol 20% w/v. Rheological studies revealed the surface tension of the PVP/PBS, PEO/PBS, and PVP/ethanol polymer–solvent systems to be 73.2, 73.9, and 22.6 mN/m, respectively. Scanning electron microscopy showed the median fibre diameters to be between 9.8 μm and 26.1 μm, with PVP producing larger fibres. Overnight Bacillus subtilis cultures were then incorporated into the chosen polymeric solutions and processed into fibres using PG. The produced cell-loaded fibres were incubated in LB broth to assess the cell viability of the encapsulated cells. Colony counts post-incubation showed the PVP/PBS 25% fibres resulted in 60% bacterial growth, and PEO/PBS 20% fibres led to 47% bacterial growth, whereas PVP/ethanol 20% fibres did not lead to any bacterial growth. Based on the results gathered during this study, it can be concluded that PG offers a promising way of encapsulating cells and other sensitive biological products while having many notable advantages compared to electrospinning. This research demonstrates proof of concept research-based evidence and showcases the potential of pressurised gyration as a key disruptive innovation in probiotic delivery system design and manufacturing. Full article

Alpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson’s disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used a range of computational algorithms such as sequence conservation, structural analysis, physicochemical properties, and machine learning. The sequence of the SNCA gene was analyzed, resulting in the mapping of 42,272 SNPs that are classified into different functional categories. A total of 177 nsSNPs were identified within the coding region; there were 20 variants that may influence the α-Syn protein structure and function. This identification was made by employing different analytical tools including SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, I-Mut, and HOPE. Three mutations, V82A, K80E, and E46K, were selected for further examinations due to their spatial positioning within the α-Syn as determined by PyMol. Results indicated that these mutations may affect the stability and function of α-Syn. Then, a molecular dynamics simulation was conducted for the SNCA wildtype and the four mutant variants (p.A18G, p.V82A, p.K80E, and p.E46K). The simulation examined temperature, pressure, density, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg). The data indicate that the mutations p.V82A, p.K80E, and p.E46K reduce the stability and functionality of α-Syn. These findings highlight the importance of understanding the impact of nsSNPs on α-syn structure and function. Our results required verifications in further protein functional and case–control studies. After being verified these findings can be used in genetic testing for the early diagnosis of PD, the evaluation of the risk factors, and therapeutic approaches. Full article

Selenium (Se) is a trace mineral found in plants with a distinct sulfuric odor that is cardioprotective and reported to have low toxicity. West Java, Indonesia, has a variety of plants with a distinct odor that are consumed raw, such as jengkol (Archidendron pauciflorum). This study is conducted to determine the Se content of jengkol using the fluorometric method, where the jengkol extract is separated, and the Se content is detected using high-pressure liquid chromatography (HPLC), combined with fluorometry. Two fractions with the highest Se concentration (A and B) are found and characterized using liquid chromatography mass spectrometry to predict the organic Se content by comparing the results with those in the external literature. The Se content of fraction (A) is found to be selenomethionine (m/z 198), gamma glutamyl-methyl-selenocysteine-(GluMetSeCys; m/z 313), and the Se-sulfur (S) conjugate of cysteine-selenoglutathione (m/z 475). Furthermore, these compounds are docked on receptors involved in cardioprotection. The receptors are peroxisome proliferator-activated receptor-γ (PPAR-γ), nuclear factor kappa-B (NF-κB), and phosphoinositide 3-kinase (PI3K/AKT). The interaction of receptor and ligan that has the lowest binding energy of the docking simulation is measured with molecular dynamic simulation. MD is performed to observe bond stability and conformation based on root mean square deviation, root mean square fluctuation, radius gyration, and MM-PBSA parameters. The results of the MD simulation show that the stability of the complex organic Se compounds tested with the receptors is lower than that of the native ligand, while the binding energy is lower than that of the native ligand based on the MM-PSBA parameter. This indicates that the predicted organic Se in jengkol, i.e., gamma-GluMetSeCys to PPAR-γ, gamma-GluMetSeCys AKT/PI3K, and Se-S conjugate of cysteine-selenoglutathione to NF-κB, has the best interaction results and provides a cardioprotection effect, compared to the molecular interaction of the test ligands with the receptors. Full article

This work uses micromodel, core floods and Field-Flow Fractionation (FFF) evaluations to estimate the behaviour and key elements for selecting polymers to address heterogenous reservoirs. One of the approaches was to construct two-layered micromodels differing six times in permeability and based on the physical characteristics of a Bentheimer sandstone. Further, the impacts of injectivity and displacement efficiency of the chosen polymers were then assessed using single- and two-phase core tests. Moreover, FFF was also used to assess the polymers’ conformity, gyration radii, and molecular weight distribution. For the polymer selection for field application, we weighted on the good laboratory performance in terms of sweep efficiency improvement, injectivity, and propagation. Based on the results, polymer B (highest MWD) performed the poorest. Full spectrum MWD measurement using Field-Flow Fractionation is a key in understanding polymer behavior. Heterogenous micromodel evaluations provided consistent data to subsequent core flood evaluations and were in alignment with FFF indications. Single-phase core floods performed higher injection velocities (5 m/d) in combination of FFF showed that narrower MWD distribution polymers (polymers A and C) have less retention and better injectivity. Two-phase core floods performed at low, reservoir representative velocities (1 ft/d) showed that Polymer B could not be injected, with pressure response staying at high values even when chase brine is injected. Adsorption values for all tested polymers at these conditions were high, however highest were observed in the case of polymer B. Overall, for the polymer selection for field application, we weighted on the good laboratory performance in terms of sweep efficiency improvement, injectivity, polymer retention, and propagation; all accounted in this work. Full article

In this paper, predictions from a theoretical model describing the rejection of a rigid spherical solute from porous membranes are compared to experimental results for a single stranded DNA (ssDNA) with 60 thymine nucleotides. Experiments were conducted with different pore size track-etched membranes at different transmembrane pressures and different NaCl concentrations. The model includes both hydrodynamic and electrostatic solute–pore wall interactions; predictions were made using different size parameters for the ssDNA (radius of gyration, hydrodynamic radius, and root mean square end-to-end distance). At low transmembrane pressures, experimental results are in good agreement with rejection predictions made using the hard sphere model for the ssDNA when the solute size is described using its root mean square end-to-end distance. When the ssDNA size is characterized using the radius of gyration or the hydrodynamic radius, the hard sphere model under-predicts rejection. Not surprisingly, the model overestimates ssDNA rejection at conditions where flow induced elongation of the DNA is expected. The results from this study are encouraging because they mean that a relatively simple hindered transport model can be used to estimate the rejection of a small DNA from porous membranes. Full article

Single-use face masks pose a threat to the environment and are not cost-effective, which prompts the need for developing reusable masks. In this study, pressurized gyration (PG) successfully produced bead-on-string polyvinylidene fluoride (PVDF) fibers with fiber diameters ranging from 2.3 μm to 26.1 μm, and bead diameters ranging from 60.9 μm to 88.5 μm by changing the solution parameters. The effect of the solution parameters on the crystalline phase was studied by Fourier-transform infrared spectroscopy (FT-IR), where the β-phase contents of PG PVDF fibers reached over 75%. The fiber morphology and β-phase contents of PG PVDF fibers indicated the potential mechanical and electrostatic filtration efficiency of PG PVDF fibers, respectively. Additionally, the hydrophobicity was investigated by static water contact angle tests, and the PVDF fibers showed superior hydrophobicity properties (all samples above 125°) over commercial polypropylene (PP) single-use masks (approximately 107°). This study supports the notion that the PG PVDF fiber mats are a promising candidate for future reusable face masks. Full article

We explored two approaches to recover uranium and plutonium from aqueous solutions at pH 4 and pH 7 using water-soluble star-like polyacrylamide polymers with a dextran core. In the first approach, a solution comprising a neutral or ionomer polymer was mixed with a radionuclide solution to form polymer–metal complexes that were then retained by ultrafiltration (UF) membranes under applied pressure. The same polymers were first deposited on the membrane in the second approach using pressure-driven flow. The applied polymers had an overall diameter of gyration of 120 nm, which exceeded the nominal diameter of the UF membrane pores. The polymers showed a high affinity to uranyl but could also be used to extract Pu from neutral or near-neutral pH solutions. Direct-flow single-step filtration and alpha spectrometry demonstrated that the UF membranes containing star-like copolymers could recover 99% of U and up to 60% of Pu from deionized water after filtering 15 mL solutions containing 25 ppm and 33 ppb of the actinides, correspondingly. The sorption capacity of the polymers for uranium could be measured as 1mg U per mg of the polymer after six subsequent filtration steps. Alpha spectroscopy of the deposited actinides revealed peculiarities of the structural organization of polymers and their complexes with U or Pu, depending on the approach. Though both approaches were efficient, the second approach (deposition of the polymer on the membrane followed by filtration) has an additional advantage of protecting the membrane pores from capillary collapse by filling them with the polymer chains. Therefore, these polymer-modified membranes could be used either in continuous or multi-step filtration process with drying after each step without deterioration of their sorption characteristics. Full article

We investigate the phase behavior of the asymmetric lipid membranes under shear flows, using the dissipative particle dynamics simulation. Two cases, the weak and strong shear flows, are considered for the asymmetric lipid microstructures. Three typical asymmetric structures, the membranes, tubes, and vesicle, are included in the phase diagrams, where the effect of two different types of lipid chain length on the formation of asymmetric membranes is evaluated. The dynamic processes are demonstrated for the asymmetric membranes by calculating the average radius of gyration and shape factor. The result indicates that different shear flows will affect the shape of the second type of lipid molecules; the shape of the first type of lipid molecules is more stable than that of the second type of lipid molecules. The mechanical properties are investigated for the asymmetric membranes by analyzing the interface tension. The results reveal an absolute pressure at the junctions of different types of particles under the weak shear flow; the other positions are almost in a state of no pressure; there is almost no pressure inside the asymmetric lipid membrane structure under the strong shear flow. The findings will help us to understand the potential applications of asymmetric lipid microstructures in the biological and medical fields. Full article

“Two ecological barriers and three shelters” (TEBTS), which has the effect of relieving ecological pressure, is the national ecological security pattern in China. Calculating the value of TEBTS ecosystem services, clarifying the synergy/trade-off relationships between ecosystem services, and maximizing the value of regional ecosystem services are of great significance for maintaining the security of the ecological civilization. At present, the research on ecosystem service synergy/trade-off has become the frontier field of ecology and related disciplines at home and abroad, and many research results have been obtained. However, there is still room and significance for continuing research to think about the synergy/trade-off relationship of ecosystems from the perspective of temporal and spatial heterogeneity: clarifying the spatial scope and spatial transmission characteristics of ecosystem service synergy/trade-off; exploring the trend of ecosystem service synergy/trade-off, and simulating the dynamic characteristics of natural factors affecting ecosystem services; and analyzing the characteristics of different spatial attributes that lead to the synergy/trade-off of ecosystem services. In this study, the Songhua River Basin (SRB), where the NFB is located, is used as the research area, the ecosystem services are simulated through the ecosystem assessment model, ecological unit (EU) is constructed as a research carrier, which is used to define the spatial scope of ecosystem services, and the influence of spatial characteristics and attribute characteristics on the change trend of the ecosystem service synergy/trade-off relationship is analyzed. The research found that water retention, soil conservation, and biodiversity did not change much from 2000 to 2015, and these ecosystem services have a greater value in the NFZ. The amount of carbon sequestration increased rapidly from 2010 to 2015. Crop production showed an increasing trend year by year. As the main grain production area, the Songnen Plain provides the main crop production function, which is greatly affected by humans. In the spatial characteristic, water retention, soil sequestration, and biodiversity present a very significant synergistic relationship, which is manifested in the obvious high-value aggregation characteristics in the NFZ, and crop production and the other four types of ecosystem services are in a trade-off relationship. At the time scale, the four types of ecosystem services, including water retention, soil conservation, biodiversity, and carbon sequestration, are synergistic, and crop production and water retention are synergistic. The vegetation types exhibiting a synergy/trade-off relationship are mainly broad-leaved forests, and the soil types are mainly luvisols and phaeozems. These EUs are mainly distributed in the NFZ and have spatial topological characteristics: the area and circumference of these EUs are smaller, the radius of gyration is also significantly smaller than that of other EUs, and the shape is more regular. By focusing on the spatial aggregation characteristics and changing trends of the ecosystem service synergy/trade-off and clarifying the influencing factors of the ecosystem service synergy/trade-off, the ecosystem services can be integrated, and the ecosystem can be optimized. Thus, the value of regional ecosystem services can be maximized, and a certain data foundation and theoretical support can be provided for major projects, such as ecological restoration and ecological environment governance, which is of great significance for improving the pattern of ecological security. Full article

The ability to generate core–sheath bicomponent polymer nanofibers in a single-step with scale-up possibilities is demonstrated using pressurised gyration manufacturing. This is the first time that nanofiber containing more than one polymer having a core–sheath configuration has been generated in this way. Water-soluble polymers polyethylene oxide (PEO) and polyvinyl pyrrolidone (PVP) are used as the core and sheath layers, respectively. Core–sheath nanofibers with a diameter in the range of 331 to 998 nm were spun using 15 wt % PEO and 15 wt % PVP polymer solutions. The forming parameters, working pressure and rotating speed, had a significant influence on the size, size distribution and the surface morphology of the nanofibers generated. Overall, fibre size decreased with increasing working pressure and rotating speed. The fibre size was normally distributed in all cases, with 0.2 MPa working pressure in particular showing narrower distribution. The fibre size distributions for 0.1 and 0.3 MPa working pressure were broader and a mean fibre size of 331 nm was obtained in the latter case. The fibre size was evenly distributed and narrower for rotating speeds of 2000 and 4000 RPMs. The distribution was broader for rotating speed of 6000 RPM with a mean value obtained at 430 nm. Continuous, smooth and bead-free fibre morphologies were obtained in each case. The fibre cross-section analysis using a focused ion beam machine showed a solid core surrounded by a sheath layer. Our findings demonstrate that the pressurised gyration could be used to produce core–sheath polymer nanofibers reliably and cost-effectively with scale-up possibilities (~4 kg h⁻¹). Full article

Hyaluronic acid (HA) has a wide range of biomedical applications including the formation of hydrogels, microspheres, sponges, and films. The modeling of HA to understand its behavior and interaction with other biomolecules at the atomic level is of considerable interest. The atomistic representation of long HA polymers for the study of the macroscopic structural formation and its interactions with other polyelectrolytes is computationally demanding. To overcome this limitation, we developed a coarse grained (CG) model for HA adapting the Martini scheme. A very good agreement was observed between the CG model and all-atom simulations for both local (bonded interactions) and global properties (end-to-end distance, a radius of gyration, RMSD). Our CG model successfully demonstrated the formation of HA gel and its structural changes at high salt concentrations. We found that the main role of CaCl₂ is screening the electrostatic repulsion between chains. HA gel did not collapse even at high CaCl₂ concentrations, and the osmotic pressure decreased, which agrees well with the experimental results. This is a distinct property of HA from other proteins or polynucleic acids which ensures the validity of our CG model. Our HA CG model is compatible with other CG biomolecular models developed under the Martini scheme, which allows for large-scale simulations of various HA-based complex systems. Full article

Injection molding is an economical and effective method for manufacturing polymer parts with nanostructures and residual stress in the parts is an important factor affecting the quality of molding. In this paper, taking the injection molding of polymethyl methacrylate (PMMA) polymer in a nano-cavity with an aspect ratio of 2.0 as an example, the formation mechanism of residual stresses in the injection molding process was studied, using a molecular dynamics simulation. The changes in dynamic stress in the process were compared and analyzed, and the morphological and structural evolution of molecular chains in the process of flow were observed and explained. The effects of different aspect ratios of nano-cavities on the stress distribution and deformation in the nanostructures were studied. The potential energy, radius of gyration and elastic recovery percentage of the polymer was calculated. The results showed that the essence of stress formation was that the molecular chains compressed and entangled under the flow pressure and the restriction of the cavity wall. In addition, the orientation of molecular chains changed from isotropic to anisotropic, resulting in the stress concentration. At the same time, with the increase in aspect ratio, the overall stress and deformation of the nanostructures after demolding also increased. Full article