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Using molecular dynamics simulation with reactive force-field (ReaxFF), we study the reactive oxygen species (ROS)-mediated damage to the core domain of human immunodeficiency virus (HIV) integrase. Our results demonstrate that with the increase in the ROS concentration, the structure of the core domain of HIV is more severely damaged, including dehydrogenation, increasing oxygen-containing groups, shorting or damaging spirals, and breaking peptide bonds. We particularly note that ROS has a significantly higher capability to abstract H atoms from N atoms than C atoms. The effects of different species of ROS on dehydrogenation and shorting or damaging spirals are not prominent. In contrast, for increasing oxygen-containing groups and breaking peptide bonds, the effect of O is more remarkable than O3 and O3 is greater than ·OH. Moreover, carboxyl dehydrogenation and nitrogen dehydrogenation are more easily dehydrogenated, resulting in higher dehydrogenation ratios for polar amino acid residues. These meticulous findings deepen our understanding of the role of ROS in regulating the structure and function of the core domain of HIV integrase and provide valuable insights into the plasma treatment of acquired immune deficiency syndrome. [ABSTRACT FROM AUTHOR]

AbstractLaccase has a wide range of substrates and the oxidation product is water, providing an ideal choice for the biological degradation and decolorization of dyeing wastewater. This study extracted laccase from the fruiting body of Agaricus bisporus, then used o-phthalaldehyde (OPA) as a cross-linking agent and added surface-aminated Fe3O4 nanoparticles (NH2-nanoFe3O4) to prepare magnetic cross-link enzyme aggregates (MCLEAs) of laccase, which was characterized by scanning electron microscope and vibrating sample magnetometer. The optimal temperature for the catalytic reaction of the MCLEAs was 35 °C, and the optimal pH was 3.0. The stability to temperature pH and storage stability were all enhanced. The immobilized laccase was utilized to treat amido black 10B solution, and the decolorization rate reached 92.48%. After five cycles of use, the MCLEAs of laccase could maintain 42.91% of the relative activity and 32.31% of the relative degradation ability to amido black 10B. [ABSTRACT FROM AUTHOR]

Because capsules exhibit viscoelasticity and shear resistance, the study of their dynamic motion under external flow is vital for biomedical and industrial applications. Toward this end, the present study uses the finite-element method to delve into the motion and deformation of viscoelastic capsules under steady and oscillating shear flow. In the steady shear, the effect of membrane viscosity is not obvious enough, which only slows the phase angle of capsules, which is consistent with previous work. However, the effect of membrane viscosity is more significant in the oscillatory shear, and we find that the deformation of capsules is affected by both viscosity and elasticity and exhibits two modes: For shear amplitudes γ0 < 0.06 or frequencies f > 0.3 Hz, the capsules essentially return to their original shape after being deformed. For amplitudes γ0 ≥ 0.06 or frequencies f ≤ 0.3 Hz, the capsules are strongly deformed and cannot return to their original state, which easily leads to membrane wrinkles and stress concentration. The results of this study systematically illustrate the dynamic behavior of viscoelastic capsules, which is critical to expound a capsule for use in drug transport, cell screening, and physiological processes. [ABSTRACT FROM AUTHOR]

Using Monte Carlo simulations, we studied the effect of bidispersity on the dynamics of polymer films capped between two neutral walls, where we chose three representative compositions for bidispersed polymer films. Our results demonstrate that the characteristic entanglement length is an important parameter to clarify the effect of the bidispersity on the dynamics of polymer films. For the short chains, shorter than the characteristic entanglement length, the average number of near-neighboring particles increases with the decrease of the film thickness and limits the diffusivity of the short chains, which is independent of the film compositions. However, the dynamics of the long chains, of which is above the characteristic entanglement length, is determined by the film's composition. In our previous paper, we inferred from the structures and entanglements of the bidisperse system with short and long chains that the constraint release contributes significantly to the relaxation mechanism of long chains. By calculating the self-diffusion coefficient of long chains, we confirmed this prediction that, with a lower weight fraction of long chains, the self-diffusion coefficient of long chains decreases slowly with the decrease of the film thickness, which is similar to that of short chains. With a higher weight fraction of long chains, the competition between the disentanglement and the increased in the local degree of confinement which resulted in the self-diffusion coefficient of long chains varying non-monotonically with the film thickness. Furthermore, for the bidisperse system with long and long chains, the diffusivity of long chains was not affected by the constraint release, which varied nonmonotonically with the decrease of the film thickness due to the competition between the disentanglement and the enhanced confinement. Herein, compared with the previous work, we completely clarified the relationship between the structures and dynamics for three representative compositions of bidisperse polymer films, which contains all possible cases for bidisperse systems. Our work not only establishes a unified understanding of the dependency of dynamics on the bidispersity of polymer films, but also helps to understand the case of polydispersity, which can provide computational supports for various applications for polymer films. [ABSTRACT FROM AUTHOR]

We study the flow-induced polymer translocation through a nanopore from a confining nanotube, using a hybrid simulation method that couples point particles into a fluctuating lattice-Boltzmann fluid. Our simulation illustrates that the critical velocity flux of the polymer linearly decreases with the decrease in the size of the confining nanotube, which corresponds well with our theoretical analysis based on the blob model of the polymer translocation. Moreover, by decreasing the size of the confining nanotube, we find a significantly favorable capture of the polymer near its ends, as well as a longer translocation time. Our results provide the computational and theoretical support for the development of nanotechnologies based on the ultrafiltration and the single-molecule sequencing.