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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]

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]

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.