Free energy calculation of single molecular interaction using Jarzynski's identity method:the case of HIV-1 protease inhibitor system

Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molec- ular dynamics （SMD） simulations to dissociate the protease of human immunodeficiency type I virus （HIV-1 protease） and its inhibitors. We showed that because of intrinsic com- plexity of the ligand-receptor system, the energy barrier pre- dicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results sug- gested that the JI method is more appropriate for reconstruct- ing free energy landscape using the data taken from experi- ments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distri- bution in SMD simulations.

Higher Harmonics Induced by Waves Propagating over A Submerged Obstacle in the Presence of Uniform Current

To investigate higher harmonics induced by a submerged obstacle in the presence of uniform current, a 2D fully nonlinear numerical wave flume（NWF） is developed by use of a time-domain higher-order boundary element method（HOBEM） based on potential flow theory. A four-point method is developed to decompose higher bound and free harmonic waves propagating upstream and downstream around the obstacle. The model predictions are in good agreement with the experimental data for free harmonics induced by a submerged horizontal cylinder in the absence of currents. This serves as a benchmark to reveal the current effects on higher harmonic waves. The peak value of non-dimensional second free harmonic amplitude is shifted upstream for the opposing current relative to that for zero current with the variation of current-free incident wave amplitude, and it is vice versa for the following current. The second-order analysis shows a resonant behavior which is related to the ratio of the cylinder diameter to the second bound mode wavelength over the cylinder. The second-order resonant position slightly downshifted for the opposing current and upshifted for the following current.

MOLECULAR UNDERSTANDING OF NATURAL POLYPHENOLS: FREE RADICAL SCAVENGING AND INTERACTION WITH BIOMEMBRANES

Quantum calculations(mainly DFT)and molecular dynamics are increasingly effective tools to evaluate the physical chemical properties of natural and bio-inspired compounds.Free Radical Scavenging Capacity.Thermodynamic parameters(mainly bond dissociation enthalpies(BDE)of the O-H phenolic bond)allowed an accurate prediction of the antioxidant capacities of

STUDY ON THE DYNAMIC BEHAVIOR OF AXIALLY MOVING RECTANGULAR PLATES PARTIALLY SUBMERSED IN FLUID

The natural frequencies, complex modes and critical speeds of an axially moving rectangular plate, which is partially immersed in a fluid and subjected to a pretension, are investigated. The effects of free surface waves, compressibility and viscidity of the fluid are neglected in the analysis. The subsection functions are used to describe the discontinuous characteristics of the system due to partial immersion. The classical thin plate theory is adopted to formulate the equations of motion of a vibrating plate. The velocity potential and Bernoulli＇s equation are used to describe the fluid pressure acting on the moving plate. The effect of fluid on the vibrations of the plate may be equivalent to the added mass on the plate. The effects of distance ratio, moving speed, immersed-depth ratio, boundary conditions, stiffness ratio and aspect ratio of the plate as well as the fluid-plate density ratios on the free vibrations of the moving plate-fluid system are investigated.