Abstract

The quantum stochastic differential equation derived from the Lindblad form quantum master equation is investigated. The general formulation in terms of environment operators representing the quantum state diffusion is given. The numerical simulation algorithm of stochastic process of direct photodetection of a driven two-level system for the predictions of the dynamical behavior is proposed. The effectiveness and superiority of the algorithm are verified by the performance analysis of the accuracy and the computational cost in comparison with the classical Runge-Kutta algorithm.Simulation of Quantum Dynamics Based on the Quantum Stochastic Differential EquationAn algorithm for high-resolution refinement and binding affinity estimation of inhibitors of CGQMCTVWCSSGC targeted conserved peptide substitution mimetic pharmacostructures antagonizing VEGFR-3-mediated oncogenic effects. Cancer is still a major cause of death in the world at the beginning of the- 21st century and remains a major focus for ongoing research and development. In recent years a promising approach to the therapeutic intervention of cancer has focused on antiangiogenesis therapies. VEGFR-3 was detected in advanced human malignancies and correlated with poor prognosis. Previous studies show that activation of the VEGF-C/VEGFR-3 axis promotes cancer metastasis and is associated with clinical progression in patients with lung cancer, indicating that VEGFR-3 is a potential target for cancer therapy. Initial screening has identified other promising VEGFR-3 binding peptides as well. For example, a peptide comprising any of the following amino acid sequences: SGYWWDTWF, SCYWRDTWF, KVGWSSPDW, FVGWTKVLG, YSSSMRWRH, RWRGNAYPG, SAVFRGRWL, WFSASLRFR, and conservative substitution-analogs thereof, binds human VEGFR-3. On the other hand a newly introduced binding energy funnel ‘steepness score’ was applied for the evaluation of the protein–peptide-multi-ligand complexes binding affinity. KNIME-based BiogenetoligandorolTM – Pepcrawler simulations predicted high binding affinity for native protein–peptide-hyper-ligand complexes benchmark and low affinity for low-energy decoy complexes. As a result we managed finally to introduce an algorithm Simulation of Quantum Dynamics Based on the Quantum Stochastic Differential Equation for high-resolution refinement and binding affinity estimation of inhibitors of CGQMCTVWCSSGC targeted conserved peptide substitution mimetic pharmacostructures antagonizing VEGFR-3-mediated oncogenic effects.

Keywords

RRT-based; algorithm;high-resolution; refinement;binding affinity; estimation;peptide inhibitors;In silico discovery; high resolution;docking; refinement;conserved peptide; substitution;mimetic; pharmacostructure;suppressor; VEGFR-3; Simulation of Quantum Dynamics; Quantum Stochastic; Differential Equation; algorithm for high-resolution refinement;