Grand Canonical Adaptive Resolution Simulation for Molecules with Electrons: A Theoretical Framework based on Physical Consistency

A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. T he Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.Comment: Computer Physics Communications (2017), in pres

Additional file 1: of Comparison of the complications of traditional 12 cores transrectal prostate biopsy with image fusion guided transperineal prostate biopsy

Multiparametric MRI Examination and Analysis. (DOCX 14 kb

Additional file 2: Figure S2. of miR-138-5p contributes to cell proliferation and invasion by targeting Survivin in bladder cancer cells

The growth curves of the bladder cancer cell xenografts. (TIFF 207 kb

Additional file 1: Figure S1. of miR-138-5p contributes to cell proliferation and invasion by targeting Survivin in bladder cancer cells

The role of siRNAs targeting Survivin and a Survivin overexpression plasmid in regulating the proliferative and invasive activities of bladder cancer cells. (A) Western blotting analysis to detect Survivin protein levels in T24 cells transfected with siRNAs targeting Survivin. (B) Western blotting analysis to detect Survivin protein levels in T24 cells transfected with the Survivin overexpression plasmid. (C) The CCK-8 viability assay was performed 12, 24, 36, and 48 hours after the transfection of T24 cells with si-Survivin#1. (D) The CCK-8 viability assay was performed 12, 24, 36, and 48 hours after the transfection of T24 cells with the Survivin overexpression plasmid. (E) and (F) Transwell analysis of invading T24 cells treated with si-Survivin#1. E: representative image; F: quantitative analysis. (G) and (H) Transwell analysis of invading T24 cells treated with the Survivin overexpression plasmid. G: representative image; H: quantitative analysis. *** p < 0.005. (TIF 5210 kb

Additional file 3: Figure S3. of miR-138-5p contributes to cell proliferation and invasion by targeting Survivin in bladder cancer cells

Effects of miR-138-5p and Survivin on the growth of bladder cancer cell xenografts in mice (supplemental animal experiment). A. Western blotting analysis of Survivin protein levels in T24 cells transduced with either lentivirus-miR-138-5p (MOI = 5) and/or different doses of the Survivin overexpression plasmid. B, Representative images of the tumors in different groups. The MOI value of lentivirus-miR-138-5p used here was 5, and the amount of pCDNA3.1-BIRC5 transfected was 9 μg/75 cm2. C, Quantitative analysis of the tumor weights. *p < 0.05; ** p < 0.01; *** p < 0.005. (TIF 5960 kb