This paper shows that in molecular dynamics (MD) when constant-energy (NVE) simulations of Newton's equations of motion are attempted using the multiple time stepping (MTS) integrator Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the longest step size is a third or possibly a fourth of the period(s) of the fastest motion(s) in the system. This is demonstrated both through a thorough set of computer experiments and through the analysis of a nonlinear model problem. The numerical experiments include not only the unconstrained dynamics simulation of a droplet of flexible water and a flexible protein, but also the constrained dynamics simulation of a solvated protein, representing a range of simulation protocols commonly in use by biomolecular modelers. The observed and predicted instabilities match exactly. Previous work has identified and explained a linear instability for Verlet-I/r-RESPA/Impulse at around half the period of the fastest motion. Mandziuk and Schlick discovered nonlinear resonances in single time stepping MD integrators, but unstable nonlinear resonances for MTS integrators are reported here for the first time. This paper also offers an explanation on the instability of MTS constrained molecular dynamics simulations of explicitly solvated proteins. More aggressive multiple step sizes are possible with mild Langevin coupling or targeted Langevin coupling, and its combination with the mollified Impulse method permits step sizes 3 to 4 times larger than Verlet-I/r-RESPA/Impulse while still retaining some accuracy.1. Introduction. This paper uncovers additional stability limitations of multiple time stepping (MTS) integrators for molecular dynamics (MD) that attempt to bridge time scales. In particular, it is shown that when constant-energy (NVE) simulations of Newton's equations of motion are attempted using the MTS integrator Verlet-I [12]/r-RESPA [42]/Impulse, there are nonlinear instabilities when the longest step size is a third or possibly a fourth of the period(s) of the fastest motion(s) in the system. This is demonstrated both through a thorough set of computer experiments and through the analysis of a nonlinear model problem. The observed and predicted instabilities match exactly.A linear instability for Verlet-I/r-RESPA/Impulse at around half the period of the fastest motion has been identified and explained by previous work [9,40]. Mandziuk and Schlick [29] discovered nonlinear resonances in single time stepping MD integrators, but unstable nonlinear resonances for MTS integrators are reported here for the first time.

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ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol's sequential performance is excellent when compared to a leading MD program, and that it scales well for moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.

A novel chitosan-based membrane that made of hydroxyethyl chitosan, gelatin and chondroitin sulfate was used as a carrier of corneal endothelial cells. The characteristics of the blend membrane including transparency, equilibrium water content, ion and glucose permeability were determined. The results showed that the optical transparency of the membrane was as good as the natural human cornea. The water content of this scaffold was 81.32% which was remarkably close to the native cornea. The membrane had a good ion permeability and its glucose permeability was even higher than natural human cornea. The cultured rabbit corneal endothelial cells formed a monolayer on the membrane. The results demonstrated that the membrane was suitable for corneal endothelial cells to attach and grow on it. In addition, the membranes in vivo could be degraded steadily with less inflammation and showed a good histocompatibility. These results demonstrated that the hydroxyethyl chitosan-chondroitin sulfate-gelatin blend membrane can potentially be used as a carrier for corneal endothelial cell transplantation.

Background. Gegen Qinlian (GGQL) decoction is a common Chinese herbal compound for the treatment of ulcerative colitis (UC). In this study, we aimed to identify its molecular target and the mechanism involved in UC treatment by network pharmacology and molecular docking. Material and Methods. The active ingredients of Puerariae, Scutellariae, Coptis, and Glycyrrhiza were screened using the TCMSP platform with drug ‐ like   properties   DL ≥ 0.18 and oral   availability   OB ≥ 30 % . To find the intersection genes and construct the TCM compound-disease regulatory network, the molecular targets were determined in the UniProt database and then compared with the UC disease differential genes with P value < 0.005 and ∣ log 2   fold   change ∣ > 1 obtained in the GEO database. The intersection genes were subjected to protein-protein interaction (PPI) construction and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. After screening the key active ingredients and target genes, the AutoDock software was used for molecular docking, and the best binding target was selected for molecular docking to verify the binding activity. Results. A total of 146 active compounds were screened, and quercetin, kaempferol, wogonin, and stigmasterol were identified as the active ingredients with the highest associated targets, and NOS2, PPARG, and MMP1 were the targets associated with the maximum number of active ingredients. Through topological analysis, 32 strongly associated proteins were found, of which EGFR, PPARG, ESR1, HSP90AA1, MYC, HSPA5, AR, AKT1, and RELA were predicted targets of the traditional Chinese medicine, and PPARG was also an intersection gene. It was speculated that these targets were the key to the use of GGQL in UC treatment. GO enrichment results showed significant enrichment of biological processes, such as oxygen levels, leukocyte migration, collagen metabolic processes, and nutritional coping. KEGG enrichment showed that genes were particularly enriched in the IL-17 signaling pathway, AGE-RAGE signaling pathway, toll-like receptor signaling pathway, tumor necrosis factor signaling pathway, transcriptional deregulation in cancer, and other pathways. Molecular docking results showed that key components in GGQL had good potential to bind to the target genes MMP3, IL1B, NOS2, HMOX1, PPARG, and PLAU. Conclusion. GGQL may play a role in the treatment of ulcerative colitis by anti-inflammation, antioxidation, and inhibition of cancer gene transcription.