In Silico Approaches to Design and Characterize Peptide-based Nanostructures
2019, Globisch, Christoph, Isele, Marc, Peter, Christine, Jain, Alok
Molecular dynamics (MD) simulations can show structural and dynamic details on an atomistic level in a native-like environment. Conventional atomistic MD simulations have been successfully applied to many problems, however, they often do not cover the necessary timescales to sufficiently explore conformational phase and reach convergence. In this study, we discuss two examples where we have employed atomistic simulations followed by either Hamiltonian replica exchange molecular dynamics (H-REMD) or coarse-grained (CG) simulations to identify the intrinsic details of nanostructure formation processes and the influence of various factors on them. We demonstrate that combining computational approaches or resolution levels is very useful to overcome the limitations of a single method, like pure atomistic simulations, while still keeping its advantages. However, it is very important to carefully select suitable methods, parameters and approaches to get meaningful results with sufficient accuracy.
Phase Behavior of n-Alkyl-substituted Polysilanes
2003-09-26, Mueller, Christian, Peter, Christine, Frey1, Holger, Schmidt, Claudia
Polysilanes are high-molecular-weight polymers with a pure silicon chain as backbone and organic side chains. The σ-conjugation of the silicon backbone leads to interesting properties, such as strong UV absorption and photoconductivity. Poly(di-n-alkylsilanes) with n-alkyl side chains longer than ethyl form mesophases, in which the polymers are hexagonally packed in two dimensions but have highly flexible backbones. Such condis (conformationally disordered) crystals, characterized by a dynamic exchange between different conformations, are also known for other polymers, for example, polysiloxanes and polyphosphazenes. A clear proof of the backbone mobility in these mesophases is provided by solid-state NMR spectroscopy.
Computational Studies of Biomembrane Systems : Theoretical Considerations, Simulation Models, and Applications
2014, Deserno, Markus, Kremer, Kurt, Paulsen, Harald, Peter, Christine, Schmid, Friederike
This chapter summarizes several approaches combining theory, simulation, and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane-mediated interactions, attraction between transmembrane proteins, and aggregation in biomembranes leading to large superstructures such as the lightharvesting complex of green plants. After a general overview of theoretical considerations and continuum theory of lipid membranes we introduce different options for simulations of biomembrane systems, addressing questions such as: What can be learned from generic models? When is it expedient to go beyond them? And, what are the merits and challenges for systematic coarse graining and quasi-atomistic coarse-grained models that ensure a certain chemical specificity?