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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact

multiscale modeling --- molecular dynamics simulations --- advanced sampling methods --- coarse grained models --- macro-biomolecules --- molecular crowding --- system biology --- bioinformatics

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The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad range of research areas. In the frame of this Research Topic, we focus on Synthetic Biology approaches that aim at rearranging biological parts/ entities in order to generate novel biochemical functions with inherent metabolic activity. This Research Topic encompasses Pathway Engineering in living systems as well as the in vitro assembly of biomolecules into nano- and microscale bioreactors. Both, the engineering of metabolic pathways in vivo, as well as the conceptualization of bioreactors in vitro, require rational design of assembled synthetic pathways and depend on careful selection of individual biological functions and their optimization. Mathematical modelling has proven to be a powerful tool in predicting metabolic flux in living and artificial systems, although modelling approaches have to cope with a limitation in experimentally verified, reliable input variables. This Research Topic puts special emphasis on the vital role of modelling approaches for Synthetic Biology, i.e. the predictive power of mathematical simulations for (i) the manipulation of existing pathways and (ii) the establishment of novel pathways in vivo as well as (iii) the translation of model predictions into the design of synthetic assemblies.

Metabolic Engineering --- reconstitution --- molecular dynamics simulations --- Membrane Transport Proteins --- Protein Engineering --- Protein scaffolds --- metabolite profiling --- Interaction domains --- Metabolic Modelling --- Starch biosynthesis

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The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad range of research areas. In the frame of this Research Topic, we focus on Synthetic Biology approaches that aim at rearranging biological parts/ entities in order to generate novel biochemical functions with inherent metabolic activity. This Research Topic encompasses Pathway Engineering in living systems as well as the in vitro assembly of biomolecules into nano- and microscale bioreactors. Both, the engineering of metabolic pathways in vivo, as well as the conceptualization of bioreactors in vitro, require rational design of assembled synthetic pathways and depend on careful selection of individual biological functions and their optimization. Mathematical modelling has proven to be a powerful tool in predicting metabolic flux in living and artificial systems, although modelling approaches have to cope with a limitation in experimentally verified, reliable input variables. This Research Topic puts special emphasis on the vital role of modelling approaches for Synthetic Biology, i.e. the predictive power of mathematical simulations for (i) the manipulation of existing pathways and (ii) the establishment of novel pathways in vivo as well as (iii) the translation of model predictions into the design of synthetic assemblies.

Metabolic Engineering --- reconstitution --- molecular dynamics simulations --- Membrane Transport Proteins --- Protein Engineering --- Protein scaffolds --- metabolite profiling --- Interaction domains --- Metabolic Modelling --- Starch biosynthesis --- Metabolic Engineering --- reconstitution --- molecular dynamics simulations --- Membrane Transport Proteins --- Protein Engineering --- Protein scaffolds --- metabolite profiling --- Interaction domains --- Metabolic Modelling --- Starch biosynthesis

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Atomistic simulations, based on ab-initio and semi-empirical approaches, are nowadays widespread in many areas of physics, chemistry and, more recently, biology. Improved algorithms and increased computational power widened the areas of application of these computational methods to extended materials of technological interest, in particular allowing unprecedented access to the first-principles investigation of their electronic, optical, thermodynamical and mechanical properties, even where experiments are not available. However, for a big impact on the society, this rapidly growing field of computational approaches to materials science has to face the unfavourable scaling with the system size, and to beat the time-scale bottleneck. Indeed, many phenomena, such as crystal growth or protein folding for example, occur in a space/time scale which is normally out of reach of present simulations. Multi-scale approaches try to combine different scale algorithms along with matching procedures in order to bridge the gap between first-principles and continuum-level simulations. This Research Topic aims at the description of recent advances and applications in these two emerging fields of ab-inito and multi-scale materials modelling for both ground and excited states. A variety of theoretical and computational techniques are included along with the application of these methods to systems at increasing level of complexity, from nano to micro. Crossing the borders between several computational, theoretical and experimental techniques, this Research Topic aims to be of interest to a broad community, including experimental and theoretical physicists, chemists and engineers interested in materials research in a broad sense.

molecular dynamics simulations --- Classical and Quantum Monte Carlo methods --- ab-initio --- macromolecular complex --- Materials characterization --- Multiscale and Hierarchical modeling --- mechanical --- Electronic and optical properties of solids --- Carbon-based systems --- materials growth --- Density-functional

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This book provides an update for the rapidly developing technology known as “optogenetics”, which is the use of genetically encoded light-sensitive molecular elements (usually derived from lower organisms) to control or report various physiological and biochemical processes within the cell. Two ongoing clinical trials use optogenetic tools for vision restoration, and optogenetic strategies have been suggested as novel therapies for several neurological, psychiatric and cardiac disorders. This Special Issue comprises two reviews and seven experimental papers on different types of light-sensitive modules widely used in optogenetic studies. These papers demonstrate the efficiency and versatility of optogenetics and are expected to be equally relevant for advanced users and beginners considering using optogenetic tools in their research.

Research & information: general --- Biology, life sciences --- optogenetic tools --- neuroscience --- calcium sensor --- voltage sensor --- neurotransmitters --- optogenetics --- channelrhodopsins --- sodium --- calcium --- DC gate --- Optogenetics --- p53 --- AsLOV2 --- LINuS --- LEXY --- MIP --- PMI --- Chlamydomonas reinhardtii --- ion channel --- electrophysiology --- molecular dynamics simulations --- membrane-protein interaction --- energy of membrane deformation --- CTMD method, residual hydrophobic mismatch --- microbial rhodopsin --- channelrhodopsin --- membrane current --- hippocampal neurons --- light stimulation --- channelrhodopsin-2 --- photoreceptor --- BLUF --- modular domain --- resonance Raman --- flash photolysis --- hybrid QM/MM simulation --- two-photon --- azobenzene --- photoswitch --- photoswitching --- photocontrol --- all-optical electrophysiology --- microbial rhodopsins --- ion channels --- LOV domains --- membrane potential --- intracellular trafficking --- protein–protein interaction --- signaling