The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

All the people I worked with gave me incredible support during these years, technical and emotional. From the first day, with my shirt decorated with bananas, to the lasts, when they had to bear my nervous and stressed mood. I thank Anna, Linda and Pierre, for the funny moments, the laughs and the many beers together. And for the precious scientific discussions, of course! Thank you also to Eethan, the living scientific encyclopedia, with (almost) always the right answer to my problems in the lab. Thank you, Enoch, for the discussions, especially those in the microscopy room. Emir, thank you for your help with the cloning, microscopy and the bacteriographs. I like your enthusiasm toward science, do not lose it! Thank you, Mehmet, for the support to the protein function prediction of my project, I appreciated the point of view from someone with a "dry biology" background and the comments on my thesis. Jeremy, Mirko, Giada, and Jara, thank you for the daily chats and jokes together. The daily routine was lighter with you around. Thank you, Dagmar, oh Dagmar, for your patience and your smiles. Lastly, thanks to the grumpy Daniel, my dear deskmate and benchmate, fellow of complains.Vorrei anche ringraziare i miei amici rimasti in Italia. Anche se ci vediamo poco, quando ci troviamo è sempre una festa. Sono fortunato a non averli persi dopo più di 5 anni passati all'estero: è anche grazie a loro che ho mantenuto la tenacia per arrivare fino alla fine. In particolare, Claudio, Stefano e Vito, grazie per la vostra vicinanza nonostante la lontananza. Grazie anche a Laura, la mia supervisor durante il mio tirocinio di tesi magistrale in Unimi, che mi ha insegnato come pensare e come muovermi nell'ambito di un progetto di ricerca: quello che ho imparato in quell'anno mi è stato molto utile durante il dottorato.Un grazie immenso alla mia famiglia e al nonno, senza i quali non sarei potuto arrivare dove sono ora, incoraggiandomi e sostenendomi sempre. E infine, Margherita, grazie per essere sempre stata al mio fianco in questi anni, anche quando non avevo occhi che per la tesi, risollevandomi dai momenti di sconforto e spazzando via i cattivi pensieri. ContributionsLeonard Ernst, a former bachelor student of the Di Ventura lab, cloned a 2-plasmid-based library composed of 5 VVD-AraC fusion proteins under IPTG induction and performed the first explorative experiments to demonstrate the light-responsiveness of the system. Emir Bora Akmeriç, technical assistant in our laboratory, helped me during the last year of my doctorate in the cloning process of some constructs and with the induction and imaging of the genes with poor or unknown function. Moreover, he took care of the Blade Runner bacteriograph, repeating it until he made it flawless.Mehmet Ali Öztürk, postdoc in our laboratory, contributed with structural biology analysis of the I1-I2 sequences rearrangements and collected, interpreted and catalogued the function and localization prediction outputs of the genes with poor or unknown function. He also provided valuable sug...

Linker histones are essential for DNA compaction in chromatin. They bind to nucleosomes in a 1:1 ratio forming chromatosomes. Alternative configurations have been proposed in which the globular domain of the linker histone H5 (gH5) is positioned either on- or off-dyad between the nucleosomal and linker DNAs. However, the dynamic pathways of chromatosome assembly remain elusive. Here, we studied the conformational plasticity of gH5 in unbound and off-dyad nucleosome-bound forms with classical and accelerated molecular dynamics simulations. We find that the unbound gH5 converts between open and closed conformations, preferring the closed form. However, the open gH5 contributes to a more rigid chromatosome and restricts the motion of the nearby linker DNA through hydrophobic interactions with thymidines. Moreover, the closed gH5 opens and reorients in accelerated simulations of the chromatosome. Brownian dynamics simulations of chromatosome assembly, accounting for a range of amplitudes of nucleosome opening and different nucleosome DNA sequences, support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent chromatosome configurations. Taken together, these findings suggest that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosome configurations through an interplay between induced fit and conformational selection.

To build or dissect complex pathways in bacteria and mammalian cells, it is often necessary to recur to at least two plasmids, for instance harboring orthogonal inducible promoters. Here we present SiMPl, a method based on rationally designed split enzymes and intein-mediated protein trans-splicing, allowing the selection of cells carrying two plasmids with a single antibiotic. We show that, compared to the traditional method based on two antibiotics, SiMPl increases the production of the antimicrobial non-ribosomal peptide indigoidine and the non-proteinogenic aromatic amino acid para-amino-L-phenylalanine from bacteria. Using a human T cell line, we employ SiMPl to obtain a highly pure population of cells double positive for the two chains of the T cell receptor, TCRα and TCRβ, using a single antibiotic. SiMPl has profound implications for metabolic engineering and for constructing complex synthetic circuits in bacteria and mammalian cells.