Transferable coarse-grained potential for de novo\textit{de novo} protein folding and design

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and folding is introduced. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences are not yet fully realistic and require further experimental testing. For an independent set of proteins, notoriously difficult to fold, the correct folding of both the designed and the natural sequences is also demonstrated. The folding properties are characterized by free energy calculations. which not only are consistent among natural and designed proteins, but we also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, this novel coarse-grained protein model is unique in the combination of its fundamental three features: its simplicity, its ability to produce natural foldable designed sequences, and its structure prediction precision. The latter demonstrated by free energy calculations. It is also remarkable that low frustration sequences can be obtained with such a simple and universal design procedure, and that the folding of natural proteins shows funnelled free energy landscapes without the need of any potentials based on the native structure

Order-disorder phase change in embedded Si nano-particles

We investigated the relative stability of the amorphous vs crystalline nanoparticles of size ranging between 0.8 and 1.8 nm. We found that, at variance from bulk systems, at low T small nanoparticles are amorphous and they undergo to an amorphous-to-crystalline phase transition at high T. On the contrary, large nanoparticles recover the bulk-like behavior: crystalline at low T and amorphous at high T. We also investigated the structure of crystalline nanoparticles, providing evidence that they are formed by an ordered core surrounded by a disordered periphery. Furthermore, we also provide evidence that the details of the structure of the crystalline core depend on the size of the nanoparticleComment: 8 pages, 5 figure

Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules

Limited bonding valence, usually accompanied by well-defined directional interactions and selective bonding mechanisms, is nowadays considered among the key ingredients to create complex structures with tailored properties: even though isotropically interacting units already guarantee access to a vast range of functional materials, anisotropic interactions can provide extra instructions to steer the assembly of specific architectures. The anisotropy of effective interactions gives rise to a wealth of self-assembled structures both in the realm of suitably synthesized nano- and micro-sized building blocks and in nature, where the isotropy of interactions is often a zero-th order description of the complicated reality. In this review, we span a vast range of systems characterized by limited bonding valence, from patchy colloids of new generation to polymer-based functionalized nanoparticles, DNA-based systems and proteins, and describe how the interaction patterns of the single building blocks can be designed to tailor the properties of the target final structures

XANES Study of Structural Disorder in Amorphous Silicon

An investigation of the structure of several amorphous silicon (a-Si) films is presented. Samples were prepared by using the ion beam sputtering technique at different substrate deposition temperatures. X-ray absorption spectroscopy and multiple scattering formalism have been used to detect structural variations of the a-Si films. The analysis of the XANES (X-ray absorption near-edge structure) spectra shows that increasing the substrate deposition temperature leads to a structural change toward a higher-level short-range order.

Different regimes of the uniaxial elongation of electrically charged viscoelastic jets due to dissipative air drag

We investigate the effects of dissipative air drag on the dynamics of electrified jets in the initial stage of the electrospinning process. The main idea is to use a Brownian noise to model air drag effects on the uniaxial elongation of the jets. The developed numerical model is used to probe the dynamics of electrified polymer jets at different conditions of air drag force, showing that the dynamics of the charged jet is strongly biased by the presence of air drag forces. This study provides prospective beneficial implications for improving forthcoming electrospinning experiments.Comment: 12 pages, 6 figure