Atomistic Calculation of Coulomb Interactions in Semiconductor Nanocrystals: Role of Surface Passivation and Composition Details

We report a theoretical investigation of electronic properties of semiconductor InAs and GaAs nanocrystals. Our calculation scheme starts with the single particle calculation using atomistic tight-binding model including spin-orbital interaction and d-orbitals. Then the exciton binding energies are calculated with screened Coulomb interaction. We study the role of surface passivation effects by varying value of surface passivation potential. We compare results obtained with dot center positioned on different lattice sites thus containing different number of anion and cations. We conclude that passivation of surface states affects significantly single particle energies and the value of electron-hole Coulomb attraction. Interestingly, due to limited screening, the short-range (on-site) contribution to the electron-hole Coulomb attraction plays significant role for small nanocrystals with radius smaller than 1 nm

Non-local effects of point mutations on the stability of a protein module

We combine experimental and theoretical methods to assess the effect of a set of point mutations on c7A, a highly mechanostable type I cohesin module from scaffoldin CipA from Clostridium thermocellum. We propose a novel robust and computationally expedient theoretical method to determine the effects of point mutations on protein structure and stability. We use all-atom simulations to predict structural shifts with respect to the native protein and then analyze the mutants using a coarse-grained model. We examine transitions in contacts between residues and find that changes in the contact map usually involve a non-local component that can extend up to 50 Å. We have identified mutations that may lead to a substantial increase in mechanical and thermodynamic stabilities by making systematic substitutions into alanine and phenylalanine in c7A. Experimental measurements of the mechanical stability and circular dichroism data agree qualitatively with the predictions provided the thermal stability is calculated using only the contacts within the secondary structures.We thank D. V. Laurents for his help with CD measurements and their analysis. This research has been supported by the ERA-NET grant ERA-IB (No. EIB.12.022) (FiberFuel) and the European Framework Programme VII NMP Grant No. 604530-2 (CellulosomePlus) and by PLGrid Infrastructure. It was also co-financed by the Polish Ministry of Science and Higher Education from the resources granted for the years 2014-2017 in support of international scientific projects. D.T. acknowledges Science Foundation Ireland (SFI) for financial support under Grant No. 15/CDA/3491 and M.Ch., M.G., and D.T. acknowledge computing resources at the SFI/Higher Education Authority Irish Centre for High-End Computing (ICHEC)

Non-local effects of point mutations on the stability of a protein module

We combine experimental and theoretical methods to assess the effect of a set of point mutations on c7A, a highly mechanostable type I cohesin module from scaffoldin CipA from Clostridium thermocellum. We propose a novel robust and computationally expedient theoretical method to determine the effects of point mutations on protein structure and stability.We use all-atom simulations to predict structural shifts with respect to the native protein and then analyze the mutants using a coarse-grained model. We examine transitions in contacts between residues and find that changes in the contact map usually involve a non-local component that can extend up to 50 Å. We have identified mutations that may lead to a substantial increase in mechanical and thermodynamic stabilities by making systematic substitutions into alanine and phenylalanine in c7A. Experimental measurements of the mechanical stability and circular dichroism data agree qualitatively with the predictions provided the thermal stability is calculated using only the contacts within the secondary structures

Topology in soft and biological matter

International audienceThe last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts. At the same time, considerable advances have been made in the description of the interplay between topological and physical properties in complex fluids, with the development of techniques that now allow researchers to control the formation of and interaction between defects in diverse classes of liquid crystals. Thanks to technological progress and the integration of experiments with increasingly sophisticated numerical simulations, topological biological and soft matter is a vibrant area of research attracting scientists from a broad range of disciplines. However, owing to the high degree of specialization of modern science, many results have remained confined to their own particular fields, with different jargon making it difficult for researchers to share ideas and work together towards a comprehensive view of the diverse phenomena at play. Compelled by these motivations, here we present a comprehensive overview of topological effects in systems ranging from DNA and genome organization to entangled proteins, polymeric materials, liquid crystals, and theoretical physics, with the intention of reducing the barriers between different fields of soft matter and biophysics. Particular care has been taken in providing a coherent formal introduction to the topological properties of polymers and of continuum materials and in highlighting the underlying common aspects concerning the emergence, characterization, and effects of topological objects in different systems. The second half of the review is dedicated to the presentation of the latest results in selected problems, specifically, the effects of topological constraints on the viscoelastic properties of polymeric materials; their relation with genome organization; a discussion on the emergence and possible effects of knots and other entanglements in proteins; the emergence and effects of topological defects and solitons in complex fluids. This review is dedicated to the memory of Marek Cieplak