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Marrink S.J.,Zernike Institute for Advanced Materials | Tieleman D.P.,University of Calgary
Chemical Society Reviews | Year: 2013

The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model. © 2013 The Royal Society of Chemistry.

van Oijen A.M.,Zernike Institute for Advanced Materials
Current Opinion in Biotechnology | Year: 2011

Single-molecule fluorescence techniques have emerged as powerful tools to study biological processes at the molecular level. This review describes the application of these methods to the characterization of the kinetics of interaction between biomolecules. A large number of single-molecule assays have been developed that visualize association and dissociation kinetics in vitro by fluorescently labeling binding partners and observing their interactions over time. Even though recent progress has been significant, there are certain limitations to this approach. To allow the observation of individual, fluorescently labeled molecules requires low, nanomolar concentrations. I will discuss how such concentration requirements in single-molecule experiments limit their applicability to investigate intermolecular interactions and how recent technical advances deal with this issue. © 2010 Elsevier Ltd.

Wilts B.D.,Zernike Institute for Advanced Materials
Proceedings. Biological sciences / The Royal Society | Year: 2012

The neotropical diamond weevil, Entimus imperialis, is marked by rows of brilliant spots on the overall black elytra. The spots are concave pits with intricate patterns of structural-coloured scales, consisting of large domains of three-dimensional photonic crystals that have a diamond-type structure. Reflectance spectra measured from individual scale domains perfectly match model spectra, calculated with anatomical data and finite-difference time-domain methods. The reflections of single domains are extremely directional (observed with a point source less than 5°), but the special arrangement of the scales in the concave pits significantly broadens the angular distribution of the reflections. The resulting virtually angle-independent green coloration of the weevil closely approximates the colour of a foliaceous background. While the close-distance colourful shininess of E. imperialis may facilitate intersexual recognition, the diffuse green reflectance of the elytra when seen at long-distance provides cryptic camouflage.

Mulder F.A.A.,University of Groningen | Filatov M.,Zernike Institute for Advanced Materials
Chemical Society Reviews | Year: 2010

In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the accuracy of different computational methods are discussed. It is anticipated that incorporating theoretical information on chemical shifts will increase the accuracy of protein structures, in the solid and liquid state alike, and extend the applicability of NMR spectroscopy to ever larger systems. © 2010 The Royal Society of Chemistry.

Greer J.R.,California Institute of Technology | De Hosson J.T.M.,Zernike Institute for Advanced Materials
Progress in Materials Science | Year: 2011

A material strength depends on its microstructure, which in turn, is controlled by an engineering process. Strengthening mechanisms like work hardening, precipitate, and grain boundary strengthening can alter the strength of a material in a predictive, quantitative manner and are readily linked to the deformation mechanism. This quantification strongly depends on the characteristic length scale of a particular microstructure, thereby dictating bulk material's strength as a function of, for example, grain or precipitate size, twin boundary spacing, or dislocation density. This microstructural, or intrinsic, size governs the mechanical properties and post-elastic material deformation at all sample dimensions, as the classical definition of "ultimate tensile strength" deems it to be "an intensive property, therefore its value does not depend on the size of the test specimen." Yet in the last 5 years, the vast majority of uniaxial deformation experiments and computations on small-scale metallic structures unambiguously demonstrated that at the micron and sub-micron scales, this definition no longer holds true. In fact, it has been shown that in single crystals the ultimate tensile strength and the yield strength scale with external sample size in a power law fashion, sometimes attaining a significant fraction of material's theoretical strength, and exhibiting the now-commonly-known phenomenon "smaller is stronger." Understanding of this "extrinsic size effect" at small scales is not yet mature and is currently a topic of rigorous investigations. As both the intrinsic (i.e. microstructural) and extrinsic (i.e. sample size) dimensions play a non-trivial role in the mechanical properties and material deformation mechanisms, it is critical to develop an understanding of their interplay and mutual effects on the mechanical properties and material deformation, especially in small-scale structures. This review focuses on providing an overview of metal-based material classes whose properties as a function of external size have been investigated and provides a critical discussion on the combined effects of intrinsic and extrinsic sizes on the material deformation behavior. © 2011 Elsevier Ltd. All rights reserved.

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