Inference of hidden structures in complex physical systems by multi-scale clustering

We survey the application of a relatively new branch of statistical physics--"community detection"-- to data mining. In particular, we focus on the diagnosis of materials and automated image segmentation. Community detection describes the quest of partitioning a complex system involving many elements into optimally decoupled subsets or communities of such elements. We review a multiresolution variant which is used to ascertain structures at different spatial and temporal scales. Significant patterns are obtained by examining the correlations between different independent solvers. Similar to other combinatorial optimization problems in the NP complexity class, community detection exhibits several phases. Typically, illuminating orders are revealed by choosing parameters that lead to extremal information theory correlations.Comment: 25 pages, 16 Figures; a review of earlier work

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase

DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA–Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA–Pol binary complex. The structure resembled existing crystal structures with regards to the downstream primer-template DNA substrate, and revealed a previously unobserved sharp bend (∼120°) in the DNA substrate; this pronounced bend was present in living cells. MD simulations and single-molecule assays also revealed that 4–5 nt of downstream gap-proximal DNA are unwound in the binary complex. Further, experiments and coarse-grained modelling showed the substrate alone frequently adopts bent conformations with 1–2 nt fraying around the gap, suggesting a mechanism wherein Pol recognises a pre-bent, partially-melted conformation of gapped DNA. We propose a general mechanism for substrate recognition by structure-specific enzymes driven by protein sensing of the conformational dynamics of their DNA substrates

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na +] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA

An Investigation into the Different Hardening Models in Reverse Forming of Thin Sheets

This paper discusses a finite element analysis of the Bauschinger effect in the reverse cup drawing process, taken from the NUMISHEET′99 (Gelin and Picart, 1999) benchmark. In order to study the Bauschinger effect, several hardening models are considered such as isotropic, kinematic, and combined forms in the linear and nonlinear cases, including the well-known Yoshida and Chaboche's model. The obtained results have been compared with some experimental results reported in literature. The various factors, namely, normalized axial stress, von Mises stress, and the punch forces, for both first and second stages have been calculated for different materials and thicknesses. Results show that the combined model had acceptable agreement with the empirical data through both stages, while the bilinear models did not show this effectiveness. Generally, the nonlinear kinematic and combined models lead to more accurate results

Numerical and field investigations of track dynamic behavior caused by light and heavy railway vehicles

Dynamic behavior of a track-train system is a function of axle loads and support stiffness because of non-linear supports. Therefore, it is expected that the support stiffness affects the behavior of the railway track during passing of a light or heavy car body. Since the effects of axle loads caused by light and heavy railway vehicles and support stiffness of ballasted railway tracks due to passing railway vehicles have not been studied adequately, therefore the present study focused on this issue. For this purpose, this issue was first investigated by passing a light and heavy car body including bogies with three axle loads as field tests. Then, numerical analyses of the railway track caused by the passing of these railway vehicles were studied, and the numerical results were compared with the field results. There was a good agreement between the values of field responses and numerical analyses. Subsequently, a series of sensitivity analyses on effects of the axle loads caused by light or heavy loading and support conditions was done on the ballasted railway track. The results indicated that the maximum vertical displacements increased by axle loads, increased sleeper distances and decreases support stiffness. Finally, equations of track behavior based on support stiffness and axle loads were derived

Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling

This chapter will provide an overview of how characterising free energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The landscapes for these complex systems are accessible through the use of accurate coarse-grained descriptions of DNA. Particular foci will be the landscapes associated with DNA self-assembly and mechanical deformation, where the latter can arise from either externally imposed forces or internal stresses

Development of fresh and fully recrystallized microstructures through friction stir processing of a rare earth bearing magnesium alloy

In the present study the friction stir processing (FSP), as an effective thermomechanical processing routine, has been conducted under the different rotational speeds on a solution treated rare earth bearing magnesium alloy. The various processing conditions result in a wide range of Zener-Holloman parameters to elaborate the desired microstructure in respect of the grain size. The obtained results indicate that applying the process on the primary solution treated material leads to the development of fully recrystallized microstructures, where the capability of refinement is directly affected through controlling the strain rate and temperature. In this regard, the resulting microstructures have been classified into "fresh and recrystallized" and "recrystallized and deformed" regions. The grain orientation speared (GOS) maps have also been employed to separate the recrystallized grains and deformed ones. Interestingly, the "recrystallized and deformed" microstructure holds a specified recrystallization texture, and exhibits unexpected hardenability during subsequent room temperature deformation. This is supported by Schmid factor analysis and fractography examinations revealing activation of basal slip and twinning systems in "recrystallized and deformed" microstructure.Web of Science775art. no. 13883