Excited States Computation of Models of Phenylalanine Protein Chains: TD-DFT and Composite CC2/TD-DFT Protocols

The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides. In contrast, only a qualitative agreement was met for the corresponding adiabatic zero-point vibrational energy (ZPVE)-corrected excitation energies. Two composite protocols combining CC2 and DFT/TD-DFT methods were then developed to improve these calculations. Both protocols substantially reduced the error compared to CC2 and experiment, and the best of both even led to results of CC2 quality at a lower cost, thus providing a reliable alternative to this method for very large systems.     

On finite-element implementation strategies of Schapery-type constitutive theories

This paper presents two new strategies for implementing Schapery-type nonlinearly viscoelastic constitutive theories into finite element codes. The first strategy uses the original differential equations that lead to the integral formulation of Schapery-type constitutive theories and Finite Difference (FD) schemes. This strategy is quite different from all the other strategies found in the literature. The second strategy is an improvement of recursive strategies, used by many authors, based on the integral formulation of the constitutive theory. The performances of the new algorithms are compared with those of existing strategies for various load histories and nonlinearities. It is shown that the newly developed strategy based on FD schemes can exhibit quadratic convergence rate when one time step is stored and 4th order convergence rate when two time steps are stored, which is a major improvement over the recursive strategies.     

Engineered Extracellular Matrices as Biomaterials of Tunable Composition and Function

Engineered and decellularized extracellular matrices (ECM) are receiving increasing interest in regenerative medicine as materials capable to induce cell growth/differentiation and tissue repair by physiological presentation of embedded cues. However, ECM production/decellularization processes and control over their composition remain primary challenges. This study reports engineering of ECM materials with customized properties, based on genetic manipulation of immortalized and death‐inducible human mesenchymal stromal cells (hMSC), cultured within 3D porous scaffolds under perfusion flow. The strategy allows for robust ECM deposition and subsequent decellularization by deliberate cell‐apoptosis induction. As compared to standard production and freeze/thaw treatment, this grants superior preservation of ECM, leading to enhanced bone formation upon implantation in calvarial defects. Tunability of ECM composition and function is exemplified by modification of the cell line to overexpress vascular endothelial growth factor alpha (VEGF), which results in selective ECM enrichment and superior vasculature recruitment in an ectopic implantation model. hMSC lines culture under perfusion‐flow is pivotal to achieve uniform scaffold decoration with ECM and to streamline the different engineering/decellularization phases in a single environmental chamber. The findings outline the paradigm of combining suitable cell lines and bioreactor systems for generating ECM‐based off‐the‐shelf materials, with custom set of signals designed to activate endogenous regenerative processes.     

Multi-Material 3D Microprinting of Magnetically Deformable Biocompatible Structures

Two-photon polymerization (2PP) allows precise 3D printing at the micrometer scale, and by associating it with magnetic materials, the creation of remotely actuatable micro-structures. Such structures attract a growing interest for biomedical applications, thanks to their size and to the biocompatibility of some photoresist materials. Gelatin methacryloyl (Gel-MA) is one such material, and can be used to create physiological scaffolds for cell culture. Here, the physico-chemical properties of two resins are exploited, the first being a silica-based hybrid polymer, the OrmoComp, and the second a Gel-MA-based hydrogel. A 2PP manufacturing protocol is defined and designed to print both materials in succession as a single structure, which is then linked to a neodymium-iron-boron (NdFeB) magnetic bead for actuation. By this combination, a magnetically deformable 3D culture substrate is created to study cells in an environment that mimics soft, curved, and dynamic properties of tissues in vivo. The structure is actuated via an external magnetic field and bends back and forth along its longest axis. Lastly, preliminary cell culture trials are conducted showing the proliferation of cells on the structures.     

WideEffHunter: An Algorithm to Predict Canonical and Non-Canonical Effectors in Fungi and Oomycetes

Newer effectorome prediction algorithms are considering effectors that may not comply with the canonical characteristics of small, secreted, cysteine-rich proteins. The use of effector-related motifs and domains is an emerging strategy for effector identification, but its use has been limited to individual species, whether oomycete or fungal, and certain domains and motifs have only been associated with one or the other. The use of these strategies is important for the identification of novel, non-canonical effectors (NCEs) which we have found to constitute approximately 90% of the effectoromes. We produced an algorithm in Bash called WideEffHunter that is founded on integrating three key characteristics: the presence of effector motifs, effector domains and homology to validated existing effectors. Interestingly, we found similar numbers of effectors with motifs and domains within two different taxonomic kingdoms: fungi and oomycetes, indicating that with respect to their effector content, the two organisms may be more similar than previously believed. WideEffHunter can identify the entire effectorome (non-canonical and canonical effectors) of oomycetes and fungi whether pathogenic or non-pathogenic, unifying effector prediction in these two kingdoms as well as the two different lifestyles. The elucidation of complete effectoromes is a crucial step towards advancing effectoromics and disease management in agriculture.     

Structural studies of the phase separation in the UO2–PuO2–Pu2O3 ternary system

In the oxygen hypo-stoichiometric range of (U_1?yPu_y)O_2?x mixed oxide MOX fuels, the U–Pu–O phase diagram is known to exhibit a large biphasic domain depending on the Pu content. However, the phase equilibria are still to be fully described as various representations are proposed in the literature.In the present work, we notify new insights into the phase separation occurring in the UO₂–PuO₂–Pu₂O₃ domain at room temperature. Our microstructural and X-ray diffraction results are compared to the different representations reported in the literature. We provide, for the first time in the hypo-stoichiometric domain, an indisputable experimental observation of a triphasic region at high Pu content, composed of two fluorite-type structures and of one α-Pu₂O₃ sesquioxyde type structure. These results are in contradiction with previous experimental representations of the U–Pu–O ternary system.     

A Coupled Euler-Lagrange Model for More Realistic Simulation of Debris Denting in Rolling Element Bearings

Abstract

The objective of this study is to investigate the effects of the contamination of lubricants on denting in rolling element bearings. A dynamic, explicit finite element model (FEM) is developed to reproduce and analyse the elastic–plastic response of the surfaces when a spherical particle passes through a heavily loaded contact area. To cope with mesh distortion issues due to the high deformation of the debris along the process, a novel Eulerian approach is used to model the particle. A parametric study is conducted with the coupled Euler-Lagrange (CEL) model to determine the influence of the debris size, bearing loading, friction coefficient, material properties, and relative sliding between the surfaces on the indentation features. The FEM results emphasize the major role of the material properties of the three bodies on the dent geometry, pointing out that the softer surface undergoes more severe damage. In the same way, the protection of one of the surfaces by a specific heat treatment such as nitriding leads to more severe damage on the other one. The results exhibit a direct link between the particle and dent sizes. For large particles, a change in the dent geometry is observed when the deformed particle size overcomes the contact width because the particle is no longer enclosed in the contact and is therefore spread more easily. The model reproduces two important aspects of the indentation in rolling element bearings, which are the asymmetry of the dent and the residual stresses distribution, providing interesting prospects for future work on the fatigue failure caused by these defects.     

Finger pad friction and its role in grip and touch

Many aspects of both grip function and tactile perception depend on complex frictional interactions occurring in the contact zone of the finger pad, which is the subject of the current review. While it is well established that friction plays a crucial role in grip function, its exact contribution for discriminatory touch involving the sliding of a finger pad is more elusive. For texture discrimination, it is clear that vibrotaction plays an important role in the discriminatory mechanisms. Among other factors, friction impacts the nature of the vibrations generated by the relative movement of the fingertip skin against a probed object. Friction also has a major influence on the perceived tactile pleasantness of a surface. The contact mechanics of a finger pad is governed by the fingerprint ridges and the sweat that is exuded from pores located on these ridges. Counterintuitively, the coefficient of friction can increase by an order of magnitude in a period of tens of seconds when in contact with an impermeably smooth surface, such as glass. In contrast, the value will decrease for a porous surface, such as paper. The increase in friction is attributed to an occlusion mechanism and can be described by first-order kinetics. Surprisingly, the sensitivity of the coefficient of friction to the normal load and sliding velocity is comparatively of second order, yet these dependencies provide the main basis of theoretical models which, to-date, largely ignore the time evolution of the frictional dynamics. One well-known effect on taction is the possibility of inducing stick–slip if the friction decreases with increasing sliding velocity. Moreover, the initial slip of a finger pad occurs by the propagation of an annulus of failure from the perimeter of the contact zone and this phenomenon could be important in tactile perception and grip function.