Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

The determination of a protein''s folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues'' side chains form a tight interaction network within the protein''s core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.     

Prediction of brittle-to-ductile transitions in polystyrene

In this study it is attempted to predict brittle-to-ductile transitions (BDTs) in polystyrene blends, induced either by an increase in temperature or by a decrease in inter-particle distance. A representative, two-dimensional volume element (RVE) of a polystyrene matrix with 20% circular voids, is deformed in tension. During deformation a hydrostatic-stress based craze-nucleation criterion [1] is evaluated. The simulations demonstrate that crazes initiate at low temperatures while a transition from crazing to shear yielding (BDT) is found around 75 °C. The numerical results correlate well with tensile tests on similar heterogeneous polystyrene. The presence of an absolute length, as experimentally found, is more difficult to explain. Near a free surface a T_g-depression is measured for polystyrene and also the resistance to indentation in polystyrene is lower than expected from bulk properties. Both observations are rationalised by an enhanced segmental mobility of chains near a free surface. As a consequence of these findings, an absolute length-scale could be incorporated in the numerical simulations. For simplicity, the length-scale is modelled by taking a temperature gradient over a thin layer near the internal free surfaces of the RVE. Deformation of the RVE with different absolute length-scales shows that indeed also the experimentally found brittle-to-ductile transition can be predicted if the ligament thickness between the inclusions (‘voids’) in polystyrene is below a critical value of ca. 15 nm.     

Dynamic crack propagation with cohesive elements: a methodology to address mesh dependency

In this paper, two brittle fracture problems are numerically simulated: the failure of a ceramic ring under centrifugal loading and crack branching in a PMMA strip. A three‐dimensional finite element package in which cohesive elements are dynamically inserted has been developed. The cohesive elements' strength is chosen to follow a modified weakest link Weibull distribution. The probability of introducing a weak cohesive element is set to increase with the cohesive element size. This reflects the physically based effect according to which larger elements are more likely to contain defects. The calculations illustrate how the area dependence of the Weibull model can be used to effectively address mesh dependency. On the other hand, regular Weibull distributions have failed to reduce mesh dependency for the examples shown in this paper. The ceramic ring calculations revealed that two distinct phenomena appear depending on the magnitude of the Weibull modulus. For low Weibull modulus, the fragmentation of the ring is dominated by heterogeneities. Whereas many cracks were generated, few of them could propagate to the outer surface. Monte Carlo simulations revealed that for highly heterogeneous rings, the number of small fragments was large and that few large fragments were generated. For high Weibull modulus, signifying that the ring is close to being homogeneous, the fragmentation process was very different. Monte Carlo simulations highlighted that a larger number of large fragments are generated due to crack branching. Copyright © 2003 John Wiley & Sons, Ltd.     

Hydrothermal Reaction Mechanism and Pathway for the Formation of K2Ti6O13 Nanowires

Calculations and detailed first principle and thermodynamic analyses have been performed to understand the formation mechanism of K₂Ti₆O₁₃ nanowires (NWs) by a hydrothermal reaction between bulk Na₂Ti₃O₇ crystals and a KOH solution. It is found that direct ion exchange between K⁺ and Na⁺ plus H⁺ interactions with [TiO₆] octahedra in Na₂Ti₃O₇ promote the formation of an intermediate H₂K₂Ti₆O₁₄ phase. The large lattice mismatch between this intermediate phase and the bulk Na₂Ti₃O₇ structure, and the large energy reduction associated with the formation of this intermediate phase, drive the splitting of the bulk crystal into H₂K₂Ti₆O₁₄ NWs. However, these NWs are not stable because of large [TiO₆] octahedra distortion and are subject to a dehydration process, which results in uniform K₂Ti₆O₁₃ NWs with narrowly distributed diameters of around 10 nm.     

Analysis of S-SEED''s characteristics in optical switch

This article introduces the basic structure of a symmetric self-electrooptic effect device （S-SEED）, and applies the Kirchoff＇ s current law and a purely equivalent capacitive model, to analyze S-SEED＇s switch characteristics. Linear approximation and N-segment approximation are utilized to obtain S-SEED＇s voltage-time （V-T） and characteristics. Theoretical analysis is verified by simulations, and the results demonstrate that the precision of S-SEED＇s switch time can satisfy the requirement in applications with linear approximation. Moreover, the simulations compare S-SEED＇s switch characteristics with different input powers and input contrast ratios, which reveal that increasing input contrast ratio is an effective way to improve S-SEED＇s switch characteristics.     

Self-Irradiation Cascade Simulations in Plutonium Metal: Model Behavior at High Energy

The Modified Embedded Atom Method model for Pu metal is revised so that it more accurately captures the behavior of the Ziegler-Biersack-Littmark model of ion-ion interactions. Two revision are tested with somewhat different stiffnesses in the 2-1000 eV range. The revised models show higher damage levels at 20 KeV than an earlier model, suggesting that the behavior of the models above 100 eV is dominating damage production, at least in the earlier stages of the cascade. Work was performed at Los Alamos National Laboratory under the auspices of the US Department of Energy, under contract DE-AC52-06NA25396.     

Computer simulation of the effective double layer occurring on a catalyst surface under electro-chemical promotion conditions

In this work, the structural and energetic properties of two typical catalytic surfaces, Na/Pt(111) and O/Pt(111), are studied by means of quantum mechanical calculations and Monte Carlo Grand Canonical simulations. The simulations were performed with electrostatic potentials at different truncation schemes. In order to elucidate the modification of catalyst surfaces produced by the backspillover of ionic species onto Pt(111), the electrostatic field at the interface due to the electric double layer was also analyzed.     

Surface adsorption of comb polymers by Monte Carlo simulations

This paper reports off-lattice Monte Carlo simulations of highly-branched comb homopolymers weakly adsorbed on a flat, featureless surface showing only covolume and dispersion interactions with the adsorbate. A minimal coarse-grained model, described by hard spheres connected by harmonic springs, was employed. The interaction energy of the adsorbed combs and linear chains is first discussed as a function of the molecular mass and of the number of beads in contact with the surface. The molecular size is then investigated as a function of backbone length and branching density at a fixed arm size. The apparent swelling exponents of the adsorbed combs are larger than those of the corresponding linear chains, and much larger than that of the free molecules. This result indicates a surface-induced stiffening of the comb backbone, further studied through the persistence length l_pers. It is found that l_pers increases upon adsorption over the free-molecule value, more so the larger is the branching density. Finally, the thickness of the adsorbed layer, the surface-induced molecular anisotropy and the molecular aspect ratio are investigated as a function of branching density and molecular mass.     

Environmental assessment of an uncontrolled sanitary landfill,Pocos de Caldas,Brazil

There are more than 20,000 uncontrolled sanitary landfill areas in Brazil. The paper reports an integrated study undertaken to develop an environmental assessment of the uncontrolled sanitary landfill area of the city of Po?os de Caldas, State of Minas Gerais, Brazil. A number of remedial alternatives were evaluated. The USGS modular 3D finite difference groundwater flow model (Modflow) and Modular 3D Finite Difference Mass Transport Model (MT3D) software were used to simulate groundwater flow and contaminant transport modelling, as well as to predict changes due to the proposed remediation measures. The remedial alternatives considered for normal conditions from 20 to 40 year periods were waste removal, vertical cut-off barriers, extraction wells and top capping. The results indicated that extraction wells and waste removal are the best alternatives because they significantly reduce both the extension and levels of the contamination plume even after 5 years. The extraction well proved a less expensive remedial alternative than waste removal.