Significant Residue Features Revealed By Eigenvalue Decomposition Analysis Of Blosum Matrices

Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI approximate to 45%. Residue hydrophobicity is a feature governing residue substitution as SI >= 45%. Whereas below this SI level, residue volume is a dominant feature. (C) 2007 Elsevier B.V. All rights reserved.

Deformation Behavior Of Fe-Based Bulk Metallic Glass During Nanoindentation

Fe-based bulk metallic glasses (BMGs) normally exhibit super high strength but significant brittleness at ambient temperature. Therefore, it is difficult to investigate the plastic deformation behavior and mechanism in these alloys through conventional tensile and compressive tests due to lack of distinct macroscopic plastic strain. In this work, the deformation behavior of Fe52Cr15Mo9Er3C15B6 BMG was investigated through instrumented nanoindentation and uniaxial compressive tests. The results show that serrated flow, the typical plastic deformation feature of BMGs, could not be found in as-cast and partially crystallized samples during nanoindentation. In addition, the deformation behavior and mechanical properties of the alloy are insensitive to the applied loading rate. The mechanism for the appearance of the peculiar deformation behavior in the Fe-based BMG is discussed in terms of the temporal and spatial characteristics of shear banding during nanoindentation.

New Deformation Twinning Mechanism Generates Zero Macroscopic Strain In Nanocrystalline Metals

Macroscopic strain was hitherto considered a necessary corollary of deformation twinning in coarse-grained metals. Recently, twinning has been found to be a preeminent deformation mechanism in nanocrystalline face-centered-cubic (fcc) metals with medium-to-high stacking fault energies. Here we report a surprising discovery that the vast majority of deformation twins in nanocrystalline Al, Ni, and Cu, contrary to popular belief, yield zero net macroscopic strain. We propose a new twinning mechanism, random activation of partials, to explain this unusual phenomenon. The random activation of partials mechanism appears to be the most plausible mechanism and may be unique to nanocrystalline fcc metals with implications for their deformation behavior and mechanical properties.

On the mechanism of void growth and the effect of straining mode in ductile materials

Finite element analysis is employed to investigate void growth embedded in elastic-plastic matrix material. Axisymmetric and plane stress conditions are considered. The simulation of void growth in a unit cell model is carried out over a wide range of triaxial tensile stressing or large plastic straining for various strain hardening materials to study the mechanism of void growth in ductile materials. Triaxial tension and large plastic strain encircling around the void are found to be of most importance for driving void growth. The straining mode of incremental loading which favors the necessary strain concentration around void for its growth can be characterized by the vanishing condition of a parameter called "the third invariant of generalized strain rate". Under this condition, it accentuates the internal strain concentration and the strain energy stored/dissipated within the material layer surrounding the void. Experimental results are cited to justify the effect of this loading parameter. (C) 2000 Elsevier Science Ltd. All rights reserved.

Investigation on mechanical properties and size effect of nanocrystalline twin copper

The stress-strain relations of nanocrystalline twin copper with variously sized grains and twins are studied by using FEM simulations based on the conventional theory of mechanism-based strain gradient plasticity (CMSG). A model of twin lamellae strengthening zone is proposed and a cohesive interface model is used to simulate grain-boundary sliding and separation. Effects of material parameters on stress-strain curves of polycrystalline twin copper are studied in detail. Furthermore, the effects of both twin lamellar spacing and twin lamellar distribution on the stress-strain relations are investigated under tension loading. The numerical simulations show that both the strain gradient effect and the material hardening increase with decreasing the grain size and twin lamellar spacing. The distribution of twin lamellae has a significant influence on the overall mechanical properties, and the effect is reduced as both the grain size and twin lamellar spacing decrease. Finally, the FEM prediction results are compared with the experimental data.

Multi-scale analysis of AFM tip and surface interactions

Thoroughly understanding AFM tip-surface interactions is crucial for many experimental studies and applications. It is important to realize that despite its simple appearance, the system of tip and sample surface involves multiscale interactions. In fact, the system is governed by a combination of molecular force (like the van der Waals force), its macroscopic representations (such as surface force) and gravitational force (a macroscopic force). Hence, in the system, various length scales are operative, from sub-nanoscale (at the molecular level) to the macroscopic scale. By integrating molecular forces into continuum equations, we performed a multiscale analysis and revealed the nonlocality effect between a tip and a rough solid surface and the mechanism governing liquid surface deformation and jumping. The results have several significant implications for practical applications. For instance, nonlocality may affect the measurement accuracy of surface morphology. At the critical state of liquid surface jump, the ratio of the gap between a tip and a liquid dome (delta) over the dome height (y(o)) is approximately (n-4) (for a large tip), which depends on the power law exponent n of the molecular interaction energy. These findings demonstrate that the multiscale analysis is not only useful but also necessary in the understanding of practical phenomena involving molecular forces. (c) 2007 Elsevier Ltd. All rights reserved.

The mechanism of pattern selection in coupled map lattices

The pattern selection of one-dimensional coupled map lattices is studied in this paper. It is shown by spatiotemporal variable separation that there exists a threshold wavelength in pattern selection which possesses wave-like structures in space and periodic chaotic motion in time.

Experimental-study on the criteria and mechanism of spallation in an aluminum-alloy

In this paper, a damage function defined by the residual strength of spalled specimens of an aluminium alloy is given to characterize the spallation of the material. Based on this function a simple method for continuously describing the spallation may be developed. Stress wave profiles showing the signal of spallation were successfully obtained with carbon gauges. Microscopic observations of the spalled aluminium alloy specimens reveal that the nucleation of spallation initiates from cracking of the second phase particles. Spallation is a process of crack nucleation, growth and coalescence to final, complete disintegration.

A study of the mechanism of consolidating metal-powder under explosive-implosive shock-waves

A study of the two-dimensional flow pattern of particles in consolidation process under explosive-implosive shock waves has been performed to further understand the mechanism of shock-wave consolidation of metal powder, in which bunched low-carbon steel wires were used instead of powder. Pressure in the compact ranges from 6 to 30 GPa. Some wires were electroplated with brass, some pickled. By this means, the flow pattern at particle surfaces was observed. The interparticle bonding and microstructure have been investigated systematically for the consolidated specimens by means of optical and electron microscopy, as well as by microhardness. The experimental results presented here are qualitatively consistent with Williamson's numerical simulation result when particle arrangement is close packed, but yield more extensive information. The effect of surface condition of particle on consolidation quality was also studied in order to explore ways of increasing the strength of the compacts. Based on these experiments, a physical model for metal powder shock consolidation has been established.

Excitation mechanism of thermocapillary oscillatory convection

It is suggested that the oscillation of thermocapillary convection may be excited by the buoyancy instability. By means of numerical simulation of the finite-element method, the temperature distributions in the liquid bridge are qualitatively analyzed. The temperature gradient in a certain flow region of liquid bridge may turn to be parallel to the direction of gravity when the temperature difference △T between two boundary rods of liquid bridge is larger than the critical value. The buoyancy instability may be excited, and then the thermocapillary oscillatory convection appears, as the temperature difference increases further. The distribution of the critical Marangoni number in the micro-gravity environment is derived from the data on the ground experiments. The results show that the onset of thermocapillary oscillatory convection is delayed in the case of smaller typical scale of liquid bridge and lower gravity environment.

The mechanism of energy storage by shearing the solar magnetic field

In this paper, a complete set of MHD equations have been solved by numerical calculations in an attempt to study the dynamical evolutionary processes of the initial equilibrium configuration and to discuss the energy storage mechanism of the solar atmosphere by shearing the magnetic field. The initial equilibrium configuration with an arch bipolar potential field obtained from the numerical solution is similar to the configuration in the vicinity of typical solar flare before its eruption. From the magnetic induction equation in the set of MHD equations and dealing with the non-linear coupling effects between the flow field and magnetic field, the quantitative relationship has been derived for their dynamical evolution. Results show that plasma shear motion at the bottom of the solar atmosphere causes the magnetic field to shear; meanwhile the magnetic field energy is stored in local regions. With the increase of time the local magnetic energy increases and it may reach an order of 4×10^25 J during a day. Thus the local storage of magnetic energy is large enough to trigger a big solar flare and can be considered as the energy source of solar flares. The energy storage mechanism by shearing the magnetic field can well explain the slow changes in solar active regions.

The dynamical process of a coronal transient associated with an eruptive prominence .1. Basic mechanism

The statistical correlation between an eruptive prominence and the coronal transient associated with this prominence implies that there should be a relationship between these two kinds of dynamical processes. This paper analyzes the dynamical effect of a plasma

A unified law of motion of lithospheric plates and the driving mechanism

From observed data on lithospheric plates, a unified empirical law for plate motion,valid for continental as well as oceanic plates, is obtained in the following form: The speedof plate motion U depends linearly on a geometric parameter T_d, ratio of the sum of effectiveridge length and trench arc length to the sum of area of continental part of plate and total areaof cold sinking slab. Based on this unified law, a simple mechanical analysis shows that, themain driving forces for lithospheric plates come from push along the mid-ocean ridge andpull by the cold sinking slab, while the main drag forces consist of the viscous traction beneaththe continental part of plate and over both faces of the sinking slab. Moreover, the specific-push along ridge and pull by slab are found to be of equal magnitude.

The permanence of density waves of galaxy and the numerical investigation of waser mechanism

This paper deals with in detail the permanence of the spiral structure of galaxies andthe characters of waser mechanism. A simplified model of galaxy is adopted. Variousdynamical characters of density waves are studied using numerical calculation method. Theresults verify very well the switch character f waser and the tunnel effect of density wavesat the potential barrier of corotation circle as is shown in a previous work of the author.

High-speed streams from coronal holes and the accelerating mechanism of the solar-wind

In this paper, the general Mach number equation is derived, and the influence of typical energy forms in the solar wind is analysed in detail. It shows that the accelerating process of the solar wind is influenced critically by the form of heating in the corona, and that the transonic mechanism is mainly the result of the adjustment of the variation of the crosssection of flowing tubes and the heat source term.The accelerating mechanism for both the high-speed stream from the coronal hole and the normal solar wind is similar. But, the temperature is low in the lower level of the coronal hole and more heat energy supply in the outside is required, hence the high speed of the solar wind; while the case with the ordinary coronal region is just the opposite, and the velocity of the solar wind is therefore lower. The accelerating process for various typical parameters is calculated, and it is found that the high-speed stream may reach 800 km/sec.