Chirality of coiled coils: elasticity matters

Coiled coils are important protein-protein interaction motifs with high specificity that are used to assemble macromolecular complexes. Their simple geometric organization, consisting of alpha helices wrapped around each other, confers remarkable mechanical properties. A geometrical and mechanical continuous model taking into account sequence effects and based on the superhelical winding of the constituent helices is introduced, and a continuous family of solutions in which the oligomerization interactions are satisfied is derived. From these solutions, geometric and structural properties, such as the chirality and pitch of the coiled coil and the location of residues, are obtained. The theoretical predictions are compared to x-ray data from the leucine zipper motif.     

激光产生温稠密物质的微观动力学过程及状态诊断

随着大型激光装置的建立和精密测量技术的发展,强激光与固体相互作用成为实验室产生温稠密物质的一个重要手段。温稠密物质的结构复杂性、瞬态性和非平衡性给理论建模和实验测量带来了巨大挑战。本文系统介绍了激光产生温稠密物质的实验手段和理论模拟方法方面的重要进展,分析了其中的电子激发动力学、电子-离子能量弛豫过程、离子动力学等物理过程,总结了温稠密物质状态诊断的实验技术和理论方法,并论述了激光产生温稠密物质的发展趋势。     

First-principles investigation of the electronic, elastic and thermodynamic properties of VC under high pressure

An investigation of the electronic,elastic and thermodynamic properties of VC under high pressure has been conducted using first-principles calculations based on density functional theory (DFT) with the plane-wave basis set,as implemented in the CASTEP code. At elevated pressures,VC is predicted to undergo a structural transition from a relatively open NaCl-type structure to a more dense CsCl-type one. The predicted transition pressure is 520 GPa. The elastic constant,Debye temperature and heat capacity each as a function of pressure and/or temperature of VC are presented for the first time.     

On the dynamics of a continuum spin system

For a one-dimensional system of classical spins with nearest neighbour Heisenberg interaction we derive the equation of motion for each three-dimensional spin vector. In the continuum limit where the spins lie dense on a line this set of equations reduces to a nonlinear partial differential equation. In addition to spin-wave solutions we obtain some other special solutions of this equation. In particular we find solitary waves having total energy localised in a finite region, with velocity of propagation inversely proportional to the width of this region. Solutions of still another type are shown to have a diffusive character. The stability of such solutions and the possibility of interaction of two or more solitary waves have not yet been studied.     

Surface chemistry of the halogen-metal interface: The interaction of chlorine with ruthenium (100)

Chlorine adsorbs on Ru(100) with high efficiency; UPS, Δφ, TD, AES and LEED data suggest that the low pressure interaction ceases with the formation of a dense chemisorbed layer of atomic Cl. This overlayer desorbs exclusively as Cl(g) with an activation energy of ~ 220 $\text{kJ}\text{mol}$. The failure of the system to grow bulk halide and the absence of molecular chlorine and ruthenium-chlorine species in the desorption products are discussed in thermochemical terms. A series of four ordered surface structures evolves with increasing coverage, and structural models are proposed which are in good quantitative accord with the results from Auger spectroscopy. As coverage deceases, it seems likely that the overlayer relaxes by the growth of ordered vacancies rather than by uniform expansion along a preferred direction.     

Emergence of modularity and disassortativity in protein-protein interaction networks

In this paper, we present a simple evolution model of protein-protein interaction networks by introducing a rule of small-preference duplication of a node, meaning that the probability of a node chosen to duplicate is inversely proportional to its degree, and subsequent divergence plus nonuniform heterodimerization based on some plausible mechanisms in biology. We show that our model cannot only reproduce scale-free connectivity and small-world pattern, but also exhibit hierarchical modularity and disassortativity. After comparing the features of our model with those of real protein-protein interaction networks, we believe that our model can provide relevant insights into the mechanism underlying the evolution of protein-protein interaction networks.     

Thermodynamics of polystyrene solutions. I. Interaction parameters and polymer order

The Maron theory was used to deduce from mostly osmotic pressure and light-scattering data the interaction parameters as a function of concentration, temperature, and polymer molecular weight for solutions of polystyrene in seven different solvents. These interaction parameters were then utilized to calculate the activity coefficients of the solvent in more concentrated solutions for comparison with experimental values deduced from vapor pressure measurements. When order was absent in the polymers (all cases but two), the agreement between calculated and observed activity coefficients was found to be very good. In the two cases where order was present, the activity coefficients observed in the concentrated solutions were higher than those calculated. These deviations were employed to find the degree of polymer order both in solution and in the original polymers.     

Theoretical investigation of high-pressure phase transitions in Mg1-xSrxO

The stability of Mg_1-xSr_xO solid solution has been analyzed using charge transfer interaction potential (CTIP) model as well as density functional theory-based ab initio approach with Perdew–Burke–Ernzerhof (PBE) type parameterized generalized gradient approximation. The present CTIP model consists of long-range part as modified coulomb interactions and charge transfer forces whereas short-range part includes the van der Waals as well as Hafemeister Flygare type overlap repulsive interactions effective up to next nearest neighbor ions. The present study finds that under the influence of pressure host binary oxides as well as their solid solutions undergo B1→B2 structural phase transition in the pressure range of 54–495 GPa. The variation of ground state properties and transition pressures have also been analyzed as a function of Sr composition. The observed results for the end point members are in agreement to their experimental counterparts and the deviations have been discussed in terms of interactions taken into consideration in two approaches.     

Liquidlike behavior of supercritical fluids

The high frequency dynamics of fluid oxygen has been investigated by inelastic x-ray scattering, at high pressures and room temperature. In spite of the markedly supercritical conditions (T approximately 2Tc, P>10(2)Pc), the sound velocity exceeds the hydrodynamic value of about 20%, a feature which is the fingerprint of liquidlike dynamics. The comparison of the present results with literature data obtained in several fluids allow us to identify the extrapolation of the liquid-vapor-coexistence line in the (P/Pc, T/Tc) plane as the relevant edge between liquidlike and gaslike dynamics. More interestingly, this extrapolation is very close to the non-metal-metal transition in hot dense fluids, at pressure and temperature values as obtained by shock wave experiments. This result points to the existence of a connection between structural modifications and transport properties in dense fluids.     

A Green's Function Approach to the Shift of Spectral Lines in Dense Plasmas

Variations of the spectral lines in high dense ion plasmas with temperature and pressure may be characterized by the broadening as well as by the shift of spectral lines. For dense hydrogen- and alkali-plasmas (free carrier density larger than 10¹⁶/cm³) one of the possible mechanisms responsible for line profiles is considered to be the Coulomb interaction with free charged carriers. Using thermodynamic Green's functions, a systematic approach to the theory of spectral lines starting from the complex dielectric function is outlined. The line shift is derived from a perturbative treatment of the two-particle Green's function in the surrounding plasma. The shift of several lines proportional to the carrier density is evaluated as a function of the temperature and compared with experimental results.     

Experimental measurement of the acousto-electric interaction signal in saline solution

Acoustic pressure alters local electrical conductivity in tissues and solutions. This work concerns the measurement of electrical conductivity in a liquid which is subjected to an acoustic pressure field created by a focused transducer. Measurements were made with four electrodes positioned in the ultrasonic focal zone, and the signal concerned is referred to as the acousto-electric interaction signal. A solution of sodium chloride in a measurement cell was subjected to ultrasound pressures of upto 1 MPa. It was shown that it is possible to quantitate the acousto-electric interaction signal once the ultrasonic vibration potential due to the Debye effect has been subtracted. The acousto-electric interaction signal was shown to be directly proportional to both the applied acoustic pressure and current. For the measurement cell used in this work, the interaction factor was found to be 5.3 microVmA(-1) MPa(-1).     

Predicted novel high-pressure phases of lithium

Under high pressure, "simple" lithium (Li) exhibits complex structural behavior, and even experiences an unusual metal-to-semiconductor transition, leading to topics of interest in the structural polymorphs of dense Li. We here report two unexpected orthorhombic high-pressure structures Aba2-40 (40 atoms/cell, stable at 60-80 GPa) and Cmca-56 (56 atoms/cell, stable at 185-269 GPa), by using a newly developed particle swarm optimization technique on crystal structure prediction. The Aba2-40 having complex 4- and 8-atom layers stacked along the b axis is a semiconductor with a pronounced band gap >0.8 eV at 70 GPa originating from the core expulsion and localization of valence electrons in the voids of a crystal. We predict that a local trigonal planar structural motif adopted by Cmca-56 exists in a wide pressure range of 85-434 GPa, favorable for the weak metallicity.     

Stationary diffusion in the membrane systems with the ongoing reversible chemical reactions

The diffusion phenomena were analyzed using the phenomenological equations of the thermodynamics of irreversible processes. The diffusion coefficient was thought to be dependent on local concentrations and pressure, unlike it was done in the linear theories. The reversible chemical reactions were modeled as intermolecular interaction. The ideal and regular solutions and solutions, described by the Margules's and Sketchard–Hammer's equations, were investigated and analytical solutions were found.     

Phase transition in a strongly nonideal deuterium plasma generated by quasi-isentropical compression at megabar pressures

High-explosive driven generators of cylindrical and plane shock waves in D2 and H2 were used for the generation of warm and dense strongly nonideal matter with an intense interparticle interaction and Fermi statistics. Highly resolved flash x-ray diagnostics were used to measure the adiabatic plasma compressibility. The thermodynamic measurements demonstrated the 20% increase of density at megabar pressure, just in the density range, where the electrical measurements indicated a sharp--5 orders of magnitude--increase of electrical conductivity due to pressure ionization in strongly coupled plasmas.     

A study of the propagation of a quasistationary relativistic electron beam in a dense gas. II. Experimental studies

Results obtained from experimental studies of the interaction between a quasistationary electron beam (300 keV, 20 A, 500 sec, 0.3 cm) and a dense gas are presented. These investigations were carried out in air at atmospheric pressure and, for the purpose of modeling the propagation of a magnetostricted REB, at reduced pressure (3–300 torr). The rarefaction dynamics of a channel heated by the beam are studied and its maximum propagation distances in a dense gas are determined. The results obtained are compared with the theoretical model examined earlier.V. I. Lenin All-Union Institute of Electrical Engineering. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 34, No. 2, pp. 190–197, February, 1991.     

A TWO-DIMENSIONAL TCHEBYCHEFF COLLOCATION METHOD FOR THE STUDY OF THE VIBRATION OF A BAFFLED FLUID-LOADED RECTANGULAR PLATE

The vibration and the acoustic radiation of a baffled rectangular plate in contact with a dense fluid is considered. By using Green's representation theorem, the original system of differential equations governing both the displacement and the acoustic sound pressure is transformed into a system of coupled boundary integral equations. The unknown functions (the displacement of the plate, the pressure jump at the surface of the plate and the boundary sources) are expanded as series of Tchebycheff polynomials. The new unknowns (the coefficients of the series) are calculated by using a collocation method. Some results, both theoretical and numerical, are given concerning the resolution properties of the Tchebycheff approximation. The numerical difficulties are presented, and solutions of these are proposed. Numerical examples are given.     

结构声辐射的振动模态分析和声辐射模态分析研究

基于辐射声功率的二次型表达式,采用有限元法、Rayleigh积分和边界元法对结构声辐射进行了振动模态分析和声辐射模态分析研究。振动模态间的耦合对辐射声功率影响的研究表明:结构各阶振动模态自身对结构辐射声功率的贡献是增大结构的辐射声功率,而振动模态间的耦合可能会增大结构辐射声功率,也可能会减小结构辐射声功率,或对辐射声功率没有影响。而且,当振动模态间的耦合作用对辐射声功率的影响不大时,采用振动模态控制可取得较好的减振降噪双重控制效果。将混合的Helmholtz积分方程方法用广义逆引入到三维复杂结构声辐射分析的声辐射模态公式中,解决了特征频率下解不唯一问题。还研究了正方形封闭空间结构声辐射模态的辐射效率和形状,并对结构声辐射的振动模态控制和声辐射模态控制进行了讨论。     

Predicting disease-related genes by topological similarity in human protein-protein interaction network

Predicting genes likely to be involved in human diseases is an important task in bioinformatics field. Nowadays, the accumulation of human protein-protein interactions (PPIs) data provides us an unprecedented opportunity to gain insight into human diseases. In this paper, we adopt the topological similarity in human protein-protein interaction network to predict disease-related genes. As a computational algorithm to speed up the identification of disease-related genes, the topological similarity has substantial advantages over previous topology-based algorithms. First of all, it provides a global measurement of similarity between two vertices. Secondly, quantity which can measure new topological feature has been integrated into the notion of topological similarity. Our method is specially designed for predicting disease-related genes of single disease-gene family. The proposed method is applied to human protein-protein interaction and hepatocellular carcinoma (HCC) data. The results show a significant enrichment of disease-related genes that are characterized by higher topological similarity than other genes.     

The structure of MgO-SiO2 glasses at elevated pressure

The magnesium silicate system is an important geophysical analogue and neutron diffraction data from glasses formed in this system may also provide an initial framework for understanding the structure-dependent properties of related liquids that are important during planetary formation. Neutron diffraction data collected in situ for a single composition (38 mol% SiO(2)) magnesium silicate glass sample shows local changes in structure as pressure is increased from ambient conditions to 8.6 GPa at ambient temperature. A method for obtaining the fully corrected, total structure factor, S(Q), has been developed that allows accurate structural characterization as this weakly scattering glass sample is compressed. The measured S(Q) data indicate changes in chemical ordering with pressure and the real-space transforms show an increase in Mg-O coordination number and a distortion of the local environment around magnesium ions. We have used reverse Monte Carlo methods to compare the high pressure and ambient pressure structures and also compare the high pressure form with a more silica-poor glass (Mg(2)SiO(4)) that represents the approach to a more dense, void-free and topologically ordered structure. The Mg-O coordination number increases with pressure and we also find that the degree of continuous connectivity of Si-O bonds increases via a collapse of interstices.     

Counterion distribution and many-body interaction in charged dendrimer solutions

Coarse-grained molecular dynamics simulations are performed to study the structural formation, counterion distribution and effective interaction on charged dendrimers in an aqueous solution. In particular, the many-body effects in triplet systems are clarified. The conformation of a dendrimer molecule depends on the size of counterions, and the counterion distribution can be scaled by the gyration radius of a dendrimer molecule. Two-body and three-body interactions have been numerically investigated, and the results indicate both similarities and differences between dendrimer solutions and other soft colloidal systems, such as star polymer solutions.