Screening of potential chemical marker with interspecific differences in Pterocarpus wood and a spatially-resolved approach to visualize the distribution of the characteristic markers.

Profiling the spatial distributions and tissue changes of characteristic compounds with interspecific differences is critical to elucidate the complex species identification during tree species traceability, wood anti-counterfeiting verification and timber trade control. In this research, in order to visualize the spatial position of characteristic compounds in two species with similar morphology (Pterocarpus santalinus and Pterocarpus tinctorius), a high coverage MALDI-TOF-MS imaging method was used to found the mass spectra fingerprints of different wood species. 2-Mercaptobenzothiazole matrix was used to spray wood tissue section to enhance the detection effect of metabolic molecules, and the mass spectrometry imaging data were obtained. Based on this technology, the spatial location of fifteen potential chemical markers with remarkable interspecific differences in 2 Pterocarpus timber species were successfully obtained. Distinct chemical signatures obtained from this method can promote rapid identification at the wood species level. Thus, matrix-assisted laser desorption/time-of-flight/ionization mass spectrometry imaging (MALDI-TOF-MSI) provides a spatial-resolved way for traditional wood morphological classification and breaking through the limitations of traditional wood identification technology.

Lignin Distribution on Cell Wall Micro-Morphological Regions of Fibre in Developmental Phyllostachys pubescens Culms.

Bamboo is a natural fibre reinforced composite with excellent performance which is, to a certain extent, an alternative to the shortage of wood resources. The heterogeneous distribution and molecular structure of lignin is one of the factors that determines its performance, and it is the key and most difficult component in the basic research into the chemistry of bamboo and in bamboo processing and utilization. In this study, the distribution of lignin components and lignin content in micro-morphological regions were measured in semi-quantitative level by age and radial location by means of visible-light microspectrophotometry (VLMS) coupled with the Wiesner and Maule reaction. There as guaiacyl lignin and syringyl lignin in the cell wall of the fibre. Lignin content of the secondary cell wall and cell corner increased at about 10 days, reached a maximum at 1 year, and then decreased gradually. From 17 days to 4 years, the lignin content of the secondary cell wall in the outer part of bamboo is higher than that in the middle part (which is, in turn, higher than that in the inner part of the bamboo). VLSM results of the micro-morphological regions showed that bamboo lignification developed by aging. Guaiacyl and syringl lignin units can be found in the cell wall of the fibre, parenchyma, and vessel. There was a difference in lignin content among different ages, different radial location, and different micro-morphological regions of the cell wall. The fibre walls were rich in guaiacyl lignin in the early stage of lignification and rich in syringyl units in the later stage of lignification. The guaiacyl and syringyl lignin deposition of bamboo green was earlier than that of the middle part of bamboo culm, and that of the middle part of bamboo culm was earlier than that of bamboo yellow. The single molecule lignin content of the thin layer is higher than that of thick layers, while the primary wall is higher than the secondary cell wall, showing that lignin deposition is consistent with the rules of cell wall formation. The obtained cytological information is helpful to understand the origin of the anisotropic, physical, mechanical, chemical, and machining properties of bamboo.

Modeling of flux, binding and substitution of urea molecules in the urea transporter dvUT.

Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model. To model the substitution of urea by the urea analogue N,N'-dimethylurea (DMU) in dvUT, we calculated the occupation probability of DMU along the urea pore and the ratio of the occupation probabilities of DMU at the external (Sext) and internal (Sint) binding sites, and we established the mutual substitution rule for binding and substitution of urea and DMU. Based on these calculations and modelings, together with the use of the Monte Carlo (MC) method, we further modeled the urea flux in dvUT, equilibrium urea binding to dvUT, and the substitution of urea by DMU in the dvUT. Our modeling results are in good agreement with the existing experimental functional data. Furthermore, the modelings have discovered the microscopic process and mechanisms of those functional characteristics. The methods and the results would help our future understanding of the underlying mechanisms of the diseases associated with impaired UT functions and rational drug design for the treatment of these diseases.

Computation and simulation of the structural characteristics of the kidney urea transporter and behaviors of urea transport.

Urea transporters are a family of membrane proteins that transport urea molecules across cell membranes and play important roles in a variety of physiological processes. Although the crystal structure of bacterial urea channel dvUT has been solved, there lacks an understanding of the dynamics of urea transport in dvUT. In this study, by using molecular dynamics simulations, Monte Carlo methods, and the adaptive biasing force approach, we built the equilibrium structure of dvUT, calculated the variation in the free energy of urea, determined the urea-binding sites of dvUT, gained insight into the microscopic process of urea transport, and studied the water permeability in dvUT including the analysis of a water chain in the pore. The strategy used in this work can be applied to studying transport behaviors of other membrane proteins.

Influences of mutations on the electrostatic binding free energies of chloride ions in Escherichia coli ClC.

Mutations in ClC channel proteins may cause serious functional changes and even diseases. The function of ClC proteins mainly manifests as Cl(-) transport, which is related to the binding free energies of chloride ions. Therefore, the influence of a mutation on ClC function can be studied by investigating the mutational effect on the binding free energies of chloride ions. The present study provides quantitative and systematic investigations on the influences of residue mutations on the electrostatic binding free energies in Escherichia coli ClC (EcClC) proteins, using all-atom molecular dynamics simulations. It was found that the change of the electrostatic binding free energy decreases linearly with the increase of the residue-chloride ion distance for a mutation. This work reveals how changes in the charge of a mutated residue and in the distance between the mutated residue and the binding site govern the variations in the electrostatic binding free energies and therefore influence the transport of chloride ions and conduction in EcClC. This work would facilitate our understanding of the mutational effects on transport of chloride ions and functions of ClC proteins and provide a guideline to estimate which residue mutations will have great influences on ClC functions.

Synthesis and properties of polyurethane foams prepared from heavy oil modified by polyols with 4,4'-methylene-diphenylene isocyanate (MDI).

The aim of the present study was to determine whether polyurethane (PU) foams can be prepared from heavy oil derived from biomass liquefaction. Since the hydroxyl number of the heavy oil was only 212 mg KOH/g, it was modified by polyols, and a hydroxyl number of 564.5 mg KOH/g was obtained. However, secondary hydroxyls rather than primary hydroxyls were introduced. As a result, when 10 wt.% activated heavy oil was added to bio-polyols, compressive strength of foams increased by 32% over that without the addition of heavy oil. When activated heavy oil wholly replaced polyethylene glycol 400, the high content of secondary hydroxyls depressed the foam reaction and resulted in partial dissociation of the heavy oil from the network structure and weakening of the thermal stability of the PU foams. Therefore, increasing the content of primary-hydroxyls by directional modification is necessary to make the process commercially feasible.

A three-state multi-ion kinetic model for conduction properties of ClC-0 chloride channel.

A three-state, multiion kinetic model was proposed to enable the conduction properties of the mammalian channel ClC-0 to be well characterized. Using this rate-theory based model, the current-voltage and conductance-concentration relations were obtained. The five parameters needed were determined by fitting the data of conduction experiments of the wild-type ClC-0 and its K519C mutant. The model was then tested against available calculation and simulation data, and the energy differences between distinct chloride-occupancy states computed agreed with an independent calculation on the binding free energies solved by using the Poisson-Boltzmann equation. The average ion number of conduction and the ion passing duration calculated closely resembled the values obtained from Brownian dynamics simulations. According to the model, the decrease of conductance caused by mutating residue K519 to C519 can be attributed to the effect of K519C mutation on translocation rate constants. Our study sets up a theoretical model for ion permeation and conductance in ClC-0. It provides a starting point for experimentalists to test the three-state model, and would help in understanding the conduction mechanism of ClC-0.

[FTIR analysis of products derived from wood liquefaction with 1-octanol].

Solvolysis is one of the important processes of biomass liquefaction. To produce superior quality liquid biofuel from biomass under mild conditions, it is essential to exploit novel reactive liquid solvent. Furthermore, the evaluation of liquefaction efficiency is carried out mainly by the means of analysis of the products derived from biomass liquefaction. In the present study, liquefaction of poplar wood powder in acidified 1-octanol was investigated with a stainless steel autoclave. Residue, heavy oil and light oil were separated from the liquefaction products by extraction with acetone and n-hexane successively. FTIR analysis was carried out on these liquefaction compositions to illuminate the liquefaction regularities and mechanisms of cellulose, hemicellulose and lignin of wood. The results showed that liquefaction oils were complex mixture containing hydroxide, carbonyl, methoxyl, aromatic and aether. Liquefactions of cellulose and hemicellulose were easier than that of lignin. Cellulose and hemicellulose were converted to light oil, however, lignin was mainly converted to heavy oil. At 150 degrees C, lignin was depolymerized and degraded into micromolecular aromatic compounds, among which condensation reactions took place when reaction temperature increased.

Cutoff variation induces different topological properties: a new discovery of amino acid network within protein.

An increasing attention has been dedicated to the characterization of complex networks within the protein world. Before now most investigations about protein structures were only considered where the interactive cutoff distance R(c)=5 or 7A. It is noteworthy that the length of peptide bond is about 1.5A, the length of hydrogen bond is about 3A, the range of London-van der Waals force is about 5A and the range of hydrophobic effect can reach to 12A in protein molecule. Present work reports a study on the topological properties of the amino acid network constructed by different interactions above. The results indicate that the small-world property of amino acid network constructed by the peptide and hydrogen bond, London-van der Waals force and the hydrophobic effect is strong, very strong and relatively weak, respectively. Besides, there exists a precise exponential relation C is proportional to k(-0.5) at R(c)=12A. It means that the amino acid network constructed by the hydrophobic effect tend to be hierarchical. Functional modules could be the cause for hierarchical modularity architecture in protein structures. This study on amino acid interactive network for different interactions facilitates the identification of binding sites which is strongly linked with protein function, and furthermore provides reasonable understanding of the underlying laws of evolution in genomics and proteomics.

Alternating morphology transitions in crystallization of NH4Cl on agar plates.

Two types of alternating morphology transitions have been observed in crystallization of NH4Cl on agar plates. One is the alternating morphology transitions between dense branching morphology and sparse branching morphology, and the other is the alternating morphology transitions between dense branching morphology and zigzag branching morphology. The appearance of them is found to depend on the mass proportion of agar to NH4Cl in the initial solution and the relative humidity. It is suggested that both the two alternating morphology transitions result from the oscillation of solute concentration in front of the growing interface caused by the competition of crystal growth and solute transfer at a moderate mass proportion. Which one of them occurs depends on the relative humidity, which controls the supersaturation.

Highly efficient avalanche multiphoton luminescence from coupled Au nanowires in the visible region.

We demonstrate highly efficient avalanche multiphoton luminescence (MPL) from ordered-arrayed gold nanowires (NWs) with low time-average excitation intensity, Iexc (5.0-9.1 kW/cm2). The intensity of avalanche MPL, IMPL, is about 10(4) times larger than that of three-photon luminescence, the slope partial differential log IMPL/ partial differential log Iexc of avalanche MPL reaches as high as 18.3, and the corresponding polarization dependence of IMPL has a form of cos50 phip. The emission dynamics of avalanche MPL and three-photon luminescence are also studied comparatively. These observations indicate that the highly efficient avalanche MPL is attributed to the giant enhancement and coupling of longitudinal surface plasmon resonance of ordered-arrayed gold NWs.

Particle-cluster aggregation on a small-world network.

To describe the aggregation behaviors on substrates with long-range jump paths, a model of particle-cluster aggregation on a two-dimensional small-world network is presented. This model is characterized by two parameters: the clustering exponent alpha and the long-range connection rate phi. The results show that there exists an asymptotic fractal dimension D(max)(f) that depends upon alpha. With decrement of alpha, D(max)(f) varies from 1.7 to 2.0, which corresponds to a crossover from diffusion-limited-aggregation-like to dense growth. The change of the aggregation pattern results from the long-range connection in the network, which reduces the effect of screening during the aggregation. When the system size is not large enough, the effective fractal dimension D(f) depends upon phi because of the finite-size effect. With primitive analysis, we obtain the expression of the effective fractal dimension D(f) with the network parameters alpha and phi.

Morphological evolution in the electrodeposition of the Pb-Sn binary system.

Morphological evolution in the electrodeposition of Pb-Sn binary system is studied. As the second component increases, the morphology of the codeposit changes from dendrite to ramification, to dense branch, and finally to fractal structure, respectively. The evolution arises from the influence of crystallographic texture, which leads to a splitting of dendritic tips and the formation of ramified morphology. This work provides direct evidence to explore the crystallographic influence on the morphological evolution in electrodeposition.

Critical behavior of efficiency dynamics in small-world networks.

Some dynamical processes in a small-world network shows a critical transition at a finite disorder phi(c) of the network, in contrast with the geometrical properties that exhibit the critical behavior at phi(c)=0. Although it has been pointed out in previous works that the transition is related to the structural properties of the network, it is still not very clear why the transition occurs at phi(c) not equal 0. In this paper we present a simple social model of efficiency dynamics in small-world networks, which also shows a transition at phi(c)>0. We obtain the critical point with phi(c) approximately equal 0.098 from the finite-size analysis. It is found that both the geometrical properties of the network and the specific dynamical characters of the model contribute to the critical transition. This work is useful for understanding this kind of transition occurring in many dynamical processes in small-world networks.

Network-induced nonequilibrium phase transition in the "game of Life".

A cellular automation model of the "game of Life" on a two-dimensional small-world network is presented in order to count in long-range interactions among living individuals in social or biological systems. The density of the life and its fluctuation are calculated, respectively. The present model exhibits a nonequilibrium phase transition from an "inactive-sparse" state to an "active-dense" one at a certain intermediate value of the network disorder. Employing finite-size scaling analysis, we estimate the location of the critical point with p(c)( infinity ) approximately 0.3685. The transition is of the "second-order" type with power-law diverging length. We obtain the critical exponents 1/nu approximately 1.70, beta approximately 0.50, and beta/nu approximately 0.85. The calculated results indicate that the present model may belong to the universality class of directed percolation.

Multiparticle random walks on a deformable medium.

Multiparticle random walks on a deformable medium have been investigated in (2+1) dimensions. The time evolution of the particle distribution is studied. The results show that the randomly distributed particles in the beginning will be self-organized into a cluster pattern in the intermediate stage, and then return to the random distribution pattern in the late stage. The dependence of the clustering degree on the stiffness parameter of medium alpha, stability parameter of systems beta, and average particle density rho(0) is also investigated. There exists an optimal clustering stability beta(p), at which the system has the strongest clustering ability and corresponds to a maximum clustering coefficient Gamma(*)(p). The dependence of the optimal clustering coefficient Gamma(*)(p) on the stiffness alpha and particle density rho(0) is obtained, and the landscape of the medium generated by particles is also investigated.

Patterns of particle distribution in multiparticle systems by random walks with memory enhancement and decay.

We investigate the pattern of particle distribution and its evolution with time in multiparticle systems using the model of random walks with memory enhancement and decay. This model describes some biological intelligent walks. With decrease in the memory decay exponent alpha, the distribution of particles changes from a random dispersive pattern to a locally dense one, and then returns to the random one. Correspondingly, the fractal dimension D(f,p) characterizing the distribution of particle positions increases from a low value to a maximum and then decreases to the low one again. This is determined by the degree of overlap of regions consisting of sites with remanent information. The second moment of the density rho(2) was introduced to investigate the inhomogeneity of the particle distribution. The dependence of rho(2) on alpha is similar to that of D(f,p) on alpha. rho(2) increases with time as a power law in the process of adjusting the particle distribution, and then rho(2) tends to a stable equilibrium value.

Directed random walks in continuous space.

The investigation on diffusion with directed motion in a two-dimensional continuous space is completed by using the model of the continuous directed random walks. The average square end-to-end distance approximately t(2nu) is calculated. The results show that this type of walks belongs asymptotically to the same class (nu=1.0) as the ballistic motions. For short time, we observe a crossover from purely random walks (nu=0.5) to ballistic motions (nu=1.0). The dependence of the crossover on the direction parameter theta is studied. There exists a scaling relation of the form approximately tf(t/theta(-2)). The return probability P00(t) is also investigated and the scaling form similar to is obtained.

Pattern formation on nonuniform surfaces by correlated random sequential absorptions.

The pattern formation on nonuniform surfaces by correlated-random sequential absorption (CRSA) process has been investigated by computer simulations. The nonuniform surfaces are represented by percolation clusters with probabilities p(s) and p(s) stands for the nonuniform degree of surfaces. The interactions between the particles and the defects in surfaces are involved by introducing a sticking coefficient s. When s-->0, the CRSA process is controlled by the absorption of surfaces and the correlation between particles. With the correlation increasing from a weak limit to a strong one, the cluster consisting of absorbed particles changes from the dispersed pattern of site percolation to correlated percolation, and then to Leath percolation clusters. When s-->1 and p(s)-->p(c), the CRSA process is dominated by the absorption of the defects, where p(c) is the threshold of percolations. The patterns appear randomly dispersed in spite of the correlation. With the decrease of s and increase of p(s), the interaction controlling the CRSA process changes from the absorption of defects to that of surface and the correlation between particles gradually. For the system s-->0, the transition correlation exponent alpha(c)=d(s), where d(s) is the fractal dimension of the percolation surfaces.

Random walk with memory enhancement and decay.

A model of random walk with memory enhancement and decay was presented on the basis of the characteristics of the biological intelligent walks. In this model, the movement of the walker is determined by the difference between the remaining information at the jumping-out site and jumping-in site. The amount of the memory information s(i)(t) at a site i is enhanced with the increment of visiting times to that site, and decays with time t by the rate e(-beta(t)), where beta is the memory decay exponent. When beta=0, there exists a transition from Brownian motion (BM) to the compact growth of walking trajectory with the density of information energy u increasing. But for beta>0, this transition does not appear and the walk with memory enhancement and decay can be considered as the BM of the mass center of the cluster composed of remembered sites in the late stage.