Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Effects of polar group saturation on physical gelation of Amphiphilic polymer solutions

Monte Carlo simulation on the basis of the comblike coarse grained nonpolar/polar (NP) model has been carried out to study the polar group saturation effect on physical gelation of amphiphilic polymer solutions. The effects of polar group saturation due to hydrogen bonding or ion bridging on the sol-gel phase diagram, microstructure of aggregates, and chain conformation of amphiphilic polymer solutions under four different solvent conditions to either the nonpolar backbone or the polar side chain in amphiphilic polymer chains have been investigated. It is found that an increase of polar group saturation results in a monotonically decreased critical concentration of gelation point, which can be qualitatively supported by the dynamic theological measurements on pectin aqueous solutions. Furthermore, various solvent conditions to either the backbone or the side chain have significant impact on both chain conformation and microstructure of aggregates. When the solvent is repulsive to the nonpolar backbone but attractive to the polar side chain, the polymer chains are collapsed, and the gelation follows the mechanism of colloidal packing; at the other solvent conditions, the gelation follows the mechanism of random aggregation.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Sedimentary changes during the Holocene in the Bohai Sea and its paleoenvironmental implication

Samples of two cores, Cores M5-5 and M7-4 in the Bohai Sea were analyzed in isotopes, grain size, heavy minerals, chemical compositions, and 14 C dating to reconstruct the sedimentation during the Holocene. Abrupt change in carbon and oxygen stable isotopes was recognized at Core M5-5 at about 6400 a BP, which was likely due to the intrusion of the Yellow Sea Warm Current (YSWC) extension into the Bohai Sea. At Core M7-4, sediments between 5900 and 6600 a BP (150-260 cm depth) became coarse-grained, containing rich garnet, high manganese content, and nil autogenic pyrite, indicating a very dynamic sedimentary event during which the ambience was transformed from reductive to oxidative, and sedimentation boosted. Meanwhile, the YSWC had invaded into the Bohai Sea indicated by rich planktonic foraminifera in this event. (c) 2008 Elsevier Ltd. All rights reserved.

Geochemical characteristics of nitrogen in the southern Yellow Sea surface sediments

Roles and distributions of various forms of nitrogen in biogeochemical cycling in the southern Yellow Sea surface sediments were investigated. The southern Yellow Sea could be divided into three regions (I, II and III) according to the proportion of fine-grained sediment in > 65%, 35-65% and < 35%, respectively. The ratios of different forms of nitrogen contents between each two of the three regions indicated that the nitrogen contents increased with the proportion of fine-grained sediment increasing. The quanta of exchangeable forms of nitrogen were similar in the three regions, while their releasing time increased from regions I to III, indicating that the cycle of nitrogen in fine-grained sediments was shorter than that in coarse-grained sediments. Nitrogen burial fluxes were also similar in these regions, while the burial efficiency increased from regions I to III. The highest burial efficiency was 30.21% in region III, indicating that more than 70% of nitrogen in the southern Yellow Sea surface sediments could be released to take part in biogeochemical recycling. When all the four forms of exchangeable nitrogen (nitrogen in ion exchangeable form (IEF-N), nitrogen in weak acid extractable form (WAEF-N), nitrogen in strong alkali extractable form (SAEF-N) and nitrogen in strong oxidant extractable form (SOEF-N)) were released to take part in recycling, their potential contributions were 80% (SOEF-N), 11% (IEF-N), 6% (SAEF-N), 3% (WAEF-N) respectively, which showed that SOEF-N was the predominant one, and its contribution to biogeochemical cycling was the highest. (c) 2004 Elsevier B.V. All rights reserved.

The release behavior of inorganic nitrogen and phosphorus in sediment during disturbance

Sediments and surface water were sampled in a tide flat in the Huiquan Bay, Qingdao, China in January 2004 to simulate the exchange of NH4-N/NO3-N/PO43- between sediments and surface water. A working system was designed with which samples were shaken at 60, 120 and 150 revolutions per minute (r/min). Experiment results show that NH4-N concentration in water at shaking rate of 60 r/min decreased gradually, while at 120 r/min increased gradually. In resuspension, fine-grained sediments contributed most NH4-N to the seawater, followed by medium-grained and coarse-grained sediments. The NO3-N concentration in water had a negative relation, with the shaking rate; the medium-grained sediments contributed more NO3-N to seawater than the coarse- and fine-grained sediments. The PO43- concentration is positively related with the shaking rate, the fine-grained sediments were the main N and P contributor to the seawater, followed by medium- and coarse-grained sediments.

芝麻坊石榴子石二辉橄榄岩多期变质演化及其地幔过程

Many garnet peridotite bodies are enclosed in ultrahigh-pressure (UHP) gneisses and/or migmatites in worldwide UHP terranes formed by subduction of continental crust. On the basis of petrochemical data, a group of garnet peridotites have been derived from depleted mantle and were subsequently metasomatized by melts and/or fluids derived from the subducted continental crust. However, their depletion and enrichment processes and tectonic evolutions are still in conflicts. New evidences for metamorphism of garnet lherzolite from Zhimafang, Donghai County, Sulu UHP terrane are reported. The garnet lherzolite have experienced a prolonged multistage metamorphic history. At least seven stages of recrystallization have been identified based on detailed analysis of reaction textures and mineral compositions. Stage I was a high-pressure and high-temperature enriched garnet lherzolite stage, which is inferred from the presence of high Ca-Cr core of garnet porphyroclast and inclusions of high-Mg clinopyroxene, high-Al-Cr orthopyroxene and high-Mg olivine. Stage II is a high-temperature and low-pressure depleted spinel-hurzbergite or spinel-dunite stage, as indicated by the presence of relict Al-rich spinel, very high-Mg and low-Ni olivine and high-Mg orthopyroxene included in the low-Cr mantle of the porphyroclastic garnet and core of fine-grained neoblastic garnet, clinopyroxene is absent in this stage. Stage III is an hydrous amphibole spinel-lherzolite stage, which recorded events of cooling and metasomatic re-enrichment, this stage is manifested by metasomatic origin of amphibole and phlogopite-bearing porphyroblastic clinopyroxene, and porphyroblastic orthopyroxene. Stage IV is a high-pressure amphibole garnet-lherzolite stage, which is indicated by the formation of low-Cr mantle of the porphyroclastic garnet and amphibole-bearing low-Cr core of neoblastic garnet. Stage V is an UHP metamorphic garnet-lherzolite stage, which is characterized by the formation of high-Cr rim of both porphyroclastic and neoblastic garnet and recrystallization of olivine, clinopyroxene and orthopyroxene in the matrix. During UHP metamorphism, the garnet lherzolite is dehydrated, hornblende decomposed to clinopyroxene and olivine. Stage VI is a high-pressure decompression amphibole garnet-lherzolite stage, indicated by formation of later coarse-grained pargasitic hornblende and phlogopite in the garnet stability field. Stage VII is a low-pressure decompression amphibole-chlorite spinel-lherzolite stage, indicated by replacement of garnet by kelyphite of high-Al orthopyroxene + aluminous spinel + tremolitic amphibole + chlorite + talc. The metamorphic evolutions of Zhimafang garnet lherzolite suggest that it displays progressive mantle wedge convection during the subduction of previous oceanic and subsequent continental slab. We propose that the Zhimafang garnet lherzolite were originated from enriched deep mantle wedge above the previously subducted oceanic slab, subduction of oceanic slab resulted in their convection to shallower back arc and sub-arc setting, decompressional melting transformed the enriched garnet-lherzolite to depleted spinel-hurzbergite or spinel-dunite, the spinel-hurzbergite or spinel dunite was then convected to the hydrous mantle wedge corner driven by corner flow and was cooled and metasomatized by slab-derived melts/fluids, and was transformed to enriched lherzolite. The lherzolites formed a downward mantle wedge layer above successively subducted continental crust. The peridotite subducted together with the underlying continental crust and suffered UHP metamorphism. Finally, the garnet-lherzolite exhumed to the earth surface together with the UHP terrane. Detailed analyses of reaction textures and mineral compositions revealed several stages of metasomatism related to continental subduction and exhumation.

矾山杂岩体成因及其与磷（铁）矿的成矿关系

The Fanshan complex consists of layered potassic ultramafic-syenite intrusions. The Fanshan apatite (-magnetite) deposit occurs in the Fanshan complex, and is an important style of phosphorus deposit in China. The Fanshan complex consists of three (First- to Third-) Phases of intrusion, and then the dikes. The First-Phase Intrusive contains ten typical layered rocks: clinopyroxenite, biotite clinopyroxenite, coarse-grained biotite clinopyroxenite, pegmatitic orthoclase-biotite clinopyroxenite, variegated orthoclase clinopyroxenite, interstitial orthoclase clinopyroxenite, biotite rock, biotite-apatite rock, biotite rock and magnetite-apatite rock. This layered intrusive consists of nine rhythmic units. Each rhythmic unit essentially comprises a pair of layers: clinopyroxenite at the bottom and biotite clinopyroxenite at the top. The apatite (-magnetite) deposit is situated near the top of rhythmic Unit no. 6 of the First-Phase Intrusive. The Second-Phase Intrusive contains three typical rocks: coarse-grained orthoclase clinopyroxenite, . coarse-grained salite syenite and schorlomite-salite syenite. The Third-Phase Intrusive includes pseudo-trachytic salite syenite, porphyritic augite syenite, fine-grained orthoclase clinopyroxenite and fine-grained salite syenite. The origin of the Fanshan complex is always paid attention to it in China. Because most layered igneous intrusion in the world not only have important deposit in it, but also carry many useful information for studying the formation of the intrusion and the evolvement of magma. Two sketch maps were drawn through orebodies along no. 25 cross-cut on 425 mL and no. 1 cross-cut on 491 mL in the Fanshan mine. Through this mapping, a small-scaled rhythmic layering (called sub-rhythmic layering in the present study) was newly found at the top of the rhythmic Unit no. 6. The concept of sub-rhythmic layering is defined in this article. The sub-rhythmic layering is recognized throughout this apatite-rich part, except for magnetite-apatite rock. Presence of the layered magnetite-apatite rock is one of the characteristics of the Fanshan apatite (-magnetite) deposit. Thus, from this layer downwards six units of sub-rhythmic layering are recognized in the present study. Each unit consists of biotite clinopyroxenite (or biotite rock and biotite-apatite rock) layer at the bottom and apatite rock layer at the top. To study this feature in detail is an important work for understanding the origin of the Fanshan complex and apatite (-magnetite) deposit. The origin of the Fanshan complex and the relation of the formation of the apatite(-magnetite)deposit will be interpreted by the study of sub-rhythmic layering on the basis of previous research works. The magma formed the Fanshan complex was rich in K2O, early crystallized pyroxene, and after this phase more biotite crystallized, but no amphibole appeared. This indicated that the activity of H2O in the magma was low. Major element compositions of biotite and clinopyroxene (on thin sections) in the sub-rhythmic layering were analyzed using electron microprobe analyzer. The analytical results indicate Mg/(Mg+Fe*+Mn) atomic ratios (Fe*, total iron) of these two minerals rhythmically changed in sub-rhythmic layering. The trends of Mg/(Mg+Fe*+Mn) atomic ratio (Fe*, total iron) of biotite and clinopyroxene indicate that the magma evolved markedly from relatively magnesian bottom layer to less magnesian top layer in each sub-rhythmic unit. A general trend through the sub-rhythmic layering sequence is both minerals becoming relatively magnesian upwards. The formation temperatures for sub-rhythmic layering yield values between 600 and 800 ℃, were calculated using the ratio of Mg/(Mg+Fe+Mn) in the salite and biotite assemblage. The equilibrium pressures in the rhythmic layers calculated using the contents of Al in the salite were plotted in the section map, shown a concave curve. This indicates that the magma formed the First-Phase Intrusive crystallized by two vis-a-vis ways, from its bottom and top to its centre, and the magnetite-apatite rock was crytallized in the latest stage. The values of equilibrium pressures in the sub-rhythmic layering were 3.6-6.8(xlO8) Pa with calculated using the contents of Al in the salite. The characteristics of geochemistry in various intrusive rocks and the rocks or apatite of sub-rhythmic layers indicated that the Fanshan complex formed by the comagmatic crystallization. The contents of immiscible elements and REEs of apatite rock at the top of one sub-rhythmic unit are more than biotite clinopyroxenite at the bottom. The contents of immiscible elements and REEs of apatite of biotite clinopyroxenite at the bottom of one sub-rhythmic unit are higher than apatite rock at the top. The curves of rocks (or apatite) in the upper sub-rhythmic units are between two curves of the below sub-rhythmic unit in the primitive mantle-normalized trace element abundance spider diagram and the primitive mantle-normalized REE pattern. The trend for the contents of immiscible elements and REEs inclines to the same contents from the bottom to the top in sub-rhythmic layering. These characteristics of geochemistry of rocks or apatites from sub-rhythmic layering indicate that the latter sub-rhythmic unit was produced by the residual magma after crystallization of the previous sub-rhythmic unit. The characteristics of petrology, petrochemistry, geochemistry in the Fanshan complex and sub-rhythmic layers and the trends of Mg/(Mg+Fe+Mn) atomic ratio of biotite and clinopyroxene in sub-rhytmic layering rejected the hypotheses, such as magma immiscibility, ravitational settling and multiple and pulse supplement of magma. The hypothesis of differentiation by crystallization lacks of evidences of field and excludes by this study. On the base of the trends of formation temperatures and pressures, the characteristics of petrology, petrochemistry, geochemistry for the Fanshan complex and the characteristics of geochemistry for the rocks (or apatites), the trends of Mg/(Mg+Fe+Mn) atomic ratio of biotite and clinopyroxene in sub-rhytmic layering, and the data of oxygen, hydrogen, strontium and neodymium isotopes, this study suggests that the magma formed the Fanshan complex was formed by low degree partial melting of mantle at a low activity of H2O, and went through the differentiation at the depth of mantle, then multiply intruded and crystallized. The rhythmic layers of the First-Phase Intrusive formed by the magma fractional crystallized in two vis-a-vis ways, from the bottom and top to the centre in-situ fractional crystallization. The apatite (-magnetite) deposit of the Fanshan complex occurs in sub-rhythmic layering sequence. The the origin of the sub-rhythmic layering is substantially the origin of the Fanshan apatite (-magnetite) deposit. The magma formed the rhythmic layers of First-Phase Intrusive was rich in H2O, F and P at the later stage of its in-situ fractional crystallization. The Fanshan apatite (-magnetite) deposit was formed by this residual magma in-situ fractional crystallization. The magnetite-apatite rock was crystallized by two vis-a-vis ways at the latest stage in-situ fractional crystallization in the rhythmic layers. The result was light apatite layer below heavy the magnetite-apatite layer, formed an "inversion" phenomenon.

Heat capacity enhancement and thermodynamic properties of nanostructured amorphous SiO2

The heat capacity of nanostructured amorphous SiO2 (na-SiO2) has been measured by adiabatic calorimetric method over the temperature range 9-354 K. TG and differential scanning calorimeter (DSC) were also employed to determine the thermal stability. Glass transition temperature (T-g) for the two same grain sizes with different specific surface of naSiO(2) samples and one coarse-grained amorphous SiO2 (ca-SiO2) sample were determined to be 1377, 1397 and 1320 K, respectively. The low temperature experimental results show that there are significant heat capacity (C-P) enhancements among na-SiO2 samples and ca-SiO2. Entropy, enthalpy, Gibbs free energy and Debye temperature (theta (D)) were obtained based on the low temperature heat capacity measurement of na-SiO2. The Cp enhancements of na-SiO2 were discussed in terms of configurational and vibrational entropy. (C) 2001 Elsevier Science B.V. All rights reserved.

Enhancement of molar heat capacity of nanostructured Al2O3

The nanosized alumina prepared by the hydrolysis method with an average particle size of 20 nm was characterized by X-ray diffraction. The heat capacity measurements of the prepared sample were carried out using an adiabatic calorimeter in the temperature range from 78 to 370 K. Enhancement of heat capacity was observed in the nanostructured materials as the heat capacity data were compared with those of the corresponding coarse-grained materials. The enhanced heat capacity was discussed on the basis of experiments. Differential scanning calorimetry and thermogravimetry were used to determine the thermal stability of the nanostructured alumina.

Adaptive Weighing Designs for Keyword Value Computation

Attributing a dollar value to a keyword is an essential part of running any profitable search engine advertising campaign. When an advertiser has complete control over the interaction with and monetization of each user arriving on a given keyword, the value of that term can be accurately tracked. However, in many instances, the advertiser may monetize arrivals indirectly through one or more third parties. In such cases, it is typical for the third party to provide only coarse-grained reporting: rather than report each monetization event, users are aggregated into larger channels and the third party reports aggregate information such as total daily revenue for each channel. Examples of third parties that use channels include Amazon and Google AdSense. In such scenarios, the number of channels is generally much smaller than the number of keywords whose value per click (VPC) we wish to learn. However, the advertiser has flexibility as to how to assign keywords to channels over time. We introduce the channelization problem: how do we adaptively assign keywords to channels over the course of multiple days to quickly obtain accurate VPC estimates of all keywords? We relate this problem to classical results in weighing design, devise new adaptive algorithms for this problem, and quantify the performance of these algorithms experimentally. Our results demonstrate that adaptive weighing designs that exploit statistics of term frequency, variability in VPCs across keywords, and flexible channel assignments over time provide the best estimators of keyword VPCs.

An application of quasi-Newton methods for the numerical solution of interface problems

Quasi-Newton methods are applied to solve interface problems which arise from domain decomposition methods. These interface problems are usually sparse systems of linear or nonlinear equations. We are interested in applying these methods to systems of linear equations where we are not able or willing to calculate the Jacobian matrices as well as to systems of nonlinear equations resulting from nonlinear elliptic problems in the context of domain decomposition. Suitability for parallel implementation of these algorithms on coarse-grained parallel computers is discussed.

Simulation of 2-D metal cutting by means of a distributed algorithm

Temperature distributions involved in some metal-cutting or surface-milling processes may be obtained by solving a non-linear inverse problem. A two-level concept on parallelism is introduced to compute such temperature distribution. The primary level is based on a problem-partitioning concept driven by the nature and properties of the non-linear inverse problem. Such partitioning results to a coarse-grained parallel algorithm. A simplified 2-D metal-cutting process is used as an example to illustrate the concept. A secondary level exploitation of further parallel properties based on the concept of domain-data parallelism is explained and implemented using MPI. Some experiments were performed on a network of loosely coupled machines consist of SUN Sparc Classic workstations and a network of tightly coupled processors, namely the Origin 2000.

A hybrid Laplace transform/finite difference boundary element method for diffusion problems

The solution process for diffusion problems usually involves the time development separately from the space solution. A finite difference algorithm in time requires a sequential time development in which all previous values must be determined prior to the current value. The Stehfest Laplace transform algorithm, however, allows time solutions without the knowledge of prior values. It is of interest to be able to develop a time-domain decomposition suitable for implementation in a parallel environment. One such possibility is to use the Laplace transform to develop coarse-grained solutions which act as the initial values for a set of fine-grained solutions. The independence of the Laplace transform solutions means that we do indeed have a time-domain decomposition process. Any suitable time solver can be used for the fine-grained solution. To illustrate the technique we shall use an Euler solver in time together with the dual reciprocity boundary element method for the space solution