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The pore-throat structure is a critical factor in the study of unconventional oil and gas reservoirs, drawing particular attention from petroleum geologists, and it is of paramount significance to analyze to enhance oil and gas production. In tight sandstone, which serves as a significant hydrocarbon reservoir, the internal pore-throat structure plays a decisive role in the storage and migration of fluids such as water, gases, and hydrocarbons. This paper employs casting thin section (CTS), field emission scanning electron microscope (FE-SEM), high-pressure mercury injection (HPMI), and low-temperature nitrogen gas adsorption (LT−N2−GA) experimental tests to qualitatively and quantitatively analyze the characteristics of the pore-throat structure in tight sandstone. The results indicate that the pore types in tight sandstone include intergranular residual pores, dissolution pores, intercrystalline pores, and microfractures, while the throat types encompass sheet-shaped, curved-sheet-shaped, and tubular throats. Analysis of the physical and structural parameters from 13 HPMI and 5 LT−N2−GA samples reveals a bimodal distribution of pore-throat radii. The complexity of the pore-throat structure is identified as a primary controlling factor for reservoir permeability. The fractal dimension (D) exhibits an average value of 2.45, displaying a negative correlation with porosity (R2 = 0.22), permeability (R2 = 0.65), the pore-throat diameter (R2 = 0.58), and maximum mercury saturation (R2 = 0.86) and a positive correlation with threshold pressure (R2 = 0.56), median saturation pressure (R2 = 0.49), BET specific surface area (R2 = 0.51), and BJH total pore volume (R2 = 0.14). As D increases, reservoir pores tend to decrease in size, leading to reduced flow and deteriorated physical properties, indicative of a more complex pore-throat structure. [ABSTRACT FROM AUTHOR]

The article discusses the recent advancements in protein structure prediction, with a focus on the achievements of AlphaFold. It explains how AlphaFold has made significant progress in accurately predicting 3D protein structures by dividing the problem into subproblems. However, the article acknowledges that there is still work to be done in mapping a single sequence to its real-world structure and dynamics. It compares AlphaFold 2 to previous methods and mentions other methods that have been developed in response. The article concludes by stating that the success of AlphaFold 2 has opened up new possibilities for structural biology research. [Extracted from the article]

Total organic carbon (TOC) and hydrocarbon generation potential (Pg) are essential parameters for the qualitative evaluation of source rock and the basis for evaluating hydrocarbon resources in petroliferous basins. However, there will be some deviations in evaluating hydrocarbon resources of overmature source rock by using TOC and Pg. The super-thick overmature source rock of the Early Cretaceous Laiyang Formation was found in well LK-1, the Riqingwei Basin. To accurately understand the oil and gas potential of the Riqingwei Basin, this paper conducted a systematic organic geochemical analysis of the overmature source rock of the Early Cretaceous Laiyang Formation found in well LK-1. Combined with the results of previous thermal simulation tests on hydrocarbon generation of low-maturity samples in the Jiaolai Basin, the original total organic carbon (TOC0) content of source rock in well LK-1 was recovered and the evaluation criteria of overmature source rock was established. Results: (1) The average TOC content of well LK-1 source-rock samples is 1.25 wt.%, and the average Pg content is 0.11 mg/g. The type of organic matter is mainly type II2, including a small amount of type II1 and type III. The average reflectance of vitrinite (Ro) is 4.35%, which belongs to overmature source rock of a poor–fair level and mixed kerogen. (2) After recovery calculation, these samples' original hydrocarbon generation potential (Pg0) contents ranged from 0.63 to 108.1 mg/g, with an average value of 6.76 mg/g. Furthermore, the TOC0 contents of the analyzed source-rock samples ranged from 0.62 to 30.6 wt.%, with an average value of 2.01 wt.%. It belongs to fair–good source rock, showing better hydrocarbon generation potential. (3) According to the relationship between the Pg0, Pg and TOC content, the evaluation standard for overmature source rock in well LK-1 was established. Under the evaluation standard of overmature source rock, a source rock with a TOC content exceeding 0.6% and a Pg content greater than 0.1 mg/g can be identified as a good source rock. This paper provides a foundation for the fine classification and evaluation of the overmature source rock of the Riqingwei Basin. [ABSTRACT FROM AUTHOR]

The Lingshan Island scientific drill confirms that two episodes (Laiyang period and Qingshan period) of rifting developed in the central Sulu orogenic belt (SOB) in Late Mesozoic. With a set of methods including fieldwork, drilling, core logging, zircon U-Pb dating and whole rock geochemistry applied, the age, the depositional sequence and the deep dynamic mechanisms of rift evolution were unraveled. The stratigraphic sequence of the Laiyang-Qingshan Groups on Lingshan Island was composed of two different rifting sequences: (1) Laiyang Group (147–125 Ma), which consists of deep-water gravity flow deposits with interlayers of intermediate volcanic rocks; and (2) Lower Qingshan Group (125–119 Ma), which unconformably overlies the former sequence and contains subaerial volcanic deposits and terrestrial deposits. The tectonic environment changed during the evolution of these two episodes of rifting: the rift was in a NNW-SSE extensional environment in the Laiyang period and showed the typical passive rifting character that "lithospheric extension and rifting preceded volcanism". The passive rifting period was ended by a short WNW-ESE compression at about 125 Ma. After that, the tectonic environment transferred to a strong NW-SE extensional environment and the rifting evolved into a volcanic arc basin in the Qingshan period. The igneous rocks are shoshonitic to high-K calc-alkaline trachyandesites to trachytes with a few intercalated lamprophyres and a rhyolite. The geochemical characteristics of the igneous rocks indicate that they are mantle-derived melts with a metasomatized mantle source and/or crustal contamination. In addition, an increased thinning of the lithosphere happened during the rifting episodes. The low-angle subduction of the Paleo-Pacific plate in the Jurassic weakened the thickened SOB lithospheric mantle. The rollback of the subducting plate started in late Jurassic to early Cretaceous, and the SOB lithospheric mantle was delaminated synchronously because of the gravity collapse. Thus, this caused passive rifting in the Laiyang period. Thereafter, the rollback and trench retreat of the high-angle subducting Paleo-Pacific plate would have achieved its climax, resulting in the strong regional extension. Passive rifting was ended by the crustal uplift caused by asthenospheric upwelling beneath the rift. The lower crust was heated by the upwelling asthenosphere and partially melted to form felsic melts, which were emplaced upwards and erupted explosively. The rift evolved into a volcanic arc basin in the Qingshan period and showed some characteristics of active rifting. Above all, a passive rifting in the Laiyang period and a volcanic arc basin in the Qingshan period developed successively in the Lingshan Island area (the central SOB). This records the transfer of the study area from the Paleo-Tethys tectonic domain to the circum-Pacific tectonic domain. The delamination of SOB lithospheric mantle and the upwelling of asthenospheric material were the deep dynamic mechanisms driving the development and evolution of two rift episodes. Additionally, the rift development was controlled remotely by the subduction of the Paleo-Pacific plate. [ABSTRACT FROM AUTHOR]

The Ri-Qing-Wei basin is located in the central Sulu Orogeny on the eastern side of the Tanlu fault zone in eastern Shandong province. To the north, the Jiaonan uplift separates it from the Jiaolai basin, where drilling in the lower Cretaceous sedimentary rock of the Laiyang group has indicated good oil and gas reserves. Drilling in the Ri-Qing-Wei basin, in contrast, is in the preliminary exploration stage. Lingke 1, the only scientific well, is on Lingshan Island on the basin boundary, and it encountered a large set of source rocks 700 m thick. The two basins were comprehensively compared and analyzed based on comprehensive fieldwork, drilling, core data, seismic profiling, sedimentary filling sequence, tectonic evolution history, basin burial history, geothermal history, and geochemical characteristics of the source rocks. The results showed three things: (1) from the late Jurassic to the early Cretaceous (the Laiyang period), subduction of the paleo-Pacific plate under the Eurasian plate delaminated the lithospheric mantle of the Sulu Orogeny, thus forming a series of passive continental rift basins. Of these, the Ri-Qing-Wei is central and the Jiaolai is its branch. After the active rift stage in the Qingshan period and the depression stage in the Wangshi period, the burial depth of the source rocks in the Ri-Qing-Wei basin was up to 6000 m, while the maximum burial depth in the Jiaolai basin was about 3000 m. The paleogeotemperature of both basins exceeded 125 °C, indicating that the source rocks were very mature. (2) A comprehensive comparison of their geochemical characteristics—organic matter abundance, type, and maturity—showed that both basins have oil-generating potential. It is worth noting that the magmatic activity in the Qingshan period had a positive effect on the evolution of the source rocks but was not the key factor: burial depth was. (3) Oil and gas failed to accumulate in the Jiaolai basin because they were destroyed by the lateral tectonic activities. During the right-lateral strike-slip stage (50 ± 5 Ma) during the late Wangshi, the Jiaolai basin was strongly uplifted over a range of more than 1000 m by the Tanlu and Wulian-Mouji fault zones along the boundary. The Wangshi group, as a cap rock, was eroded, and oil and gas overflowed along the fault that reached the surface. The late Wangshi period uplift of the Ri-Qing-Wei basin was less than 1000 m because the source rock was deeper, and the reverse faults in the basin were sealed well. The uplift did little damage to the oil in the Ri-Qing-Wei basin. Above all, tectonic evolution was the main controlling factor of oil accumulation in the study area, and the layers of the Laiyang group in the Ri-Qing-Wei basin have oil and gas potential, making it a prospective target for unconventional offshore oil and gas exploration. [ABSTRACT FROM AUTHOR]

Lower Cretaceous sedimentary rocks of Lingshan Island, located along the continental margin of East Asia, have received increased attention. The Lingke-1 core mainly belongs to the Lower Cretaceous Laiyang Group. We investigate provenance, tectonic setting, palaeoclimate and palaeoredox conditions in the study area using elemental geochemistry, thereby elucidating the depositional history of the Lower Cretaceous sediments and reconstructing the palaeo-environment. To achieve this, 90 siltstones and 76 mudstones were sampled from this core and other outcrops on Lingshan Island. The chemical index of alternation (CIA) values for the majority of the samples and the bivariate diagrams indicate that the sedimentary rocks were subjected to minor weathering processes. Geochemical results suggest that source rocks for the region are felsic igneous and metamorphic rocks, along with minor proportions of intermediate igneous rocks. Major- and trace-element discrimination diagrams, deciphering the tectonic history, indicate that source rocks mainly originated from the continental island-arc and active continental margin. Several representative geochemical indices and the bivariate plots based on elemental contents show that the Laiyang Group was predominantly deposited in arid conditions. Sr/Ba values suggest a palaeosalinity transition from brackish to saline, demonstrating a depositional transformation from lacustrine facies for the lower Laiyang Group to marine facies in the upper Laiyang Group. U/Th and V/(V+Ni) ratios and Ce anomalies in the rocks indicate anoxic conditions. We conclude that the conspicuous decline in the trends of the above three geochemical indices, ranging between 400 and 800 m, may be related to the latest Hauterivian oceanic anoxic event. [ABSTRACT FROM AUTHOR]

The depositional environment and tectonic setting of the newly identified Ri‐Qing‐Wei Basin are the focus of controversy. In order to solve these questions, the geochemical characteristics of siltstones from Laiyang Group in Taolin area are analysed in detail. The siltstones present similar contents of SiO2 and Al2O3 compared with upper continental crust (UCC) and post‐Archean Australian Shale (PAAS) and are classified as wacke on chemical classification plot of clastic rocks. The trace elements are characterized by the depletion of transition elements (Sc, V, Cr, Ni, and Cu). The chondrite‐normalized REE patterns exhibit the enrichment of LREE and depletion of HREE, as well as significant negative Eu anomalies. Relative high Index of Compositional Variability (ICV) values suggest the siltstones are compositionally immature and the sediments of first‐cycle. The low Chemical Index of Alteration (CIA) and Plagioclase Index of Alteration (PIA) values of the samples indicate the weak source weathering condition. Moreover, the characteristics of A‐CN‐K plot suggest K‐metasomatism occurred after burial. A series of palaeo‐environment indexes imply that the Laiyang Group were deposited in a reducing marine environment with hot and arid climate. Major‐ and trace‐based tectonic setting discriminant diagrams all indicate that the Ri‐Qing‐Wei Basin was formed in an active continental margin setting; this conclusion is also supported by the analysis of the coeval igneous rocks. Based on the investigations of the subduction of the Palaeo‐Pacific plate and the development of Cretaceous basins on the eastern Eurasia, we propose that Ri‐Qing‐Wei Basin was formed in response to the delamination of the North China Craton and the subduction of Izanagi plate. [ABSTRACT FROM AUTHOR]

Protein topology, which refers to the arrangement of secondary structures of proteins, has been extensively investigated to examine its role in protein folding. However, recent studies show that topology alone cannot account for the variation of folding behaviors observed in some proteins of the same structural family. In a recent work, we showed that the native structure of the second β hairpin of protein G predicts a folding mechanism that is different from topology-based models. Here, we continue to examine how much one can learn about folding mechanism from native structure. This work focuses on fragment B of Staphylococcal protein A (BpA) - a three-helix (H[SUB1], H[SUB2], and H[SUB3]) bundle protein. Using a recently developed all-atom (except nonpolar hydrogen) Go model interacting with simple discontinuous potentials, the folding of the model BpA was observed in 112 out of 249 trajectories within 50 h of CPU times on a Pentium PC (1 GHz). The model successfully captured several specific properties of BpA that have been observed experimentally. These include the higher stability of H[SUB3] compared to H[SUB1] and H[SUB2], and the higher stability of the H[SUB2]-H[SUB3] microdomain compared to the H[SUB1]-H[SUB2] microdomain. These specific details were not produced by a topology-based square-well model of BpA. Thus, the result further supports the important role of sidechain packing in determining the specific pathway of protein folding. Additional 96000 short simulations were performed to locate the transition states of the two folding pathways. The limitation of the Go model and its possible improvement are also discussed. [ABSTRACT FROM AUTHOR]

We explore the distance fluctuation criterion (“Lindemann criterion”) for melting transitions. Distances from average positions in accord with Lindemann, or interparticle distances, in accord with Jellinek and Berry or Etters and Kaelberer, are examined. The primary goal is to determine which of these offers the more useful criterion. The choice of origin can sometimes effect the significance of the index. We study three systems with two kinds of potentials. They are all composed of 64 particles: (a) and (b), a homopolymer and a cluster that consist of beads interacting pairwise through square-well potentials, and (c) a cluster of particles interacting pairwise through Morse potentials. For each of the noncrystalline structures, in contrast to the crystals originally studied by Lindemann, the fluctuation parameter based on interparticle distances gives a clearer separability of liquid and solid phases than that based on fluctuations from average positions. The solid-like forms of the Morse cluster, the square-well cluster, and the square-well homopolymer have similar behavior, indicating that a broad class of systems can be evaluated with this index. In these systems, relative fluctuation parameters provide a suitable criterion for the melting transition. The critical values for the interparticle distance criterion, which are in the range of 0.03–0.05, are smaller than those for the Lindemann criterion (0.1–0.15). © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A new method for calculating thermodynamics of any square-well systems by umbrella sampling of the corresponding hard-sphere systems is proposed. The removal of energetic barriers leads to an efficient configurational sampling. As an illustrative example, the method is applied to a square-well chain of freely-jointed 64 beads. Results indicate that it produces fast and more accurate thermodynamic results than either the direct molecular dynamics simulation or the umbrella sampling of the square-well chain. The new method, which provides a new route for accurate heat-capacity and free energy calculations, can be easily extended to a system interacting with the Lennard-Jones or any other continuous potentials. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The geological units in Shandong Province, North China are important parts of the North China Craton and offer important insights into their crustal evolutionary history. This work compiled 611 sets of Nd isotopic data of Archean-Mesozoic rocks from Shandong including the Luxi, Jiaobei, and Sulu terranes, which provided important constraints for crustal growth and reactivation. Nd-depleted mantle model ages (TDM) of Archean rocks with positive εNd(t) values showed that ca. 2.9 and 2.8-2.7 Ga were the most important periods of crustal growth in the Jiaobei and Luxi terranes, respectively, while the period of ca. 2.6-2.5 Ga in the Jiaobei terrane likely indicated a coherent event of crustal growth and reworking. During the Proterozoic, multi-stage rifting and collisional orogenic events possibly led to the reworking of Archean crust in the source region. The Nd isotopic data of the Paleoproterozoic and Neoproterozoic rocks from Sulu indicated significant reworking of older crust with juvenile magmatic input. Crustal reactivation occurred during the Mesozoic. The younger TDM ages of the Mesozoic rocks with low negative εNd(t) values indicated that a juvenile crustal/mantle component was added to the ancient basement. The reactivation reflected significant crust-mantle interaction via the mechanism of crustal subduction and mantle-derived magma un-derplating, or possibly asthenospheric upwelling. Our work also attempted to establish the crustal correlation between Shandong and Korea (including the Gyeonggi massif, Ogcheon belt, and Yeongnam massif). The TDM age distribution provided evidence favoring the affinity relationship between the Gyeonggi massif and Ogcheon belt of South Korea and the Jiaobei and Sulu terranes of Shandong, while the Yeongnam massif was more correlated with the South China Block. [ABSTRACT FROM AUTHOR]

Early Cretaceous sedimentary rocks in the Sulu Orogen (SO) have been a popular topic in recent years. The provenances of sedimentary rocks can help elucidate the tectonic history of the SO, China. The Dingzi Bay and Taolin areas in the SO have always been poorly known. Thus, we date detrital zircons from four sedimentary rock samples including sandstone, siltstone, and greywacke collected in both areas. Age distributions from Dingzi Bay exhibit three major age populations including Palaeoproterozoic (1900–1800 Ma), Neoproterozoic (800–700 Ma), and Early Cretaceous (136–106 Ma) ages and small age populations including early Mesozoic, Palaeozoic, and Palaeoproterozoic–Archean ages, while age distributions in the Taolin area show the largest age population of Early Cretaceous (132–102 Ma) with minor early Mesozoic, Palaeozoic, and Neoproterozoic populations. The youngest detrital zircon populations yield weighted mean ages of ca. 116 Ma in Dingzi Bay and ca. 120 Ma in the Taolin area as the maximum depositional ages, which correspond to the Early Cretaceous Lower Qingshan Group. Age distributions in both areas indicate that the local SO served as the primary source area, whereas the Yangtze Block might have been a lesser source of detrital zircons. The comparison of geochronological, geochemical, and sedimentary data among Dingzi Bay, Taolin, Laoshan, and Lingshan Island suggests an Early Cretaceous marine basin formed over the SO. Further, considering previous regional tectonic history, we propose a two‐stage (Laiyang and Qingshan stages) evolutionary model for this marine basin. We suggest that transpression between the Laiyang and Qingshan stages due to subduction of the Pacific Plate might have caused rapid uplift of the south‐eastern SO and closing of the marine basin. Correspondingly, this process influenced the input of the source material from the Yangtze Block to the marine basin during the Qingshan stage. [ABSTRACT FROM AUTHOR]

We find that first-order thermodynamic perturbation theory (TPT1) which incorporates the reference monomer fluid used in the generalized Flory–AB (GF–AB) theory yields an equation of state for fused hard-sphere (FHS) chain fluids that has accuracy comparable to the GF–AB and GF–dimer–AC theories. The new TPT1 equation of state is significantly more accurate than other extensions of the TPT1 theory to FHS chain fluids. The TPT1 is also extended to two-dimensional fused hard-disk chain fluids. For the fused hard-disk dimer fluid, the extended TPT1 equation of state is found to be more accurate than the Boublík hard-disk dimer equation of state. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A multiplicative interpolation scheme (MIS) for the cavity function of associating hard-core particles is proposed and applied to the case of our shielded sticky-point model in which the particles associate into fused hard-sphere diatomic molecules (hard dumbbells). The results indicate that the MIS is a significant improvement over the simple interpolation scheme (SIS) of our earlier paper when the bonding length is much less than the hard-core diameter. The MIS is also applied to the case of a weak electrolyte modelled by shielded sticky-point particles that are charged, which associate into hard dipolar dumbbells. Using a near-exact hard-sphere cavity function along with the mean spherical approximation (MSA) for the electrostatic part of the activity coefficient, we find that the resulting version of the MIS is already in reasonable agreement with the experimental data for monochloroacetic acid, despite the equal-diameter restriction of the simple version of the model that we are using. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We report Monte Carlo simulation results for the bulk pressure of fused-hard-sphere (FHS) chain fluids with bond-length-to-bead-diameter ratios ≊ 0.4 at chain lengths n=4, 8 and 16. We also report density profiles for FHS chain fluids at a hard wall. The results for the compressibility factor are compared to results from extensions of the Generalized Flory (GF) and Generalized Flory Dimer (GFD) theories proposed by Yethiraj et al. and by us. Our new GF theory, GF-AB, significantly improves the prediction of the bulk pressure of fused-hard-sphere chains over the GFD theories proposed by Yethiraj et al. and by us although the GFD theories give slightly better low-density results. The GFD-A theory, the GFD-B theory and the new theories (GF-AB, GFD-AB, and GFD-AC) satisfy the exact zero-bonding-length limit. All theories considered recover the GF or GFD theories at the tangent hard-sphere chain limit. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The pairing mean spherical approximation (PMSA) developed in the previous paper of this series is applied to a binary mixture of hard spheres and ions of the restricted primitive model. The resulting equation of state is used to investigate the phase equilibrium for the binary mixture. It is found that the model exhibits type-III phase behavior. This work serves as the basis for more realistic models. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A new method, which improves upon the mean spherical approximation (MSA), is developed by including the ionic-pairing contribution using a recent theory of association. The association constant of the new approximation is obtained through the second ionic virial coefficient. In the simplest version of our theory, which we call the pairing MSA 1 (PMSA1), we neglect the activity coefficient of the fully associated ionic-pairs, which are regarded as a separate dipolar species, and obtain the critical point (ρc*, Tc*) at (0.025, 0.075). In the second PMSA ( or PMSA2), we include the activity coefficient of these dipolar particles at the MSA level. The new critical point is located at (0.023, 0.073). In the third PMSA ( or PMSA3), we further include the effect of the presence of the dipolar-particle cores. The final critical point is located at (0.0245, 0.0745). These critical points are considerably closer than the MSA result (0.014, 0.079) to the most recent Monte Carlo estimates of ρc* from 0.025 to 0.04 and Tc* from 0.053 to somewhat over 0.057. Both PMSA2 and PMSA3 appear to improve the critical values of pressure and the degree of association significantly over PMSA1. All expressions for the thermodynamic properties in the PMSA1, PMSA2, and PMSA3 are of simple analytic form. The equation of state in the PMSA3 reduces to the very accurate Carnahan-Starling equation of state for hard spheres if the charges are turned off, and it reduces to an accurate equation of state for a mixture of hard spheres and hard dumbbells if the charges of the associated pairs are turned off. A comparison is made between our theory and that of a recent approach of Fisher and Levin, which is in good agreement with the simulation results if the hard-core contribution to the thermodynamics is neglected, but which falls out of agreement when an accurate core contribution is included. A discussion of the importance of an accurate core term in the treatment of the restrictive... [ABSTRACT FROM AUTHOR]

The exact asymptotic behavior of the particle–particle direct correlation function for dissociative dipolar dumbbells is discussed. It reveals the sense in which the complete association limit is like a critical point and suggests several approximations as well as the conditions under which they can be expected to be useful. The simplest of these is an extended mean spherical approximation (EMSA) that can be solved analytically for a model liquid of symmetric dissociative dipolar dumbbells with two centers (each bearing a point charge of opposite sign) a distance L apart, when σ/3≤L≤σ/2, where σ is the diameter of the spheres that consistute the dumbbells. The analytical expressions for the Born solvation free energy of a symmetric dipolar dumbbell in a symmetric dipolar dumbbell solvent and in a dipolar hard-sphere solvent are also obtained. Such expressions can be expected to be useful in investigating intramolecular electron-transfer reactions. Results for σ/2≤L≤σ that have a somewhat different conceptual status are obtained as well. They suggest a new interpretation of the Percus–Yevick solution to the sticky-sphere model considered by Baxter. [ABSTRACT FROM AUTHOR]

Exact equations which relate the cavity function to excess solvation free energies and equilibrium association constants are rederived by using a thermodynamic cycle. A zeroth-order approximation, derived previously by us as a simple interpolation scheme, is found to be very accurate if the associative bonding occurs on or near the surface of the repulsive core of the interaction potential. If the bonding radius is substantially less than the core radius, the approximation overestimates the association degree and the association constant. For binary association, the zeroth-order approximation is equivalent to the first-order thermodynamic perturbation theory (TPT) of Wertheim. For n-particle association, the combination of the zeroth-order approximation with a ‘‘linear’’ approximation (for n-particle distribution functions in terms of the two-particle function) yields the first-order TPT result. Using our exact equations to go beyond TPT, near-exact analytic results for binary hard-sphere association are obtained. Solvent effects on binary hard-sphere association and ionic association are also investigated. A new rule which generalizes Le Chatelier’s principle is used to describe the three distinct forms of behaviors involving solvent effects that we find. The replacement of the dielectric-continuum solvent model by a dipolar hard-sphere model leads to improved agreement with an experimental observation. Finally, equation of state for an n-particle flexible linear-chain fluid is derived on the basis of a one-parameter approximation that interpolates between the generalized Kirkwood superposition approximation and the linear approximation. A value of the parameter that appears to be near optimal in the context of this application is obtained from comparison with computer-simulation data. [ABSTRACT FROM AUTHOR]

The zeroth order (hydrostatic) nonlocal integral-equation approximation is applied here to Lennard-Jones (LJ) fluids. Systems of homogeneous LJ fluids are investigated, as well as LJ fluids near a hard wall, a model CO2 wall, and inside two model CO2 walls. The hydrostatic hypernetted chain (HHNC) approximation is shown to be better than both the Percus–Yevick and the hypernetted chain approximations when compared with computer simulations. The phenomena of solid wetting by liquid, solid wetting by gas, and capillary condensation are predicted by the HHNC approximation. [ABSTRACT FROM AUTHOR]

A formally exact nonlocal density-functional expansion procedure for direct correlation functions developed earlier by Stell for a homogeneous system, and extended by Blum and Stell, Sullivan and Stell, and ourselves to various inhomogeneous systems, is used here to derive nonlocal integral-equation approximations. Two of the simplest of these approximations (zeroth order), which we shall characterize here as the hydrostatic Percus–Yevick (HPY) approximation and the hydrostatic hypernetted-chain (HHNC) approximation, respectively, are shown to be capable of accounting for wetting transitions on the basis of general theoretical considerations. Before turning to such transitions, we investigate in this first paper of a series the case of homogeneous hard-sphere fluids and hard spheres near a hard wall as well as the case of hard spheres inside a slit pore. Numerical results show that the HHNC approximation is better than the HNC approximation for both the homogeneous and inhomogeneous systems considered here while the HPY approximation appears to overcorrect the PY approximation. [ABSTRACT FROM AUTHOR]

Analytical equations are obtained for the pair correlation functions in the mean spherical approximation (MSA) for two charged hard-sphere ions in a model molecular solvent. Model solvents of dipolar dumbbells (which may be partially dissociative) or charged hard-spheres fused in a tetrahedral configuration are treated in an extended MSA. The resulting expressions for the Born solvation free energy of an ion are very similar to that obtained earlier by Chan et al. for a charged hard-sphere ion in a dipolar hard-sphere solvent. The solvent averaged ion–ion potentials are obtained in the hypernetted chain approximation. Comparisons among results of various solvents are also made. In order of increasing oscillation amplitudes of the solvent averaged ion–ion potential for given molecular density and dipole moment we have continuum ≪dumbbell≤tetrahedral

The Born solvation free energy (BSFE) of two ions at a fixed distance from one another in a model polar solvent is obtained via two approaches. In the interaction-site approach, the two ions are modeled as a rigid extended dipolar dumbbell. Analytical expressions for the BSFE for such a dumbbell model in a dipolar dumbbell and a dipolar hard-sphere solvent are obtained under a mean spherical approximation (MSA). In the second approach, a thermodynamic cycle is established such that the BSFE for two ions a fixed distance apart can be expressed in terms of the solvent-averaged potential between the two ions and other known quantities. The results obtained via these two approaches are reasonably consistent, with the thermodynamic-cycle BSFE as a function of distance exhibiting more of the structure one expects to find in a molecular solvent. Both BSFE functions are substantially different from the corresponding continuum-solvent result. When the distance between two ions goes to infinity, our results reduce to earlier results for the single-ion BSFE obtained by us for a dipolar dumbbell solvent and by Chan et al. for a dipolar hard-sphere solvent. The BSFE of two ions in an ionic solution with a dielectric-continuum solvent is also obtained; it is found that the contribution of other ionic particles to the total BSFE is usually negligible if the dielectric constant of the solution is assumed to be unchanged. [ABSTRACT FROM AUTHOR]

The observation that the intramolecular direct-correlation-function matrix is very closely approximated by its large-r form for rigid diatomics suggests an approximation such that the site–site Ornstein–Zernike equation becomes analytically solvable for several molecular models of interest. Alternatively, approximation of the particle–particle direct correlation function by its asymptotic form directly yields the same approximation, in particle–particle (in contrast to site–site) language. Applications of this approximation, which can be regarded as an extended mean spherical approximation when viewed in particle–particle terms, are made to rigid hard diatomics, dipolar diatomics, and a tetrahedral molecular model. The close but subtle connections between our approximation procedure and earlier approximations are discussed. [ABSTRACT FROM AUTHOR]

The solvation dynamics of a pair of ions rigidly held a fixed distance from each other in either a dipolar hard-sphere solvent or a dipolar dumbbell solvent is investigated under the mean spherical approximation (MSA) applied to an interaction-site model in which the pair of ions is treated as a rigid extended dipolar dumbbell. An analytical expression for the reorganization free energy for a charge transfer reaction is obtained and compared with numerical results obtained via a thermodynamic cycle. Solvent effects on the rate of a charge transfer reaction are also investigated using the dielectric Green-function theory developed by Newton and Friedman. [ABSTRACT FROM AUTHOR]

A simple approximation scheme is given for the association constant of a family of models of associating particles introduced and considered by Cummings and Stell, Rasaiah et al., and Stell. The result correctly reduces to the law of mass action at low concentrations. For the ionic-species version, the theory requires accurate assessment of the cavity function of charged hard spheres, for which we develop a recipe. We show the close similarity (and some differences) between the above models and those considered by Wertheim, through a simple extensions of his models. We also note the equivalence of our approximation and Wertheim’s first-order thermodynamic perturbation theory. [ABSTRACT FROM AUTHOR]

The system of a fluid in the presence of a spherical semipermeable vesicle (SPV) with the freely mobile nonpermeating species inside the vesicle is investigated via an integral-equation approach. This system can be used to model certain feature of a biological cell, permeable to simple ions, in which solute proteins inside the cell are unable to permeate its walls. As an illustrative example of the use of our integral equations, the analytical solution for density profiles in the mean-spherical approximation/Debye–Hückel approximation (MSA/DH) is obtained, where the MSA is used to obtain the density profiles near a membrane and the DH approximation to obtain the bulk pair correlation functions. A method which applies to nonmobile protein fixed inside a cell is also considered. [ABSTRACT FROM AUTHOR]

An exact integral-equation formalism for a system of a binary hard-sphere mixture interacting with a spherical semipermeable vesicle (SPV) and plane semipermeable membrane (SPM) is derived by using the Ornstein–Zernike (OZ) equation with appropriate closures. The Percus–Yevick (PY) closure or the hypernetted chain (HNC) closure, in which the bulk correlation is obtained by the PY approximation, are considered as examples. We refer to these as the PY/PY and HNC/PY approximations, respectively. The mixture contains solvent particles, which are permeable to the membrane, and solute particles (‘‘protein’’ or ‘‘polymer’’ particles), which can not pass through the membrane. We develop an exact general formalism for this problem and as an illustration of its use give quantative results for solvent and solute particles modeled as hard spheres of different diameters. An analytical expression for the density ratio in the PY/PY and HNC/PY approximations between two sides of a plane SPM is obtained. Results obtained from these expressions agree very well with results obtained by equating chemical potentials in the region of interest. It turns out that the protein–membrane direct correlation function can be given by a simple analytic expression for the limit of a point solvent in the PY/PY approximation. The osmotic pressure and density profiles for the system containing an ideal spherical SPV or plane SPM in the PY/PY approximation are evaluated. Extension to the nonlocal density-functional closures previously introduced by Blum and Stell is discussed. Finally, we note that certain impenetrable-wall problems previously considered elsewhere can be regarded as semipermeable membrane problems treated via McMillan–Mayer formalism in the continuum–solvent approximation. [ABSTRACT FROM AUTHOR]

Integral equations that yield the charge and density profiles are derived for a Donnan system, in which an ionic solution is separated into two regions by a semipermeable membrane (SPM) or a spherical semipermeable vesicle (SPV). These equations are obtained from the Ornstein–Zernike (OZ) equation. We show how quantitative results can be obtained from either the mean spherical approximation (MSA) closure or the hypernetted-chain (HNC) closure for profiles. Use is made of bulk-correlation input obtained by means of the Debye–Hückel approximation, the MSA approximation, or the HNC approximation. The resulting approximations will be referred as MSA/DH, HNC/DH, MSA/MSA, etc. The system on which we focus contains three charged hard-sphere species: cation, anion, and a large ion (a protein or polymer ion) separated by a plane SPM, through which the large ion cannot pass, and to one side of which all large ions are confined, or a spherical SPV, outside of which the large ions are confined. Analytical expressions for the bulk density ratio between the two sides of a plane membrane as well as the membrane potential in various approximations are obtained. Results obtained from these expresssions are compared with the results obtained by equating electrochemical potentials. A new contact-value theorem is provided for the plane SPM system. Analytical solutions for the charge profile and the potential profile in the MSA/DH approximation are obtained. It turns out that results obtained in the HNC/DH approximation are exactly the same as those obtained by using 1D nonlinear Poisson–Boltzmann equations if the repulsive cores of the macroions are neglected. [ABSTRACT FROM AUTHOR]

We investigate the partition of ionic species in a system of two phases that are immiscible even in the limit of vanishing ionic concentrations. An analytic expression for the solvation free energy and for the standard free energy of transfer is obtained for dipolar hard-sphere solvents in the mean spherical approximation. We find that both dipolar hard-sphere solvents and continuum solvent models yield an electric potential difference (equilibrium junction potential) between two pure solvents in contact that is identically zero. Simple analytic expressions for partition coefficients and junction potentials are obtained in the ideal-solution limit for these solvent models. We note that for the junction potential the ideal solution limits differ in general from the pure-solvent values. For nonideal solutions, approximations based on the mean spherical approximation can be applied conveniently to calculate the activities of ionic species and to obtain the partition coefficients. [ABSTRACT FROM AUTHOR]

Studies the equilibrium thermodynamics of homopolymers and clusters with square-well interactions through constant-temperature discontinuous molecular dynamics (DMD) and Monte Carlo simulations. Monte Carlo results for chains of fixed-bond lengths; DMD results for chains with flexible bond lengths; Square-well cluster of 64 square-well beads.

Motivation: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processes, functional mechanisms, and drug discovery. Protein-peptide interactions can be analyzed by studying the structures of protein-peptide complexes. However, only a small portion has known complex structures and experimental determination of protein-peptide interaction is costly and inefficient. Thus, predicting peptide-binding sites computationally will be useful to improve efficiency and cost effectiveness of experimental studies. Here, we established a machine learning method called SPRINT-Str (Structure-based prediction of protein-Peptide Residue-level Interaction) to use structural information for predicting protein-peptide binding residues. These predicted binding residues are then employed to infer the peptide-binding site by a clustering algorithm. Results: SPRINT-Str achieves robust and consistent results for prediction of protein-peptide binding regions in terms of residues and sites. Matthews' Correlation Coefficient (MCC) for 10-fold cross validation and independent test set are 0.27 and 0.293, respectively, as well as 0.775 and 0.782, respectively for area under the curve. The prediction outperforms other state-of-the-art methods, including our previously developed sequence-based method. A further spatial neighbor clustering of predicted binding residues leads to prediction of binding sites at 20-116% higher coverage than the next best method at all precision levels in the test set. The application of SPRINT-Str to protein binding with DNA, RNA and carbohydrate confirms the method's capability of separating peptide-binding sites from other functional sites. More importantly, similar performance in prediction of binding residues and sites is obtained when experimentally determined structures are replaced by unbound structures or quality model structures built from homologs, indicating its wide applicability. Availability and implementation: http://sparks-lab.org/server/SPRINT-Str. [ABSTRACT FROM AUTHOR]

Turbidites of the Early Cretaceous Lingshandao Formation on Lingshan Island, eastern China, show numerous soft-sediment deformation structures. The turbidites accumulated in a rift basin plain on the distal part of a low-energy fan, together with autochthonous fine-grained sediments that settled from suspension. Occasionally, sets of both types of sediments slumped down the basin slope. The turbidites were studied in two sections. Paleocurrent directions, measured from sole marks at the base of the sandy turbidites, indicate a slope from SE to NW; this is consistent with the dip direction of the axial planes of the major slump folds. Among the numerous types of soft-sediment deformation structures that are present, two types are of special interest because of their specific genesis, viz. rip-up clasts and dome structures. It appears that rapid sedimentation must be considered as the main trigger behind these deformations: the rapid accumulation of particularly the sandy turbidites resulted in overloading of the underlying beds and then consequently in an increase in their pore-water pressure that induced liquefaction and fluidization, which triggered the formation of the rip-up clasts and dome structures. The downslope movement of freshly deposited turbidites after slope failure over the inclined sedimentary surface induced shear stresses, which resulted in the complication of the rip-up clasts and the preferred orientation of some dome structures. Both the dip directions of the axial planes of some of the dome structures and microfolds within the rip-up clasts are consistent with the paleocurrent direction indicated by the sole marks and the slump folds. [ABSTRACT FROM AUTHOR]

RNA is essential for a variety of biological processes, including protein synthesis and gene regulation. Understanding RNA structure-dependent regulatory mechanisms and cellular functions could help develop better RNA-based therapeutics. The structural flexibility, target binding, and environmental circumstances are just a few examples of the many variables that may affect RNA function. Given their complexity and dynamic nature, it is difficult to predict and analyze RNA structure and function accurately. Many fields have benefited significantly from advances in artificial intelligence (AI) technology, which has also opened previously unimaginable possibilities for understanding RNA structure and function. Recent progress in AI-based techniques for predicting RNA structure and function as well as RNA design provide directions and insights for future research on the sequence–structure–function relation of RNAs. RNA functions by interacting with its intended targets structurally. However, due to the dynamic nature of RNA molecules, RNA structures are difficult to determine experimentally or predict computationally. Artificial intelligence (AI) has revolutionized many biomedical fields and has been progressively utilized to deduce RNA structures, target binding, and associated functionality. Integrating structural and target binding information could also help improve the robustness of AI-based RNA function prediction and RNA design. Given the rapid development of deep learning (DL) algorithms, AI will provide an unprecedented opportunity to elucidate the sequence–structure–function relation of RNAs. [ABSTRACT FROM AUTHOR]

A simple interpolation scheme (SIS) suggested in an earlier paper is used to obtain the excess Helmholtz free energy and the equation of state for the shielded sticky-shell model and the shielded sticky-point model of associative fluids. It is found that the equation of state under the SIS for a fully associated homonuclear dumbbell fluid is quite accurate as long as L*=L/σ≥0.8. For ionic association, the excess Helmholtz free energy in this work reduces to that of Bjerrum’s theory in the ideal limit. An analytical equation of state for associative ions is evaluated. [ABSTRACT FROM AUTHOR]

Protein structure prediction is a long-standing problem in molecular biology. Due to lack of an accurate energy function, it is often difficult to know whether the sampling algorithm or the energy function is the most important factor for failure of locating near-native conformations of proteins. This article examines the size dependence of sampling effectiveness by using a perfect 'energy function': the root-mean-squared distance from the target native structure. Using protein targets up to 460 residues from critical assessment of structure prediction techniques (CASP11, 2014), we show that the accuracy of near native structures sampled is relatively independent of protein sizes but strongly depends on the errors of predicted torsion angles. Even with 40% out-of-range angle prediction, 2 Å or less near-native conformation can be sampled. The result supports that the poor energy function is one of the bottlenecks of structure prediction and predicted torsion angles are useful for overcoming the bottleneck by restricting the sampling space in the absence of a perfect energy function. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Astronomical forcing has been shown to be a fundamental driver of climate change through geological time. Pelagic, bedded cherts deposited in Mesozoic ocean basins with chert–mudstone cycles have been shown to contain the imprint of Milankovitch astronomical climate forcing. In the Chaohu region, South China, we studied a Middle Permian radiolarian chert sequence (Gufeng Formation) with chert–mudstone couplets reminiscent of the Mesozoic cherts, but deposited on a continental shelf. Spectral analysis of lithologic bed thickness data from two sections of this chert sequence reveals that 13 cm to 20 cm chert–mudstone cycles in the stratigraphic domain match theoretical 32-kyr Middle Permian obliquity cycling, together with a hierarchy of other cycles with 12 cm, 9 cm, 7 cm, 6.6 cm and 5.4 cm wavelengths. Tuning the 13 cm to 20 cm stratigraphic cycles to Earth's obliquity cycle periodicity indicates that the cm-scale cycles are precession-scale variations with a strong ∼400 kyr amplitude modulation. Tuning to theoretical precession terms provides further support for the astronomical forcing of the chert sequence. We propose that monsoon-controlled upwelling contributed to the development of the chert–mudstone cycles. A seasonal monsoon controlled by astronomical forcing (i.e., insolation) influenced the intensity of upwelling. Stronger upwelling increased radiolarian productivity in the surface ocean, increasing silica deposition. Glacio-eustatic oscillations from ice sheet dynamics in southern Gondwana modulated terrigenous mud flux to the basin. The two processes jointly contributed to the astronomical rhythms of these tropical chert–mudstone sequences, which are characterized by comparably strong obliquity and precession responses. Subsequent diagenesis distorted the chert and mudstone layering, but not enough to destroy the original stratigraphic patterns. The resulting astronomical time scale (ATS) assumes a Roadian/Wordian boundary age of 268.8 Ma for the onset of the first chert layer at the base of the sequence and ends at 264.1 Ma, for a total duration of 4.7 myr. [ABSTRACT FROM AUTHOR]

We describe the development of new force fields for protein side chain modeling called optimized side chain atomic energy (OSCAR). The distance-dependent energy functions (OSCAR-d) and side-chain dihedral angle potential energy functions were represented as power and Fourier series, respectively. The resulting 802 adjustable parameters were optimized by discriminating the native side chain conformations from non-native conformations, using a training set of 12,000 side chains for each residue type. In the course of optimization, for every residue, its side chain was replaced by varying rotamers, whereas conformations for all other residues were kept as they appeared in the crystal structure. Then, the OSCAR-d were multiplied by an orientation-dependent function to yield OSCAR-o. A total of 1087 parameters of the orientation-dependent energy functions (OSCAR-o) were optimized by maximizing the energy gap between the native conformation and subrotamers calculated as low energy by OSCAR-d. When OSCAR-o with optimized parameters were used to model side chain conformations simultaneously for 218 recently released protein structures, the prediction accuracies were 88.8% for χ, 79.7% for χ, 1.24 Å overall root mean square deviation (RMSD), and 0.62 Å RMSD for core residues, respectively, compared with the next-best performing side-chain modeling program which achieved 86.6% for χ, 75.7% for χ, 1.40 Å overall RMSD, and 0.86 Å RMSD for core residues, respectively. The continuous energy functions obtained in this study are suitable for gradient-based optimization techniques for protein structure refinement. A program with built-in OSCAR for protein side chain prediction is available for download at . © 2011 Wiley Periodicals, Inc. J Comput Chem 2011 [ABSTRACT FROM AUTHOR]

Abstract: Worldwide structural genomics projects are increasing structure coverage of sequence space but have not significantly expanded the protein structure space itself (i.e., number of unique structural folds) since 2007. Discovering new structural folds experimentally by directed evolution and random recombination of secondary-structure blocks is also proved rarely successful. Meanwhile, previous computational efforts for large-scale mapping of protein structure space are limited to simple model proteins and led to an inconclusive answer on the completeness of the existing observed protein structure space. Here, we build novel protein structures by extending naturally occurring circular (single-loop) permutation to multiple loop permutations (MLPs). These structures are clustered by structural similarity measure called TM-score. The computational technique allows us to produce different structural clusters on the same naturally occurring, packed, stable core but with alternatively connected secondary-structure segments. A large-scale MLP of 2936 domains from structural classification of protein domains reproduces those existing structural clusters (63%) mostly as hubs for many nonredundant sequences and illustrates newly discovered novel clusters as islands adopted by a few sequences only. Results further show that there exist a significant number of novel potentially stable clusters for medium-size or large-size single-domain proteins, in particular, >100 amino acid residues, that are either not yet adopted by nature or adopted only by a few sequences. This study suggests that MLP provides a simple yet highly effective tool for engineering and design of novel protein structures (including naturally knotted proteins). The implication of recovering new-fold targets from critical assessment of structure prediction techniques (CASP) by MLP on template-based structure prediction is also discussed. Our MLP structures are available for download at the publication page of the Web site http://sparks.informatics.iupui.edu. [Copyright &y& Elsevier]

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward. [ABSTRACT FROM AUTHOR]

Fluid inclusions have recorded the history of degassing in basalt. Some fluid inclusions in olivine and pyroxene phenocrysts of basalt were analyzed by micro-thermometry and Raman spectroscopy in this paper. The experimental results showed that many inclusions are present almost in a pure CO2 system. The densities of some CO2 inclusions were computed in terms of Raman spectroscopic characteristics of CO2 Fermi resonance at room temperature. Their densities change over a wide range, but mainly between 0.044 g/cm3 and 0.289 g/cm3. Their micro-thermometric measurements showed that the CO2 inclusions examined reached homogenization between 1145.5°C and 1265°C. The mean value of homogenization temperatures of CO2 inclusions in basalts is near 1210°C. The trap pressures (depths) of inclusions were computed with the equation of state and computer program. Distribution of the trap depths makes it know that the degassing of magma can happen over a wide pressure (depth) range, but mainly at the depth of 0.48 km to 3.85 km. This implicates that basalt magma experienced intensive degassing and the CO2 gas reservoir from the basalt magma also may be formed in this range of depths. The results of this study showed that the depth of basalt magma degassing can be forecasted from CO2 fluid inclusions, and it is meaningful for understanding the process of magma degassing and constraining the inorganogenic CO2 gas reservoir. [ABSTRACT FROM AUTHOR]

Statistical energy functions are discrete (or stepwise) energy functions that lack van der Waals repulsion. As a result, they are often applied directly to a given structure (native or decoy) without further energy minimization being performed to the structure. However, the full benefit (or hidden defect) of an energy function cannot be revealed without energy minimization. This paper tests a recently developed, all-atom statistical energy function by energy minimization with a fixed secondary helical structure in dihedral space. This is accomplished by combining the statistical energy function based on a distance-scaled finite ideal-gas reference (DFIRE) state with a simple repulsive interaction and an improper torsion energy function. The energy function was used to minimize 2000 random initial structures of 41 small and medium-sized helical proteins in a dihedral space with a fixed helical region. Results indicate that near-native structures for most studied proteins can be obtained by minimization alone. The average minimum root-mean-squared distance (rmsd) from the native structure for all 41 proteins is 4.1 Å. The energy function (together with a simple clustering of similar structures) also makes a reasonable selection of near-native structures from minimized structures. The average rmsd value and the average rank for the best structure in the top five is 6.8 Å and 2.4, respectively. The accuracy of the structures sampled and the structure selections can be improved significantly with the removal of flexible terminal regions in rmsd calculations and in minimization and with the increase in the number of minimizations. The minimized structures form an excellent decoy set for testing other energy functions because most structures are well-packed with minimum hard-core overlaps with correct hydrophobic/hydrophilic partitioning. They are available online at . [ABSTRACT FROM AUTHOR]

Cooperative binding of ligands to proteins can serve to increase their efficiency and to regulate their activity. Thus, understanding of the mechanism of cooperativity is one of the central concerns of molecular biology. For the tetrameric human hemoglobin (HbA), the cooperative mechanism involves a reasonably well understood combination of tertiary and quaternary changes that occur during the binding process. The dimeric hemoglobin of Scapharca (HbI), which is composed of subunits with the same fold as in HbA, is also highly cooperative but the structural changes on ligand binding are small. A re-orientation of Phe97 in the binding pocket and changes in the number of interfacial water moleculess have been implicated in the cooperative mechanism. To explore the role of these factors, we have investigated models of partially liganded intermediate states of HbI with molecular dynamics simulation methods. Since, unlike HbA, no structures for intermediates are available, they were constructed by combining subunits from the unliganded and liganded dimers. Two structurally distinct intermediates were examined, and it was shown that the transition between the two intermediates is directly coupled to the number of interfacial water molecules. Further, it was found that there is a well-defined water channel that connects the interface between the subunits to bulk water. The bottleneck (gate) of the channel, which can be open or closed, is made of hydrophilic residues. The implication of the present results for the cooperative mechanism of HbI is discussed. [Copyright &y& Elsevier]

Reports on the use of C alpha-based three-helix bundle-like protein model with a realistic thermodynamic phase diagram to calculate several hundred folding trajectories of helical proteins.

Examines the folding thermodynamics of a simple off-lattice three-helix-bundle protein model under equilibrium conditions. Details on the protein transition; Understanding the thermodynamics of proteins; Details on the phase behavior of proteins; Details on the study.

Exact results are obtained for isolated, freely jointed, square-well trimers bonded with an infinitely deep square-well potential. Bond flexibility is found to have small but detectable effects on structural and thermodynamic properties. A larger chain size, a higher heat capacity, and a sharper collapse transition with a lower transition temperature are observed for a flexibly bonded chain, relative to an infinitely stiff trimer. [ABSTRACT FROM AUTHOR]

Sedimentary chert phases from the Archean to the present are widely used to trace sedimentary environments and tectonic settings. Recently, chert nodules occurring within carbonates have been the subject of possible hydrothermal or biogenic origin, in lieu of a diagenetic origin. However, chert nodules from a vast cratonic basin represent extremely rich silica accumulations but less noted is how they respond to submarine hydrothermal activity (and/or surface siliceous organism productivity). The links between the cratonic‐type chert depositions and environmental changes regarding cratonic evolution need to be revisited at a large temporal‐spatial scale. The chert nodules are widespread throughout the Lower Permian Taiyuan Formation in the North China Craton (NCC). Several Taiyuan chert‐rich successions across the NCC have been selected to study possible links between chert deposition and cratonic evolution in scenario of partial cratonic activation of the northern NCC margin during the Late Paleozoic. Based on stratigraphic correlation, the chert nodules are ubiquitously, evenly distributed throughout the Taiyuan Formation at a large craton‐basin scale from the northern to southern interior NCC. Petrological results, elemental abundances, together with silicon and oxygen isotopic compositions of chert samples infer significant hydrothermal contributions for the silica accumulations. Therefore, the cratonic‐scale chert depositions of hydrothermal origin infer a giant and remote silica reservoir, linking to the large igneous province and magmatism in the NCC northern margins. The Taiyuan chert nodules could be unique marine sedimentary archives recording the Late Paleozoic NCC partial activation, which also generated continental records of igneous rocks, bauxites and tuffs. The strong tectonics of the northern margin, south‐dipping topography and northward transgression of the Early Permian NCC facilitated the chert deposition on the shallow marine platform in the cratonic interior. [ABSTRACT FROM AUTHOR]

The article presents a study which examines the reservoir forming conditions and exploration potential of Upper Paleozoic in Eastern Linqing Depression in China. Results of the investigation revealed that coal and mudstone of Upper Paleozoic could act as source rocks which have gone through six stages and classify to three burial history types. The gas-generating intensity of coal-bearing source rock has been cited in the study as the key factor to predict favorable hydrocarbon accumulation.

This paper examines the folding mechanism of an individual β-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel β-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single β-hairpin in literature is confirmed to be useful in describing β-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, β1-β2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of β2-β3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent. [ABSTRACT FROM AUTHOR]