Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand...Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand interactions.The major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure.With these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.展开更多
Generic polymer models capturing the chain connectivity and excluded-volume interactions between polymer segments can be classified, according to whether or not the 3D integral of the latter diverges, into hard- and s...Generic polymer models capturing the chain connectivity and excluded-volume interactions between polymer segments can be classified, according to whether or not the 3D integral of the latter diverges, into hard- and soft-core models. Taking homogeneous systems of compressible homopolymer melts (or equivalently homopolymer solutions in an implicit, good solvent) in the continuum as an example, we recently compared the correlation effects on the structural and thermodynamic properties of the hard- and soft-core models given by the polymer reference interaction site model (PRISM) theory with the Percus-Yevick (PY) closure (Polymers 2023, 15, 1180). Here we analyzed in detail the numerical errors and behavior of the interchain pair correlation functions (PCFs) given by the PRISM-PY calculations of these models using an efficient numerical approach that we proposed. Our numerical approach has the least number of independent variables to be iteratively solved, analytically treats the discontinuities caused by the non-bonded pair potential (such as that of the hard spheres) and takes only the inverse Fourier transform of the interchain indirect PCF between polymer segments (which is continuous and decays towards 0 with increasing wavenumber much faster than both the interchain direct and total PCFs), and is essential for us to accurately solve the PRISM-PY theory for chain length N as large as 106. To capture the correlation-hole effect, the real-space cut-off in the PRISM calculations should be proportional to the square root of N.展开更多
As part of a larger project to examine the richness and distribution of wildlife in Kumtag Desert area, we conducted camera trapping surveys during the period 2010–2012 at seven watering sites in an arid region of th...As part of a larger project to examine the richness and distribution of wildlife in Kumtag Desert area, we conducted camera trapping surveys during the period 2010–2012 at seven watering sites in an arid region of the Altun Mountains in western China. Information on activity patterns of the wild bactrian camel (Camelus ferus), kiang (Equus kiang), goitered gazelle (Gazella subgutturosa), argali (Ovis ammon), blue sheep (Pseudois nayaur), red fox (Vulpes vulpes), and wolf (Canis lupus) was obtained. We found that the wild camel, kiang, goitered gazelle, argali, and blue sheep were predominantly diurnal at watering sites, whereas red fox and wolf were nocturnal. Five herbivores partitioned the use of watering sites in a temporal manner to minimize the risk of predation by carnivores. The wild camel was the dominant herbivorous species at the watering sites. The kiang, goitered gazelle, argali, and blue sheep displayed adaptive water use by altering spatial or temporal patterns based on the presence or absence of wild camel, to minimize the risk of interspecific strife. These results are suggestive of the differences in activity patterns that might modulate water partitioning by different species, and provide insights for the development of conservation strategies for integrated species and decisions regarding water development in the Altun Mountains.展开更多
The spin-orbit interaction of the 5d electron needs to be taken into account to give the proper energy structure for the 4fN-1 5d configuration of heavy lanthanide ions occupying a site with ligands forming an octahed...The spin-orbit interaction of the 5d electron needs to be taken into account to give the proper energy structure for the 4fN-1 5d configuration of heavy lanthanide ions occupying a site with ligands forming an octahedron. This paper derives theoretical results for the energy structure by treating the t2 orbitals as quasi p orbitals and then using angular-momentum coupling techniques. An analytic expression for the electric dipole absorption line strengths between 4fN multiplets and 4fN- 1 5d states is given in terms of various angular-momentum quantum numbers and re-coupling coefficients. The result is then applied to interpret the excitation spectrum of Cs2NaYF6：Er3＋. Tbe high-spin and lowspin states of Cs2NaYF6：Er3＋ are discussed in terms of the wavefunctions obtained by using the developed theoretical model.展开更多
Time-dependent diffusion coefficient and conventional diffusion constant are calculated and analyzed to study diffusion of nanoparticles in polymer melts. A generalized Langevin equa- tion is adopted to describe the d...Time-dependent diffusion coefficient and conventional diffusion constant are calculated and analyzed to study diffusion of nanoparticles in polymer melts. A generalized Langevin equa- tion is adopted to describe the diffusion dynamics. Mode-coupling theory is employed to calculate the memory kernel of friction. For simplicity, only microscopic terms arising from binary collision and coupling to the solvent density fluctuation are included in the formalism. The equilibrium structural information functions of the polymer nanocomposites required by mode-coupling theory are calculated on the basis of polymer reference interaction site model with Percus-Yevick closure. The effect of nanoparticle size and that of the polymer size are clarified explicitly. The structural functions, the friction kernel, as well as the diffusion coefficient show a rich variety with varying nanoparticle radius and polymer chain length. We find that for small nanoparticles or short chain polymers, the characteristic short time non-Markov diffusion dynamics becomes more prominent, and the diffusion coefficient takes longer time to approach asymptotically the conventional diffusion constant. This constant due to the microscopic contributions will decrease with the increase of nanoparticle size, while increase with polymer size. Furthermore, our result of diffusion constant from mode- coupling theory is compared with the value predicted from the Stokes-Einstein relation. It shows that the microscopic contributions to the diffusion constant are dominant for small nanoparticles or long chain polymers. Inversely, when nanonparticle is big, or polymer chain is short, the hydrodynamic contribution might play a significant role.展开更多
基金supported in part by the National Natural Science Foundation of China(Grant Nos.T2225007 and T2222012)the Foundation for Innovative Research Groups of State Key Laboratory of Microbial Technology,China(Grant No.WZCX2021-03).
文摘Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand interactions.The major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure.With these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.
基金the donors of The American Chemical Society Petroleum Research Fund for partial support of this research
文摘Generic polymer models capturing the chain connectivity and excluded-volume interactions between polymer segments can be classified, according to whether or not the 3D integral of the latter diverges, into hard- and soft-core models. Taking homogeneous systems of compressible homopolymer melts (or equivalently homopolymer solutions in an implicit, good solvent) in the continuum as an example, we recently compared the correlation effects on the structural and thermodynamic properties of the hard- and soft-core models given by the polymer reference interaction site model (PRISM) theory with the Percus-Yevick (PY) closure (Polymers 2023, 15, 1180). Here we analyzed in detail the numerical errors and behavior of the interchain pair correlation functions (PCFs) given by the PRISM-PY calculations of these models using an efficient numerical approach that we proposed. Our numerical approach has the least number of independent variables to be iteratively solved, analytically treats the discontinuities caused by the non-bonded pair potential (such as that of the hard spheres) and takes only the inverse Fourier transform of the interchain indirect PCF between polymer segments (which is continuous and decays towards 0 with increasing wavenumber much faster than both the interchain direct and total PCFs), and is essential for us to accurately solve the PRISM-PY theory for chain length N as large as 106. To capture the correlation-hole effect, the real-space cut-off in the PRISM calculations should be proportional to the square root of N.
基金funded by National Nonprofit Institute Research Grant of Chinese Academy of Forestry (CAFYBB2011003)the Administrative Bureau of Xinjiang Lop Nur Wild Camel National Nature Reservethe Administrative Bureau of Gansu Annanba Wild Camel National Nature Reserve for their support of this study
文摘As part of a larger project to examine the richness and distribution of wildlife in Kumtag Desert area, we conducted camera trapping surveys during the period 2010–2012 at seven watering sites in an arid region of the Altun Mountains in western China. Information on activity patterns of the wild bactrian camel (Camelus ferus), kiang (Equus kiang), goitered gazelle (Gazella subgutturosa), argali (Ovis ammon), blue sheep (Pseudois nayaur), red fox (Vulpes vulpes), and wolf (Canis lupus) was obtained. We found that the wild camel, kiang, goitered gazelle, argali, and blue sheep were predominantly diurnal at watering sites, whereas red fox and wolf were nocturnal. Five herbivores partitioned the use of watering sites in a temporal manner to minimize the risk of predation by carnivores. The wild camel was the dominant herbivorous species at the watering sites. The kiang, goitered gazelle, argali, and blue sheep displayed adaptive water use by altering spatial or temporal patterns based on the presence or absence of wild camel, to minimize the risk of interspecific strife. These results are suggestive of the differences in activity patterns that might modulate water partitioning by different species, and provide insights for the development of conservation strategies for integrated species and decisions regarding water development in the Altun Mountains.
基金supported by the National Natural Science Foundation of China(Grant Nos 10874173 and 10774140)
文摘The spin-orbit interaction of the 5d electron needs to be taken into account to give the proper energy structure for the 4fN-1 5d configuration of heavy lanthanide ions occupying a site with ligands forming an octahedron. This paper derives theoretical results for the energy structure by treating the t2 orbitals as quasi p orbitals and then using angular-momentum coupling techniques. An analytic expression for the electric dipole absorption line strengths between 4fN multiplets and 4fN- 1 5d states is given in terms of various angular-momentum quantum numbers and re-coupling coefficients. The result is then applied to interpret the excitation spectrum of Cs2NaYF6：Er3＋. Tbe high-spin and lowspin states of Cs2NaYF6：Er3＋ are discussed in terms of the wavefunctions obtained by using the developed theoretical model.
基金This work was supported by the National Natural Science Foundation of China （No.21173152）, the Ministry of Education of China （No.NCET-11-0359 and No.2011SCU04B31）, and the Science and Technology Department of Sichuan Province （No.2011HH0005）.
文摘Time-dependent diffusion coefficient and conventional diffusion constant are calculated and analyzed to study diffusion of nanoparticles in polymer melts. A generalized Langevin equa- tion is adopted to describe the diffusion dynamics. Mode-coupling theory is employed to calculate the memory kernel of friction. For simplicity, only microscopic terms arising from binary collision and coupling to the solvent density fluctuation are included in the formalism. The equilibrium structural information functions of the polymer nanocomposites required by mode-coupling theory are calculated on the basis of polymer reference interaction site model with Percus-Yevick closure. The effect of nanoparticle size and that of the polymer size are clarified explicitly. The structural functions, the friction kernel, as well as the diffusion coefficient show a rich variety with varying nanoparticle radius and polymer chain length. We find that for small nanoparticles or short chain polymers, the characteristic short time non-Markov diffusion dynamics becomes more prominent, and the diffusion coefficient takes longer time to approach asymptotically the conventional diffusion constant. This constant due to the microscopic contributions will decrease with the increase of nanoparticle size, while increase with polymer size. Furthermore, our result of diffusion constant from mode- coupling theory is compared with the value predicted from the Stokes-Einstein relation. It shows that the microscopic contributions to the diffusion constant are dominant for small nanoparticles or long chain polymers. Inversely, when nanonparticle is big, or polymer chain is short, the hydrodynamic contribution might play a significant role.
