Based on the knot theory and researching of network structures of glucomannan molecules, the polysaccharides were analyzed. The link prediction analysis is to further reveal the interactions between polysaccharides, t...Based on the knot theory and researching of network structures of glucomannan molecules, the polysaccharides were analyzed. The link prediction analysis is to further reveal the interactions between polysaccharides, to elaborate QSAR of polysaccharides, and to analyze the network conformation relationships among polysaccharides. We made a classification for glucomannan molecules based on the related domestic and international theories, and investigated their network structures and application prospects. The knot theory and the link predictions not only simplify the glucomannan microscopic descriptions but also play a guiding role in predicting and regulating the structures.展开更多
The knots frequently occur in biopolymer and their diffusion plays an active role in the gene regulation.In this work,Langevin dynamics simulations were carried out to detect the diffusion behaviours of a knot along a...The knots frequently occur in biopolymer and their diffusion plays an active role in the gene regulation.In this work,Langevin dynamics simulations were carried out to detect the diffusion behaviours of a knot along a tensioned polymer in different spatial constraints.The polymer accommodating a knot was tethered to two macrospheres to block the unravelling of the knot.As a result,the curves for the diffusion coefficients of the knot with different bending stiffness as a function of the tension in different spatial constraints were obtained.In the space without constraints or with weak constraints,the corresponding curves for the knot with relatively large bending stiffness exhibited two turnover behaviours.On the contrary,for the knot with relatively small bending stiffness,the diffusion coefficients were monotonically reduced with increasing tension.However,in a space with strong constraints,all the curves showed one turnover behaviour regardless of the bending stiffness.The turnover behaviours divided the curves into different regimes,and the dominant diffusion mechanisms in the regimes,namely,knot-region breathing,self-reptation,and internal friction,were clearly identified.The effective friction coefficientsξof the knots with 3_(1),4_(1),5_(1) and 5_(2) types as a function of the knot size N at a fixed tension were well fitted by the relationξ∝N.The effective friction coefficients of the knots at relatively large tension f>3 sharply increased with the knot complexity,which is not dependent on the spatial constraints.By contrast,the values of these coefficients at relatively small tension f≤3 were remarkably dependent on the spatial constraints.Our work not only provides valuable simulation results to assist the understanding of the diffusion of DNA knot,but also highlights the single-molecule design for the manipulation of DNA knots in future.展开更多
Understanding the factors that contribute to population stability in long-distance migrant birds is increasingly important, particularly given global climate change, sea level rise, and loss or disturbance at essentia...Understanding the factors that contribute to population stability in long-distance migrant birds is increasingly important, particularly given global climate change, sea level rise, and loss or disturbance at essential habitats. While the populations of most shorebirds are declining worldwide, those that migrate through Delaware Bay, New Jersey and Delaware, are declining at the most rapid rate despite conservation efforts. In this paper, we 1) provide background information on population declines of red knots (Calidris canutus rufa) using Delaware Bay, threats to their foraging, and efforts to reduce threats, 2) summarize briefly our studies of the effects of human activities on knots and other shorebirds, 3) present data on management efforts to protect knots and other shorebirds from the activities of people, and 4) discuss the efficacy of such efforts (usually referred to as “decreasing the effect of human disturbances”). The Shorebird Project on Delaware Bay is over 25 years old and provides long-term data to help assess the status of shorebird numbers, particularly for red knot, as well as the density of horseshoe crabs (Limulus polyphemus) and their eggs. Red knots have continued to decline even more precipitously in the last few years, presenting cause for concern. Protective efforts have been successful in reducing human disruption on the N.J. Delaware Bay beaches, but the lack of uniformity in implementation across the New Jersey side, and across the whole Bay have hampered further improvements. Implementation of signs, fencing, and stewards on some beaches significantly enhanced the use of these beaches by red knots, determined by examining the use of beaches pre- and post-implementation. Implementation of fencing and stewards had the greatest effect. From 1986 to 2018, there was a significant shift in the percent of Delaware Bay red knots using the NJ side, where protection efforts had been implemented on many of the beaches. Merely restricting access (without fencing or other efforts) did not res展开更多
基金Supported by the National Natural Science Foundation of China(31271837 and 31071518)Specialized Research Fund for the Doctoral Program of Higher Education jointly funded by Ministry of Education(20113515110010)+2 种基金Special Research Funds from Ministry of Science and Technology(2012GA7200022)Major projects of industries,universities and research in Fujian Province(2013N5003)Natural Science Foundation of Fujian Province(2011J0101)
文摘Based on the knot theory and researching of network structures of glucomannan molecules, the polysaccharides were analyzed. The link prediction analysis is to further reveal the interactions between polysaccharides, to elaborate QSAR of polysaccharides, and to analyze the network conformation relationships among polysaccharides. We made a classification for glucomannan molecules based on the related domestic and international theories, and investigated their network structures and application prospects. The knot theory and the link predictions not only simplify the glucomannan microscopic descriptions but also play a guiding role in predicting and regulating the structures.
基金The National Natural Science Foundation of China under Grant Nos.11864006, 11874309, 12164007, and 12204118
文摘The knots frequently occur in biopolymer and their diffusion plays an active role in the gene regulation.In this work,Langevin dynamics simulations were carried out to detect the diffusion behaviours of a knot along a tensioned polymer in different spatial constraints.The polymer accommodating a knot was tethered to two macrospheres to block the unravelling of the knot.As a result,the curves for the diffusion coefficients of the knot with different bending stiffness as a function of the tension in different spatial constraints were obtained.In the space without constraints or with weak constraints,the corresponding curves for the knot with relatively large bending stiffness exhibited two turnover behaviours.On the contrary,for the knot with relatively small bending stiffness,the diffusion coefficients were monotonically reduced with increasing tension.However,in a space with strong constraints,all the curves showed one turnover behaviour regardless of the bending stiffness.The turnover behaviours divided the curves into different regimes,and the dominant diffusion mechanisms in the regimes,namely,knot-region breathing,self-reptation,and internal friction,were clearly identified.The effective friction coefficientsξof the knots with 3_(1),4_(1),5_(1) and 5_(2) types as a function of the knot size N at a fixed tension were well fitted by the relationξ∝N.The effective friction coefficients of the knots at relatively large tension f>3 sharply increased with the knot complexity,which is not dependent on the spatial constraints.By contrast,the values of these coefficients at relatively small tension f≤3 were remarkably dependent on the spatial constraints.Our work not only provides valuable simulation results to assist the understanding of the diffusion of DNA knot,but also highlights the single-molecule design for the manipulation of DNA knots in future.
文摘Understanding the factors that contribute to population stability in long-distance migrant birds is increasingly important, particularly given global climate change, sea level rise, and loss or disturbance at essential habitats. While the populations of most shorebirds are declining worldwide, those that migrate through Delaware Bay, New Jersey and Delaware, are declining at the most rapid rate despite conservation efforts. In this paper, we 1) provide background information on population declines of red knots (Calidris canutus rufa) using Delaware Bay, threats to their foraging, and efforts to reduce threats, 2) summarize briefly our studies of the effects of human activities on knots and other shorebirds, 3) present data on management efforts to protect knots and other shorebirds from the activities of people, and 4) discuss the efficacy of such efforts (usually referred to as “decreasing the effect of human disturbances”). The Shorebird Project on Delaware Bay is over 25 years old and provides long-term data to help assess the status of shorebird numbers, particularly for red knot, as well as the density of horseshoe crabs (Limulus polyphemus) and their eggs. Red knots have continued to decline even more precipitously in the last few years, presenting cause for concern. Protective efforts have been successful in reducing human disruption on the N.J. Delaware Bay beaches, but the lack of uniformity in implementation across the New Jersey side, and across the whole Bay have hampered further improvements. Implementation of signs, fencing, and stewards on some beaches significantly enhanced the use of these beaches by red knots, determined by examining the use of beaches pre- and post-implementation. Implementation of fencing and stewards had the greatest effect. From 1986 to 2018, there was a significant shift in the percent of Delaware Bay red knots using the NJ side, where protection efforts had been implemented on many of the beaches. Merely restricting access (without fencing or other efforts) did not res
