The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approa...The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.展开更多
A closed analytical relation is derived for the two-center nuclear attraction integrals over Slater type orbitals (STOs) in terms of binomial coefficients. This formula can be used in highly accurate calculations of t...A closed analytical relation is derived for the two-center nuclear attraction integrals over Slater type orbitals (STOs) in terms of binomial coefficients. This formula can be used in highly accurate calculations of the nuclear at-traction integrals. The relationships obtained are valid for arbitrary values of quantum numbers and screening con-stants of STOs and location of nuclei.展开更多
We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments.By combining an atomic-interaction based coarse-grained model with an all-a...We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments.By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm,we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations.We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy.These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.展开更多
文摘The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.
文摘A closed analytical relation is derived for the two-center nuclear attraction integrals over Slater type orbitals (STOs) in terms of binomial coefficients. This formula can be used in highly accurate calculations of the nuclear at-traction integrals. The relationships obtained are valid for arbitrary values of quantum numbers and screening con-stants of STOs and location of nuclei.
基金the National Natural Science Foundation of China(Grant Nos.11974173 and 11934008)the HPC Center of Nanjing University。
文摘We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments.By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm,we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations.We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy.These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.
