The dynamics of tracers in crowded matrix is of interest in various areas of physics, such as the diffusion of proteins in living cells. By using two-dimensional (2D) Langevin dynamics simulations, we investigate th...The dynamics of tracers in crowded matrix is of interest in various areas of physics, such as the diffusion of proteins in living cells. By using two-dimensional (2D) Langevin dynamics simulations, we investigate the diffusive properties of a tracer of a diameter in crowded environments caused by randomly distributed crowders of a diameter. Results show that the emergence of subdiffusion of a tracer at intermediate time scales depends on the size ratio of the tracer to crowders a. If a falls between a lower critical size ratio and a upper one, the anomalous diffusion occurs purely due to the molecular crowding, tqlrther analysis indicates that the physical origin of subdiffusion is the "cage effect". Moreover, the subdiffusion exponent α decreases with the increasing medium viscosity and the degree of crowding, and gets a minimum αmin=0.75 at δ=1. At long time scales, normal diffusion of a tracer is recovered. For δ≤1, the relative mobility of tracers is independent of the degree of crowding. Meanwhile, it is sensitive to the degree of crowding for δ〉l. Our results are helpful in deepening the understanding of the diffusive properties of biomacromolecules that lie within crowded intracellular environments, such as proteins, DNA and ribosomes.展开更多
Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium visc...Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders. By contrast, the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders. Notably, the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36-0.44. We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.展开更多
Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional (3D) Langevin dynamics simulations, we investigate adsorption behaviors of m...Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional (3D) Langevin dynamics simulations, we investigate adsorption behaviors of multivalent polymer chains to a surface with receptors. Multivalent polymer chains display superselective adsorption. Furthermore, the range of density of surface receptors at which a multivalent polymer chain displays a superselective behavior, narrows down for chains with higher density of ligands. Meanwhile, the optimal density of surface receptors where the highest superselectivity is achieved, decreases with increasing the density of ligands. Then, the conformational properties of bound multivalent chains are studied systematically. Interestingly, we find that the equilibrium radius of gyration Rg and its horizontal component have a maximum as a function of the density of surface receptors. The scaling exponents of Rg with the length of chain suggest that with increasing the density of surface receptors., the conformations of a bound multivalent polymer chain first fall in between those of a two-dimensional (2D) and a 3D chain, while it is slightly collapsed subsequently.展开更多
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics ...Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation [J. Chem. Phys. 147, 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended "middle" scheme [J. Chem. Phys. 147, 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation thermostatting processes with molecular is proposed for understanding efficient stochastic dynamics.展开更多
We recently reported several driver genes of biliary tract carcinoma(BTC) that are known to play important roles in oncogenesis and disease progression. Although the need for developing novel therapeutic strategies is...We recently reported several driver genes of biliary tract carcinoma(BTC) that are known to play important roles in oncogenesis and disease progression. Although the need for developing novel therapeutic strategies is increasing, there are very few BTC cell lines and xenograft models currently available for conducting preclinical studies. Using a total of 88 surgical BTC specimens and 536 immunodeficient mice, 28 xenograft models and 13 new BTC cell lines, including subtypes, were established. Some of our cell lines were found to be resistant to gemcitabine, which is currently the first choice of treatment, thereby allowing highly practical preclinical studies to be conducted. Using the aforementioned cell lines and xenograft models and a clinical pathological database of patients undergoing BTC resection, we can establish a preclinical study system and appropriate parameters for drug efficacy studies to explore new biomarkers for practical applications in the future studies.展开更多
In this article, the dynamical process of the dielectric particle in the optical tweezer using the counter-propagating Gaussian pulses is investigated by the Langevin equation concerning the Brownian motion. The tempo...In this article, the dynamical process of the dielectric particle in the optical tweezer using the counter-propagating Gaussian pulses is investigated by the Langevin equation concerning the Brownian motion. The temporal stabilities of particle is simulated. The influence of the duration, repetition period and delay time between pulses on stability is discussed.展开更多
The stochastic systems without detailed balance are common in various chemical reaction systems, such as metabolic network systems. In studies of these systems, the concept of potential landscape is useful However, wh...The stochastic systems without detailed balance are common in various chemical reaction systems, such as metabolic network systems. In studies of these systems, the concept of potential landscape is useful However, what are the su^cient and necessary conditions of the existence of the potential function is still an open problem. Use Hodge decomposition theorem in differential form theory, we focus on the general chemical Langevin equations, which reitect complex chemical reaction systems. We analysis the conditions for the existence of potential landscape of the systems. By mapping the stochastic differential equations to a Hamiltonian mechanical system, we obtain the Fokker-Planck equation of the chemical reaction systems. The obtained Fokker-Planck equation can be used in further studies of other steady properties of complex chemical reaction systems, such as their steady state entropies.展开更多
When visiting Kazakhstan,President Xi Jinping proposed the strategic project to build the" Silk Road economic zone" . Under this background,the study of postgraduate students' English teaching is very important.Thi...When visiting Kazakhstan,President Xi Jinping proposed the strategic project to build the" Silk Road economic zone" . Under this background,the study of postgraduate students' English teaching is very important.This paper analyzes the historical status of the Silk Road,the significance of culture teaching of Silk Road countries,presents the study of the main elements and its implementation approaches of the Silk Road culture teaching in postgraduate students' English class,with the purpose of making more educators to participate in the" Silk Road economic zone" construction.展开更多
The paper analyzes the distribution pattern of resources, ecological environment, society and economy, and holds that it is conducive to Silk Road countries to carry out Omni-directional and multi-level economic coope...The paper analyzes the distribution pattern of resources, ecological environment, society and economy, and holds that it is conducive to Silk Road countries to carry out Omni-directional and multi-level economic cooperation. Then the article puts forth main modes and paths of sustainable economic development for the Silk Road Economic Belt (SREB): ecological civilization mode, regional economic integration mode, transportation economic belt mode and international tourism economic zone mode. Finally, the article summarizes the key scientific issues for the sustainable development in the SREB and puts forward several action projects which include establishing International Scientists League and Think Tanks, establishing international information sharing platform and scientific policy-making system of ecological environment and sustainable development of the SREB, starting international science cooperation and technology traineeship program of the SREB, founding the international cooperation committee in the SREB and founding transnational construction and win-win cooperation mechanism of coping with climate change and ecological environment.展开更多
The silkworm,Bombyx mori,played an important role in the old Silk Road that connected ancient Asia and Europe.However,to date,there have been few studies of the origins and domestication of this species using molecula...The silkworm,Bombyx mori,played an important role in the old Silk Road that connected ancient Asia and Europe.However,to date,there have been few studies of the origins and domestication of this species using molecular methods.In this study,DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives.All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm.Domestication was estimated to have occurred about 4100 years ago(ya),and the radiation of the different geographic strains of B.mori about 2000 ya.The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya.These estimates are in good agreement with the fossil evidence and historical records.In addition,we show that the domesticated silkworm experienced a population expansion around 1000 ya.The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics,in the genetic analysis of domestic animals,and for understanding the spread of human civilizations.展开更多
So far, three reversals have occurred in the history of Western metaphysics. The first was the reversal from the "metaphysics of presence" represented by Platonism to the "metaphysics of subjectivity" represented ...So far, three reversals have occurred in the history of Western metaphysics. The first was the reversal from the "metaphysics of presence" represented by Platonism to the "metaphysics of subjectivity" represented by Descartes, Kant and Hegel. The second occurred within the framework of the metaphysics of subjectivity and marked the transformation from the "metaphysics of reason" represented by Descartes, Kant and Hegel to the "metaphysics of will" represented by Schopenhauer and Nietzsche. The third reversal was from the "metaphysics of being-there" of the earlier phase of Hcidegger's philosophy to his later "metaphysics of the world-fourfold."展开更多
Socialism with Chinese characteristics is a product of the integration of the basic tenets of Marxism with Chinese realities and the primary stage of socialism in China, marked by reform and opening up. In this stage ...Socialism with Chinese characteristics is a product of the integration of the basic tenets of Marxism with Chinese realities and the primary stage of socialism in China, marked by reform and opening up. In this stage capital and market exist and play important roles and capitalism is utilized for the Chinese modernization drive under the leadership of the Communist Party. With changes in historical conditions, the ideal of scientific socialism raised by Marx and Engels is confronted with a lot of challenges. It is the historical mission of Chinese Marxists to take up the gauntlet in response to these challenges and solve the historical enigma of human development in contemporary society.展开更多
基金This work is supported by the National Natural Science Foundation of China (No.21225421 and No.21474099), the National Basic Research Program of China (No.2014CB845605).
文摘The dynamics of tracers in crowded matrix is of interest in various areas of physics, such as the diffusion of proteins in living cells. By using two-dimensional (2D) Langevin dynamics simulations, we investigate the diffusive properties of a tracer of a diameter in crowded environments caused by randomly distributed crowders of a diameter. Results show that the emergence of subdiffusion of a tracer at intermediate time scales depends on the size ratio of the tracer to crowders a. If a falls between a lower critical size ratio and a upper one, the anomalous diffusion occurs purely due to the molecular crowding, tqlrther analysis indicates that the physical origin of subdiffusion is the "cage effect". Moreover, the subdiffusion exponent α decreases with the increasing medium viscosity and the degree of crowding, and gets a minimum αmin=0.75 at δ=1. At long time scales, normal diffusion of a tracer is recovered. For δ≤1, the relative mobility of tracers is independent of the degree of crowding. Meanwhile, it is sensitive to the degree of crowding for δ〉l. Our results are helpful in deepening the understanding of the diffusive properties of biomacromolecules that lie within crowded intracellular environments, such as proteins, DNA and ribosomes.
基金This work is supported by the Fundamental Research Funds for the Central Universities of China (No.WK2060200020) and the China Postdoctoral Science Foundation (No.2015M581998).
文摘Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders. By contrast, the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders. Notably, the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36-0.44. We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.
文摘Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional (3D) Langevin dynamics simulations, we investigate adsorption behaviors of multivalent polymer chains to a surface with receptors. Multivalent polymer chains display superselective adsorption. Furthermore, the range of density of surface receptors at which a multivalent polymer chain displays a superselective behavior, narrows down for chains with higher density of ligands. Meanwhile, the optimal density of surface receptors where the highest superselectivity is achieved, decreases with increasing the density of ligands. Then, the conformational properties of bound multivalent chains are studied systematically. Interestingly, we find that the equilibrium radius of gyration Rg and its horizontal component have a maximum as a function of the density of surface receptors. The scaling exponents of Rg with the length of chain suggest that with increasing the density of surface receptors., the conformations of a bound multivalent polymer chain first fall in between those of a two-dimensional (2D) and a 3D chain, while it is slightly collapsed subsequently.
文摘Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation [J. Chem. Phys. 147, 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended "middle" scheme [J. Chem. Phys. 147, 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation thermostatting processes with molecular is proposed for understanding efficient stochastic dynamics.
文摘We recently reported several driver genes of biliary tract carcinoma(BTC) that are known to play important roles in oncogenesis and disease progression. Although the need for developing novel therapeutic strategies is increasing, there are very few BTC cell lines and xenograft models currently available for conducting preclinical studies. Using a total of 88 surgical BTC specimens and 536 immunodeficient mice, 28 xenograft models and 13 new BTC cell lines, including subtypes, were established. Some of our cell lines were found to be resistant to gemcitabine, which is currently the first choice of treatment, thereby allowing highly practical preclinical studies to be conducted. Using the aforementioned cell lines and xenograft models and a clinical pathological database of patients undergoing BTC resection, we can establish a preclinical study system and appropriate parameters for drug efficacy studies to explore new biomarkers for practical applications in the future studies.
文摘In this article, the dynamical process of the dielectric particle in the optical tweezer using the counter-propagating Gaussian pulses is investigated by the Langevin equation concerning the Brownian motion. The temporal stabilities of particle is simulated. The influence of the duration, repetition period and delay time between pulses on stability is discussed.
基金Supported in part by the National Basic Research Program of China(973 Program)under Grants No.2007CB935903the National Nature Science Foundation of China under Grant No.11074259
文摘The stochastic systems without detailed balance are common in various chemical reaction systems, such as metabolic network systems. In studies of these systems, the concept of potential landscape is useful However, what are the su^cient and necessary conditions of the existence of the potential function is still an open problem. Use Hodge decomposition theorem in differential form theory, we focus on the general chemical Langevin equations, which reitect complex chemical reaction systems. We analysis the conditions for the existence of potential landscape of the systems. By mapping the stochastic differential equations to a Hamiltonian mechanical system, we obtain the Fokker-Planck equation of the chemical reaction systems. The obtained Fokker-Planck equation can be used in further studies of other steady properties of complex chemical reaction systems, such as their steady state entropies.
文摘When visiting Kazakhstan,President Xi Jinping proposed the strategic project to build the" Silk Road economic zone" . Under this background,the study of postgraduate students' English teaching is very important.This paper analyzes the historical status of the Silk Road,the significance of culture teaching of Silk Road countries,presents the study of the main elements and its implementation approaches of the Silk Road culture teaching in postgraduate students' English class,with the purpose of making more educators to participate in the" Silk Road economic zone" construction.
基金National Natural Science Foundation of China(4127155641101117)+1 种基金National Natural Science Foundation of China and Russian Foundation for Basic Research(414110106515-56-53037)
文摘The paper analyzes the distribution pattern of resources, ecological environment, society and economy, and holds that it is conducive to Silk Road countries to carry out Omni-directional and multi-level economic cooperation. Then the article puts forth main modes and paths of sustainable economic development for the Silk Road Economic Belt (SREB): ecological civilization mode, regional economic integration mode, transportation economic belt mode and international tourism economic zone mode. Finally, the article summarizes the key scientific issues for the sustainable development in the SREB and puts forward several action projects which include establishing International Scientists League and Think Tanks, establishing international information sharing platform and scientific policy-making system of ecological environment and sustainable development of the SREB, starting international science cooperation and technology traineeship program of the SREB, founding the international cooperation committee in the SREB and founding transnational construction and win-win cooperation mechanism of coping with climate change and ecological environment.
基金supported by the National Natural Science Foundation of China(Grant No. 30671587)the Programme for Introducing Talents of Discipline to Universities(Grant No.B07045)+1 种基金the Doctorial Innovation Fund of Southwest University(Grant No.Kb2009019)supported by grants from the U.S.National Science Foundation(Grant Nos.0531769, 0531626,and DEB-0212910)
文摘The silkworm,Bombyx mori,played an important role in the old Silk Road that connected ancient Asia and Europe.However,to date,there have been few studies of the origins and domestication of this species using molecular methods.In this study,DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives.All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm.Domestication was estimated to have occurred about 4100 years ago(ya),and the radiation of the different geographic strains of B.mori about 2000 ya.The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya.These estimates are in good agreement with the fossil evidence and historical records.In addition,we show that the domesticated silkworm experienced a population expansion around 1000 ya.The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics,in the genetic analysis of domestic animals,and for understanding the spread of human civilizations.
文摘So far, three reversals have occurred in the history of Western metaphysics. The first was the reversal from the "metaphysics of presence" represented by Platonism to the "metaphysics of subjectivity" represented by Descartes, Kant and Hegel. The second occurred within the framework of the metaphysics of subjectivity and marked the transformation from the "metaphysics of reason" represented by Descartes, Kant and Hegel to the "metaphysics of will" represented by Schopenhauer and Nietzsche. The third reversal was from the "metaphysics of being-there" of the earlier phase of Hcidegger's philosophy to his later "metaphysics of the world-fourfold."
文摘Socialism with Chinese characteristics is a product of the integration of the basic tenets of Marxism with Chinese realities and the primary stage of socialism in China, marked by reform and opening up. In this stage capital and market exist and play important roles and capitalism is utilized for the Chinese modernization drive under the leadership of the Communist Party. With changes in historical conditions, the ideal of scientific socialism raised by Marx and Engels is confronted with a lot of challenges. It is the historical mission of Chinese Marxists to take up the gauntlet in response to these challenges and solve the historical enigma of human development in contemporary society.