X-ray photon correlation spectroscopy(XPCS)has emerged as a powerful tool for probing the nanoscale dynamics of soft condensed matter and strongly correlated materials owing to its high spatial resolution and penetrat...X-ray photon correlation spectroscopy(XPCS)has emerged as a powerful tool for probing the nanoscale dynamics of soft condensed matter and strongly correlated materials owing to its high spatial resolution and penetration capabilities.This technique requires high brilliance and beam coherence,which are not directly available at modern synchrotron beamlines in China.To facilitate future XPCS experiments,we modified the optical setup of the newly commissioned BL10U1 USAXS beamline at the Shanghai Synchrotron Radiation Facility(SSRF).Subsequently,we performed XPCS measurements on silica suspensions in glycerol,which were opaque owing to their high concentrations.Images were collected using a high frame rate area detector.A comprehensive analysis was performed,yielding correlation functions and several key dynamic parameters.All the results were consistent with the theory of Brownian motion and demonstrated the feasibility of XPCS at SSRF.Finally,by carefully optimizing the setup and analyzing the algorithms,we achieved a time resolution of 2 ms,which enabled the characterization of millisecond dynamics in opaque systems.展开更多
We use the Brownian dynamics with hydrodynamic interactions simulation in order to describe the movement of an elastically coupled dimer Brownian motor in a ratchet potential. The only external forces considered in ou...We use the Brownian dynamics with hydrodynamic interactions simulation in order to describe the movement of an elastically coupled dimer Brownian motor in a ratchet potential. The only external forces considered in our system were the load, the random thermal noise and an unbiased thermal fluctuation. We observe differences in the dynamic behaviour if hydrodynamic interactions are considered as compared with the case without them. In conclusion, hydrodynamic interactions influence substantially the dynamics of a ratchet dimer Brownian motor;consequently they have to be considered in any theory where the molecular motors are in a liquid medium.展开更多
It is well known that potassium ion channels have higher permeability than K ions, and the permeable rate of a single K ion channel is about 108 ions per second. We develop a hierarchical model of potassium ion channe...It is well known that potassium ion channels have higher permeability than K ions, and the permeable rate of a single K ion channel is about 108 ions per second. We develop a hierarchical model of potassium ion channel permeation involving ab initio quantum calculations and Brownian dynamics simulations, which can consistently explain a range of channel dynamics. The results show that the average velocity of K ions, the mean permeable time of K ions and the permeable rate of single channel are about 0.92nm/ns, 4.35ns and 2.30 ×10^8 ions/s, respectively.展开更多
We investigated the effect of hydrodynamic interaction（HI） on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately contro...We investigated the effect of hydrodynamic interaction（HI） on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long po- lymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stret- ching, both of which play an important role in translocation process.展开更多
Using Brownian dynamics simulation, we studied the effect of histone modifications On conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows...Using Brownian dynamics simulation, we studied the effect of histone modifications On conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ＂cross-talking＂ interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.展开更多
Alzheimer’s disease (AD) is considered a slow neuronal dysfunction process through hypoxia, ischemia and leads to apoptosis mediated senile plaques and neurofibrillary tangles (NFTs). Due to non-invasive approach of ...Alzheimer’s disease (AD) is considered a slow neuronal dysfunction process through hypoxia, ischemia and leads to apoptosis mediated senile plaques and neurofibrillary tangles (NFTs). Due to non-invasive approach of plaque characterization, computational techniques based on Brownian dynamics simulation are unique to speculate the electrostatic and kinetic properties of Acetylcho-linesterase (AChE). Typically the MRI spectros-copy high choline peak and enzyme specific to Alzheimer’s Disease (specificity constant (kcat/Km) of AChE) appeared associated with apoptosis and hypoxia. A simple display between synergy of cytokines, apoptosis, elevated AChE and choline is postulated as initial events. The events may be distributed heterogeneously within the senile plaques and neurofibrillary tangles (NFTs) of Alzheimer’s Disease (AD). The role of decreased brain AChE and synergy was associated with specific Magnetic Resonance Spectroscopic (MRS) pattern profiles in AD. These findings suggest that that the altered AChE and early apoptosis events in AD may be associated with specific MR spectral peak patterns. This study opens the possibility of reduced AChE levels causing high choline and reduced N-acetyl ace-tate (NAA) neurotransmitter by MRS after initial apoptosis and/or inflammation to make amyloid plaques in the cerebral tissue of Alzheimer’s disease (AD) patients. These results can be useful in clinical trials on AD lesions.展开更多
We study the conformation of an amphiphilic comb-like copolymer in a selective solvent by using Brownian dynamics simulations.Our results demonstrate that,there is an optimal total degree of polymerization to form sph...We study the conformation of an amphiphilic comb-like copolymer in a selective solvent by using Brownian dynamics simulations.Our results demonstrate that,there is an optimal total degree of polymerization to form spherical micelles.Only when the total degree of polymerization is less than the optimal total degree of polymerization,a unimolecular spherical micelle can be formed,otherwise,the spherical micelle will be transformed into a cylindrical micelle.When the total degree of polymerization is less than the optimal total degree of polymerization,the radius of gyration and the stretching factor meet an exponential relationship,where the power exponent decreases with the increase of the length of hydrophilic side chains.The fundamental principles uncovered here afford insights for the optimization of molecular design of amphiphilic comb-like copolymers in various applications.展开更多
Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformat...Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformations.When the ratio of hydrophilic and hydrophobic segments is N_(g,g)∶N_(g,r)=3∶1,no core-shell structure is observed,and unsegregated chains or clusters are substituted.When N_(g,g)∶N_(g,r)=3∶2or 3∶3,the core-shell comb-like chains can be assembled into single micelles or structures where several small micelles are strung together by the backbone,which is similar to the pearl-necklace structure formed by the polyelectrolytes in poor solvent.With the increase of backbone length or grafting density,the probability of forming single micelles becomes lower,but the structures of two,three or more small micelles strung together are more observed.Our results indicate how to obtain the desired self-assembled structures of core-shell comb-like chains by regulating the architectural parameters,which could provide insights for the optimization of molecular design in various applications.展开更多
钾离子通道作为细胞中阳离子浓度的调节器之一,在神经细胞动作电位去极化及复极化过程中起着重要作用.KcsA(K^(+)conduction and selectivity architecture)通道结构简单又具有钾离子通道的共性,常作为钾通道研究的模板.本文采用布朗动...钾离子通道作为细胞中阳离子浓度的调节器之一,在神经细胞动作电位去极化及复极化过程中起着重要作用.KcsA(K^(+)conduction and selectivity architecture)通道结构简单又具有钾离子通道的共性,常作为钾通道研究的模板.本文采用布朗动力学数值方法,系统地对KcsA钾通道的电学特性进行模拟.得到静电场作用下通道内离子的平均势能分布、均匀与非均匀溶液的电流-电压特性曲线、通道轴向的离子浓度分布曲线以及电导-浓度曲线.研究结果发现,KcsA钾离子通道选择性过滤区域几乎完全阻隔了Cl–通过,呈现倾向于K^(+)通过的特异选择特性;其电流-电压曲线基本呈线性分布,电导-浓度曲线呈现先增大后平缓的趋势,基本规律与实验现象一致.另外,还模拟分析了太赫兹场对通道K^(+)电流的影响,相比于仅施加同幅值静电场,选定的0.6 THz,1.2 THz,5 THz的太赫兹场可通过影响离子对之间的相互作用势能,降低通道平均力势,从而增大K^(+)电流.本文的研究不但加深了对于KcsA钾离子通道的规律性认识,还为其他类型离子通道以及太赫兹场对离子通道特性影响的研究提供了新思路.展开更多
基金This work was supported by National Natural Science Foundation of China(No.12075304)Natural Science Foundation of Shanghai(No.22ZR1442100)National Key Research and Development Program of China(No.2022YFB3503904).
文摘X-ray photon correlation spectroscopy(XPCS)has emerged as a powerful tool for probing the nanoscale dynamics of soft condensed matter and strongly correlated materials owing to its high spatial resolution and penetration capabilities.This technique requires high brilliance and beam coherence,which are not directly available at modern synchrotron beamlines in China.To facilitate future XPCS experiments,we modified the optical setup of the newly commissioned BL10U1 USAXS beamline at the Shanghai Synchrotron Radiation Facility(SSRF).Subsequently,we performed XPCS measurements on silica suspensions in glycerol,which were opaque owing to their high concentrations.Images were collected using a high frame rate area detector.A comprehensive analysis was performed,yielding correlation functions and several key dynamic parameters.All the results were consistent with the theory of Brownian motion and demonstrated the feasibility of XPCS at SSRF.Finally,by carefully optimizing the setup and analyzing the algorithms,we achieved a time resolution of 2 ms,which enabled the characterization of millisecond dynamics in opaque systems.
文摘We use the Brownian dynamics with hydrodynamic interactions simulation in order to describe the movement of an elastically coupled dimer Brownian motor in a ratchet potential. The only external forces considered in our system were the load, the random thermal noise and an unbiased thermal fluctuation. We observe differences in the dynamic behaviour if hydrodynamic interactions are considered as compared with the case without them. In conclusion, hydrodynamic interactions influence substantially the dynamics of a ratchet dimer Brownian motor;consequently they have to be considered in any theory where the molecular motors are in a liquid medium.
基金Supported by the National Natural Science Foundation of China under Grant Nos 10474018 and 10375016, the Hebei Provincial Natural Science Foundation under Grant Nos C2005000011 and A2004000005, the Subsidization for Construction Programme of Key Subjects in Universities and Colleges of Hebei Province, and the Hebei Provincial Doctoral Foundation under Grant No 2006148.
文摘It is well known that potassium ion channels have higher permeability than K ions, and the permeable rate of a single K ion channel is about 108 ions per second. We develop a hierarchical model of potassium ion channel permeation involving ab initio quantum calculations and Brownian dynamics simulations, which can consistently explain a range of channel dynamics. The results show that the average velocity of K ions, the mean permeable time of K ions and the permeable rate of single channel are about 0.92nm/ns, 4.35ns and 2.30 ×10^8 ions/s, respectively.
基金Supported by the National Basic Research Program of China（No.2009CB930100）, the National Natural Science Foundation of China（Nos.21234007, 21304097, 51473168） and the Joint Research Fund for Overseas Chinese, Hong Kong and Macao Young Scientists of the National Natural Science Foundation of China（No.51028301）.
文摘We investigated the effect of hydrodynamic interaction（HI） on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long po- lymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stret- ching, both of which play an important role in translocation process.
基金Project supported by the National Natural Science Foundation of China (Grants Nos. 10834014 and 10674173)the National Basic Research Program of China (Grant No. 2009CB930704)
文摘Using Brownian dynamics simulation, we studied the effect of histone modifications On conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ＂cross-talking＂ interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.
文摘Alzheimer’s disease (AD) is considered a slow neuronal dysfunction process through hypoxia, ischemia and leads to apoptosis mediated senile plaques and neurofibrillary tangles (NFTs). Due to non-invasive approach of plaque characterization, computational techniques based on Brownian dynamics simulation are unique to speculate the electrostatic and kinetic properties of Acetylcho-linesterase (AChE). Typically the MRI spectros-copy high choline peak and enzyme specific to Alzheimer’s Disease (specificity constant (kcat/Km) of AChE) appeared associated with apoptosis and hypoxia. A simple display between synergy of cytokines, apoptosis, elevated AChE and choline is postulated as initial events. The events may be distributed heterogeneously within the senile plaques and neurofibrillary tangles (NFTs) of Alzheimer’s Disease (AD). The role of decreased brain AChE and synergy was associated with specific Magnetic Resonance Spectroscopic (MRS) pattern profiles in AD. These findings suggest that that the altered AChE and early apoptosis events in AD may be associated with specific MR spectral peak patterns. This study opens the possibility of reduced AChE levels causing high choline and reduced N-acetyl ace-tate (NAA) neurotransmitter by MRS after initial apoptosis and/or inflammation to make amyloid plaques in the cerebral tissue of Alzheimer’s disease (AD) patients. These results can be useful in clinical trials on AD lesions.
基金financially supported by the Scientific Research Project of Yili Normal University(No.2022YSYB009)。
文摘We study the conformation of an amphiphilic comb-like copolymer in a selective solvent by using Brownian dynamics simulations.Our results demonstrate that,there is an optimal total degree of polymerization to form spherical micelles.Only when the total degree of polymerization is less than the optimal total degree of polymerization,a unimolecular spherical micelle can be formed,otherwise,the spherical micelle will be transformed into a cylindrical micelle.When the total degree of polymerization is less than the optimal total degree of polymerization,the radius of gyration and the stretching factor meet an exponential relationship,where the power exponent decreases with the increase of the length of hydrophilic side chains.The fundamental principles uncovered here afford insights for the optimization of molecular design of amphiphilic comb-like copolymers in various applications.
基金financially supported by the Scientific Research Project of Yili Normal University(No.2022YSYB009)the National Natural Science Foundation of China(No.2019M651340)。
文摘Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformations.When the ratio of hydrophilic and hydrophobic segments is N_(g,g)∶N_(g,r)=3∶1,no core-shell structure is observed,and unsegregated chains or clusters are substituted.When N_(g,g)∶N_(g,r)=3∶2or 3∶3,the core-shell comb-like chains can be assembled into single micelles or structures where several small micelles are strung together by the backbone,which is similar to the pearl-necklace structure formed by the polyelectrolytes in poor solvent.With the increase of backbone length or grafting density,the probability of forming single micelles becomes lower,but the structures of two,three or more small micelles strung together are more observed.Our results indicate how to obtain the desired self-assembled structures of core-shell comb-like chains by regulating the architectural parameters,which could provide insights for the optimization of molecular design in various applications.
