We employ finite element method to investigate the kinematics of non-axially positioned vesicles through a pore.To complete the coupling between fluid flow and the vesicle membranes,we use the fluid structure interact...We employ finite element method to investigate the kinematics of non-axially positioned vesicles through a pore.To complete the coupling between fluid flow and the vesicle membranes,we use the fluid structure interactions with the arbitrary Lagrangian Eulerian method.Our results demonstrate that the vesicles show different deformations in migration process,in turn an oblique ellipse-shape,slipper-shape,oval-shape.We find that the rotation angle of non-axially positioned vesicles mainly shows the trend of increase,besides the small fluctuation induced by deformation relaxation.Moreover,when the vesicles move towards the axis of the channel,the rotation angle exhibits a decrease because of the decrease of the shear force.However,rotation of axially positioned vesicles hardly occur due to symmetrical shear force.Our results further indicate that the rotation is faster nearby the pore for non-axially positioned vesicles.Our work answers the mapping between the positions of vesicles and deformed states,as well as the change of rotation angle and rotation velocity,which can provide helpful information on the utilization of vesicles in pharmaceutical,chemical,and physiological processes.展开更多
We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random sel...We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0（N）-N^-0.8.展开更多
Polyurethane micelles（PM）-based nanovehicles have shown great potential in targeted delivery of therapeutics and diagnostics into tumors.However,the pathways of PMs entering cancer cells and the action mechanism of ...Polyurethane micelles（PM）-based nanovehicles have shown great potential in targeted delivery of therapeutics and diagnostics into tumors.However,the pathways of PMs entering cancer cells and the action mechanism of targeting ligands have yet to be understood.In this contribution,the actively-targeted PM were developed using trastuzumab as a model targeting group.It was found that PM were mainly taken up by SKOV-3 tumor cells via a micropinocytosis process,while the incorporation of trastuzumab to PM enabled a receptor-mediated endocytosis of nanocarriers in cancer cells,leading to more efficient cell entry and enhanced anticancer efficacy of chemotherapeutic drugs both in vitro and in vivo.This study is advantageous to the understanding of the action mechanism of trastuzumab,and significant for the construction of improved formulations for targeted delivery and precise therapy.展开更多
In order to find more biologically active substances, we have carefully investigated the chemical constituents of Pterocypsela elata. One new guaianolide, （4S）-ll-methoxycarbonyl-guaiane- l（10）,5（6）,7（11）,8（9...In order to find more biologically active substances, we have carefully investigated the chemical constituents of Pterocypsela elata. One new guaianolide, （4S）-ll-methoxycarbonyl-guaiane- l（10）,5（6）,7（11）,8（9）-tetraen-6,12-olide was isolated from the EtOAc extracts of the roots of P. elata. Its structure was elucidated by various spectroscopic methods and confirmed by X-ray crystallographic analysis.展开更多
Using a hybrid simulation approach that combines a finite difference method with a Brownian dynamics,we investigated the motion of charged polymers.Owing to the fact that polymer-solution systems often contain a large...Using a hybrid simulation approach that combines a finite difference method with a Brownian dynamics,we investigated the motion of charged polymers.Owing to the fact that polymer-solution systems often contain a large number of particles and the charged palymer chains are in a state of random motion,it is a time consuming task to calculate the electrostatic interaction of the system.Accordingly,we propose a new strategy to shorten the CPU time by reducing the iteration area.Our simulation results ilustrate the effect of preset parameters on CPU time and accuracy,and demonstrate the feasibility of the"local iteration"method.Importantly,we find that the increase in the number of charged beads has no signifiant infuence on the time of global iterations and local iterations.For a number of 80×80×80 grids,when the relative error is controlled below 1.5%,the computational efficiency is increased by 8.7 times in the case that contains 500 charged beads.In adition,for a number of 100×100×100 grids with 100 charged beads,the computational efciency can be increased up to 12 times.Our work provides new insights for the optimization of iterative algorithms in special problems.展开更多
Nanopore sequencing harnesses changes in ionic current as nucleotides traverse a nanopore,enabling real-time decoding of DNA/RNA sequences.The instruments for the dynamic behavior of substances in the nanopore on the ...Nanopore sequencing harnesses changes in ionic current as nucleotides traverse a nanopore,enabling real-time decoding of DNA/RNA sequences.The instruments for the dynamic behavior of substances in the nanopore on the molecular scale are still very limited experimentally.This study employs all-atom molecular dynamics(MD)simulations to explore the impact of charge densities on graphene nanopore in the translocation of single-stranded DNA(ssDNA).We find that the magnitude of graphene’s charge,rather than the charge disparity between ssDNA and graphene,significantly influences ssDNA adsorption and translocation speed.Specifically,high negative charge densities on graphene nanopores are shown to substantially slow down ssDNA translocation,highlighting the importance of hydrodynamic effects and electrostatic repulsions.This indicates translocation is crucial for achieving distinct ionic current blockades,which plays a central role for DNA sequencing accuracy.Our findings suggest that negatively charged graphene nanopores hold considerable potential for optimizing DNA sequencing,marking a critical advancement in this field.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
基金This work was financially supported by the National Natural Science Foundation of China(No.21604086)Jlin Provincial science and technology development program(No.20190103124JH)and Key Research Program of Frontier Sciences,CAS(No.QYZDY-SSW-SLH027).
文摘We employ finite element method to investigate the kinematics of non-axially positioned vesicles through a pore.To complete the coupling between fluid flow and the vesicle membranes,we use the fluid structure interactions with the arbitrary Lagrangian Eulerian method.Our results demonstrate that the vesicles show different deformations in migration process,in turn an oblique ellipse-shape,slipper-shape,oval-shape.We find that the rotation angle of non-axially positioned vesicles mainly shows the trend of increase,besides the small fluctuation induced by deformation relaxation.Moreover,when the vesicles move towards the axis of the channel,the rotation angle exhibits a decrease because of the decrease of the shear force.However,rotation of axially positioned vesicles hardly occur due to symmetrical shear force.Our results further indicate that the rotation is faster nearby the pore for non-axially positioned vesicles.Our work answers the mapping between the positions of vesicles and deformed states,as well as the change of rotation angle and rotation velocity,which can provide helpful information on the utilization of vesicles in pharmaceutical,chemical,and physiological processes.
基金financially supported by the National Basic Research Program of China(No.2009CB930100)the National Natural Science Foundation of China(Nos.21234007,21304097 and 51473168)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 investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0（N）-N^-0.8.
基金financially supported by the National Natural Science Foundation of China(Nos.51273126 and 51573112)the National Science Fund for Distinguished Young Scholars of China(No.51425305)the Youth Science and Technology Innovation Team of Sichuan Province(No.2015TD0001)
文摘Polyurethane micelles（PM）-based nanovehicles have shown great potential in targeted delivery of therapeutics and diagnostics into tumors.However,the pathways of PMs entering cancer cells and the action mechanism of targeting ligands have yet to be understood.In this contribution,the actively-targeted PM were developed using trastuzumab as a model targeting group.It was found that PM were mainly taken up by SKOV-3 tumor cells via a micropinocytosis process,while the incorporation of trastuzumab to PM enabled a receptor-mediated endocytosis of nanocarriers in cancer cells,leading to more efficient cell entry and enhanced anticancer efficacy of chemotherapeutic drugs both in vitro and in vivo.This study is advantageous to the understanding of the action mechanism of trastuzumab,and significant for the construction of improved formulations for targeted delivery and precise therapy.
基金supported by the National Natural Science Foundation of China(No.81172953)
文摘In order to find more biologically active substances, we have carefully investigated the chemical constituents of Pterocypsela elata. One new guaianolide, （4S）-ll-methoxycarbonyl-guaiane- l（10）,5（6）,7（11）,8（9）-tetraen-6,12-olide was isolated from the EtOAc extracts of the roots of P. elata. Its structure was elucidated by various spectroscopic methods and confirmed by X-ray crystallographic analysis.
基金the National Natural!Science Foundation of China(No.21604086)Jilin Provincial science and technology development program(No.20190103124JH)Key Research Program of Frontier Sciences,CAS(No.QYZDY-SSW-SLH027).
文摘Using a hybrid simulation approach that combines a finite difference method with a Brownian dynamics,we investigated the motion of charged polymers.Owing to the fact that polymer-solution systems often contain a large number of particles and the charged palymer chains are in a state of random motion,it is a time consuming task to calculate the electrostatic interaction of the system.Accordingly,we propose a new strategy to shorten the CPU time by reducing the iteration area.Our simulation results ilustrate the effect of preset parameters on CPU time and accuracy,and demonstrate the feasibility of the"local iteration"method.Importantly,we find that the increase in the number of charged beads has no signifiant infuence on the time of global iterations and local iterations.For a number of 80×80×80 grids,when the relative error is controlled below 1.5%,the computational efficiency is increased by 8.7 times in the case that contains 500 charged beads.In adition,for a number of 100×100×100 grids with 100 charged beads,the computational efciency can be increased up to 12 times.Our work provides new insights for the optimization of iterative algorithms in special problems.
基金This work was financially supported by the National Natural Science Foundation of China(Nos.22373025 and 22227804).
文摘Nanopore sequencing harnesses changes in ionic current as nucleotides traverse a nanopore,enabling real-time decoding of DNA/RNA sequences.The instruments for the dynamic behavior of substances in the nanopore on the molecular scale are still very limited experimentally.This study employs all-atom molecular dynamics(MD)simulations to explore the impact of charge densities on graphene nanopore in the translocation of single-stranded DNA(ssDNA).We find that the magnitude of graphene’s charge,rather than the charge disparity between ssDNA and graphene,significantly influences ssDNA adsorption and translocation speed.Specifically,high negative charge densities on graphene nanopores are shown to substantially slow down ssDNA translocation,highlighting the importance of hydrodynamic effects and electrostatic repulsions.This indicates translocation is crucial for achieving distinct ionic current blockades,which plays a central role for DNA sequencing accuracy.Our findings suggest that negatively charged graphene nanopores hold considerable potential for optimizing DNA sequencing,marking a critical advancement in this field.
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.
