The persistence length and the overlap concentration(c~*) of poly(ethylene oxide)(PEO) and hydroxyethylcellulose(HEC) with similar molecular weight in 1×TBE buffer were studied by laser light scattering and visco...The persistence length and the overlap concentration(c~*) of poly(ethylene oxide)(PEO) and hydroxyethylcellulose(HEC) with similar molecular weight in 1×TBE buffer were studied by laser light scattering and viscometry.Their effect on DNA separation was investigated by capillary electrophoresis.It was determined that the persistence length of HEC was at least 5 times higher than that of PEO.Therefore,the c~* of HEC was smaller than that of PEO by a factor of ca.2.5.It was also found that the c~* values deter...展开更多
Surface effects on the persistence length of quasi-one-dimensional nanomaterials are investigated by using the theory of surface elasticity and the core-shell model of nanobeams. A simple and unified expression is pro...Surface effects on the persistence length of quasi-one-dimensional nanomaterials are investigated by using the theory of surface elasticity and the core-shell model of nanobeams. A simple and unified expression is provided to determine the persistence length of nanowires and nanotubes with any regular polygonal cross-sections. It is demonstrated that surface effects have a distinct in- fluence on the persistence length when the characteristic sizes of materials shrink to nanometers. This work is helpful not only for understanding the size-dependent behavior of nanomaterials but also for the design of devices based on nanotubes or nanowires.展开更多
DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA.A series of experiments pointed out that,in the DNA condensa...DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA.A series of experiments pointed out that,in the DNA condensation process by multivalent cations,the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration.At the same time,single molecule experiments carried out in solution with multivalent cations(such as spermidine,spermine)indicated that DNA persistence length strongly depends on the ionic concentration.In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation,a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided.The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations.With an increase in ion concentration,the first periodic oscillation contained in the autocorrelation function shifts,the number of segment contained in the first periodic oscillation decreases gradually.According to the experiments,the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further.The relation between long-axis length and ionic concentration matches the experimental results qualitatively.展开更多
Despite the significance of the high flexibility exhibited by short DNAs,there remains an incomplete understanding of their anomalous persistence length.In this study,we propose to model each basic unit of gene sequen...Despite the significance of the high flexibility exhibited by short DNAs,there remains an incomplete understanding of their anomalous persistence length.In this study,we propose to model each basic unit of gene sequences within short DNAs as a transversely isotropic ring.Our comprehensive model analysis successfully replicates the observed high flexibility of short DNAs and also displays the impact of sequence dependence,aligning with experimental findings.Furthermore,our analysis suggests that the bending behavior of short DNAs can be effectively described by the Timoshenko beam theory with the consideration of shear.展开更多
Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein recognition.By all-atom molecular dynamics simulations,we investigated the bendin...Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein recognition.By all-atom molecular dynamics simulations,we investigated the bending elasticity of DNA with three typical sequences including poly(A)-poly(T)(AA-TT),poly(AT)-poly(TA)(AT-TA),and a generic sequence(GENE).Our calculations indicate that,AA-TT has an apparently larger bending persistence length(P~63 nm)than GENE(P~49 nm)and AT-TA(P~48 nm)while the persistence length of AT-TA is only very slightly smaller than that of GENE,which agrees well with those from existing works.Moreover,through extensive electrostatic calculations,we found that the sequence-dependent bending elasticity is attributed to the sequence-dependent electrostatic bending energy for AA-TT,AT-TA and GENE,which is coupled to their backbone structures.Particularly,the apparently stronger bending stiffness of AA-TT is attributed to its narrower minor groove.Interestingly,for the three DNAs,we predicted the non-electrostatic persistence length of~17 nm,thus electrostatic interaction makes the major contribution to DNA bending elasticity.The mechanism of electrostatic energy dominating sequence effect in DNA bending elasticity is furtherly illustrated through the electrostatic calculations for a grooved coarse-grained DNA model where minor groove width and other microscopic structural parameters can be artificially adjusted.展开更多
Two soluble isomerized polyimides（PIs） synthesized from 2,2＇-bis（3,4-dicarboxyphenyl）hexafluoropropane dianhydride（6FDA） with either 2,2＇-dimethylbenzidine（2,2＇-DMB） or 3,3＇-DMB were investigated by means ...Two soluble isomerized polyimides（PIs） synthesized from 2,2＇-bis（3,4-dicarboxyphenyl）hexafluoropropane dianhydride（6FDA） with either 2,2＇-dimethylbenzidine（2,2＇-DMB） or 3,3＇-DMB were investigated by means of size-exclusion chromatography coupled with multi-angle laser light scattering,a viscometer and a refractive index detector in tetrahydrofuran（THF） with tetrabutylammonium bromide（TBAB） at 35 ℃.The corresponding parameters related to conformations α and ν,evaluated from the scaling relationships [η]=K η M α and R g =K g M ν,respectively,were 0.66±0.01 and 0.55±0.02 for poly（6FDA/3,3＇-DMB）,and 0.67±0.01 and 0.56±0.01 for poly（6FDA/2,2＇-DMB）,indicating a random coil conformation for both the samples in this mobile system.The persistence length l p and shift factor M L（relative molecular weight per unit contour length） were estimated from the relationship between intrinsic viscosity and molecular weight for the wormlike cylinder model proposed by Bohdanecky.Both l p and M L showed that the two PIs in THF are flexible chains and exhibit some local rigidity to some extent.展开更多
A new method for characterizing fiber bending flexibility was developed by worm-like chain model proposed by Kratky-Porod,[1]which was first introduced to the pulp and paper field in this study.For the three types of ...A new method for characterizing fiber bending flexibility was developed by worm-like chain model proposed by Kratky-Porod,[1]which was first introduced to the pulp and paper field in this study.For the three types of pulps,the experimental results were compared with the KP chain model,and the resulting determination coefficients were all above 0.95,which proved that the model was feasible to be applied to these three fibers.The relation between fiber bending rigidity and that of cellulosic chains inside was discussed to deduce the fiber bending flexibility.The flexibility of an individual fiber can be approximated as the contribution of that of all the cellulose chains inside.By this method,the fiber flexibility values were determined to be in the range of 0.6×10^(11)-3.5×10^(11)N^(-1)·m^(-2),which was comparable to that of the conventional methods recorded in the literature.展开更多
A new and computationally efficient version of the immersed boundary method,which is combined with the coarse-graining method,is introduced for modeling inextensible filaments immersed in low-Reynolds number flows.Thi...A new and computationally efficient version of the immersed boundary method,which is combined with the coarse-graining method,is introduced for modeling inextensible filaments immersed in low-Reynolds number flows.This is used to represent actin biopolymers,which are constituent elements of the cytoskeleton,a complex network-like structure that plays a fundamental role in shape morphology.An extension of the traditional immersed boundary method to include a stochastic stress tensor is also proposed in order to model the thermal fluctuations in the fluid at smaller scales.By way of validation,the response of a single,massless,inextensible semiflexible filament immersed in a thermally fluctuating fluid is obtained using the suggested numerical scheme and the resulting time-averaged contraction of the filament is compared to the theoretical value obtained from the worm-like chain model.展开更多
A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit...A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit counterions.The agreement on the radius of gyration of the PCEs with experiments shows that our model can be useful in studying the equilibrium sizes of PCEs in solution.The effects of ionic strength,side-chain number,and side-chain length on the conformational behavior of PCEs in solution are explored.Single-chain equilibrium properties,including the radius of gyration,end-to-end distance and persistenee length of the polymer backbone,shape-asphericity parameter,and the mean span dimension,are determined.It is found that with the increase of ionic strength,the equilibrium sizes of the polymers decrease only slightly,and a linear dependenew of the persistence length of backbone on the Debye screening length is found,in good agreement with the theory developed by Dobrynin.Increasing side-chain numbers and/or side-chain lengths increases not only the equilibrium sizes(radius of gyration and mean span)of the polymer as a whole,but also the persistence length of the backbone due to excluded volume interactions.展开更多
Understanding how small molecules interface with amyloid fibrils at the nanoscale is of importance for developing therapeutic treatments against amyloid-based diseases. Here, we show for the first time that human isle...Understanding how small molecules interface with amyloid fibrils at the nanoscale is of importance for developing therapeutic treatments against amyloid-based diseases. Here, we show for the first time that human islet amyloid polypeptides （LAPP） in the fibrillar form are polymorphic, ambidextrous, and possess multiple periodicities. Upon interfacing with the small molecule epigallocatechin gallate （EGCG）, IAPP aggregation was rendered off-pathway and assumed a form with soft and disordered clusters, while mature IAPP fibrils displayed kinks and branching but conserved the twisted fibril morphology. These nanoscale phenomena resulted from competitive interactions between EGCG and the IAPP amyloidogenic region, as well as end capping of the fibrils by the small molecule. This information is crucial in delineating IAPP toxicity implicated in type 2 diabetes and for developing new inhibitors against amyloidogenesis.展开更多
基金supported by the National Natural Science Foundation of China(No20504001)
文摘The persistence length and the overlap concentration(c~*) of poly(ethylene oxide)(PEO) and hydroxyethylcellulose(HEC) with similar molecular weight in 1×TBE buffer were studied by laser light scattering and viscometry.Their effect on DNA separation was investigated by capillary electrophoresis.It was determined that the persistence length of HEC was at least 5 times higher than that of PEO.Therefore,the c~* of HEC was smaller than that of PEO by a factor of ca.2.5.It was also found that the c~* values deter...
基金supported by the National Natural Science Foundation of China(11472035 and11432008)973 Program of MOST(2010CB631005 and 2012CB934001)
文摘Surface effects on the persistence length of quasi-one-dimensional nanomaterials are investigated by using the theory of surface elasticity and the core-shell model of nanobeams. A simple and unified expression is provided to determine the persistence length of nanowires and nanotubes with any regular polygonal cross-sections. It is demonstrated that surface effects have a distinct in- fluence on the persistence length when the characteristic sizes of materials shrink to nanometers. This work is helpful not only for understanding the size-dependent behavior of nanomaterials but also for the design of devices based on nanotubes or nanowires.
基金Supported by National Natural Science Foundation of China under Grant Nos.11047022,11204045,11464004 and 31360215The Research Foundation from Ministry of Education of China(212152)+4 种基金Guizhou Provincial Tracking Key Program of Social Development(SY20123089SZ20113069)The General Financial Grant from the China Postdoctoral Science Foundation(2014M562341)The Research Foundation for Young University Teachers from Guizhou University(201311)The West Light Foundation(2015)and College Innovation Talent Team of Guizhou Province,(2014)32
文摘DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA.A series of experiments pointed out that,in the DNA condensation process by multivalent cations,the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration.At the same time,single molecule experiments carried out in solution with multivalent cations(such as spermidine,spermine)indicated that DNA persistence length strongly depends on the ionic concentration.In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation,a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided.The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations.With an increase in ion concentration,the first periodic oscillation contained in the autocorrelation function shifts,the number of segment contained in the first periodic oscillation decreases gradually.According to the experiments,the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further.The relation between long-axis length and ionic concentration matches the experimental results qualitatively.
基金supported by Zhejiang Provincial Natural Science Foundation of China(Grant No.LZ23A020004)the National Natural Science Foundation of China(Grant Nos.12372318 and 11872334).
文摘Despite the significance of the high flexibility exhibited by short DNAs,there remains an incomplete understanding of their anomalous persistence length.In this study,we propose to model each basic unit of gene sequences within short DNAs as a transversely isotropic ring.Our comprehensive model analysis successfully replicates the observed high flexibility of short DNAs and also displays the impact of sequence dependence,aligning with experimental findings.Furthermore,our analysis suggests that the bending behavior of short DNAs can be effectively described by the Timoshenko beam theory with the consideration of shear.
基金supported by grants from the National Science Foundation of China(Grant Nos.11774272,and 12075171)。
文摘Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein recognition.By all-atom molecular dynamics simulations,we investigated the bending elasticity of DNA with three typical sequences including poly(A)-poly(T)(AA-TT),poly(AT)-poly(TA)(AT-TA),and a generic sequence(GENE).Our calculations indicate that,AA-TT has an apparently larger bending persistence length(P~63 nm)than GENE(P~49 nm)and AT-TA(P~48 nm)while the persistence length of AT-TA is only very slightly smaller than that of GENE,which agrees well with those from existing works.Moreover,through extensive electrostatic calculations,we found that the sequence-dependent bending elasticity is attributed to the sequence-dependent electrostatic bending energy for AA-TT,AT-TA and GENE,which is coupled to their backbone structures.Particularly,the apparently stronger bending stiffness of AA-TT is attributed to its narrower minor groove.Interestingly,for the three DNAs,we predicted the non-electrostatic persistence length of~17 nm,thus electrostatic interaction makes the major contribution to DNA bending elasticity.The mechanism of electrostatic energy dominating sequence effect in DNA bending elasticity is furtherly illustrated through the electrostatic calculations for a grooved coarse-grained DNA model where minor groove width and other microscopic structural parameters can be artificially adjusted.
基金Supported by the National Natural Science Foundation of China(No.20674085)the Funds for Creative Researth Groups of China(No.50921062)the Project of Bureau of Science and Technology of Jilin Province,China(No.20101535)
文摘Two soluble isomerized polyimides（PIs） synthesized from 2,2＇-bis（3,4-dicarboxyphenyl）hexafluoropropane dianhydride（6FDA） with either 2,2＇-dimethylbenzidine（2,2＇-DMB） or 3,3＇-DMB were investigated by means of size-exclusion chromatography coupled with multi-angle laser light scattering,a viscometer and a refractive index detector in tetrahydrofuran（THF） with tetrabutylammonium bromide（TBAB） at 35 ℃.The corresponding parameters related to conformations α and ν,evaluated from the scaling relationships [η]=K η M α and R g =K g M ν,respectively,were 0.66±0.01 and 0.55±0.02 for poly（6FDA/3,3＇-DMB）,and 0.67±0.01 and 0.56±0.01 for poly（6FDA/2,2＇-DMB）,indicating a random coil conformation for both the samples in this mobile system.The persistence length l p and shift factor M L（relative molecular weight per unit contour length） were estimated from the relationship between intrinsic viscosity and molecular weight for the wormlike cylinder model proposed by Bohdanecky.Both l p and M L showed that the two PIs in THF are flexible chains and exhibit some local rigidity to some extent.
基金financially supported by the National Natural Science Foundation of China (No. 21534002)National Key R&D Program of China (No. 2019YFC1520402)
文摘A new method for characterizing fiber bending flexibility was developed by worm-like chain model proposed by Kratky-Porod,[1]which was first introduced to the pulp and paper field in this study.For the three types of pulps,the experimental results were compared with the KP chain model,and the resulting determination coefficients were all above 0.95,which proved that the model was feasible to be applied to these three fibers.The relation between fiber bending rigidity and that of cellulosic chains inside was discussed to deduce the fiber bending flexibility.The flexibility of an individual fiber can be approximated as the contribution of that of all the cellulose chains inside.By this method,the fiber flexibility values were determined to be in the range of 0.6×10^(11)-3.5×10^(11)N^(-1)·m^(-2),which was comparable to that of the conventional methods recorded in the literature.
文摘A new and computationally efficient version of the immersed boundary method,which is combined with the coarse-graining method,is introduced for modeling inextensible filaments immersed in low-Reynolds number flows.This is used to represent actin biopolymers,which are constituent elements of the cytoskeleton,a complex network-like structure that plays a fundamental role in shape morphology.An extension of the traditional immersed boundary method to include a stochastic stress tensor is also proposed in order to model the thermal fluctuations in the fluid at smaller scales.By way of validation,the response of a single,massless,inextensible semiflexible filament immersed in a thermally fluctuating fluid is obtained using the suggested numerical scheme and the resulting time-averaged contraction of the filament is compared to the theoretical value obtained from the worm-like chain model.
文摘A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit counterions.The agreement on the radius of gyration of the PCEs with experiments shows that our model can be useful in studying the equilibrium sizes of PCEs in solution.The effects of ionic strength,side-chain number,and side-chain length on the conformational behavior of PCEs in solution are explored.Single-chain equilibrium properties,including the radius of gyration,end-to-end distance and persistenee length of the polymer backbone,shape-asphericity parameter,and the mean span dimension,are determined.It is found that with the increase of ionic strength,the equilibrium sizes of the polymers decrease only slightly,and a linear dependenew of the persistence length of backbone on the Debye screening length is found,in good agreement with the theory developed by Dobrynin.Increasing side-chain numbers and/or side-chain lengths increases not only the equilibrium sizes(radius of gyration and mean span)of the polymer as a whole,but also the persistence length of the backbone due to excluded volume interactions.
文摘Understanding how small molecules interface with amyloid fibrils at the nanoscale is of importance for developing therapeutic treatments against amyloid-based diseases. Here, we show for the first time that human islet amyloid polypeptides （LAPP） in the fibrillar form are polymorphic, ambidextrous, and possess multiple periodicities. Upon interfacing with the small molecule epigallocatechin gallate （EGCG）, IAPP aggregation was rendered off-pathway and assumed a form with soft and disordered clusters, while mature IAPP fibrils displayed kinks and branching but conserved the twisted fibril morphology. These nanoscale phenomena resulted from competitive interactions between EGCG and the IAPP amyloidogenic region, as well as end capping of the fibrils by the small molecule. This information is crucial in delineating IAPP toxicity implicated in type 2 diabetes and for developing new inhibitors against amyloidogenesis.
