EFFECT OF OVERLAP CONCENTRATION AND PERSISTENCE LENGTH ON DNA SEPARATION IN POLYMER SOLUTIONS BY ELECTROPHORESIS

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...

Surface effects on the persistence length of nanowires and nanotubes

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.

Chain Conformation and Local Rigidity of Soluble Polyimides(II):Isomerized Polyimides in THF

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.

A Hybrid Immersed Boundary/Coarse-Graining Method for Modeling Inextensible Semi-Flexible Filaments in Thermally Fluctuating Fluids Dedicated to Professor Karl Stark Pister for his 95th birthday

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.

Temperature Dependence of Chain Conformation and Local Rigidity of Isomerized Polyimides in Dimethyl Formamide

Temperature dependence of chain conformation and local rigidity of two soluble isomerized polyimides （PIs）, poly（hexafluorodianhydride/3,3＇-dimethylbenzidine）[poly（6FDA/3,3＇-DMB）] and poly（hexafluorodianhy- dride/2,2＇-dimethylbenzidine）[poly（6FDA/2,2＇-DMB）] were investigated by dilute solution viscosity, size exclusion chromatography（SEC） coupled with multi-angle laser light scattering, viscometer, and refractive index detector in dimethylformamide（DMF） with either 0.1 mol/L LiBr or 3.1 mmol/L tetrabutylammonium bromide（TBAB） in the temperature range of 30 to 50 ~C. The scaling relationships of [t/]=K^M~ and Rg=KgMv obtained are employed to in- vestigate the temperature dependence of chain conformation for the two polyimides. The values of a and v are in the range of 0.66--0.69 and 0.53--0.56, respectively, for poly（6FDA/3,3＇-DMB）, meanwhile they are in the range of 0.64--0.68 and 0.53--0.56, respectively, for poly（6FDAJ2,2＇-DMB）. These results reveal that random coil conforma- tions for both Pls are not affected visibly with increasing temperature from 30 ~C to 50 ~C. However, values of more exact intrinsic viscosity from dilute solution measurement indicate there is only tiny coil extension or shrinkage for both PIs with temperature rising. Parameters related to chain flexibility of polymer, including persistence length lp, shift factor ME（relative molecular weight per unit contour length） and backbone diameter d are estimated from the relationship between intrinsic viscosity and molecular weight for the continuous wormlike cylinder model, which indicates that two samples are flexible chains, only the chain of poly（6FDA/3,3＇-DMB） is stiffer than that of poly（6FDA/2,2＇-DMB） slightly.

Nanoscale inhibition of polymorphic and ambidextrous lAPP amyloid aggregation with small molecules

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.

Understanding sequence effect in DNA bending elasticity by molecular dynamic simulations

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.

Fiber Bending Flexibility Evaluation by Worm-like Chain Model

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.

Conformational Properties of Comb-shaped Polyelectrolytes with Negatively Charged Backbone and Neutral Side Chains Studied by a Generic Coarse-grained Bead-and-Spring Model

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.