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Sample records for kratkie soobshcheniya oiyai

  1. Understanding the stiffness of macromolecules: From linear chains to bottle-brushes

    NASA Astrophysics Data System (ADS)

    Binder, K.; Hsu, H.-P.; Paul, W.

    2016-07-01

    The intrinsic local stiffness of a polymer is characterized by its persistence length. However, its traditional definition in terms of the exponential decay of bond orientational correlations along the chain backbone is accurate only for Gaussian phantom-chain-like polymers. Also care is needed to clarify the conditions when the Kratky-Porod wormlike chain model is applicable. These problems are elucidated by Monte Carlo simulations of simple lattice models for polymers in both d = 2 and d = 3 dimensions. While the asymptotic decay of the bond orientational correlations for real polymers always is of power law form, the Kratky-Porod model is found to be applicable for rather stiff (but not too long) thin polymers in d = 3 (but not in d = 2). However, it does not describe thick chains, e.g., bottle-brush polymers, where stiffness is due to grafted flexible side-chains, and the persistence length grows proportional to the effective thickness of the bottle-brush. A scaling description of bottle-brushes is validated by simulations using the bond fluctuation model.

  2. Stretching semiflexible polymer chains: evidence for the importance of excluded volume effects from Monte Carlo simulation.

    PubMed

    Hsu, Hsiao-Ping; Binder, Kurt

    2012-01-14

    Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice (d = 3 dimensions) and square lattice (d = 2 dimensions), varying chain stiffness by an energy penalty ε(b) for chain bending. In the absence of excluded volume interactions, the persistence length l(p) of the polymers would then simply be l(p) = l(b)(2d - 2)(-1)q(b) (-1) with q(b) = exp(-ε(b)/k(B)T), the bond length l(b) being the lattice spacing, and k(B)T is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both q(b) and the chain length N are varied over a wide range (0.005 ≤ q(b) ≤ 1, N ≤ 50,000), and also a stretching force f is applied to one chain end (fixing the other end at the origin). In the absence of this force, in d = 2 a single crossover from rod-like behavior (for contour lengths less than l(p)) to swollen coils occurs, invalidating the Kratky-Porod model, while in d = 3 a double crossover occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and then to coils that are swollen due to the excluded volume interaction. If the stretching force is applied, excluded volume interactions matter for the force versus extension relation irrespective of chain stiffness in d = 2, while theories based on the Kratky-Porod model are found to work in d = 3 for stiff chains in an intermediate regime of chain extensions. While for q(b) ≪ 1 in this model a persistence length can be estimated from the initial decay of bond-orientational correlations, it is argued that this is not possible for more complex wormlike chains (e.g., bottle-brush polymers). Consequences for the proper interpretation of experiments are briefly discussed. PMID:22260610

  3. Solution X-ray scattering analysis of cold- heat-, and urea-denatured states in a protein, Streptomyces subtilisin inhibitor.

    PubMed

    Konno, T; Kataoka, M; Kamatari, Y; Kanaori, K; Nosaka, A; Akasaka, K

    1995-08-01

    Streptomyces subtilisin inhibitor (SSI), a homo-dimeric protein with a subunit of 113 residues with two disulfide bonds, is known to exist at low pH in at least three distinct thermodynamic states namely, the native (N), cold-denatured (D') and heat-denatured (D). Small-angle X-ray scattering was used to analyze and to compare overall chain conformations of SSI in typical, N, D', D and urea-denatured states (Durea). Molecular masses were determined from scattering intensities extrapolated to a scattering angle of zero, which showed that SSI exists as a homo-dimer in the N state, but as dissociated monomers in the D', D and Durea states. From Guinier plots of the scattering intensities, radii of gyration (Rg) were determined to be 20.1(+/- 1.8) A for N, and 20.7(+/- 1.3), 25.8(+/- 1.5) and 32 to 35 A for D', D and Durea, respectively. Kratky plots for both N and D' exhibited a bell-shape indicating that the polypeptide chain has a globular part not only in N but also in D', while Kratky plots for D and Durea showed that the polypeptide chain has no globular part either in Durea or D. Combined with the results from circular dichroism and 1H NMR spectra, a picture emerges for the polypeptide chain conformation of SSI such that in N it is a globular dimer close to that in the crystal, in Durea it is totally disordered and expanded nearly to a fully random chain with restrictions only from the disulfide bridges, in D the entire chain is disordered and expanded but with considerable local intra-chain interactions, and in D' the chain consists of a part with a unique tertiary structure and a part disordered and expanded to a degree comparable to D. PMID:7643393

  4. Scattering function of semiflexible polymer chains under good solvent conditions.

    PubMed

    Hsu, Hsiao-Ping; Paul, Wolfgang; Binder, Kurt

    2012-11-01

    Using the pruned-enriched Rosenbluth Monte Carlo algorithm, the scattering functions of semiflexible macromolecules in dilute solution under good solvent conditions are estimated both in d = 2 and d = 3 dimensions, considering also the effect of stretching forces. Using self-avoiding walks of up to N = 25,600 steps on the square and simple cubic lattices, variable chain stiffness is modeled by introducing an energy penalty ε(b) for chain bending; varying q(b) = exp (-ε(b)∕k(B)T) from q(b) = 1 (completely flexible chains) to q(b) = 0.005, the persistence length can be varied over two orders of magnitude. For unstretched semiflexible chains, we test the applicability of the Kratky-Porod worm-like chain model to describe the scattering function and discuss methods for extracting persistence length estimates from scattering. While in d = 2 the direct crossover from rod-like chains to self-avoiding walks invalidates the Kratky-Porod description, it holds in d = 3 for stiff chains if the number of Kuhn segments n(K) does not exceed a limiting value n(K)(*) (which depends on the persistence length). For stretched chains, the Pincus blob size enters as a further characteristic length scale. The anisotropy of the scattering is well described by the modified Debye function, if the actual observed chain extension (end-to-end distance in the direction of the force) as well as the corresponding longitudinal and transverse linear dimensions - (2), are used. PMID:23145745

  5. Structure of bottle brush polymers on surfaces: weak versus strong adsorption.

    PubMed

    Hsu, Hsiao-Ping; Paul, Wolfgang; Binder, Kurt

    2011-12-01

    Large-scale Monte Carlo simulations are presented for a coarse-grained model of cylindrical molecular brushes adsorbed on a flat structureless substrate, varying both the chain length N of the side chains and the backbone chain length N(b). For the case of good solvent conditions, both the cases of weak adsorption (only 10 to 15% of the monomers being bound to the surface) and strong adsorption (~40% of the monomers being bound to the surface, forcing the bottle brush into an almost 2D conformation) are studied. We focus on the scaling of the total linear dimensions of the cylindrical brush with both chain lengths N and N(b), demonstrating a crossover from rod-like behavior (for not very large N(b)) to the scaling of 2D self-avoiding walks. Despite the fact that snapshot pictures suggest a "worm-like" picture as a coarse-grained description of such cylindrical brushes, the Kratky-Porod worm-like chain model fails because there is no regime where Gaussian statistics applies. We compare the stiffness (orientational correlations of backbone bonds, persistence length estimates, etc.) of the adsorbed bottle brush polymers with their corresponding 3D nonadsorbed counterparts. Consequences for the discussion of pertinent experiments are briefly discussed. PMID:21751800

  6. Nonlinear Behavior of Gelatin Networks Reveals a Hierarchical Structure.

    PubMed

    Yang, Zhi; Hemar, Yacine; Hilliou, Loic; Gilbert, Elliot P; McGillivray, Duncan J; Williams, Martin A K; Chaieb, Sahraoui

    2016-02-01

    We investigate the strain hardening behavior of various gelatin networks-namely physical gelatin gel, chemically cross-linked gelatin gel, and a hybrid gel made of a combination of the former two-under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillations shear protocols. Further, the internal structures of physical gelatin gels and chemically cross-linked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically cross-linked network whereas, in the physical gelatin gels, a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as the correlation length (ξ), the cross-sectional polymer chain radius (R(c)) and the fractal dimension (d(f)) of the gel networks. The fractal dimension d(f) obtained from the SANS data of the physical and chemically cross-linked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized nonlinear elastic theory that has been used to fit the stress-strain curves. The chemical cross-linking that generates coils and aggregates hinders the free stretching of the triple helix bundles in the physical gels. PMID:26667303

  7. Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment.

    PubMed

    Henriques, João; Cragnell, Carolina; Skepö, Marie

    2015-07-14

    An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014, 10, 5113 - 5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment. PMID:26575776

  8. Rouse-Bueche Theory and The Calculation of The Monomeric Friction Coefficient in a Filled System

    NASA Astrophysics Data System (ADS)

    Martinetti, Luca; Macosko, Christopher; Bates, Frank

    According to flexible chain theories of viscoelasticity, all relaxation and retardation times of a polymer melt (hence, any dynamic property such as the diffusion coefficient) depend on the monomeric friction coefficient, ζ0, i.e. the average drag force per monomer per unit velocity encountered by a Gaussian submolecule moving through its free-draining surroundings. Direct experimental access to ζ0 relies on the availability of a suitable polymer dynamics model. Thus far, no method has been suggested that is applicable to filled systems, such as filled rubbers or microphase-segregated A-B-A thermoplastic elastomers at temperatures where one of the blocks is glassy. Building upon the procedure proposed by Ferry for entangled and unfilled polymer melts, the Rouse-Bueche theory is applied to an undiluted triblock copolymer to extract ζ0 from the linear viscoelastic behavior in the rubber-glass transition region, and to estimate the size of Gaussian submolecules. At iso-free volume conditions, the so-obtained matrix monomeric friction factor is consistent with the corresponding value for the homopolymer melt. In addition, the characteristic Rouse dimensions are in good agreement with independent estimates based on the Kratky-Porod worm-like chain model. These results seem to validate the proposed approach for estimating ζ0 in a filled system. Although preliminary tested on a thermoplastic elastomer of the A-B-A type, the method may be extended and applied to filled homopolymers as well.

  9. Characterizing Flexible and Instrinsically Unstructured Biological Macromolecules by SAS using the Porod-Debye Law

    PubMed Central

    Rambo, Robert P.; Tainer, John A.

    2011-01-01

    Unstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X-ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. Here, we consider the Porod-Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod-Debye region fundamentally describes the nature of the scattering intensity decay, which captures information needed for distinguishing between folded and flexible particles. Particularly for comparative SAS experiments, application of the law, as described here, can distinguish between discrete conformational changes and localized flexibility relevant to molecular recognition and interaction networks. This approach aids insightful analyses of fully and partly flexible macromolecules that is more robust and conclusive than traditional Kratky analyses. Furthermore, we demonstrate for prototypic SAXS data that the ability to calculate particle density by the Porod-Debye criteria, as shown here, provides an objective quality assurance parameter that may prove of general use for SAXS modeling and validation. PMID:21509745

  10. Experimental and numerical studies of tethered DNA dynamics in shear flow

    NASA Astrophysics Data System (ADS)

    Lueth, Christopher A.

    Polymer physics has a rich tradition spanning nearly two centuries. In the 1830s, Henri Braconnot and coworkers were perhaps the first to work on what is today known as polymer science when they derived semi-synthetic materials from naturally occurring cellulose. However, the true nature of polymers, as long chain molecules, had not been proposed until 1910 by Pickles. It was not until the 1950's when polymer models were developed using statistical mechanics. Recently, the field has been revitalized by the ability to study individual polymer molecules for the first time. The development of DNA single molecule fluorescence microscopy coupled with ever increasing computational power has opened the door to molecular level understanding of polymer physics, resolving old disputes and uncovering new interesting phenomena. In this work, we use a combination of theoretical predictions and lambda-phage DNA single molecule fluorescence microscopy to study the behavior of polymers tethered to surfaces. Brownian dynamics simulations of a number of coarse-grained polymer models---dynamic and equilibrium Kratky-Porod chains as well as bead-spring chains---were completed and compared with analytical and experimental results. First, an expression is developed for the entropic exclusion force experienced by a tethered polymer chain. We propose that, for a freely jointed chain, a modification to the free entropic force of kBT/y is needed in the direction normal to the surface. Analogously, we propose that for a wormlike chain, a modification of 2kBT/y is needed, due to the finite curvature of the model. Then, the reliability of discretized bead spring simulations containing this modified entropic force are analyzed using Kratky-Porod simulations and are found to reproduce most statistics, except for those very near the surface, such as end-wall contact. Next, experiments of tethered lambda-phage DNA in shear flow are presented for the first time in the flow-gradient plane. The

  11. Structural Plasticity of Staphylococcal Nuclease Probed by Perturbation with Pressure and pH

    PubMed Central

    Kitahara, Ryo; Hata, Kazumi; Maeno, Akihiro; Akasaka, Kazuyuki; Chimenti, Michael; Bertrand Garcia-Moreno, E; Schroer, Martin A.; Jeworrek, Christoph; Tolan, Metin; Winter, Roland; Roche, Julien; Roumestand, Christian; de Guillen, Karine Montet; Royer, Catherine A.

    2012-01-01

    The ionization of internal groups in proteins can trigger conformational change. Despite this being the structural basis of most biological energy transduction, these processes are poorly understood. SAXS and NMR spectroscopy experiments at ambient and high hydrostatic pressure were used to examine how the presence and ionization of Lys-66, buried in the hydrophobic core of a stabilized variant of staphylococcal nuclease, affect conformation and dynamics. NMR spectroscopy at atmospheric pressure showed previously that the neutral Lys-66 affects slow conformational fluctuations globally, whereas the effects of the charged form are localized to the region immediately surrounding position 66. Ab initio models from SAXS data suggest that when Lys-66 is charged the protein expands, which is consistent with results from NMR spectroscopy. The application of moderate pressure (< 2 kbar) at pH values where Lys-66 is normally neutral at ambient pressure left most of the structure unperturbed but produced significant non-linear changes in chemical shifts in the helix where Lys-66 is located. Above 2 kbar pressure at these pH values the protein with Lys-66 unfolded cooperatively adopting a relatively compact, albeit random structure according to Kratky analysis of the SAXS data. In contrast, at low pH and high pressure the unfolded state of the variant with Lys-66 is more expanded than that of the reference protein. The combined global and local view of the structural reorganization triggered by ionization of the internal Lys-66 reveals more detectable changes than were previously suggested by NMR spectroscopy at ambient pressure. PMID:21254234

  12. Structural characterization of intramolecular Hg2+ transfer between flexibly-linked domains of mercuric ion reductase

    SciTech Connect

    Johs, Alexander; Harwood, Ian M; Parks, Jerry M; Nauss, Rachel; Smith, Jeremy C; Liang, Liyuan; Miller, Susan M

    2011-01-01

    The enzyme mercuric ion reductase, MerA, is the central component of bacterial mercury resistance encoded by the mer operon. Many MerA proteins possess a metallochaperone-like N-terminal domain, NmerA, that can transfer Hg2+ to the catalytic core (Core) for reduction to Hg0. These domains are tethered to the homodimeric Core by ~30-residue linkers that are subject to proteolysis, which has limited structural and functional characterization of the interactions of these domains. Here, we report purification of homogeneous full-length MerA using a fusion protein construct and combine small-angle X-ray and neutron scattering with molecular dynamics simulation to characterize the structure of constructs that mimic the system before and during handoff of Hg2+ from NmerA to the Core. The radii of gyration, distance distribution functions and Kratky plots derived from the small-angle X-ray scattering data are consistent with full-length MerA adopting elongated conformations resulting from flexibility in the linkers to the NmerA domains. The scattering profiles are best reproduced using an ensemble of linker conformations. This flexible attachment of NmerA may facilitate fast and efficient removal of Hg2+ from diverse protein substrates. Using a specific mutant of MerA allowed determination of the position and relative orientation of NmerA to the Core during Hg2+ handoff. The small buried surface area at the site of interaction suggests molecular recognition may be of less importance for the integrity of metal ion transfers between tethered domains than for transfers between separate proteins in metal trafficking pathways.

  13. Lattice Monte Carlo simulations of polymer melts

    NASA Astrophysics Data System (ADS)

    Hsu, Hsiao-Ping

    2014-12-01

    We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction 0.5. In order to reduce the local density fluctuations, we test a pre-packing process for the preparation of the initial configurations of the polymer melts, before the excluded volume interaction is switched on completely. This process leads to a significantly faster decrease of the number of overlapping monomers on the lattice. This is useful for simulating very large systems, where the statistical properties of the model with a marginally incomplete elimination of excluded volume violations are the same as those of the model with strictly excluded volume. We find that the internal mean square end-to-end distance for moderately stiff chains in a melt can be very well described by a freely rotating chain model with a precise estimate of the bond-bond orientational correlation between two successive bond vectors in equilibrium. The plot of the probability distributions of the reduced end-to-end distance of chains of different stiffness also shows that the data collapse is excellent and described very well by the Gaussian distribution for ideal chains. However, while our results confirm the systematic deviations between Gaussian statistics for the chain structure factor Sc(q) [minimum in the Kratky-plot] found by Wittmer et al. [EPL 77, 56003 (2007)] for fully flexible chains in a melt, we show that for the available chain length these deviations are no longer visible, when the chain stiffness is included. The mean square bond length and the compressibility estimated from collective structure factors depend slightly on the stiffness of the chains.

  14. A New Efficient Method for Generating Conformations of Unfolded Proteins with Diverse Main-Chain Dihedral-Angle Distributions.

    PubMed

    Seki, Yasutaka; Shimbo, Yudai; Nonaka, Takamasa; Soda, Kunitsugu

    2011-07-12

    A new method for generating polypeptide-chain conformations has been developed for studying structural characteristics of unfolded proteins. It enables us to generate a large number of conformations very rapidly by avoiding atomic collisions efficiently with the use of main-chain dihedral-angle distributions derived from a crystal-structure database of proteins. In addition, combining main-chain dihedral-angle distributions for the amino acid residues incorporated in different secondary structures, we can obtain diverse conformational ensembles with different structural features. Structural characteristics of proteins denatured in high-concentration denaturant solution were analyzed by comparing predictions from this method with results from solution X-ray scattering (SXS) measurement. Analysis of the dependence of the mean square radius (Rsq) of protein on the number of residues and the shape of its Kratky profile has confirmed that the highly denaturing solvent serves as a good solvent in accordance with previous reports. It was also found that, in order for a conformational ensemble to reproduce experimental data, the percentage in which main-chain dihedral angles are found in the α region must be in the range of 20-40%. It agrees with studies on the (3)JHNα coupling constant using the multidimensional NMR method. These results confirm that our method for generating diverse conformations of polypeptide chains is very useful to the conformational analysis of unfolded protein, because it enables us to analyze comprehensively both of the local structural features obtained from NMR and the global ones obtained from SXS. PMID:26606484

  15. Penta-L-lysine Potentiates Fibrin-Independent Activity of Human Tissue Plasminogen Activator.

    PubMed

    Rehan, Mohammad; Sagar, Amin; Sharma, Vandna; Mishra, Sanskruti; Ashish; Sahni, Girish

    2015-10-22

    The therapeutic action of tissue plasminogen activator (t-PA) is a two-step process: (1) binding to lysine-rich fibrin (Km event) and (2) converting local plasminogen into plasmin (Kcat event). Overcoming limitations of other structural biophysics methods, we wanted to employ small-angle X-ray scattering (SAXS) to visualize what shape changes occur/accompany t-PA activation, but the prime hurdle was the polydisperse nature of the fibrin, which occluded scattering information from t-PA. Earlier, larger polylysine peptides have been used to potentiate activation of t-PA, so while screening short polylysine peptides as alternatives to fibrin or larger peptides, we found that penta-polylysine (P5) specifically activates t-PA in a dose-dependent manner, averaging to almost 3-fold more than in the absence of any peptide. SAXS data analysis confirmed that P5 does not induce association of t-PA molecules, and a narrower peak profile of the Kratky plot indicated that P5 binding quenches inherent motion in t-PA. Shape reconstruction of t-PA ∓ P5 revealed that P5 closes the "gap" between the two gross domains of t-PA, viz. fused F/E, K1 and K2 domains, and the P domain. Docking experiments suggested that, while other polylysine peptides preferentially interacted with the surfaces of kringle domains, P5 "slipped into" the gap/groove between K2 and P domains, thereby mediating a substantial increase in the number of long-range interactions between the K2 domain and exosites in the P domain. We report here dissection of shape events involved in between Km/Kcat steps of t-PA activation, which can pave the way toward the search for small molecule function regulator(s) of t-PA. PMID:26447340

  16. Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase.

    PubMed

    Johs, Alexander; Harwood, Ian M; Parks, Jerry M; Nauss, Rachel E; Smith, Jeremy C; Liang, Liyuan; Miller, Susan M

    2011-10-28

    The enzyme mercuric ion reductase MerA is the central component of bacterial mercury resistance encoded by the mer operon. Many MerA proteins possess metallochaperone-like N-terminal domains (NmerA) that can transfer Hg(2+) to the catalytic core domain (Core) for reduction to Hg(0). These domains are tethered to the homodimeric Core by ~30-residue linkers that are susceptible to proteolysis, the latter of which has prevented characterization of the interactions of NmerA and the Core in the full-length protein. Here, we report purification of homogeneous full-length MerA from the Tn21 mer operon using a fusion protein construct and combine small-angle X-ray scattering and small-angle neutron scattering with molecular dynamics simulation to characterize the structures of full-length wild-type and mutant MerA proteins that mimic the system before and during handoff of Hg(2+) from NmerA to the Core. The radii of gyration, distance distribution functions, and Kratky plots derived from the small-angle X-ray scattering data are consistent with full-length MerA adopting elongated conformations as a result of flexibility in the linkers to the NmerA domains. The scattering profiles are best reproduced using an ensemble of linker conformations. This flexible attachment of NmerA may facilitate fast and efficient removal of Hg(2+) from diverse protein substrates. Using a specific mutant of MerA allowed the formation of a metal-mediated interaction between NmerA and the Core and the determination of the position and relative orientation of NmerA to the Core during Hg(2+) handoff. PMID:21893070

  17. Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles

    NASA Astrophysics Data System (ADS)

    Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt

    2015-12-01

    The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs

  18. Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles.

    PubMed

    Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt

    2015-12-28

    The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs