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The thermoresponsive nature of aqueous solutions of poly(N‐isopropylacrylamide) (PNIPAAM) star polymers containing 2, 3, 4, and 6 arms has been investigated by turbidity, dynamic light scattering, rheology, and rheo‐SALS. Simulations of the thermosensitive nature of the single star polymers have also been conducted. Some of the samples form aggregates even at temperatures significantly below the lower critical solution temperature (LCST) of PNIPAAM. Increasing concentration and number of arms promotes associations at low temperatures. When the temperature is raised, there is a competition between size increase due to enhanced aggregation and a size reduction caused by contraction. Monte Carlo simulations show that the single stars contract with increasing temperature, and that this contraction is more pronounced when the number of arms is increased. Some samples exhibit a minimum in the turbidity data after the initial increase at the cloud point. The combined rheology and rheo‐SALS data suggest that this is due to a fragmentation of the aggregates followed by re‐aggregation at even higher temperatures. Although the 6‐arm star polymer aggregates more than the other stars at low temperatures, the more compact structure renders it less prone to aggregation at temperatures above the cloud point., How many arms? Aqueous solutions of poly(N‐isopropylacrylamide) (PNIPAAM) star polymers exhibit a complex thermosensitive behavior. Increasing the number of arms promotes aggregation below the cloud point. When the temperature is raised, there is a competition between size increase due to enhanced aggregation and a size reduction caused by contraction. Some of the samples exhibits fragmentation of the aggregates at temperatures above the cloud point, followed by re‐aggregation at even higher temperatures.

The adsorption of the thermoresponsive positively charged copolymer poly(N-isopropylacrylamide)-block-poly(3-acrylamidopropyl)trimethylammonium chloride, PNIPAAM48-b-PAMPTMA6(+), onto negatively charged gold nanoparticles can provide stability to the nanoparticles and make the emerging structure tunable by temperature. In this work, we characterize the nanocomposite formed by gold nanoparticles and copolymer chains and study the influence of the copolymer on the expected aggregation process that undergoes those nanoparticles at high ionic strength. We also determine the lower critical solution temperature (LCST) of the copolymer (around 42 °C) and evaluate the influence of the temperature on the nanocomposite. For those purposes, we use dynamic light scattering, UV-vis spectroscopy and transmission electron microscopy. At the working PNIPAAM48-b-PAMPTMA6(+) concentration, we observe the existence of copolymer structures that trap the gold nanoparticles and avoid the formation of nanoparticles aggregates. Finally, we discuss how these structures can be useful in catalysis and nanoparticles recovery.

23 pags., 5 figs., 3 tabs. -- This article belongs to the Special Issue Structural, Functional and Folding Strategies of Oligomeric Proteins, The histidine phosphocarrier protein (HPr) kinase/phosphorylase (HPrK/P) modulates the phosphorylation state of the HPr protein, and it is involved in the use of carbon sources by Gram-positive bacteria. Its X-ray structure, as concluded from crystals of proteins from several species, is a hexamer; however, there are no studies about its conformational stability, and how its structure is modified by the pH. We have embarked on the conformational characterization of HPrK/P of Bacillus subtilis (bsHPrK/P) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, small-angle X-ray-scattering (SAXS) and dynamic light-scattering (DLS)). bsHPrK/P was mainly a hexamer in solution at pH 7.0, in the presence of phosphate. The protein had a high conformational stability, with an apparent thermal denaturation midpoint of ~70 °C, at pH 7.0, as monitored by fluorescence and CD. The protein was very pH-sensitive, precipitated between pH 3.5 and 6.5; below pH 3.5, it had a molten-globule-like conformation; and it acquired a native-like structure in a narrow pH range (between pH 7.0 and 8.0). Guanidinium hydrochloride (GdmCl) denaturation occurred through an oligomeric intermediate. On the other hand, urea denaturation occurred as a single transition, in the range of concentrations between 1.8 and 18 µM, as detected by far-UV CD and fluorescence., This research was funded by Spanish Ministry of Economy and Competitiveness and European ERDF Funds (MCIU/AEI/FEDER, EU) [RTI2018-097991-B-I00 to JLN, BIO2016-78020-R to ACA and CTQ2017-85425-P to JGHC]; JGHC thanks Fundación Séneca, Región de Murcia for funding (20933/PI/18).

The assembly of the protein complex of cytochrome c oxidase (COX), which participates in the mitochondrial respiratory chain, requires a large number of accessory proteins (the so-called assembly factors). Human COX assembly factor 3 (hCOA3), also known as MITRAC12 or coiled-coil domain-containing protein 56 (CCDC56), interacts with the first subunit protein of COX to form its catalytic core and promotes its assemblage with the other units. Therefore, hCOA3 is involved in COX biogenesis in humans and can be exploited as a drug target in patients with mitochondrial dysfunctions. However, to be considered a molecular target, its structure and conformational stability must first be elucidated. We have embarked on the description of such features by using spectroscopic and hydrodynamic techniques, in aqueous solution and in the presence of detergents, together with computational methods. Our results show that hCOA3 is an oligomeric protein, forming aggregates of different molecular masses in aqueous solution. Moreover, on the basis of fluorescence and circular dichroism results, the protein has (i) its unique tryptophan partially shielded from solvent and (ii) a relatively high percentage of secondary structure. However, this structure is highly flexible and does not involve hydrogen bonding. Experiments in the presence of detergents suggest a slightly higher content of nonrigid helical structure. Theoretical results, based on studies of the primary structure of the protein, further support the idea that hCOA3 is a disordered protein. We suggest that the flexibility of hCOA3 is crucial for its interaction with other proteins to favor mitochondrial protein translocation and assembly of proteins involved in the respiratory chain.

10 pags., 6 figs., 1 tab., Plakophilin 1 (PKP1) is a member of the armadillo repeat family of proteins. It serves as a scaffold component of desmosomes, which are key structural components for cell–cell adhesion. We have embarked on the biophysical and conformational characterization of the ARM domain of PKP1 (ARM-PKP1) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, analytical ultracentrifugation (AUC), dynamic light scattering (DLS) and differential scanning calorimetry (DSC)). ARM-PKP1 was a monomer in solution at physiological pH, with a low conformational stability, as concluded from DSC experiments and thermal denaturations followed by fluorescence and CD. The presence or absence of disulphide bridges did not affect its low stability. The protein unfolded through an intermediate which has lost native-like secondary structure. ARM-PKP1 acquired a native-like structure in a narrow pH range (between pH 6.0 and 8.0), indicating that its adherent properties might only work in a very narrow pH range., This work was supported by Spanish Ministry of Economy and Competitiveness and European ERDF Funds (MCIU/AEI/ERDF, EU) [RTI2018-097991-B-I00 to JLN, BIO2016-78020-R to ACA, CTQ2017-85425-P to JGHC] and by the PAIDI program, Group BIO309 (Junta de Andalucía) to MEFV. JGHC thanks Fundación Séneca, Región de Murcia for funding (20933/PI/18).

In a previous work, we described a multi-scale protocol for the simulation of the conformation and dynamics of macromolecules that was applied to dendrimer molecules proving its predictive capability by comparison with experimental data. That scheme is now employed in order to predict conformational properties (radius of gyration) and overall hydrodynamic properties (translational diffusion and intrinsic viscosity) of hyperbranched molecules in dilute solution. For that purpose, we use a very simple coarse-grained bead-and-spring model whose parameters are not adjusted against experimental properties but they are obtained from previous atomic-level (Langevin) simulations of small fragments of real hyperbranched polymers. In addition, we devise a method to generate structures with different degree of branching. The Monte Carlo simulation technique was used to generate the set conformations of the coarse-grained model. In spite of the difficulties of reproducing experimental data of highly polydisperse entities (in terms of both molecular weight and topology) without using adjustable parameters, the results of this paper show that the proposed methodology allows for qualitative predictions of the behavior of such complex systems and lead us to conclude that, after some improvement, acceptable quantitative predictions can be achieved.

The LrtA protein of Synechocystis sp. PCC 6803 intervenes in cyanobacterial post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family of proteins, involved in protein synthesis. In this work, we studied the conformational preferences and stability of isolated LrtA in solution. At physiological conditions, as shown by hydrodynamic techniques, LrtA was involved in a self-association equilibrium. As indicated by Nuclear Magnetic Resonance (NMR), circular dichroism (CD) and fluorescence, the protein acquired a folded, native-like conformation between pH 6.0 and 9.0. However, that conformation was not very stable, as suggested by thermal and chemical denaturations followed by CD and fluorescence. Theoretical studies of its highly-charged sequence suggest that LrtA had a Janus sequence, with a context-dependent fold. Our modelling and molecular dynamics (MD) simulations indicate that the protein adopted the same fold observed in other members of the HPF family (&beta, &alpha, &beta, ) at its N-terminal region (residues 1&ndash, 100), whereas the C terminus (residues 100&ndash, 197) appeared disordered and collapsed, supporting the overall percentage of overall secondary structure obtained by CD deconvolution. Then, LrtA has a chameleonic sequence and it is the first member of the HPF family involved in a self-association equilibrium, when isolated in solution.

Two chain models, a Gaussian chain and a touching-beads (wormlike) chain, are used to represent a flexible polyelectrolyte (sodium polystyrene sulfonate) and a semiflexible polyelectrolyte (sodium alginate), respectively. Monte Carlo and Brownian dynamics simulations of those models were carried out to obtain the ionic strength dependence of some conformational and hydrodynamic properties expressed in form of equivalent radii. Electrostatic interactions were taken into account by the Debye–Huckel potential, thus counterions are not considered explicitly. In the case of the sodium polystyrene sulfonate model, a linear dependence of the equivalent radii with the ionic strength is found for a region of intermediate to low enough ionic strength values, whereas for high values of the ionic strength the equivalent radii reach a plateau with a value equal to that of the uncharged chain. Thus, an extrapolation to infinite ionic strength of the linear region would not report the actual property value of the uncharged chain. In the case of the sodium alginate model such a linear dependence is not so clearly appreciated. Our simulation results show a good agreement with several experimental data which support the validity of the Debye–Huckel approximation to model different types of polyelectrolyte solutions in a simple way.

This review elucidates several aspects on the behavior of charged polysaccharides and mucin. Viscosification of dilute aqueous solutions of hyaluronan (HA) occurs in the course of time at low shear flow, whereas shear thinning as time evolves is found at moderate shear rates. Hydrogen bonds and electrostatic interaction play an important role for the emergence of these features. No time effect of the viscosity is observed for semidilute HA solutions. A degradation of HA is observed at low and high pH and this effect continues over long times, and it is only in the approximate interval 5

A bead-and-spring model has been used to simulate the behavior of thermoresponsive asymmetric diblock amphiphilic copolymers with aid of Monte Carlo simulations. The alteration of the thermodynamic conditions was mimicked by using a Lennard-Jones potential, which was related to the measured temperatures by comparison with experimental data for aqueous solutions of two sets of diblock copolymers, namely methoxypoly(ethylene glycol)-block-poly(N-isopropylacrylamide), one with different lengths of the hydrophilic block (MPEG(n)-b-PNIPAAM(71)) and one with varying lengths of the hydrophobic block (MPEG(57)-b-PNIPAAM(m)). The influence of the length of both the thermoresponsive and the hydrophilic block on the size and conformation of single molecules at various temperatures was studied by means of simulations. The temperature-induced contraction of the copolymer (MPEG(n)-b-PNIPAAM(71)) entities is only modestly affected by changing the length of the hydrophilic block, whereas for the MPEG(57)-b-PNIPAAM(m) copolymer both the transition temperature and the magnitude of the compression of the molecules are strongly influenced by the length of the thermosensitive block. When the MPEG chain fully covers the hydrophobic core, the copolymer moieties are stabilized, whereas poorly covered cores can promote interchain aggregation at elevated temperatures.

The calculation of solution properties of flexible macromolecules and other nanoparticles requires, in addition to the hydrodynamic formalisms needed for the sedimentation coefficient and other transport properties, the consideration of the conformational statistics and internal dynamics. The latter aspects can be handled with simulation methods like Monte Carlo and Brownian dynamics. An example of a Monte Carlo simulation for a model specific of DNA is illustrated with results for the several solution properties over an extremely wide range of molecular weight. The convenience of having computational tools of a quite general applicability has prompted us to implement the simulation and hydrodynamic treatments in software packages, MONTEHYDRO for Monte Carlo, and SIMUFLEX for Brownian dynamics which — with a scope similar to the HYDRO suite for rigid particles — can handle a variety of situations. As an application of the new methodology to a yet unclear problem in analytical ultracentrifugation, in a simple application of the SIMU-FLEX software, we present a simulation of the so-called anomalous sedimentation of very long DNA molecules, obtaining results for the experimentally observable rotor-speed-dependence of the sedimentation coefficient.

A computer programs suite, SIMUFLEX, has been constructed for the calculation of solution properties of flexible macromolecules modeled as bead-and-connector models of arbitrary topology. The suite consists mainly of two independent programs, BROWFLEX that generates the macromolecular trajectory by using the Brownian dynamics technique and ANAFLEX that analyzes that trajectory to get solution properties of the macromolecule. In this paper, we describe theoretical aspects about the macromolecular model and the Brownian dynamics algorithm used and describe some of the numerous properties that can be evaluated. In order to provide examples of the application of the methodology, we present simulations of dynamic properties of DNA with length ranging from 10 to 10(5) base pairs. SIMUFLEX is able to run simulations with more or less coarse-grained models, thus enabling such multiple-scale studies.

This paper describes a computational exercise at undergraduate level that demonstrates the employment of Monte Carlo simulation to study the conformational statistics of flexible polymer chains, and to predict solution properties. Three simple chain models, including excluded volume interactions, have been implemented in a public-domain computer program that is the tool on which this exercise is based. The first stage considers fundamental aspects of polymer chain statistics, such as the distribution of end-to-end distance and the exponents in the power laws that relate properties to chain length, for both ideal, phantom chains and also with excluded volume effects. The numerical results are employed to predict properties of real polymer/solvent systems, such as polystyrene in cyclohexane and toluene, which are then compared to experimental data.

The determination of the intrinsic viscosity by single-point determinations, like that based on the Solomon–Ciuta equation, have been proposed as efficient alternatives to dilution procedures. With a basis on theoretical analysis and computer simulation, we evaluate the systematic and global bias of the Solomon–Ciuta result and show how it depends on the strength of the concentration dependence of the solution viscosity (represented by the intrinsic viscosity and the Huggins constant) and the concentration of the single measured solution. We propose that an estimated Huggins constant can be employed in a corrected Solomon–Ciuta procedure, which may yield results for the intrinsic viscosity that are even more accurate than those from the Huggins extrapolation. This gives support and utility to the use of the single-point procedure when the intrinsic viscosity has to be determined for a unique concentration. We also pinpoint specific circumstances where the dilution–extrapolation procedures should be preferred.

Chitosan (CS) is a biocompatible polysaccharide with positive charge that is widely used as a coating agent for negatively charged nanoparticles. However, the types of structures that emerge by combining CS and nanoparticles as well as their behaviour are still poorly understood. In this work, we characterize the nanocomposites formed by gold nanoparticles (AuNPs) and CS and study the influence of CS in the expected aggregation process that should experience those nanoparticles under the favourable conditions of low pH and high ionic strength. Thus, at the working CS concentration, we observe the existence of CS structures that quickly trap the AuNPs and avoid the formation of nanoparticle aggregates in environmental conditions that, otherwise, would lead to such an aggregation.

30 p.-14 fig. Zhao, Huaying, et alt., Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.

Background The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations. Results That scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed. Conclusions The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics. Electronic supplementary material The online version of this article (doi:10.1186/s13628-015-0025-7) contains supplementary material, which is available to authorized users.

In this work, we propose simple physical models and simulation methodologies for the simulation of solution properties of dendrimer molecules. We employ a multi-scale approach, in which the basic entities in the bead-and-connector models are first parameterized by comparison of the outcome from fully atomic molecular dynamics simulation with that of Monte Carlo calculations of the simple model. Employing experimental data of the radius of gyration for this parameterization, the calculated values of other properties, like the intrinsic viscosity and hydrodynamic radius are in good agreement with experimental data. The dynamics of our simple physical model can be studied by Brownian dynamics with hydrodynamic interaction. Thus one can make predictions for other dynamic properties of the dendrimer molecules, like NMR relaxation and rheology. Copyright © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.

Polymer orientation in dilute solutions undergoing shear flow is investigated computationally by means of the Brownian dynamics simulation technique applied to the bead-spring chain model. The dependence of the degree of orientation on the shear intensity is evaluated through a quantity called orientation resistance. All simulations were performed using non-preaveraged hydrodynamic interaction (HI). The spring type (Gaussian or FENE) is shown to strongly determine the shear flow behavior of the chain orientation. Solvent quality (Θ, good or bad), represented by a suitable Lennard-Jones intramolecular potential, does not affect the flow behavior but influences the values of the orientation resistance. Hence, the orientability of the polymer molecule is, in a way, related to the flow intensity.

The evaluation of the effect of saline aqueous media in the aggregation of colloidal gold nanoparticles (AuNP) suspensions has been followed by means of both dynamic light scattering and UV–Vis spectroscopy techniques. A wide range of ionic strengths from 0 to 1 M has been covered for suspensions of AuNPs with a hydrodynamic radius of 6.5 nm. The growth of the clusters over time is described by a power law whose exponent varies with the ionic strength. Two main aggregation regimes are found in qualitative agreement with predictions of the DLVO theory. At low ionic strength, AuNPs form small aggregates that are long-term stable. When a critical electrolyte concentration is exceeded, big clusters are formed rapidly and then colloidal suspension becomes unstable and precipitation occurs. That so-called critical coagulation concentration was estimated by analyzing the time evolution of both the nanoparticle size (determined by DLS) and the plasmon peak (determined by UV–Vis spectroscopy), thus showing the validity of both techniques for such a purpose. The stability is also studied in terms of the zeta potential which approaches zero when salt concentration is above the critical coagulation concentration.

The behavior of polymer chains in dilute solution under a steady, homogeneous elongational flow has been studied employing Brownian dynamics simulation. We first consider the dependence of polymer properties in steady state on the elongational rate, e. When this rate exceeds some critical value, e c , the properties show a dramatic change from the values typical of the coil state to those of a stretched conformation. We describe the dependence of e c on chain length for different polymer/solvent conditions. Following the trajectories of individual molecules, we have characterized dynamic aspects of the coil-stretch transition. Each chain suffer the transition after some time, t trans , has elapsed after the flow start-up. The values of t trans vary remarkably from one molecule to another, and we have characterized the statistical distribution of this quantity. We also determine the kinetics of the coil-to-stretch process, which seems to follow a first-order kinetics after some induction time. The dependence of the statistical and kinetic parameters on chain length and elongational rate has been determined.

15 pags, 7 figs, 1 tab, The phosphotransferase system (PTS) is involved in the use of carbon sources in bacteria. Bacillus sphaericus, a bacterium with the ability to produce insecticidal proteins, is unable to use hexoses and pentoses as the sole carbon source, but it has ptsHI genes encoding the two general proteins of the PTS: enzyme I (EI) and the histidine phosphocarrier (HPr). In this work, we describe the biophysical and structural properties of HPr from B. sphaericus, HPrbs, and its affinity towards EI of other species to find out whether there is inter-species binding. Conversely to what happens to other members of the HPr family, HPrbs forms several self-associated species. The conformational stability of the protein is low, and it unfolds irreversibly during heating. The protein binds to the N-terminal domain of EI from Streptomyces coelicolor, EINsc, with a higher affinity than that of the natural partner of EINsc, HPrsc. Modelling of the complex between EINsc and HPrbs suggests that binding occurs similarly to that observed in other HPr species. We discuss the functional implications of the oligomeric states of HPrbs for the glycolytic activity of B. sphaericus, as well as a strategy to inhibit binding between HPrsc and EINsc. © 2013 Doménech et al., This work was supported by the Spanish Ministerio de Ciencia e Innovación (MCINN) (CTQ2011-24393, and CSD2008-00005 to JLN; BIO2009-13261-C02- 01/02 and P09-CVI-5063, with Fondo Social Europeo (ESF) to ACA; and BFU2010-19451 to AVC), Diputación General de Aragón (PI044/09 to AVC), intramural BIFI 2011 projects (to AVC and JLN), Junta de Andalucía (BIO-328 to ACA), and by grants from the Agencia Nacional de Promoción Científica y Tecnológica Argentina (ANPCyT; PICT-2011-2778) (to CNC). SMR was supported by the CSD2008-00005. The stays of RD in the laboratory of AVC were supported by the Spanish Ministerio de Ciencia e Innovación (BFU2008-02302-BMC).

The hydrodynamic interaction is an essential effect to consider in Brownian dynamics simulations of polymer and nanoparticle dilute solutions. Several mathematical approaches can be used to build Brownian dynamics algorithms with hydrodynamic interaction, the most common of them being the exact but time demanding Cholesky decomposition and the Chebyshev polynomial expansion. Recently, Geyer and Winter [J. Chem. Phys. 130, 1149051 (2009)]10.1063/1.3089668 have proposed a new approximation to treat the hydrodynamic interaction that seems quite efficient and is increasingly used. So far, a systematic comparison among those approaches has not been clearly made. In this paper, several features and the efficiency of typical implementations of those approaches are evaluated by using bead-and-spring chain models. The different sensitivity to the bead overlap detected for the different implementations may be of interest to select the suitable algorithm for a given simulation.

The calculation of solution properties of flexible macromolecules and other nanoparticles requires, in addition to the hydrodynamic formalisms needed for the sedimentation coefficient and other transport properties, the consideration of the conformational statistics and internal dynamics. The latter aspects can be handled with simulation methods like Monte Carlo and Brownian dynamics. An example of a Monte Carlo simulation for a model specific of DNA is illustrated with results for the several solution properties over an extremely wide range of molecular weight. The convenience of having computational tools of a quite general applicability has prompted us to implement the simulation and hydrodynamic treatments in software packages, MONTEHYDRO for Monte Carlo, and SIMUFLEX for Brownian dynamics which-with a scope similar to the HYDRO suite for rigid particles-can handle a variety of situations. As an application of the new methodology to a yet unclear problem in analytical ultracentrifugation, in a simple application of the SIMUFLEX software, we present a simulation of the so-called anomalous sedimentation of very long DNA molecules, obtaining results for the experimentally observable rotor-speed-dependence of the sedimentation coefficient.

We propose a multiscale protocol for the simulation of conformation and dynamics of dendrimer molecules in dilute solution. Conformational properties (radius of gyration, mass distribution, and scattering intensities) and overall hydrodynamic properties (translational diffusion and intrinsic viscosity) are predicted by means of a very simple coarse-grained bead-and-spring model, whose parameters are not adjusted against experimental properties, but rather they are obtained from previous, atomic-level simulations which are also quite simple, performed with small fragments and Langevin dynamics simulation. The scheme is described and applied systematically to four different dendrimer molecules with up to seven generations. The predictive capability of this scheme is tested by comparison with experimental data. It is found that the predicted geometric and hydrodynamic radii of the dendrimer molecules are in agreement (typical error is about 4%) with a large set experimental values of the four dendrimers with various numbers of generations. Agreement with some X-ray scattering experimental intensities also confirms the good prediction of the internal structure. This scheme is easily extendable to study more complex molecules (e.g., functionalized dendrimers) and to simulate internal dynamics.

The formation of associative networks in semidilute aqueous solutions of hydrophobically modified hydroxyethylcellulose (HM-HEC) is dependent on intermolecular hydrophobic interactions. Addition of hydroxypropyl-beta-cyclodextrin (HP-beta-CD) monomers to the system provides decoupling of these associations via inclusion complex formation with the polymer hydrophobic tails. Results from viscosity, polymer NMR self-diffusion, and dynamic light scattering (DLS) measurements show that the hydrophobic interactions in HM-HEC solutions are effectively suppressed when the level of HP-beta-CD addition increases. Small-angle neutron scattering (SANS) results reveal that the large-scale association complexes in HM-HEC solutions are strongly diminished when the concentration of HP-beta-CD rises. The time correlation data obtained from the DLS experiments unveiled the existence of two relaxation modes: one single exponential at short times followed by a stretched exponential at longer times. The fast mode is always diffusive, whereas the slow mode exhibits progressively stronger wavevector dependence as the intensity of the hydrophobic interactions increases. This feature, as well as the accompanying drop of the stretched exponential beta as the HP-beta-CD concentration decreases, is attributed to enhanced hydrophobic interactions and can be well rationalized in the framework of the coupling model of Ngai.

Effects of temperature on the association behavior in aqueous solutions of a series of thermosensitive poly(N-isopropylacrylamide)-block-poly(ethylene glycol)-block-poly(N-isopropylacrylamide) triblock copolymers (PNIPAAMm-b-PEGn-b-PNIPAAMm) with the length of the PNIPAAM block fixed (m ≈ 67) and with different lengths of the PEG block (n = 23, 34, 77, and 165) have been studied with the aid of turbidity, dynamic light scattering (DLS), and Monte Carlo simulations. The turbidity results show that the sharp transition to high turbidity values is shifted to higher temperatures when the length of the PEG spacer is increased from 23 to 77, whereas no transition is observed for the longest PEG block. These findings are consistent with the DLS results, which suggest the formation of large association structures at temperatures well above the cloud point. The simulation results indicate that a long PEG-block portion separating the PNIPAAM blocks in the triblock copolymer reduces the tendency of the polymer forming interchain associations at elevated temperatures. Simulation shows that for a long PEG spacer, the copolymer moiety is rather extended even at high temperatures, whereas for copolymers with a short PEG length the thermoresponsive block copolymer undergoes a transition from an extended to a compact conformation.