Equilibrium conformational dynamics of a polymer in a solvent

Molecular dynamics simulations were used to study the conformational dynamics of a bead-spring model polymer in an explicit solvent under good solvent conditions. The dynamics of the polymer chain were investigated using an analysis of the time autocorrelation functions of the Rouse coordinates of the polymer chain. We have investigated the variation of the correlation functions with polymer chain length N, solvent density rho, and system size. The measured initial decay rates gamma(p) of the correlation functions were compared with the predictions from a theory of polymer dynamics which uses the Oseen tensor to describe hydrodynamic interactions between monomers. Over the range of chain lengths considered (N = 30-60 monomers), the predicted scaling of gamma(p) proportional to N(-3nu) was observed at high rho, where nu is the polymer scaling exponent. The predicted gamma(p) are generally higher than the measured values. This discrepancy increases with decreasing rho, as a result in the breakdown in the conditions required for the Oseen approximation. The agreement between theory and simulation at high rho improves considerably if the theoretical expression for gamma(p) is modified to avoid sum-to-integral approximations, and if the values of (R(p)2), which are used in the theory, are taken directly from the simulation rather than being calculated using approximate scaling relations. The observed finite-size scaling of gamma(p) is not quantitatively consistent with the theoretical predictions.     

A nanotumbleweed: breaking away a covalently tethered polymer molecule by noncovalent interactions

A covalently tethered polymer molecule can spontaneously break away from the surface when polymer/surface interaction is sufficiently unfavorable. This is demonstrated in surface-initiated polymerization of a hydrophilic polymer, hyperbranched polyglycidol, from minority surface sites embedded in a hydrophobic self-assembled monolayer. As each hyperbranched polyglycidol molecule grows larger, it encounters more unfavorable interaction with the hydrophobic surface, and this leads to spontaneous bond rupture and desorption. This finding challenges the traditional view on noncovalent interaction of macromolecules with the local environment at interfaces and has broad implications for the understanding, design, synthesis, and applications of surface-tethered macromolecules.     

Modeling a tethered polymer in Poiseuille flow

We investigate the behavior of a tethered polymer in Poiseuille flow using a multiscale algorithm. The polymer, treated using molecular dynamics, is coupled to a solvent modeled by the stochastic rotation algorithm, a particle-based Navier-Stokes integrator. The expected series of morphological transitions of the polymer: sphere to distorted sphere to trumpet to stem and flower to rod are recovered, and we discuss how the polymer extension depends on the flow velocity. Backflow effects cause an effective increase in viscosity, which appears to be primarily due to the fluctuations of the free end of the polymer.     

Postsynthetic modification at the focal point of a hyperbranched polymer

Functionalization at the focal point of hyperbranched polyester was achieved using a series of amines and a postsynthetic reaction utilizing an activated p-nitrophenyl ester unit. An element of dense packing was also detected, as evident from differences in levels of incorporation between linear and bulky reagents.     

Load drop at the upper yield point of a polymer

The stress-system curves have been measured for isotropic and oriented specimens of poly(ethylene terephthalate) in extension, shear, and compression. It was found that for all these types of deformations there was an intrinsic yield drop, i.e., a fall in true stress. It is concluded therefore that the stress for initiation is greater than the stress for propagation of yielding.     

Elucidation of conformational hysteresis on a giant DNA

The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for folding and unfolding processes, by increasing and decreasing the concentration of condensing agent (polyethylene glycol) (PEG), respectively. To elucidate the observed hysteresis, a semiflexible chain model is studied by using Monte Carlo simulations for the coil-globule transition. In the simulations, the hysteresis loop emerges for stiff enough chains, indicating distinct pathways for folding and unfolding processes. Also, our results show that globular state is thermodynamically more stable than coiled state in the hysteresis loop. Our findings suggest that increasing chain stiffness may reduce the chain conformations relevant to the folding pathway, which impedes the folding process.     

Dynamical hysteresis in a self-oscillating polymer gel

An ionic polymer gel may undergo rhythmical swelling-deswelling kinetics induced by chemical oscillation. We demonstrate that the gel admits of dynamical hysteresis, which is manifested in the non-vanishing area of the response function-concentration (of reaction substrate) hysteresis loop, the response function being the integrated probability of residence of the polymer in any one of the swelled or deswelled states. The loop area depends on temperature and exhibits a turnover as a function of the strength of thermal noise-a phenomenon reminiscent of stochastic resonance. The numerical simulations agree well with our proposed analytical scheme.     

Contact angle hysteresis at the nanoscale: a molecular dynamics simulation study

In this paper, the contact angle hysteresis (CAH) of nanodroplets on both rigid and flexible substrates with different wettabilities was studied using molecular dynamics (MD) simulations. The critical shear stress (CSS) that determines the motion of the contact line (CL) was investigated. A theoretical correlation between CAH and CSS was proposed. Both CAH and CSS reflect the energy dissipation at the CL of the droplet in response to the exerted force. MD results of CAH are qualitatively consistent with the theoretical model. Simulation results also show that, for the same liquid–solid interactions, CAH on the flexible substrate is larger than that on the rigid substrate. These findings aim to enhance our understanding of the mechanism of the CAH at the nanoscale.     

A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

 In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA–DNA attractions. Received: 30 November 2000 / Accepted: 7 February 2001 / Published online: 22 May 2001     

Influence of conformational asymmetry on the surface enrichment of polymer blends II

We reexamine the influence of statistical segment length asymmetry on the surface segregation of homopolymer blends in a mean field thread model of polymer melts. By developing numerical self-consistent field solutions of the Edwards-Helfand equations, we demonstrate that the component with the smaller value of the parameter β² = a²/(6ν) (a is the statistical segment length and ν is the segment volume) is enriched at a neutral, impenetrable surface. Qualitatively, this finding is in agreement with our earlier analytical work and with experiment. However, in contrast to our earlier work, we find that the absolute magnitude of the segregation is a sensitive function of the chain lengths of the two species and of the compressibility of the system. © 1995 John Wiley & Sons, Inc.     

Stability of a protein tethered to a surface

Surface-tethered proteins are increasingly being used in a variety of experimental situations, and they are the basis for many new technologies. Nevertheless, a thorough understanding of how a surface can impact the native state stability of an attached protein is lacking. In this work, the authors use molecular dynamics simulations of a model beta-barrel protein to investigate how surface tethering influences native state stability. They find that stability, as measured by the folding temperature Tf, can be either increased, decreased, or remain unchanged as a result of tethering. Observed shifts are highly dependent on the location of residue used as the tether point, and stability is influenced by a number of factors, both energetic and entropic. These factors include native state vibrations, loss of bulk unfolded conformations, changes to the unfolded state ensemble, and the emergence of an entropic term not present for the bulk protein. They discuss each of these contributions in detail and comment on their relative importance and connection to experiment.     

Magneto-hydrodynamical numerical simulation of heat transfer in MHD stagnation point flow of Cross fluid model towards a stretched surface

Here formulation and computations are presented to introduce the novel concept of activation energy in chemically reacting stagnation point flow towards a stretching sheet. Constitutive expression for Cross liquid is taken into account. Magnetic field is utilised in the transverse direction. Application of suitable variables generates the non-linear differential systems. Numerical solution by Runge–Kutta–Fehlberg approach is presented. Characteristics for the significant variables like Weissenberg number, Hartmann number, Schmidt number, activation energy chemical reaction parameter, velocity ratio parameter and Prandtl number on the physical quantities are addressed through graphs and tables. Our computations reveal that species concentration rises via larger activation energy parameter whereas it decays when Schmidt number is incremented. The Weissenberg number has opposite characteristics for local Nusselt and Sherwood numbers when compared with surface drag force.     

Reversible pH-driven conformational switching of tethered superoxide dismutase with gold nanoparticle enhanced surface plasmon resonance spectroscopy

A new class of surface-immobilized protein nanomachines can be reversibly actuated by cycling the solution pH between 2.5 and 12.3, which induces a conformational change, thereby modulating the thickness of superoxide dismutase (SOD1) tethered to the Au thin film. By placing Au nanoparticles (AuNP) atop the immobilized SOD1 by means of a gold-thiol assembly, the nanoscale motion of SOD1 at the interface produces mechanical work to lift and then lower the AuNP from the Au substrate by a distance of ca. 3 nm and transduces this motion into an easily measurable reflectivity change in the surface plasmon resonance (SPR) spectrum. As-made supported conjugate consisting of SOD1 and AuNP is quite robust and stable, and its operation in response to pH variations, which mirrors the conformational changes of responsive SOD1 at the interface, is found to be highly reversible and reproducible. This is the first demonstration of the development of novel solid-state sensors and/or switching devices based on substrate-bound protein conformational changes and AuNP enhanced SPR spectroscopy.     

Single molecules reveal the dynamics of heterogeneities in a polymer at the glass transition

The notion of heterogeneous dynamics in glasses, that is, the spatial and temporal variations of structural relaxation rates, explains many of the puzzling features of glass dynamics. The nature and the dynamics of these heterogeneities, however, have been very controversial. Single rhodamine B molecules in poly(vinyl acetate) at the glass transition reorient through sudden jumps. With a statistical search for the most likely break points in the logarithm of the ratio of the two perpendicular fluorescence polarizations, we determine the times of these angular jumps. We interpret these jumps as an indication for individual glass rearrangements in the vicinity of the probe molecule. Time-series analysis of the resulting sequence of waiting times between jumps shows that dynamic heterogeneities in the matrix exist, but are short lived. From the correlation of the logarithm of the waiting time between subsequent jumps, we determine an upper limit for the lifetime of heterogeneities in the sample. The correlation time of τ(het) = 32 s is three times shorter than the orientational correlation time of the probe molecule, τ(orient) = 90 s, in the sample at this temperature, but 13 times longer than the structural relaxation time, τ(α) = 2.5 s, estimated for this sample from dielectric experiments. We present a model for glass dynamics in which each rearrangement in one region causes a random change in the barrier height for subsequent rearrangements in a neighboring region. This model, which equates the dynamics of the heterogeneities with the dynamics of the glass itself and thus implies a factor of one between heterogeneity lifetime and structural relaxation time, successfully reproduces the statistics of the experimentally observed waiting time sequences.     

Polymer conformation at the polymer melt surface

Due to the symmetry which characterizes the surroundings of each chain segment in the amorphous melt all (but end) segments are equivalent in their embedment in space. Energetic interactions between segments are confined to segments in contact. Hence, in the presence of a surface only the segments actually in the surface layer will be affected and will have a statistical weight and Boltzmann factor different from segments in the bulk. The number of segments so involved is fixed, since the extent of the surface is controlled. The partition function is comprised of factors which depend neither upon the order of the segments in the chain nor upon the conformation of any particular chain. Only segments finding themselves in the surface contribute to the surface tension, with the largest contribution deriving from the density transition in the interface. This, at most temperatures, is confined to a lamella one segment layer, or less, thick. For polymer of high enough molecular weight end-effects can be neglected and no allowance for the presence of ends is made here. It is then possible to reach a representation of surface tension in reduced coordinates, as shown already by Posner and Sanchez. Changes in chain conformation near the surface are calculated.     

Light-induced surface wettability of a tethered DNA base

We show that the DNA base thymine and other uracil derivatives, when alkylated with a hydrocarbon chain and assembled at a gold interface, dimerize when subjected to UV irradiation. The process is robust and reversible and is accompanied by a substantial decrease in wettability as well as a marked decrease in acidity constant when the dimer is formed. There is a concerted molecular reorientation that accompanies photodimerization, with the dimer displaying a marked affinity for the gold surface. The spatial requirements for this reorganization are satisfied during dimerization by the reduction in intermolecular distance that occurs when the cyclobutane ring is formed between adjacent bases. The structural changes observed here for a tethered DNA base provide a direct route for exploring reactions, in two dimensions, that are of central interest in biology.     

Structure and dynamics of water at a clay surface from molecular dynamics simulation

We report a molecular dynamics study of the structure and dynamics of water at a clay surface. The negative charge of the surface and the presence of surface oxygen atoms perturbs water over two to three molecular layers, while the nature of the counterions (Na(+)or Cs(+)) has only a small effect. In the first molecular layer, approximately half of the water molecules are H-bonded to the surface. We also analyze the H-bond network between surface water molecules. The diffusion of water molecules along the surface is slowed down compared to the bulk case. As far as the orientational order and dynamics of the water dipole are concerned, only the component normal to the clay surface is perturbed. We investigate the surface H-bond formation and dissociation dynamics and their coupling to the release of molecules from the first molecular layer. We introduce a simple kinetic model in the spirit of Luzar and Chandler [Nature, 1996, 379, 55] to allow for a comparison with bulk water dynamics. This model semi-quantitatively reproduces the molecular simulation results and suggests that H-bond formation is faster with the surface than in the bulk, while H-bond dissociation is slower.     

Morphological dynamics of swelling-induced surface patterns in metal-capped polymer bilayer

We report on the morphological dynamics of surface patterns induced by swelling of metal-capped polymer bilayer on a substrate. When the bilayer is subject to solvent vapor, the strain is generated in the polymer layer that is confined by the substrate and the metal capping layer. An increase in the strain induces the development of the stress in the bilayer to deform the lower polymer layer perpendicularly to the surface of the bilayer. Isotropic surface wave patterns results from the stress relaxation, the wave number of the patterns shows a characteristic temporal dependency on the swelling time, such that km(t) approximately t(-1/8). This temporal evolution accompanied by the morphological dynamics gives smaller value of the growth rate of the characteristic wavelength than that of the case of swelling of gel.     

A Monte Carlo study of a tethered polymer chain in a uniform field

We study the non‐uniform stretching and relaxation of a long flexible end‐anchored polymer chain of N monomers (32 ≤ N ≤ 1 024) in a uniform field B by means of an off‐lattice bead‐spring Monte Carlo model. Our simulational results for the case of a Rouse‐like polymer in the good solvent regime confirm the existence of “trumpet”‐ and “flower”‐type chain conformations, predicted recently by scaling analysis based on the notion of Pincus tensile blobs. The observed elongation of the chain and the critical fields, separating three different regimes of chain deformation, are found to obey the predicted scaling behavior. The segment density distribution matches that of a DNA molecule pulled from one end at constant velocity in a good solvent. As expected, the relaxation of the stretch to coil transition of the polymer of length N is determined by the typical Rouse time τ ∝ N^2ν+1.