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Register a new userInfluence of Bonded Interactions on Structural Phases of Flexible Polymers
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We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states obtained in advanced replica-exchange Monte Carlo simulations is analyzed by employing the recently developed generalized microcanonical inflection-point analysis method, which enables the identification of diverse structural phases and the construction of a suitably parameterized hyperphase diagram. It reveals that icosahedral phases dominate for polymers with asymmetric and narrow bond potentials, whereas polymers with symmetric and more elastic bonds tend to form amorphous structures with non-icosahedral cores. We also observe a hierarchy in the freezing transition behavior associated with the formation of the surface layer after nucleation.
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The thermodynamic and elastic properties of a flexible polymer in the presence of dipole interactions are studied via Monte Carlo simulations. The structural coil-globular, solid-globular, and solid-solid transitions are mapped in the hyperphase diagram, parameterized by the dipole concentration, $eta$, and temperature, $T$. Polymer flexibility is usually quantified by the persistent length, $ell_p$, which is defined as the length on which the bond-bond correlation is lost. Non-monotonic flexibility of polymeric complexes as a function of $eta$ has been interpreted as a cooperative effect under the Worm-Like Chain model. Instead of the usual exponential behavior, $langle Cleft(kright)ranglepropto e^{-k/ell_p}$, here we show that the bond-bond correlation follows a power law decay, $langle Cleft(kright)rangleapprox c_0k^{-omega}$. The power law regime holds even at the coil-globular transition, where a Gaussian limit is expected, originated from non-leading terms due to monomer-monomer connectivity. The exponent $omega$ monotonically converges to the mbox{SAW} limit for large $eta$, if the isotherm pathway is constructed at the coil phase. The deviation from ideality in better probed at the chain segment size, and the expected $Theta-$condition at the $(T,eta)$ pathway near the coil-globular transition is not observed.
We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.
Lipid bilayers composed of non-alpha hydroxy sphingosine ceramide (CER NS), cholesterol (CHOL), and free fatty acids (FFA), which are components of the human skin barrier, are studied via molecular dynamics simulations. Since mixtures of these lipids exist in dense gel phases with little molecular mobility at physiological conditions, care must be taken to ensure that the simulations become decorrelated from the initial conditions. Thus, we propose and validate an equilibration protocol based on simulated tempering in which the simulation takes a random walk through temperature space, allowing the system to break out of metastable configurations and hence become decorrelated form its initial configuration. After validating the equilibration protocol, the effects of the lipid composition and ceramide tail length on bilayer properties are studied. Systems containing pure CER NS, CER NS + CHOL, and CER NS + CHOL + FFA, with the CER fatty acid tail length varied within each CER NS-CHOL-FFA composition, are simulated. The bilayer thickness is found to depend on the structure of the center of the bilayer, which arises as a result of the tail length asymmetry between the lipids studied. The hydrogen bonding between the lipid headgroups and with water is found to change with the overall lipid composition, but is mostly independent of the CER fatty acid tail length. Subtle differences in the lateral packing of the lipid tails are also found as a function of CER tail length. Overall, these results provide insight into the experimentally observed trend of altered barrier properties in skin systems where there are more ceramides with shorter tails present.
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different sort of short range order. In the high temperature regime, the 2-point correlation functions of the object are identical to worm-like chains, while in the low temperature regime they are different due to a twist structure. In the low temperature phase, the polymers develop a kink-rod structure which could clarify some recent puzzling experiments on actin.
It has been shown that a nanoliter chamber separated by a wall of asymmetric obstacles can lead to an inhomogeneous distribution of self-propelled microorganisms. Although it is well established that this rectification effect arises from the interaction between the swimmers and the non-centrosymmetric pillars, here we demonstrate numerically that its efficiency is strongly dependent on the detailed dynamics of the individual microorganism. In particular, for the case of run-and-tumble dynamics, the distribution of run lengths, the rotational diffusion and the partial preservation of run orientation memory through a tumble are important factors when computing the rectification efficiency. In addition, we optimize the geometrical dimensions of the asymmetric pillars in order to maximize the swimmer concentration and we illustrate how it can be used for sorting by swimming strategy in a long array of parallel obstacles.
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