We investigate the properties of magnetic supracolliodal polymers -- magnetic filaments (MFs) -- with super-paramagnetic monomers, with and without Van der Waals (VdW) attraction between them. We employ molecular dynamics (MD) simulations to elucidate the impact of crosslinking mechanism on the structural and magnetic response of MFs to an applied external homogeneous magnetic field. We consider two models: plain crosslinking, which results in a flexible backbone; and constrained crosslinking, which provides significant stiffens against bending. We find that for plain crosslinking, even a slight increase of the central attraction leads to collapsed MF conformations. Structures that initially exhibit spherical symmetry evolve into cylindrically symmetric ones, with growing magnetic field strength. Plain crosslinking also allows for conformational bistability. MFs with constrained crosslinking tend to, instead, unravel in field. In both crosslinking scenarios, central attraction is able to hinder low-field magnetic response of MFs, albeit the bistability of plainly crosslinked MFs manifests itself also in the high-field region.
Diverse polymer crosslinking techniques allow the synthesis of linear polymer-like structures whose monomers are colloidal particles. In the case where all or part of these colloidal particles are magnetic, one can control the behaviour of these supracolloidal polymers, known as magnetic filaments (MFs), by applied magnetic fields. However, the response of MFs strongly depends on the crosslinking procedure. In the present study, we employ Langevin dynamics simulations to investigate the influence of the type of crosslinking and the distribution of magnetic particles within MFs on their respons…
Unlike Stockmayer fluids, that prove to undergo gas-liquid transition on cooling, the system of dipolar hard or soft spheres without any additional central attraction so far has not been shown to have a critical point. Instead, in the latter, one observes diverse self-assembly scenarios. Crosslinking dipolar soft spheres into supracolloidal magnetic polymer-like structures (SMPs) changes the self-assembly behaviour. Moreover, aggregation in systems of SMPs strongly depends on the constituent topology. For Y- and X-shaped SMPs, under the same conditions in which dipolar hard spheres would form …
We study the dynamics and conformation of polymers composed by active monomers. By means of Brownian dynamics simulations we show that when the direction of the self-propulsion of each monomer is aligned with the backbone, the polymer undergoes a coil-to-globule-like transition, highlighted by a marked change of the scaling exponent of the gyration radius. Concurrently, the diffusion coefficient of the center of mass of the polymer becomes essentially independent of the polymer size for sufficiently long polymers or large magnitudes of the self-propulsion. These effects are reduced when the se…
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially shrinks with active force, which starts swelling on further increase in force. The shrinkage followed by swelling is attributed purely to excluded-volume interactions among the monomers. In the swelling regime, chain shows a cross-over from the self-avoiding behavior to Rouse-behavior with scaling exponent $ν_a \simeq 1/2$ for end-to-end distance. The non-monoton…
Static Properties of a Simulated Supercooled Polymer Melt: Structure Factors, Monomer Distributions Relative to the Center of Mass, and Triple Correlation Functions
Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with the spatial positions of the monomer units. The geometrical patterns of lamellae, hexagonally packed cylinders, and balls arranged in a body-centered cubic lattice are considered as typical microphase-separated morphologies of block copolymers. Random trajectories of polymer chains are described by the diffusion-type equations and, in parallel, simulated in…
Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects
我们进一步开发了耦合DNA中的变性和链构象的统计模型（Palmeri J，Manghi M和Destainville N 2007 Phys. Rev. Lett. 99 088103）。我们的离散螺旋蠕虫链模型明确考虑了三个弹性自由度，即聚合物的拉伸，弯曲和扭转。通过整合这些外部变量，构象熵有助于气泡成核（碱基对的打开），这揭示了DNA解链机制。由于单体长度、弯曲模量和扭转模量的值在dsDNA和ssDNA中显著不同，因此这些效应是重要的。此外，我们探讨在这种情况下，一个额外的循环熵的作用和分析有限尺寸的影响，在实验的情况下，polydA-polydT是由两个G-C链，以及自由聚合物夹紧。
We study the dynamics and conformations of a single active semiflexible polymer whose monomers experience a propulsion force perpendicular to the local tangent, with the end beads being different from the inner beads ("end-tailored"). Using Langevin simulations, we demonstrate that, apart from sideways motion, the relative propulsion strength between the end beads and the polymer backbone significantly changes the conformational properties of the polymers as a function of bending stiffness, end-tailoring and propulsion force. Expectedly, for slower ends the polymer curves away from the moving …
We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the mean-field approximation, we find that the phase transition between the swollen-disordered state and the compact-ordered state is discrete; it is first-order as in the long-range Potts model, but with a significantly larger jump in magnetization (i.e., mark coherence) upon the ordering transition. The results imply how small changes in epigenetic writer concentrati…
Via molecular dynamics simulation with Langevin thermostat we study the structure and dynamics of a flexible bead-spring active polymer model after a quench from good to poor solvent conditions. The self propulsion is introduced via a Vicsek-like alignment activity rule which works on each individual monomer in addition to the standard attractive and repulsive interactions among the monomeric beads. We observe that the final conformations are in the globular phase for the passive as well as for all the active cases. By calculating the bond length distribution, radial distribution function, etc…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where monomer pairs are connected randomly. We obtain asymptotic formulas for the steady-state variance, encounter probability, the radius of gyration, instantaneous displacement and the mean first encounter time between any two monomers. The analytical results are confirmed by Brownian simulations. Finally, the present results can be used to extract the minimum n…
The conformational and dynamical properties of active polymers in solution are determined by the nature of the activity, and the behavior of polymers with self-propelled, active Brownian particle-type monomers differs qualitatively from that of polymers with monomers driven externally by colored noise forces. We present simulation and theoretical results for polymers in solution in the presence of external active noise. In simulations, a semiflexible bead-spring chain is considered, in analytical calculations, a continuous linear wormlike chain. Activity is taken into account by independent mo…
We present a simple analytical theory of flexible polymer chain dissolved in a good solvent, carrying permanent freely oriented dipoles on the monomers. We take into account the dipole correlations within the random phase approximation (RPA), as well as a dielectric heterogeneity in the internal polymer volume relative to the bulk solution. We demonstrate that the dipole correlations of monomers can be taken into account as pairwise ones only when the polymer chain is in a coil conformation. In this case the dipole correlations manifest themselves through the Keesom interactions of the permane…
G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions G4s undergo multimerization. Here, we address the structural, conformational and energetic features of G4 multimers formed in solutions by the human telomere sequence. A novel multi-technique approach is used combining Small Angle X-ray Scattering (SAXS) and circular dichroism experiments with coarse-graine…
We develop a theory to probe the effect of non-equilibrium fluctuation-induced forces on the size of a polymer confined between two horizontal thermally conductive plates subject to a constant temperature gradient, $\nabla T$. We assume that (a) the solvent is good and (b) the distance between the plates is large so that in the absence of a thermal gradient the polymer is a coil whose size scales with the number of monomers as $N^ν$, with $ν\approx 0.6$. We predict that above a critical temperature gradient, $\nabla T_c \sim N^{-\frac{5}{4}}$, favorable attractive monomer-monomer interaction d…
Alterations in Conformations of Poly(3-hexylthiophene) on Au(111) Induced by Annealing
Albert-Ludwigs-Universität Freiburg（弗莱堡大学）；Université de Haute-Alsace（上阿尔萨斯大学）；CNRS, Institut de Science des Matériaux de Mulhouse（法国国家科学研究中心，米卢斯材料科学研究所）
In the present work, we study the equilibrium conformations of linear polyelectrolytes tethered onto a spherical, oppositely charged core in equilibrium with an ionic reservoir of fixed concentration. Particular focus is placed on the situation of stretched chains, where the monomer concentration is known to display an inverse square-law decay far away from the spherical surface, which is then further extrapolated all the way down to the grafting core. While the equilibrium distributions of mobile ions are computed in the framework of a classical Density Functional Theory (cDFT) that incorpora…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the poly…
Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the \textit{trans}-side. Under the influence of pre-stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields …
The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete linear chain composed of active Brownian particles is considered, analytically, a continuous linear semiflexible polymer with active velocities changing diffusively. The force-free nature of active monomers is accounted for - no Stokeslet fluid flow induced by active forces - and higher order hydrodynamic multipole moments are neglected. The nonequilibrium chara…
We present a new simple self-consistent field theory of the polarizable flexible polymer chain under the external constant electric field with account for the many-body electrostatic dipole correlations. We show the effect of electrostatic dipole correlations on the electric field-induced globule-coil transition. We demonstrate that only when the polymer chain is in the coil conformation, the electrostatic dipole correlations of monomers can be considered as pairwise. However, when the polymer chain is in collapsed state, the dipole correlations have to be considered at the many-body level.
Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins
蛋白质聚集与许多疾病有关，当单体进入准备形成淀粉样纤维的流氓构象时，蛋白质聚集就开始了。我们表明，使用模拟的src SH 3域，机械力增强人口的聚集倾向（$N^*$）状态，这是很少填充的力自由原生条件下，但编码的频谱原生波动。SH 3作为变性剂浓度（$[C]$），机械力（$f$）和温度的函数的折叠相图表现出明显的两态行为，而没有揭示难以捉摸的$N^*$状态的存在。有趣的是，在所有[C]和$f$处分离折叠态和未折叠态的相边界落在主曲线上，这可以使用磁场中的超导体的类比来定量描述。作为分子延伸（$R$）的函数的自由能分布（$R$），其在牵拉实验（$R$）中可获得，揭示了具有无序溶剂暴露的氨基末端$β$ -链的天然样$N^*$的存在。$N^*$状态的结构与通过NMR分散实验在Fyn SH 3中发现的结构相同。我们发现，原纤维形成的时间尺度可以估计从人口的$N^*$状态，由分离的天然结构和$N^*$状态的自由能隙，发现可用于评估原纤维形成的蛋白质的倾向。$N^*$状态的结构用于显示低聚物形成和可能的原纤维路线通过SH 3结构域中的结构域交换机制发生。
