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Register a new userMonte Carlo SImulation of Polymers: Coarse-Grained Models
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A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific polymer and reflect the underlying atomistic details to some extent, and those which retain only the most basic features of a polymer chain (chain connectivity, short-range excluded-volume interactions, etc.). In this review we mainly focus on the second class of generic polymer models, while the first class of specific coarse-grained models is only touched upon briefly.
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During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein concentration at a range of low (native phase) to high (denature phase) temperatures. Visual inspections show distinct structures, i.e. isolated globular bundles to entangled network on multiple length scales in dilute to crowded protein concentrations. In native phase, the radius of gyration of the protein does not vary much with the protein concentration while that of its inner segment increases systematically. In contrast, the radius of gyration of the protein shows enormous growth with the concentration due to entanglement while that of the inner segment remains almost constant in denatured phase. The multi-scale morphology of the collective assembly is quantified by estimating the effective dimension D of protein from scaling of the structure factor: collective assembly from inner segments remains globular (D aroud 3) at almost all length scales in its native phase while that from protein chains shows sparsely distributed morphology with D around 2 in entire temperature range due to entanglement except in crowded environment at low temperature where D around 2.6. Higher morphological response of chains with only the inner-segments due to selective interactions in its native phase may be more conducive to self-organizing mechanism than that of the remaining segments of the protein chains.
Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight backbone, both radial density profiles of monomers and side chain ends are obtained, as well as structure factors describing the scattering from a single side chain and from the total bottle-brush polymer. To describe the structure in the interior of a very long bottle-brush, a periodic boundary condition in the direction along the backbone is used, and to describe effects due to the finiteness of the backbone length, a second set of simulations with free ends of the backbone is performed. In the latter case, the inhomogeneity of the structure in the direction along the backbone is carefully investigated. We use these results to test various phenomenological models that have been proposed to interpret experimental scattering data for bottle-brush macromolecules. These models aim to extract information on the radial density profile of a bottle-brush from the total scattering via suitable convolution approximations. Possibilities to improve such models, guided by our simulation results, are discussed.
Frustrated spin systems generically suffer from the negative sign problem inherent to Monte Carlo methods. Since the severity of this problem is formulation dependent, optimization strategies can be put forward. We introduce a phase pinning approach in the realm of the auxiliary field quantum Monte Carlo algorithm. If we can find an anti-unitary operator that commutes with the one body Hamiltonian coupled to the auxiliary field, then the phase of the action is pinned to $0$ and $pi$. For generalized Kitaev models, we can successfully apply this strategy and observe a remarkable improvement of the average sign. We use this method to study thermodynamical and dynamical properties of the Kitaev-Heisenberg model down to temperatures corresponding to half of the exchange coupling constant. Our dynamical data reveals finite temperature properties of ordered and spin-liquid phases inherent to this model.
Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich physicochemical characteristics, including structural and dynamic heterogeneity. The significance of electrostatic interactions in RTILs results in long characteristic length- and timescales, and has motivated the development of a number of coarse-grained (CG) simulation models. In this study, we aim to better understand the connection between certain CG parametrization strategies and the dynamical properties and transferability of the resulting models. We systematically compare five CG models: a model largely parametrized from experimental thermodynamic observables; a refinement of this model to increase its structural accuracy; and three models that reproduce a given set of structural distribution functions by construction, with varying intramolecular parametrizations and reference temperatures. All five CG models display limited structural transferability over temperature, and also result in various effective dynamical speedup factors, relative to a reference atomistic model. On the other hand, the structure-based CG models tend to result in more consistent cation-anion relative diffusion than the thermodynamic-based models, for a single thermodynamic state point. By linking short- and long-timescale dynamical behaviors, we demonstrate that the varying dynamical properties of the different coarse-grained models can be largely collapsed onto a single curve, which provides evidence for a route to constructing dynamically-consistent CG models of RTILs.
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