STOCK: Structure mapper and online coarse‐graining kit for molecular simulations

We present a web toolkit STructure mapper and Online Coarse‐graining Kit for setting up coarse‐grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, for example, all‐atom, to low, that is, coarse‐grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse‐graining packages, for example, Versatile Object‐oriented Toolkit for Coarse‐graining Applications and DL_CGMAP. Our second tool generates effective potentials for coarse‐grained simulations preserving the structural properties, for example, radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse‐grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse‐graining web toolkit is available at http://stock.cmm.ki.si . © 2014 Wiley Periodicals, Inc.     

Behavior of mixed ZnO and SiO2 nano-particles in magnetic field assisted fluidization

The fluidization behavior of ZnO nano-particles in magnetic fluidized bed （MFB） by adding coarse magnetic particles was investigated, followed by the co-fluidization of mixtures of ZnO and SiO2 nano-particles. For such co-fluidization, bed expansion was found to change smoothly with gas velocity through a range of stable operation. By measuring the bed expansion ratio and pressure drop, a stability diagram for the mixture in MFB was obtained. Within this stable operation range, with increasing gas velocity the pressure drop hardly changes as the bed expands, up to an expansion ratio of more than 4.     

On the Use of a Supramolecular Coarse‐Grained Model for the Solvent in Simulations of the Folding Equilibrium of an Octa‐β‐peptide in MeOH and H2O

Molecular dynamics (MD) simulation can give a detailed picture of conformational equilibria of biomolecules, but it is only reliable if the force field used in the simulation is accurate, and the sampling of the conformational space accessible to the biomolecule shows many (un)folding transitions to allow for precise averages of observable quantities. Here, the use of coarse‐grained (CG) solvent MeOH and H₂O models to speed up the sampling of the conformational equilibria of an octa‐β‐peptide is investigated. This peptide is thought to predominantly adopt a 3₁₄‐helical fold when solvated in MeOH, and a hairpin fold when solvated in H₂O on the basis of the NMR data. Various factors such as the chirality of a residue, a force‐field modification for the solute, coarse‐graining of the solvent model, and an extension of the nonbonded interaction cut‐off radius are shown to influence the simulated conformational equilibria and the agreement with the experimental NMR data for the octa‐β‐peptide.     

LemPel-Ziv复杂度算法中粗粒化方法分析及改进

为了提高Lempel-Ziv复杂度(LZC)的抗干扰能力和稳定性,提出用等概率粗粒化方法计算LZC的思想,介绍其具体算法,分析二值粗粒化阈值与LZC的关系.用Logistic映射生成87个序列进行抗干扰试验,计算这些序列加噪前后所得LZC序列的相关系数和相对变异系数,作为LZC指标抗干扰能力的测度,用10个脑电图进行LZC稳定性测试.结果表明,用等概率粗粒化方法时的相关系数都大于0.998,相对变异系数较小,脑电的LZC稳定性好.该方法可明显提高LZC的抗干扰能力和稳定性.     

Remarks on coarse embeddings of metric spaces into uniformly convex Banach spaces

We study the support and convergence conditions for a metric space to be coarsely embeddable into a uniformly convex Banach space. By using ultraproducts we also show that the coarse embeddability of a metric space into a uniformly convex Banach space is determined by its finite subspaces.     

The coarse geometric Novikov conjecture and uniform convexity

The coarse geometric Novikov conjecture provides an algorithm to determine when the higher index of an elliptic operator on a noncompact space is nonzero. The purpose of this paper is to prove the coarse geometric Novikov conjecture for spaces which admit a (coarse) uniform embedding into a uniformly convex Banach space.     

Implicit solvent coarse‐grained model of polyamidoamine dendrimers: Role of generation and pH

Highly branched polymers such as polyamidoamine (PAMAM) dendrimers are promising macromolecules in the realm of nanobiotechnology due to their high surface coverage of tunable functional groups. Modeling efforts of PAMAM can provide structural and morphological properties, but the inclusion of solvents and the exponential growth of atoms with generations make atomistic simulations computationally expensive. We apply an implicit solvent coarse‐grained model, called the Dry Martini force field, to PAMAM dendrimers. The reduced number of particles and the absence of a solvent allow the capture of longer spatiotemporal scales. This study characterizes PAMAM dendrimers of generations one through seven in acidic, neutral, and basic pH environments. Comparison with existing literature, both experimental and theoretical, is done using measurements of the radius of gyration, moment of inertia, radial distributions, and scaling exponents. Additionally, ion coordination distributions are studied to provide insight into the effects of interior and exterior protonation on counter ions. This model serves as a starting point for future designs of larger functionalized dendrimers. © 2015 Wiley Periodicals, Inc.     

Hybrid particle‐field molecular dynamics simulations: Parallelization and benchmarks

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self‐consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle‐field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD‐SCF program profiles, serial MD‐SCF and parallel MD‐SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. © 2012 Wiley Periodicals, Inc.     

Coarse grained approach for volume conserving models

Volume conserving surface (VCS) models without deposition and evaporation, as well as ideal molecular-beam epitaxy models, are prototypes to study the symmetries of conserved dynamics. In this work we study two similar VCS models with conserved noise, which differ from each other by the axial symmetry of their dynamic hopping rules. We use a coarse-grained approach to analyze the models and show how to determine the coefficients of their corresponding continuous stochastic differential equation (SDE) within the same universality class. The employed method makes use of small translations in a test space which contains the stationary probability density function (SPDF). In case of the symmetric model we calculate all the coarse-grained coefficients of the related conserved Kardar–Parisi–Zhang (KPZ) equation. With respect to the symmetric model, the asymmetric model adds new terms which have to be analyzed, first of all the diffusion term, whose coarse-grained coefficient can be determined by the same method. In contrast to other methods, the used formalism allows to calculate all coefficients of the SDE theoretically and within limits numerically. Above all, the used approach connects the coefficients of the SDE with the SPDF and hence gives them a precise physical meaning.     

The maximal coarse Baum–Connes conjecture for spaces which admit a fibred coarse embedding into Hilbert space

We introduce a notion of fibred coarse embedding into Hilbert space for metric spaces, which is a generalization of Gromov?s notion of coarse embedding into Hilbert space. It turns out that a large class of expander graphs admit such an embedding. We show that the maximal coarse Baum–Connes conjecture holds for metric spaces with bounded geometry which admit a fibred coarse embedding into Hilbert space.