Carsten Svaneborg

Scattering from block copolymer micelles

Small-angle neutron and X-ray scattering are techniques, which are frequently used for studying the structure and interactions of block copolymer micelles. Recent developments of models for the analysis of small-angle scattering data are reviewed. The most recent models, based on Monte Carlo simulations, are able to provide information on shape, aggregation number, polydispersity, core size, core solvation, corona shape/size, and on the interactions between the chains in the corona.

Stress Relaxation in Entangled Polymer Melts

We present an extensive set of simulation results for the stress relaxation in equilibrium and step-strained bead-spring polymer melts. The data allow us to explore the chain dynamics and the shear relaxation modulus, G(t), into the plateau regime for chains with Z=40 entanglements and into the terminal relaxation regime for Z=10. Using the known (Rouse) mobility of unentangled chains and the melt entanglement length determined via the primitive path analysis of the microscopic topological state of our systems, we have performed parameter-free tests of several different tube models. We find excellent agreement for the Likhtman-McLeish theory using the double reptation approximation for constraint release, if we remove the contribution of high-frequency modes to contour length fluctuations of the primitive chain.

Strain-Dependent Localization, Microscopic Deformations, and Macroscopic Normal Tensions in Model Polymer Networks

We use molecular dynamics simulations to investigate the microscopic and macroscopic response of model polymer networks to uniaxial elongations. By studying networks with strand lengths ranging from N(s)=20 to 200 we cover the full crossover from cross-link to entanglement dominated behavior. Our results support a recent version of the tube model which accounts for the different strain dependence of chain localization due to chemical cross-links and entanglements.

A Monte Carlo study on the effect of excluded volume interactions on the scattering from block copolymer micelles

Effects of excluded volume interaction on the form factor of a block copolymer micelle model have been investigated by performing Monte Carlo simulations. The micelles are modeled as a corona of semi-flexible chains tethered to a spherical core. Simulated form factors are analyzed using the model proposed by Pedersen and Gerstenberg. A slightly modified model is presented, in which chains consists of a radially pointing rigid rod, onto which a Gaussian chain is attached. The straight section emulates chain stretching near the micelle core. Both models are fitted to the simulation data using two parameters, that describes the individual chains: the radius of gyration, and the average center-of-mass distance to the micelle core. Based on a comparison between parameters obtained from fits, and those obtained directly from the simulation, it is concluded that the models provide good estimates for the radius of gyration and the chain center-of-mass distance for a low surface coverage, while systematic deviatio...

LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA

Abstract We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Program summary Program title: LAMMPS Framework for Directional Dynamic Bonding Catalogue identifier: AEME_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Hours to days. The examples provided in the distribution take just seconds to run.

Generating minimal living systems from non-living materials and increasing their evolutionary abilities

We review lessons learned about evolutionary transitions from a bottom-up construction of minimal life. We use a particular systemic protocell design process as a starting point for exploring two fundamental questions: (i) how may minimal living systems emerge from non-living materials? and (ii) how may minimal living systems support increasingly more evolutionary richness? Under (i), we present what has been accomplished so far and discuss the remaining open challenges and their possible solutions. Under (ii), we present a design principle we have used successfully both for our computational and experimental protocellular investigations, and we conjecture how this design principle can be extended for enhancing the evolutionary potential for a wide range of systems. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.

Multiscale approach to equilibrating model polymer melts

We present an effective and simple multiscale method for equilibrating Kremer Grest model polymer melts of varying stiffness. In our approach, we progressively equilibrate the melt structure above the tube scale, inside the tube and finally at the monomeric scale. We make use of models designed to be computationally effective at each scale. Density fluctuations in the melt structure above the tube scale are minimized through a Monte Carlo simulated annealing of a lattice polymer model. Subsequently the melt structure below the tube scale is equilibrated via the Rouse dynamics of a force-capped Kremer-Grest model that allows chains to partially interpenetrate. Finally the Kremer-Grest force field is introduced to freeze the topological state and enforce correct monomer packing. We generate 15 melts of 500 chains of 10.000 beads for varying chain stiffness as well as a number of melts with 1.000 chains of 15.000 monomers. To validate the equilibration process we study the time evolution of bulk, collective, and single-chain observables at the monomeric, mesoscopic, and macroscopic length scales. Extension of the present method to longer, branched, or polydisperse chains, and/or larger system sizes is straightforward.

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is represented by a single interaction site. Complementary sites can reversibly hybridize and dehybridize during a simulation. This bond dynamics induces a dynamics of the angular and dihedral bonds, that model the collective effects of chemical structure on the hybridization dynamics. We use the DNA model to perform simulations of the self-assembly kinetics of DNA tetrahedra, an icosahedron, as well as strand displacement operations used in DNA computation.

A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units.

We present a formalism for the scattering of an arbitrary linear or acyclic branched structure build by joining mutually non-interacting arbitrary functional sub-units. The formalism consists of three equations expressing the structural scattering in terms of three equations expressing the sub-unit scattering. The structural scattering expressions allow composite structures to be used as sub-units within the formalism itself. This allows the scattering expressions for complex hierarchical structures to be derived with great ease. The formalism is generic in the sense that the scattering due to structural connectivity is completely decoupled from internal structure of the sub-units. This allows sub-units to be replaced by more complex structures. We illustrate the physical interpretation of the formalism diagrammatically. By applying a self-consistency requirement, we derive the pair distributions of an ideal flexible polymer sub-unit. We illustrate the formalism by deriving generic scattering expressions for branched structures such as stars, pom-poms, bottle-brushes, and dendrimers build out of asymmetric two-functional sub-units.

Assembling living materials and engineering life-like technologies

Von Neumann, the inventor of the modern computer, realized that if life is a physical process, it should be possible to implement life in other media than biochemistry. In the 1950s, he was one of the first to propose the possibility of implementing genuine living processes in computers and robots. This perspective, while still controversial, is rapidly gaining momentum in many science and engineering communities. Below, we summarize our recent activities to create artificial life from scratch in physicochemical systems. We also outline the nature of the grand science and engineering challenges faced as we seek to realize Von Neumanns vision: Integration of information processing and material production from the nano- to the macroscale in technical systems.