Carsten Svaneborg

Center for Fundamental Living Technology
Department of Physics, Chemistry and Farmacy
University of Southern Denmark
Campusvej 55
5230 Odense M
Denmark

FAX: +45 6550 4470
PHONE: +45 6550 3523
Email: scienceatzqex.dk or zqexatsdu.dk
Web: Personal home page

 

Research Interest

My interests and competences lie in developing and applying state-of-the-art models and computational techniques to obtain new insights into the fundamental physics of complex systems such as soft-condensed matter. This class of materials is essentially everything that is intermediate between elastic solids and viscous liquids and also includes all the materials that evolution has chosen as the building blocks of living organisms.

Typical for soft-matter is the emergence of mesoscopic self-assembled structures, and it is the dynamics of these mesoscopic structures which produces the exotic properties of these materials. For instance surfactants can form a large variety of micellar aggregates, a particular type of surfactants lipids is the major component of all cell membranes. Using the simulation data, I do not only want to understand the molecular model I'm simulating, but I also want to learn how we can use the simulation insights to improve state-of-the art theories and experiments done on these systems. This approach creates strong scientific synergies.

My Ph.D. was a computational study of self-assembled block-copolymer micelles. The methods I developed remain the state-of-the-art for the analysis of experimental scattering data from such systems. As a post-doc and assistant professor, I used computational techniques to study the molecular origin of viscoelasticity in polymer materials, and the molecular response to deformation of these materials. The Science paper and two Physical Review Letters, that I have authored or coauthored remain state-of-the art in the field. At present, I'm developing and applying new methodologies for simulating DNA hybridization dynamics and metabolic dynamics in coarse-grained molecular models. The aim is to design a set of molecules, metabolic reactions and molecular interactions that will spontaneously self-assemble into a system (a protocell), which has the ability to self-replicate when fed with the right precursor molecules. The protocell is furthermore equipped with a genotype-phenotype relation and hence should be capable of evolution. This would be physical-chemically realistic simulation of a minimal life form.

 

 Research:

  • Statistical mechanics: Coarse-graining, free energy calculations modelling.
  • Computational physics: Methodologies, optimization, coarse-graining, analysis methods, modelling.
  • Soft-condensed matter: Self-assembly and non-equilibrium phenomena. Material properties.
  • DNA: Hybridization and zippering dynamics, melting, sequence specific interactions.
  • Polymers: Static and dynamic properties, elastic and viscoelastic material properties, rheology.
  • Scattering: Theory and analysis of experimental x-ray, neutron, and light scattering spectra.

Competencies:

  • Natural science: Analyse complex problems. Create, analyse, learn and apply knowledge.
  • Physics: Computational physics, statistical mechanics, soft-condensed matter, scattering techniques, viscoelasticity.
  • Modelling. Computer modelling of complex systems such as soft-condensed matter.
  • Numerics: Techniques for numerical simulation of physical problems, optimization, visualization.
  • Communication: University lectures, conference presentations, popular science articles.
  • Organization: Organized workshops and symposia. Created and organized university courses.
  • Languages: Fluent English. Reads/understands German and Swedish.
  • Programming: High level languages e.g. C++, Perl, Mathematica, Python, and SQL.
  • IT experience: 20+ years with computers and programming. 19 years Linux experience.
  • Graphics: Raytracing, openGL/GLUT programming. 3D visualisation.

Employments

My contract at FLinT is expected to expire around 1/1 2013, so if you find my work interesting, let me know.

15/6 2011-31/12 2012: Associate professor at the Center for Fundamental Living Technology, SDU.
15/6 2010-15/6 2011: Assistant professor at the Center for Fundamental Living Technology, SDU.
1/7 2009-31/1 2010: Assistant professor, Dept. of Chemistry, AU. Funded by ENS-Lyon.
1/4 2006-30/6 2009: Assistant professor, Dept. of Chemistry, AU. Funded by a FNU Steno grant.
1/8 2003-31/3 2006: Post-doc at the Max Planck Institute for Complex Systems, Dresden, Germany.
1/7 2001-30/7 2003: Post-doc at the Max Planck Institute for Polymer Research, Mainz, Germany.
1/3 1998-28/2 2001: Employed as a Ph. D. student at Risø National Laboratory, Roskilde, Denmark

Publication list

''Simulation of migration and coalescence of metal inclusions in homogeneous and isotropic media''. C. Svaneborg, S. Steenstrup, and K.K. Bourdelle. Nuclear Instruments and Methods B 142, 89 (1998).

''A Monte Carlo study on the effect of excluded volume interactions on the scattering from block copolymer micelles''.C. Svaneborg and J.S. Pedersen. Journal of Chemical Physics 112, 9661 (2000).

''Block Copolymer micelle coronas as quasi two-dimensional dilute or semi-dilute polymer solutions''. C. Svaneborg and J.S. Pedersen. Physical Review E (rapid communications) 63, 10802 (2001).

''Form factors of block copolymer micelles with excluded volume interactions of the corona chains determined by Monte Carlo simulations''. C. Svaneborg and J.S. Pedersen. Macromolecules 35, 1028 (2002).

''Scattering from block copolymer micelles''. J.S. Pedersen and C. Svaneborg. Curr. Opinion in Colloid and Interface Science 7, 158 (2002).

''A small-angle neutron and X-ray contrast variation scattering study of the structure of block copolymer micelles: Corona shape and excluded volume interactions''. J.S. Pedersen, C. Svaneborg, K. Almdalm I.W. Hamley, and R.N. Young. Macromolecules 36, 416 (2003)

''Rheology and Microscopic Topology of Entangled Polymeric Liquids''. R. Everaers, S.K. Sukumaran, G.S. Grest, C. Svaneborg, A. Sivasubramanian, and K. Kremer. Science 303, 823 (2004)

''Monte Carlo simulations and analysis of scattering from neutral and polyelectrolyte polymer and polymer-like systems''. C. Svaneborg and J.S. Pedersen. Current Opinion in Colloid and Interface Science 8, 507 (2004).

''Strain-Dependent Localization, Microscopic Deformations, and Macroscopic Normal Tensions in Model Polymer Networks''. C. Svaneborg, G.S. Grest, and R. Everaers. Physical Review Letters 93, 257801 (2004)

''Disorder effects on the strain response of model polymer networks''. C. Svaneborg, G.S. Grest, and R. Everaers. Polymer 46, 4283, (2005).

''Scattering from polymer networks under elongational strain''. C. Svaneborg, G.S. Grest, and R. Everaers. Europhysics Letters 72, 760 (2005)

''Permanent Set of Crosslinking Networks: Comparison of Theory with Molecular Dynamics Simulations''. D. R. Rottach, J. G. Curro, J. Budzien, G. S. Grest, C. Svaneborg and R. Everaers. Macromolecules 39, 5521 (2006).

''Molecular Dynamics Simulations of Polymer Networks Undergoing Sequential Cross-Linking and Scission Reactions".D. R. Rottach, J. G. Curro, J. Budzien, G. S. Grest, C. Svaneborg and R. Everaers. Macromolecules 40, 131 (2007).

''Connectivity and Entanglement Stress Contributions in Strained Polymer Networks''. C. Svaneborg, R. Everaers, G.S. Grest, and J.G. Curro. Macromolecules 41, 4920 (2008).

''Microphase separation in cross-linked polymer blends: Efficient replica RPA post-processing of simulation data for homopolymer networks”. A.V. Klopper, C. Svaneborg, and R. Everaers. European Physics Journal E. 28, 89 (2009).

”Stress Relaxation in Entangled Polymer Melts”. J.-X. Hou, C. Svaneborg, R. Everaers, and G.S. Grest. Physical Review Letters 105, 068301 (2010)

”A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units”. C. Svaneborg and J.S. Pedersen. Journal of Chemical Physics 136, 104105 (2012) and republished in Virtual Journal of Biological Physics Research (2012).

”A formalism for scattering of complex composite structures 2. Distributed reference points”. C. Svaneborg and J.S. Pedersen. Journal of Chemical Physics 136, 154907 (2012) and republished in Virtual Journal of Nanoscale Science & Technology (2012).

”LAMMPS Framework for Dynamic Bonding an Application Modeling DNA”. C. Svaneborg. Computer Physics Communications 183, 1793 (2012).

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model. C. Svaneborg, H. Fellermann, and S. Rasmussen. Lecture Notes in Computer Science 7433, 123 (2012) Eds. D. Stafanovic and A. Tuberfield.

 

Other Publications

LAMMPS Framework for Dynamic Bonding and DNA dynamics examples C. Svaneborg. Computer Physics Communications Program Library (2012)

Fra syntetisk liv til levende teknologi C. Svaneborg, A.N. Albertsen, H. Fellermann, and S. Rasmussen. videnskab.dk (2012)

Modelling DNA Dynamics, Self-Assembly and Computation. C. Svaneborg, H. Fellermann, and S. Rasmussen. Computational Bioscience Minisymposium, University of Southern Denmark, Odense, Denmark. April 11, 2012

Fra syntetisk liv til levende teknologi. C. Svaneborg, A.N. Albertsen, H. Fellermann, and S. Rasmussen. Aktuel Naturvidenskab (Sept. 2011)

 

Current scientific activities

Below are some videos from some of my current simulation studies.

  1. Atomistic DNA simulations
  2. Self-assembly of DNA nano-structures
  3. Template based replication of DNA molecules
  4. Self-assembly of soft-condensed matter
  5. Modelling metabolic reactions in soft-matter
  6. DNA tagged soft-matter
  7. Protocell models

Atomistic Simulations

I use NAMD to perform simulations of single and double stranded DNA at various conditions. By calculating the centres of mass of the nucleosides (green spheres), we can use the simulations to learn about the interaction potentials (potentials of mean force) that should be used in one bead per nucleoside coarse-grained DNA models. The video below is a 40 bp long poly-AT strand at T=300K.

Self-assembly of DNA nano-structures

Complimentary single strands hybridize forming a double strand. This can be used to program the molecular self-assembly of desired nano-structures. For instance, by crafting 4 different types of 3-armed single strand complexes with the right complementary DNA sequences, these can be made to self-assemble into well-defined structures such as a tetrahedron.

Using instead 12 5-functional DNA constructs, they can be made to self-assemble into an icosahedron as shown below.

Template based replication of DNA

This video shows a dynamic bonded DNA model ["LAMMPS Framework for Dynamic Bonding an Application Modeling DNA". C. Svaneborg. Computer Physics Communications 183, 1793 (2012).] The video illustrates how complimentary oligomers docks on a template, subsequently nearby oligomers ligate with each other. The final result is the production of a strand with the complimentary sequence of the template. Periodically the system is heated for brief period to melt of the copy, such that the template based replication can continue.

Soft-condensed matter

Soft-condensed matter systems shows spontaneous emergence of self-assembled mesoscopic structures. Typical constituents are oil, water, surfactants, polymers etc. The simulations below investigates different soft-matter systems using Dissipative Particle Dynamics

Oil-surfactant-water mixture with excess surfactant.

Oil-surfactant-water mixture with excess oil.

Self-assembly of stiff bola-amphiphile molecules. The red mid sections are hydrophobic. To avoid contact with water (not shown) they self-assemble into micellar structures

Simulation of metabolic reactions

The video is a Dissipative Particle dynamics simulation of the metabolic digestion of an oil droplet. The droplet consists of dimeric oil molecules (grey molecules) in a water medium (not shown). The red-blue molecule represent an energy harvesting and catalytic functionality respectively. When these are co-localized the catalytic bead (blue) can digest nearby oil molecules and convert them into surfactant (green molecules). The result is the progressive digestion of oil (core volume) into surfactant (droplet surface). The metabolic dynamics leads to the progressive breakup of the oil droplet into surfactant micelles.

Simulation of DNA tagged droplets

The simulations below are of a number of DNA labelled oil droplets. The only difference is that in the first simulation DNA tags hybridize to form a double stranded bridge between the two droplets. In the latter simulation, I have reversed the direction of one sequence. Hence, the hybridization is tip-to-tether on both strands, this induces fast fusion between the two droplets.

Protocell model 62

The central dogma of FLiNT is that a minimal living protocell can be realised through the functional integration of just three components: a self-assembled soft-matter container, a chemical metabolism, and information carrying molecules. The container colocalizes the information molecules and the metabolism and provides the protocell with an genetic identitity and a boundary to the environment. The metabolism converts environmental ressources into the chemical constituents of comprising the protocell itself. This enables the protocell to grow and replicate itself. The information molecules are used to actively regulate the metabolism and hence the protocell division process.

In this protocell model, a surfactant stabilized oil-droplet acts as the container. The information molecules are anchored to the container by a hydrophobic anchor. Between the anchor and the information molecule are a red or blue particle. These represent a light harvesting and a catalytic molecule, respectively, that model the metabolism used in the laboratory. When they are colocalized by being tethered to complimentary information molecules, the metabolic rate is maximised, and the metabolism acts by converting oil in the core into surfactant, hence driving the droplet to divide. Unfortunately, the droplet does not just divide but also fuses, which leads to undersired mixing of information molecules between different containers. Even though these model are quite primitive, they adequately illustrates the complexity of integrating self-assembly, sequence information, and metabolic reactions in these materials.