Research overview dr. A.J. Markvoort


Lipid membranes

Membranes are important in all organisms as the plasma membrane of cells forms the protective barrier between the cytosol and the exterior. Membranes, which constitute mainly of lipids and proteins, exhibit interesting phenomena on a wide range of scales. For each problem, the appropriate modeling technique should be chosen.

Electronic Structure Calculations


Atomistic Molecular Dynamics



Coarse Grained Molecular Dynamics




Continuum Modeling

The main constituent of these membranes are phospholipids, which are aggregated in a bilayer. We show that even using a relatively simple model for lipids many properties of such bilayers can be elucidated, like their self-assembly, the spontaneous formation of vesicles, the fusion of such vesicles as well as the occurrence of diverse vesicle shapes and different fission pathways.

Modeling reversible polymerizations

Whereas phospholipids mainly aggregate into two-dimensional aggregates, i.e., bilayers, other molecules aggregate into one dimensional aggregates, i.e., filaments or supramolecular polymers. Examples of such molecules include proteins like actin. Here we study such filament formation using two synthetic molecules, namely BTA's and OPV's. Both of these molecules can form one dimensional helical supramolecular polymers, where the helicity can be both left-handed and right-handed.

Achiral monomers will form aggregates of both helicities in equal amount, while chiral information in the monomers results in a preference for one helicity in the aggregates. We study both the thermodynamic equilibrium of these supramolecular polymerizations, for instance showing the important role of the monomer pool in chiral amplification, as well as the kinetics, where we for instance observed that not always the thermodynamically most stable aggregate is formed first.

Another interesting example of reversible polymerization is the Fischer-Tropsch reaction, i.e., a heterogeneous catalytic reaction that converts synthesis gas (a mixture of carbon monoxide and hydrogen which can be derived from natural gas, coal, or biomass) into diesel quality liquid fuels. Taking the reversibility of the hydrocarbon chain growth into account using similar approaches as used for the supramolecular polymerizations, new insight into the behavior of this catalytic reaction is provided.

Nanoparticles

The precise control of the folded structure of synthetic polymers is commonly sought after in the development of nanomaterials for diverse applications. We use Wang-Landau Monte Carlo simulations of coarse-grained copolymers to explore the design parameters of these systems on their pathway to collapse, as well as a lattice based Monte Carlo technique to study the self-assembly of such collapsed single-chain, polymeric nanoparticles upon evaporation.

Synthetic biology

The rapid progress in synthetic biology has stimulated research into reconstituted minimal biological systems that display complex spatiotemporal behavior. Central to this bottom-up strategy is the fundamental understanding of important biological design rules critical to a specific cellular function, constructed from a minimal set of components. An interesting way to study the spatiotemporal pattern formation arising via coupling of reaction and diffusion, which is increasingly recognized as an important driving force for intra- and intercellular organization, is using wet stamping experiments in combination with modeling.

Bioinformatics

Within CTMM's PREDICCt project we are working on a proteomics data analysis on Type 2 Diabetes Mellitus, studying the effect of a very low calorie diet on diabetic patients. Here we use various (graph) algorithms in order to study not only individual proteins, but also relations between proteins and complete pathways.

Multi-scale modeling

Like also mentioned above for lipid membranes, many systems exhibit important features at multiple spatial and/or temporal scales. Instead of limiting to one scale, multiscale modeling and simulation is a recent trend in which different modeling methods are combined in one multiscale model in which the advantages of the different methods are tried to be used. For instance, in order to perform more efficient, though accurate, simulations, we work, in collaboration with colleagues from Mechanical Engineering, on the development of a simulation method that combines the advantages of molecular dynamics and the Monte Carlo simulations. We apply this in the context of heat transfer, by simulating particles near an interface using the molecular dynamics technique to obtain accurate results at that interface, and the Monte Carlo technique for the particles in the bulk where it yields the same results as MD but at a much lower computational cost. This is achieved by dividing our simulation domain into subdomains, where we use either MD or MC, and a coupling between these subdomains.