A numerical study on the enhancement and suppression of crystal nucleation
Thesis defense by Koos van Meel on 20 October 2009
First-order phase transitions, such as condensation or crystallization, start with nucleation. This refers to the spontaneous formation of a microscopic amount of the new phase, a so-called nucleus, due to thermal fluctuations. If such a nucleus exceeds a critical size it has a high probability to grow all the way to macroscopic dimensions. Although this process is reasonably well understood from a phenomenological perspective, more insight on the molecular mechanism is required to actively control the process. This Thesis investigates the molecular mechanism of nucleation for various model systems by means of numerical many-particle simulations. A particular emphasis is on the physical aspects of homogeneous and heterogeneous nucleation, which refers to the absence or presence, respectively, of foreign objects such as seeds or surfaces. Some of the results of these chapters are potentially applicable to the design of novel materials or to protein crystallization for structure determination. Another focus of this Thesis is on various aspects of the numerical simulation. In particular, it is shown that graphic processing units for designed 3D video games can be programmed to significantly speed up a molecular dynamics simulation.
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Proton transfer in the photocycle of the photoactive yellow protein
Thesis defense of Elske Leenders on 12 September 2008
The photoactive yellow protein (PYP) is a widely used model protein. It is a typical, easy to study, example of photoactive and other signalling proteins. For this reason, PYP has been studied extensively using experiments and simulations. PYP is triggered by UV light: this starts the photocycle, in which the protein changes its shape to transduct the signal to its bacterial host. The photocycle consists of several steps and starts with the excitation and isomerisation of the chromophore. This chromophore, p-coumaric acid (pCA), is attached to the protein through the cysteine residue at position 69 via a thioester bond. When the protein is at rest in its ground state (pG), pCA is in the trans configuration. It is deproto- nated; its negative charge is stabilised inside the protein by hydrogen bonds donated by tyrosine at position 42 and glutamic acid at position 46. A positively charged arginine at position 52 is in plane with the chromophore ring and provides extra stabilisation as well.
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The dynamics of polymers by novel mesoscopic models
Promotion on 9 September 2008
The research presented in this thesis mainly considers the
results of meso-scopic computer simulations on polymer
solutions. This can be broken down into two parts, namely
computer simulations and the behaviour of polymer chains in
solution. Consequently, in the first two chapters we give an
introduction to these topics. First, in chapter 1, we try to
do this on a very basic level. We aim to make these concepts
accessible to non-experts. Next, in chapter 2, we discuss the
topics in more detail. In this chapter we describe for
instance how and why we use a dissipative ideal gas coupled to
a Lowe-Andersen thermostat as our simulation
method. Furthermore, we introduce some of the important
concepts in polymer physics, for instance the Gaussian chain
and the excluded volume effect.
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Computational Modeling of Oxidation Catalysis
Promotion on 27 May 2008
The Fenton reaction is a very elegant and environmentally
friendly way to oxidize organic substances using Fe2+
ions and hydrogen peroxide (H2O2) in water,
and has been known since the late 19th century. However, the
mechanism by which the Fenton reaction occurs is not completely
known, and there has been a long-lasting debate on the subject.
Fenton's reagent is a rather strong but unspecific oxidation
catalyst, and its main use is found in the oxidation of
wastewater, besides several other industrial
applications. Manuel J. Louwerse investigated the oxidation
mechanisms of Fenton's reaction focussing on the active role
that the aqueous solution molecules play as well as the
influence of the metal ligands on the reaction. He will defend
his thesis on these first-principles (Car-Parrinello) molecular
dynamics simulation studies on Tuesday, May 27 at the VU
University of Amsterdam.
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Proteins in Action
Promotion on 29 May 2008
"Proteins in Action, simulations of conformational changes in small proteins" is the title of the PhD thesis that Jaroslaw (Jarek) Juraszek will defend on Thursday, May 29. Jarek investigated, under guidance of his promotor, Peter Bolhuis, folding and unfolding of small proteins by computer simulation. He wrote the following summary of his work on the back of his thesis: "Even though at least trillions of proteins have just folded in the time...
Hypervalence & Aromaticity
Promotion on 2 June 2008
Hypervalence and aromaticity are two fundamental chemical
concepts that deal with the propensity of a system to localize
or delocalize bonds. Typically, so-called hypervalent and aromatic
molecules have highly symmetrical structures with equal-sized
bonds in contrast to the geometries of non-hypervalent and
anti-aromatic species which are usually asymmetric with
alternating short and long bonds. S. C. A. H. (Simon) Pierrefixe
investigated how hypervalence and aromaticity can be understood
and represented within the electronic structure framework of
Kohn-Sham molecular orbital theory. His objective is to...