Multi-scale simulation of reaction-diffusion systems

Thesis defense by Adithya Vijaykumar on 24 October 2017

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Hydration layer dynamics and association mechanisms of food and antifreeze proteins

Thesis defense by Z.Faidon Brotzakis on 7 March 2017

By the time the reader reads this line, billions of protein association events just occurred in our body, such as the ones regulating cell communication, signaling pathways, or in initiating a self-assembly processes, such as tissue fabrication, etc. The timescale of such transitions is slow, compared to atom vibrations and such events are termed rare, the reason being that protein or/and solvent interactions have to be disrupted and reformed in order for the transition to occur. In other words there is a barrier for the transition to occur. Having an atomistic insight into rare transitions and their respective important interactions is pivotal for understanding and experimentally controlling such processes. Water is an important agent on its own in facilitating protein folding, recognizing ice crystal planes (anti-freeze proteins) and in mediating protein association. By using molecular simulations we better understand the role of water at the hydration shell of single proteins in terms of structure and dynamics, we resolve the mechanisms of association and first steps of self-assembly food and anti-freeze proteins, and elucidate the role of water during protein association. Finally, in order to improve the efficiency of rare event sampling we develop a new algorithm which efficiently samples complex rare transitions as well as gives insight into the barrier region of the transition.

Self-assembly via anisotropic interactions

Thesis defense by Arhtur Newton on 26 January 2017

Self-assembly, the non-dissipative spontaneous formation of structural order spans many length scales, from amphiphilic molecules forming micelles to stars forming galaxies. This thesis mainly deals with systems on the colloidal length scale where the size of a particle is between a nanometer and a micrometer. As such, this thesis focuses on the self-assembly of colloidal particles made in the laboratory forming supracolloidal structures in a capillary and making the link to proteins forming complexes or virus shells. Whereas retrosynthetic analysis gives a handle on how atoms form molecules and subsequently how molecules form even bigger molecules, similar design principles are lacking for assembling micrometer particles. Last decade has witnessed great advances in the synthesis of micrometer particle building blocks. It is currently possible to make colloids anisotropic in shape, or anisotropic in surface properties, so-called patchy particles. Patchy particles show great promise in the design of new building blocks, possibly applicable in novel functional materials. Moreover, patchy particles have also shown to be good models for globular proteins. This thesis discusses mainly two topics using advanced computer simulation techniques. The first part of this thesis deals with the extraction of an effective potential for anisotropic colloidal dumbbell particles interacting through the critical Casimir force. The second part deals with how the kinetics and mechanism of formation of simple colloidal or protein structures are influenced by changing the interaction between or the dynamics of patchy particles.

Succes for Amsterdam Center for Multiscale Modeling in computational sciences call

3 October, 2014 - Three collaborative UvA/VU proposals granted

Three proposals of chemistry researchers from the Amsterdam Universities were selected for the final matching phase of the ‘Computational Sciences for Energy Research' public-private partnership, a multi-million euro research initiative of Shell, the Netherlands Organisation for Scientific Research NWO and the Foundation for Fundamental Research on Matter (FOM).

The successful call demonstrates the strength of the collaborative research of the Amsterdam science faculties, a collaboration pioneered by the joint Amsterdam Center for Multiscale Modeling (ACMM). The projects will be executed within the ACMM. Two of them were proposed by researchers Bernd Ensing and Evert Jan Meijer, respectively, both of the University of Amsterdam (UvA) and ACMM. In the third project Koop Lammertsma and Matthias Bickelhaupt, both of VU University and ACMM, will collaborate with Wybren Jan Buma of the UvA Molecular Photonics research group. The projects will add to an earlier successful CSER call in which an ACMM proposal by Peter Bolhuis (UvA) and Pieter-Rein ten Wolde (VU/AMOLF) was granted.

Talented Indian researchers

The Computational Sciences for Energy Research initiative CSER is a a joint large-scale public-private partnership in fundamental research in the energy domain. It was established in 2012 by Shell, the Netherlands Organization for Scientific Research (NWO) and the Foundation for Fundamental Research on Matter (FOM). Shell will invest circa 20 million euro to fund a total of 75 PhD positions at Dutch universities. NWO's investment will amount to approximately 21 million euro.

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Matthias Bickelhaupt member of the Royal Holland Society of Sciences and Humanities

Friday, 17 February, 2014 - Members promote science in the broadest sense.

Professor Matthias Bickelhaupt of the Division of Theoretical Chemistry has been appointed member of the Royal Holland Society of Sciences and Humanities (KHMW) as per 17 February. The KHMW is the oldest Learned Society of the Netherlands and was established in 1752 with the aim to promote science in the broadest sense. Between 1754 and 1793, the society published the complete works of Christiaan Huygens. The designation "royal" was granted...

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Understanding the role of aqueous solution in chemical reactions - A computational study

Thesis defense by Anna Pavlova on 30 October 2013

Water is a unique solvent due its structure and reactivity. The ability of a water molecule to form hydrogen bonds is its most important characteristic. In liquid water, each molecule typically donates and accepts two hydrogen bonds. This structure significantly enhances water’s ability to accept or donate protons. In addition, the lone pair electrons of the water oxygen can be involved in stronger bonds, for example when a water molecule acts as a ligand in a metal catalyst. Water is one of the most important solvents in (bio)chemistry. Due to its properties, solvent effects in aqueous chemical reactions are often significant. Both beneficial and negative effects of water in chemical reactions are well documented. Compared to the organic alternatives, water is an environmentally friendly, cheap and safe solvent. To date, the role of the solvent in aqueous chemical reactions is only partially understood. A full understanding on a detailed molecular level is often completely absent. This issue is the central theme of the present thesis where we report molecular simulation studies of two prototype aqueous chemical reactions. These reactions are not only of fundamental interest, but have also a significant importance in technological applications. In our study...

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From peptide chains to chains of peptides - multiscale modelling of self-assembling polypeptides

Thesis defense by Marieke Schor on 20 September 2011

Amyloid-like fibrils are long, insoluble threads of protein. The fibrils typically consist of two to six protofilaments, each two to five nm in diameter, twisting together to form rope-like fibrils with a length of several tens of nanometers. In each protofilament, the proteins or peptides form β-strands running perpendicular to the fibril axis. The formation of amyloid-like fibrils is related to the process of protein folding. Protein folding is often discussed in terms of a free energy landscape in which minima represent stable or metastable structures. The free energy landscape for a given polypeptide sequence depends largely on the environment. Changes in polypeptide concentration, pH, salt concentration, temperature etc. affect the landscape significantly and can shift the free energy minimum towards the fibril state as was proposed by Astbury. The kinetics of fibril formation is generally thought of as a nucleation-and-growth process. The nucleation step involves the formation of a small, energetically unfavourable aggregate usually called a nucleus or seed. Once this nucleus is formed....

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On the Stability of Old and Novel Carbon Phases; A computational study

Thesis defense by Francesco Colonna on 7 June 2011

Carbon is one of the most abundant elements on Earth, where it is present in a great variety of molecules and materials. A remarkable feature of carbon is that it can adopt different forms. For centuries, graphite and diamond have been the only known crystalline forms of carbon. Since the discovery of fullerenes in the 80s of the last century, however, a completely new "world of carbon" has been unfolding before the eyes of scientists, and a multitude of previously unknown carbon structures have been discovered. Most of these new structures are "nano-materials", meaning that their size is on the scale of the nano-meter. Because of their unusual mechanical and electronic properties, carbon-based nano-materials are expected to have a major impact on technology. It is hard to predict...

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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...

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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...

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