Prof. Jocelyne Vreede (associate professor)

"My simulations of protein unfolding need computing power - lots of computing power. My calculations concern molecules made up of 30,000 atoms that change shape over the course of a million little steps. So that takes rather a lot of computing power."

"When I first started studying chemistry I had never even worked on a computer. I was still writing up all my papers by hand. And I had never imagined myself in a research job involving entire days spent building models. It was lab work I wanted to pursue. But I enrolled in a few subjects dealing with molecular simulations and enjoyed them so much that I wanted to keep going in that direction."

"After I obtained my PhD in the Microbiology research group at SILS (Swammerdam Institute or Life Sciences), I started working as a postdoc researcher in the Computational Physics and Chemistry group at HIMS (Van 't Hoff Institute for Molecular Sciences). My work there focused on a bacterial protein called Photoactive Yellow Protein, or PYP for short. The way this protein behaves is an illustration of observing signals on a molecular scale. PYP acts something like a trigger. It can detect harmful UV radiation and sets off a series of reactions in response. This response is prompted by a change in the protein's internal structure, which puts it into what is known as the signal state. Of course, the protein had already been sequenced, and various experiments had also revealed exactly how the protein was folded in space."

"When you have a set of particles, they "feel" each other, as it were. I describe each bond, the angle of the atoms' placement relative to each other and the torsions. Next, I factor in the electrostatic interactions - positively charged particles repel each other; positive and negative attract - and the Van der Waal interactions, which quickly decay as distance grows. The result is a model which I refer to as a ‘force field': an extensive set of interactions between the particles inside the molecule."

"It takes no more than a few milliseconds for PYP to unfold. The structural changes that occur are modelled on the basis of the force field description and use increments of femtoseconds. That means I would need to make around 1011 calculations to reconstruct the entire process of unfolding - not exactly time-efficient, considering that if it took me one second to do each increment, the entire calculation would take 15,000 years. Luckily, there are a few tricks I can use to speed up the reaction, such as using a higher temperature. For a protein like PYP to unfold, there has to be some sort of activation pushing it to cross the barrier from a stable state. That barrier is lower at higher temperatures, when atoms move much faster. Consequently, the simulation of the unfolding speeds up significantly. I've set up 64 unfolding simulations for PYP, each at a different temperature. By switching these temperatures, I was able to reconstruct how the molecule would look if it had been unfolding at room temperature. In the final model, the light-activated group had moved to the protein's exterior and several helixes had uncoiled. A number of other researchers carried out additional experiments with a mutant of PYP to check whether this conformation was valid. This mutant protein has a more stable signal state, enabling my colleagues to study it using an experimental technique. Their findings validate the PYP conformation I found."

"But one major question remained: What is the actual course of the unfolding process? To find out, I used a method called Transition Path Sampling. This is a simulation technique designed around 10 years ago by my group's head researcher, Prof. Peter Bolhuis, whilst working at Berkeley. It starts off on a reaction path from another simulation, in this case a high temperature unfolding. Naturally that's not the real reaction path, but it is a reasonable guess. New reaction paths can also be calculated on the basis of this reaction path at any given point in the conformational change. The algorithm automatically saves the reaction paths that would put the protein in either the inactive or signal state. Reaction paths leading nowhere are rejected by the program. The successful reaction paths can be used to generate new paths in turn, with the process repeating until a path representing the probable unfolding is found. With 125 amino acids, PYP is a comparatively large protein to use in simulations, as it unfolds in a series of steps. Moreover, it is a molecule that is biologically relevant. My article on the unfolding even made it into the columns of the reputable journal Proceedings of the National Academy of Sciences (PNAS)."

"I have now widened my focus to include transitions in biological proteins that are even larger and more complex than PYP. In 2008 I received a Veni grant from the Netherlands Organisation for Scientific Research (NWO) for this research. One of my current projects is on so-called ‘coiled coils': two helix-shaped proteins that are coiled around each other."

"It's logical that simulations do not always hit their mark right away. One of my programs might have a bug, for example, or I could make an error when inputting a bond. That's just as much a part of research as errors you make in the lab. It is the theory that is really key in this work. You always have to keep thinking about the chemical reality. Your steps have to be logical. In the end, a simulation program is never more than a tool."

Abstract:

Asphaltenes are the heaviest component of crude oil, causing the formation of a stable oil–water emulsion. Even though asphaltenes are known to behave as an emulsifying agent for emulsion formation, their arrangement at the oil–water interface is poorly understood. We investigated the effect of asphaltene structure (island type vs archipelago type) and heteroatom type (Oxygen-O, Nitrogen-N, and Sulfur-S) on their structural behavior in the oil–water system. Out of six asphaltenes studied here, only three asphaltenes remain at the oil–water interface while others are soluble in the oil phase. Molecular orientation of asphaltene at the interface, position, and angle of asphaltene with the interface has also been determined. We observed that the N-based island type asphaltene is parallel, while the O-based island type asphaltene and N-based archipelago type are perpendicular to the interface. These asphaltene molecules are anchored at the interface by the heteroatom. The S-based asphaltenes (both island and archipelago type) and O-based archipelago type asphaltenes are soluble in the oil phase due to their inability to form a hydrogen bond with water and steric crowding near the heteroatom. This study will help in understanding the role of asphaltenes in oil–water emulsion formation based on its structure and how to avoid it.

https://pubs.acs.org/doi/10.1021/acs.energyfuels.8b01648

MOFs:

https://www.nakulrampal.com/research

ABSTRACT:

Twin polymerization [1] represents a new synthesis route to create nano-porous hybrid materials for a large number of different compositions containing organic and inorganic structure domains of 0.5 to 3 nm. Although first theoretical and experimental investigations have been performed, the open question still remains: How does the structure formation process of twin polymerization, yielding these interweaved organic-inorganic nanoporous hybrid materials, takes place in detail? Understanding the occurring effects and processes of the structure formation opens up the possibility to design (organic and/or inorganic) nanoporous materials with desired properties for industry. E.g. nanoporous materials are of great interest in applications like gas filter systems, catalyst or fuel cells.
In this framework we investigate different approaches on different length scales, i.e. coarse grained reactive bond fluctuation models [2], reaction kinetics models [3], reactive molecular dynamics [4], and density functional theory calculations [5]. Based on this broad range of methods we discuss our insights to the reaction mechanism itself, the resulting structure formation process, corresponding influence factors and its relation to experimental data.

References
[1] T. Ebert, A. Seifert, S. Spange, Macromol. Rapid Commun. 2015, 36(18):1623–1639
[2] C. Huster, K. Nagel, S. Spange, J. Prehl, Chem. Phys. Lett. accepted
[3] J. Prehl, R. Masser, P. Salamon, K. H. Hoffmann, J. Non-Equilib. Thermody. 2018
43(4):347–357
[4] J. Prehl, T. Schönfelder, J. Friedrich, S. Spange, K. H. Hoffmann, J. Chem. Phys. C 2017
121(29): 15984–15992
[5] I. Tchernook, J. Prehl, J. Friedrich, Polymer 2015, 60:241–251.

Abstract and references: 

Perfluorinated proton-exchange polymers form the basis of standard high-performance PEMFCs but difficult synthetic chemistry hampers further materials development. Hydrocarbon proton-exchange materials, on the other hand, are founded on well-established and versatile synthetic chemistry that allows for rapid materials development, and offer a less expensive alternative to perfluorinated polymers. In the corollary case of Anion Exchange Membrane Fuel Cells, the search continues for an alkaline-stable, polymeric hydroxide-conducting medium. Solutions to these challenges require the undertaking of rigorous systematic studies on model polymers and representative materials of known and controllable molecular structure and preferred nano-morphology. In this presentation, the evolution and properties of unique proton- and hydroxide-conducting polymers will be described together with mass transport phenomenon of PEMs and AEMs that might be of interest to the NTNU group.

References:

• “Structurally-Defined, Sulfo-Phenylated, Oligophenylenes and Polyphenylenes”, J. Am. Chem. Soc, 137 (2015) 12223-12226.

• “Hydroxide-Stable Ionenes”, ACS Macro Letters, 3 (5) (2014) 444-447.

• "Poly(phenylene) and m-Terphenyl as Powerful Protecting Groups for the Preparation of Stable Organic Hydroxides”, Angewandte Chemie, 55 (2016), 4818-4821.

• “The Control and Effect of Pore Size Distribution in AEMFC Catalyst Layers”, J. Electrochem. Soc, 163 (5) (2016) F1-F6.

• “Fuel Cell Catalyst Layers” Chem. Mater., Invited perspective commemorating 25th year of Chemistry of Materials, 2014, 26 (1), 381–39.

• "Thickness dependence of water permeation through proton exchange membranes”, J. Membr. Sci. 364 (2010) 183–193.

• Electrochemical reduction of dissolved oxygen in alkaline, solid polymer electrolyte films, J. Amer. Chem. Soc. 138 (2016) 15465-15472.

The main research topics of Prof. Jaakko Akola  are:

• Amorphous semiconductor materials in nonvolatile memory applications, especially chalcogenide alloys (DVD-RAM, DVD-RW, Blu-ray Disc, Phase-change RAM, Conductive-bridging RAM)
• Glasses in general: Novel oxide-based materials, chalcogens, pnictides, etc.
• Noble metal nanoparticles (Au, Ag, Pt, Pd) with various coatings and environments (surface, solution and biological environment)
• H2020-NMP project CritCat: Size-selected metal clusters as replacements of the Platinum Group Metals in heterogeneous and electrocatalysis (hydrogen energy, CO2 chemistry)
• Intermetallic alloys based on aluminum; clustering, precipitate formation and hardening effects

For more information please refer to the website: https://www.ntnu.edu/employees/jaakko.akola.

Abstract:

"The Nasal Geometry of the Reindeer Nose Gives Energy-Efficient Respiration"

Abstract:

"Reindeer in the arctic region live under very harsh conditions, and may face temperatures below 233 K. Therefore, efficient conservation of body heat and water is important for their survival. Alongside their insulating fur, the reindeer nasal mechanism for heat and mass exchange during respiration plays a fundamental role. We present a dynamic model to describe the heat and mass transport that takes place inside the reindeer nose, where we account for the complicated geometrical structure of the subsystems that are part of the nose. The model correctly captures the trend in experimental data for the temperature, heat and water recovery in the reindeer nose during respiration. As a reference case, we model a nose with a simple cylindrical-like geometry, where the total volume and contact area are the same as those determined in the reindeer nose. A comparison of the reindeer nose with the reference case shows that the nose geometry has a large influence on the velocity, temperature and water content of the air inside the nose. For all investigated cases, we find that the total entropy production during a breathing cycle is lower for the reindeer nose than for the reference case. The same trend is observed for the total energy consumption. The reduction in the total entropy production caused by the complicated geometry is higher (up to -20%) at more extreme ambient conditions, when energy efficiency is presumably more important for the maintenance of energy balance in the animal. In the literature, a hypothesis has been proposed, which states that the most energy efficient design of a system is characterized by equipartition of the entropy production. In agreement with this hypothesis, we find that the local entropy production during a breathing cycle is significantly more uniform for the reindeer nose than for the reference case. This suggests that natural selection has favored designs that give uniform entropy production when energy efficiency is an issue. Animals living in the harsh arctic climate, such as the reindeer, can therefore serve as inspiration for a novel industrial design with increased efficiency."

Reference to paper: Elisa Magnanelli, Øivind Wilhelmsen, Mario Acquarone, Lars P. Folkow, and Signe Kjelstrup. "The Nasal Geometry of the Reindeer Gives Energy-Efficient Respiration." Journal of Non-Equilibrium Thermodynamics 42, no. 1 (2017): 59-78.

TWIN POLYMERiZATION: Reactive Molecular Dynamics and other approaches

Karl Heinz Hoffmann¹

¹ Institut für Physik, Technische Universität Chemnitz, D-09107 Chemnitz, Germany,

e-mail: hoffmann@physik.tu-chemnitz.de

Polymer hybrid materials, i.e. materials combining organic polymer structures with inorganic components on the nanoscale, play an important role in reinforcing, coating and barrier materials. The production of such nanostructured polymer hybrid materials is a challenging task, since two different components must be merged together, while suppressing phase separation processes on the molecular level.

In recent years a more elegant technique called twin polymerization [1] has been developed to synthesize these hybrid materials with organic and inorganic structure domains. Twin polymerization is a special process that utilizes twin monomers containing differently polymerizable groups in one molecule, where only one initialization step is necessary to start the process.

The theoretical understanding of the overall twin polymerization process and especially of the structure formation of the composite material is still at the beginning. After introducing the basic concepts of twin polymerization, different modeling approaches for the complex reaction mechanism of twin polymerization will be shown. The utilized methods include reactive molecular dynamics simulation [3] and reactive Bond-Fluctuation-Models (rBFM).

Antonio Rizzo is a theoretical and computation chemist, his main research interests concern structural and response properties of atomic and molecular systems under intense laser pulses (http://h2.pi.ipcf.cnr.it/rizzo/ar.html). He is a senior research at the "Istituto per processi chimico-fisici" of the CNR (Consiglio nazionale delle ricerche) in Pisa.