Material design using Martini:Accelerating discovery through coarse-grained simulations

Advanced materials are a fundamental aspect of our modern everyday life. From batteries to solar cells and vaccines, the development of new functional materials is key in addressing societal challenges of the 21st century, yet the development process is often slow and expensive. Computational studies can accelerate this process but to fully realize their potential, they require infrastructure in the form of software, protocols, and benchmarks of these protocols. The thesis at hand starts with an in-depth review of the current usage of the Martini coarse-grained (CG) simulation technique in the field of material science. Subsequently, it lays the groundwork to realize the next stage of the rational design of complex heterogeneous materials utilizing Martini CG simulations. In particular, two newly developed software tools are introduced to facilitate high-throughput workflows. The open-source Vermouth python library and Polyply software suite efficiently automate the simulation setup of complex materials and sharing of simulation input parameters. Subsequently, two libraries of simulation parameters for carbohydrates and synthetic polymers are presented and benchmarked. Finally, a proof-of-concept method is presented to incorporate pH effects in Martini simulations. This protocol allows to study the response of materials to changes in pH, which is a common mechanism to functionalize materials. Taken together these developments enable the simulation of highly complex materials and offer a comprehensive collection of Martini (bio)-polymer parameters

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3

Water Losses During Technical Snow Production: Results From Field Experiments

Alpine as well as Nordic skiing tourism strongly depend on the production of machine-made snow for the timely opening of the winter season. However, it is likely that sublimation, evaporation, wind drift, and the discharge of unfrozen water to the ground will result in the loss of significant parts of the water used. The relation between these water losses and the ambient meteorological conditions is poorly understood. We present results from a series of 12 detailed snow-making field tests performed in a ski resort near Davos, Switzerland. Water inflows, measured at the snow machine, are related to the mass of snow deposited on the ground. Snow amounts are calculated from accumulated volumes, measured with terrestrial laser scanning (TLS), and manually sampled snow densities. Additionally, samples of liquid water contents (LWCs) of the produced snow are presented. We find that 7 to 35 ± 7% (mean 21%) of the consumed water was lost during snow-making and that the loss is strongly related to the ambient meteorological conditions. Linear regression analysis shows that water losses increase with air temperature (TA). Combining our data with observations from earlier field measurements shows similar correlations

Defect healing at room temperature in pentacene thin films and improved transistor performance

We report on a healing of defects at room temperature in the organic semiconductor pentacene. This peculiar effect is a direct consequence of the weak intermolecular interaction which is characteristic of organic semiconductors. Pentacene thin-film transistors were fabricated and characterized by in situ gated four-terminal measurements. Under high vacuum conditions (base pressure of order 10E-8 mbar), the device performance is found to improve with time. The effective field-effect mobility increases by as much as a factor of two and mobilities up to 0.45 cm2/Vs were achieved. In addition, the contact resistance decreases by more than an order of magnitude and there is a significant reduction in current hysteresis. Oxygen/nitrogen exposure and annealing experiments show the improvement of the electronic parameters to be driven by a thermally promoted process and not by chemical doping. In order to extract the spectral density of trap states from the transistor characteristics, we have implemented a powerful scheme which allows for a calculation of the trap densities with high accuracy in a straightforward fashion. We show the performance improvement to be due to a reduction in the density of shallow traps <0.15 eV from the valence band edge, while the energetically deeper traps are essentially unaffected. This work contributes to an understanding of the shallow traps in organic semiconductors and identifies structural point defects within the grains of the polycrystalline thin films as a major cause.Comment: 13 pages, 13 figures, to be published in Phys. Rev.

pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer

[Image: see text] The photosystem II PsbS protein triggers the photoprotective mechanism of plants by sensing the acidification of the thylakoid lumen. Despite the mechanism of action of PsbS would require a pH-dependent monomerization of the dimeric form, a clear connection between the pH-induced structural changes and the dimer stability is missing. Here, by applying constant pH coarse-grained and all-atom molecular dynamics simulations, we investigate the pH-dependent structural response of the PsbS dimer. We find that the pH variation leads to structural changes in the lumen-exposed helices, located at the dimeric interface, providing an effective switch between PsbS inactive and active form. Moreover, the monomerization free energies reveal that in the neutral pH conformation, where the network of H-bond interactions at the dimeric interface is destroyed, the protein–protein interaction is weaker. Our results show how the pH-dependent conformations of PsbS affect their dimerization propensity, which is at the basis of the photoprotective mechanism

Polyply:A python suite for facilitating simulations of macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle

Strategies for Enhancing the Dielectric Constant of Organic Materials

High dielectric constant organic semiconductors, often obtained by the use of ethylene glycol (EG) side chains, have gained attention in recent years in the efforts of improving the device performance for various applications. Dielectric constant enhancements due to EGs have been demonstrated extensively, but various effects, such as the choice of the particular molecule and the frequency and temperature regime, that determine the extent of this enhancement require further understanding. In this work, we study these effects by means of polarizable molecular dynamics simulations on a carefully selected set of fullerene derivatives with EG side chains. The selection allows studying the dielectric response in terms of both the number and length of EG chains and also the choice of the group connecting the fullerene to the EG chain. The computed time- and frequency-dependent dielectric responses reveal that the experimentally observed rise of the dielectric constant within the kilo/megahertz regime for some molecules is likely due to the highly stretched dielectric response of the EGs: the initial sharp increase over the first few nanoseconds is followed by a smaller but persistent increase in the range of microseconds. Additionally, our computational protocol allows the separation of different factors that contribute to the overall dielectric constant, providing insights to make several molecular design guides for future organic materials in order to enhance their dielectric constant further

Dynamics of chromosome organization in a minimal bacterial cell

Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM. </p

Martini 3 Coarse-Grained Force Field for Carbohydrates

The Martini 3 force field is a full re-parametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance it allows for more accurate description of condensed phase systems. In the present work we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme that decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals are developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the poly-glucoses dextran (water soluble) and cellulose (water insoluble, but soluble in ionic-liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids, being able to reproduce membrane properties and to induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach

Molecular dynamics simulation of an entire cell

The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell’s components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell’s spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future