Johannes Zeman

Nudged-elastic band used to find reaction coordinates based on the free energy

Transition paths characterize chemical reaction mechanisms. In this paper, we present a new method to find mean reaction paths based on the free energy. A nudged elastic band (NEB) is optimized using gradients and Hessians of the free energy, which are obtained from umbrella integration. The transition state can be refined by a Newton-Raphson search starting from the highest point of the NEB path. All optimizations are done using Cartesian coordinates. Independent molecular dynamics (MD) runs are performed at each image used to discretize the path. This makes the method intrinsically parallel. In contrast to other free energy methods, the algorithm does not become more expensive when including more degrees of freedom in the active space. The method is applied to the alanine-dipeptide as a test case and compared to pathways that have been derived from metadynamics and forward flux sampling.

Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA

Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonucleotide, which has important consequences for osmotic regulation mechanisms.

Preferential solvation and ion association properties in aqueous dimethyl sulfoxide solutions

We study the solvation and the association properties of ion pairs in aqueous dimethyl sulfoxide (DMSO) solution by atomistic molecular dynamics (MD) simulations. The ion pair is composed of two lithium and a single sulfonated diphenyl sulfone ion whose properties are studied under the influence of different DMSO concentrations. For increasing mole fractions of DMSO, we observe a non-ideal behavior of the solution as indicated by the derivatives of the chemical activity. Our findings are complemented by dielectric spectra, which also verify a complex DMSO-water mixing behavior. In agreement with these results, further simulation outcomes reveal an aqueous homoselective solvation of the ion species which fosters the occurrence of pronounced ion association constants at higher DMSO mole fractions. The consequences of this finding are demonstrated by lower ionic conductivities for increasing concentrations of DMSO.

A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

First-Principles Parametrization of Polarizable Coarse-Grained Force Fields for Ionic Liquids

We present an ab initio parametrization scheme for explicitly dipole-polarizable force fields for the simulation of molecular liquids. The scheme allows for, in principle, arbitrarily coarse-grained representations. All parameters in the force field are derived from first-principles, based on simple physical arguments. Only one fit parameter enters the parametrization, a global scaling factor for the size of the particles, which is adjusted to reproduce the experimental mass density. As important examples and for the first time, polarizable coarse-grained force fields are derived for 1-alkyl-3-methylimidazolium cations with varying alkyl-chain lengths (alkyl = ethyl, butyl, hexyl) and hexafluorophosphate and tetrafluoroborate anions. Our findings are in good agreement with experimental results and results of further atomistic simulations. Hence, the force fields can be faithfully used where polarizability is expected to play a significant role, such as simulations of energy storage devices.

Validation of Trimethylamine-N-oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions

Five molecular models for trimethylamine N-oxide (TMAO) to be used in conjunction with compatible models for liquid water are evaluated by comparison of molecular dynamics (MD) simulation results to experimental data as functions of TMAO molality. The experimental data comprise thermodynamic properties (density, apparent molar volume, and partial molar volume at infinite dilution), transport properties (self-diffusion and shear viscosity), structural properties (radial distribution functions and degree of hydrogen bonding), and dielectric properties (dielectric spectra and static permittivity). The thermodynamic and transport properties turned out to be useful in TMAO model discrimination while the influence of the water model and the TMAO-water interaction are effectively probed through the calculation of dielectric spectra.

It’s a match! Simulating compatibility-based learning in a network of networks

In this article, we develop a new way to capture knowledge diffusion and assimilation in innovation networks by means of an agent-based simulation model. The model incorporates three essential characteristics of knowledge that have not been covered entirely by previous diffusion models: the network character of knowledge, compatibility of new knowledge with already existing knowledge, and the fact that transmission of knowledge requires some form of attention. We employ a network-of- networks approach, where agents are located within an innovation network and each agent itself contains another network composed of knowledge units (KUs). Since social learning is a path-dependent process, in our model, KUs are exchanged among agents and integrated into their respective knowledge networks depending on the received KUs’ compatibility with the currently focused ones. Thereby, we are also able to endogenize attributes such as absorptive capacity that have been treated as an exogenous parameter in some of the previous diffusion models. We use our model to simulate and analyze various scenarios, including cases for different degrees of knowledge diversity and cognitive distance among agents as well as knowledge exploitation vs. exploration strategies. Here, the model is able to distinguish between two levels of knowledge diversity: heterogeneity within and between agents. Additionally, our simulation results give fresh impetus to debates about the interplay of innovation network structure and knowledge diffusion. In summary, our article proposes a novel way of modeling knowledge diffusion, thereby contributing to an advancement of the economics of innovation and knowledge.

A polarizable MARTINI model for monovalent ions in aqueous solution

We present a new polarizable coarse-grained martini force field for monovalent ions, called refIon, which is developed mainly for the accurate reproduction of electrostatic properties in aqueous electrolyte solutions. The ion model relies on full long-range Coulomb interactions and introduces satellite charges around the central interaction site in order to model molecular polarization effects. All force field parameters are matched to reproduce the mass density and the static dielectric permittivity of aqueous NaCl solutions, such that experimental values are well-reproduced up to moderate salt concentrations of 2   m o l / l . In addition, an improved agreement with experimentally measured ionic conductivities is observed. Our model is validated with regard to analytic solutions for the ion distribution around highly charged rod-like polyelectrolytes in combination with atomistic simulations and experimental results concerning structural properties of lipid bilayers in the presence of distinct salt concentrations. Further results regarding the coordination numbers of counterions around dilute poly(styrene sulfonate) and poly(diallyldimethylammonium) polyelectrolyte chains also highlight the applicability of our approach. The introduction of our force field allows us to eliminate heuristic scaling factors, as reported for previous martini ion models in terms of effective salt concentrations, and in consequence provides a better agreement between simulation and experimental results. The presented approach is specifically useful for recent martini attempts that focus on highly charged systems-such as models of DNA, polyelectrolytes or polyelectrolyte complexes-where precise studies of electrostatic effects and charge transport processes are essential.

Viral ice buckets: A memetic perspective on the ALS Ice Bucket Challenge’s diffusion

Abstract This paper presents an exploratory memetic perspective on the diffusion pattern of the ALS Ice Bucket Challenge. More precisely, the paper contributes to research on social learning, cultural evolution, and social contagion by shedding light on endogenous (meme-related) as well as exogenous (structural) properties that may have influenced the Ice Bucket Challenge’s diffusion. In a first pillar, we present a descriptive memetic analysis of the diffusion pattern, including an evaluation of the Ice Bucket Challenge according to memetic criteria for successful replication. In the second pillar, we present an agent-based simulation model designed to illuminate the influence of particular social network characteristics on the Ice Bucket Challenge’s diffusion. By combining these two pillars, we contribute to the advancement of memetic theory, narrowing the gap between a solely meme-centered perspective and social network analysis.