Peter A. J. Hilbers

Pathway complexity in supramolecular polymerization

Self-assembly provides an attractive route to functional organic materials, with properties and hence performance depending sensitively on the organization of the molecular building blocks. Molecular organization is a direct consequence of the pathways involved in the supramolecular assembly process, which is more amenable to detailed study when using one-dimensional systems. In the case of protein fibrils, formation and growth have been attributed to complex aggregation pathways that go beyond traditional concepts of homogeneous and secondary nucleation events. The self-assembly of synthetic supramolecular polymers has also been studied and even modulated, but our quantitative understanding of the processes involved remains limited. Here we report time-resolved observations of the formation of supramolecular polymers from π-conjugated oligomers. Our kinetic experiments show the presence of a kinetically favoured metastable assembly that forms quickly but then transforms into the thermodynamically favoured form. Quantitative insight into the kinetic experiments was obtained from kinetic model calculations, which revealed two parallel and competing pathways leading to assemblies with opposite helicity. These insights prompt us to use a chiral tartaric acid as an auxiliary to change the thermodynamic preference of the assembly process. We find that we can force aggregation completely down the kinetically favoured pathway so that, on removal of the auxiliary, we obtain only metastable assemblies.

Adaptive Ensemble Models of Extreme Learning Machines for Time Series Prediction

In this paper, we investigate the application of adaptive ensemble models of Extreme Learning Machines (ELMs) to the problem of one-step ahead prediction in (non)stationary time series. We verify that the method works on stationary time series and test the adaptivity of the ensemble model on a nonstationary time series. In the experiments, we show that the adaptive ensemble model achieves a test error comparable to the best methods, while keeping adaptivity. Moreover, it has low computational cost.

An equilibrium model for chiral amplification in supramolecular polymers

We describe a model that rationalizes amplification of chirality in cooperative supramolecular copolymerization. The model extends nucleation-elongation based equilibrium models for growth of supramolecular homopolymers to the case of two monomer and aggregate types. Using the principle of mass-balance for the two monomer types, we derive a set of two nonlinear equations, describing the thermodynamic equilibrium state of the system. These equations can be solved by numerical methods, but also analytical approximations are derived. The equilibrium model allows two-sided growth of the aggregates and can be applied to symmetric supramolecular copolymerizations, corresponding to the situation in which the monomers are enantiomerically related, as well as to the more general case of nonsymmetric supramolecular copolymerizations. In detail, so-called majority-rules phenomena in supramolecular systems with isodesmic as well as cooperative growth are analyzed. Comparison of model predictions with experimental data shows that the model gives a very good description of both titration and melting curves. When the system shows cooperative growth, the model leads to a phase diagram in which the presence of the various aggregate types is given as a function of composition and temperature.

Kinetics of the Fischer–Tropsch Reaction

Long carbon chains: Self-assembly of monomeric carbon intermediates into long-chain hydrocarbons on catalytically reactive surface was studied when full reversibility of the chain growth is included in the kinetic model. Using Brønsted-Evans-Polanyi relations, the maximum chain growth as a function of the surface reactivity is predicted.

Magnitude and control of mitochondrial sensitivity to ADP

The transduction function for ADP stimulation of mitochondrial ATP synthesis in skeletal muscle was reconstructed in vivo and in silico to investigate the magnitude and origin of mitochondrial sensitivity to cytoplasmic ADP concentration changes. Dynamic in vivo measurements of human leg muscle phosphocreatine (PCr) content during metabolic recovery from contractions were performed by (31)P-NMR spectroscopy. The cytoplasmic ADP concentration ([ADP]) and rate of oxidative ATP synthesis (Jp) at each time point were calculated from creatine kinase equilibrium and the derivative of a monoexponential fit to the PCr recovery data, respectively. Reconstructed [ADP]-Jp relations for individual muscles containing more than 100 data points were kinetically characterized by nonlinear curve fitting yielding an apparent kinetic order and ADP affinity of 1.9 +/- 0.2 and 0.022 +/- 0.003 mM, respectively (means +/- SD; n = 6). Next, in silico [ADP]-Jp relations for skeletal muscle were generated using a computational model of muscle oxidative ATP metabolism whereby model parameters corresponding to mitochondrial enzymes were randomly changed by 50-150% to determine control of mitochondrial ADP sensitivity. The multiparametric sensitivity analysis showed that mitochondrial ADP ultrasensitivity is an emergent property of the integrated mitochondrial enzyme network controlled primarily by kinetic properties of the adenine nucleotide translocator.

Synthesis, biological evaluation, and molecular modeling of 1-benzyl-1H-imidazoles as selective inhibitors of aldosterone synthase (CYP11B2).

Reducing aldosterone action is beneficial in various major diseases such as heart failure. Currently, this is achieved with mineralocorticoid receptor antagonists, however, aldosterone synthase (CYP11B2) inhibitors may offer a promising alternative. In this study, we used three-dimensional modeling of CYP11B2 to model the binding modes of the natural substrate 18-hydroxycorticosterone and the recently published CYP11B2 inhibitor R-fadrozole as a rational guide to design 44 structurally simple and achiral 1-benzyl-1H-imidazoles. Their syntheses, in vitro inhibitor potencies, and in silico docking are described. Some promising CYP11B2 inhibitors were identified, with our novel lead MOERAS115 (4-((5-phenyl-1H-imidazol-1-yl)methyl)benzonitrile) displaying an IC(50) for CYP11B2 of 1.7 nM, and a CYP11B2 (versus CYP11B1) selectivity of 16.5, comparable to R-fadrozole (IC(50) for CYP11B2 6.0 nM, selectivity 19.8). Molecular docking of the inhibitors in the models enabled us to generate posthoc hypotheses on their binding modes, providing a valuable basis for future studies and further design of CYP11B2 inhibitors.

An MR-compatible bicycle ergometer for in-magnet whole-body human exercise testing

An MR‐compatible ergometer was developed for in‐magnet whole‐body human exercise testing. Designed on the basis of conventional mechanically braked bicycle ergometers and constructed from nonferrous materials, the ergometer was implemented on a 1.5‐T whole‐body MR scanner. A spectrometer interface was constructed using standard scanner hardware, complemented with custom‐built parts and software to enable gated data acquisition during exercise. High‐quality 31P NMR spectra were reproducibly obtained from the medial head of the quadriceps muscle of the right leg of eight healthy subjects during two‐legged high‐frequency pedaling (80 revolutions per minute) at three incremental workloads, including maximal. Muscle phosphocreatine content dropped 82%, from 32.2 ± 1.0 mM at rest to 5.7 ± 1.1 mM at maximal workload (mean ± standard error; n = 8), indicating that the majority of quadriceps motor units were recruited. The cardiovascular load of the exercise was likewise significant, as evidenced by heart rates of 150 (±10%) beats per minute, measured immediately afterward. As such, the newly developed MR bicycling exercise equipment offers a powerful new tool for clinical musculoskeletal and cardiovascular MR investigation. The basic design of the ergometer is highly generic and adaptable for application on a wide selection of whole‐body MR scanners. Magn Reson Med, 2010.

Prediction of muscle energy states at low metabolic rates requires feedback control of mitochondrial respiratory chain activity by inorganic phosphate

The regulation of the 100-fold dynamic range of mitochondrial ATP synthesis flux in skeletal muscle was investigated. Hypotheses of key control mechanisms were included in a biophysical model of oxidative phosphorylation and tested against metabolite dynamics recorded by 31P nuclear magnetic resonance spectroscopy (31P MRS). Simulations of the initial model featuring only ADP and Pi feedback control of flux failed in reproducing the experimentally sampled relation between myoplasmic free energy of ATP hydrolysis (ΔGp = ΔGp o′+RT ln ([ADP][Pi]/[ATP]) and the rate of mitochondrial ATP synthesis at low fluxes (<0.2 mM/s). Model analyses including Monte Carlo simulation approaches and metabolic control analysis (MCA) showed that this problem could not be amended by model re-parameterization, but instead required reformulation of ADP and Pi feedback control or introduction of additional control mechanisms (feed forward activation), specifically at respiratory Complex III. Both hypotheses were implemented and tested against time course data of phosphocreatine (PCr), Pi and ATP dynamics during post-exercise recovery and validation data obtained by 31P MRS of sedentary subjects and track athletes. The results rejected the hypothesis of regulation by feed forward activation. Instead, it was concluded that feedback control of respiratory chain complexes by inorganic phosphate is essential to explain the regulation of mitochondrial ATP synthesis flux in skeletal muscle throughout its full dynamic range.

Quantifying the Composition of Human Skin for Glucose Sensor Development

Background: Glucose is heterogeneously distributed within human skin. In order to develop a glucose measurement method for human skin, both a good quantification of the different compartments of human skin and an understanding of glucose transport processes are essential. This study focused on the composition of human skin. In addition, the extent to which intersubject variability in skin composition alters glucose dynamics in human skin was investigated. Methods: To quantify the composition of the three layers of human skin—epidermis, dermis, and adipose tissue—cell and blood vessel volumes were calculated from skin biopsies. These results were combined with data from the literature. The composition was applied as input for a previously developed computational model that calculates spatiotemporal glucose dynamics in human skin. The model was used to predict the physiological effects of intersubject variability in skin composition on glucose profiles in human skin. Results: According to the model, the lag time of glucose dynamics in the epidermis was sensitive to variation in the volumes of interstitial fluid, cells, and blood of all layers. Data showed most variation/uncertainty in the volume composition of the adipose tissue. This variability mainly influences the dynamics in the adipose tissue. Conclusions: This study identified the intersubject variability in human skin composition. The study shows that this variability has significant influence on the glucose dynamics in human skin. In addition, it was determined which volumes are most critical for the quantification and interpretation of measurements in the different layers.

Self-Reproduction of Fatty Acid Vesicles: A Combined Experimental and Simulation Study

Dilution of a fatty acid micellar solution at basic pH toward neutrality results in spontaneous formation of vesicles with a broad size distribution. However, when vesicles of a defined size are present before dilution, the size distribution of the newly formed vesicles is strongly biased toward that of the seed vesicles. This so-called matrix effect is believed to be a key feature of early life. Here we reproduced this effect for oleate micelles and seed vesicles of either oleate or dioleoylphosphatidylcholine. Fluorescence measurements showed that the vesicle contents do not leak out during the replication process. We hypothesized that the matrix effect results from vesicle fission induced by an imbalance of material across both leaflets of the vesicle upon initial insertion of fatty acids into the outer leaflet of the seed vesicle. This was supported by experiments that showed a significant increase in vesicle size when the equilibration of oleate over both leaflets was enhanced by either slowing down the rate of fatty acid addition or increasing the rate of fatty acid transbilayer movement. Coarse-grained molecular-dynamics simulations showed excellent agreement with the experimental results and provided further mechanistic details of the replication process.