Modeling of uncertainties in biochemical reactions

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Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

The corrosion mechanisms of a Roman iron bezel ring were investigated by in-depth characterization of its uncommon corrosion pattern and thermodynamic modelling. A silver foil and altered glass remnants were identified, covered with thick strata of magneti ...

vanishing viscosity, networks. This work has received funding from the Alexander von Humboldt-Professorship program, the Transregio 154 Project "Mathematical Modelling, Simulation and Optimization Using the Example of Gas Networks" of the DFG, the grant PI ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytically optimal operating conditions of any complex enzyme m ...

Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed a ...

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

Empowered by ever-increasing computational power and algorithmic developments, electronic-structure simulations continue to drive research and innovation in materials science. In this context, ab-initio calculations offer an unbiased platform for the under ...

Genome duplication, transcription, and translation are among many crucial cellular processes that need to be performed with high fidelity. However, those extremely low error rates cannot be explained with simple equilibrium thermodynamic considerations. Th ...

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

This paper studies the effect of temperature on the phase assemblages of belite-ye'elimite cement. A comparison is made between thermodynamic modelling and experimental data at 28 and 180 days of hydration at 5, 20, 40, and 60 degrees C. The fast reaction ...

Machine learning is often cited as a new paradigm in control theory, but is also often viewed as empirical and less intuitive for students than classical model-based methods. This is particularly the case for reinforcement learning, an approach that does n ...

In the context of SARS-CoV-2 pandemic, mathematical modelling has played a funda-mental role for making forecasts, simulating scenarios and evaluating the impact of pre-ventive political, social and pharmaceutical measures. Optimal control theory represent ...

Glucose sensing in pancreatic D-cells depends on oxidative phosphorylation and mitochondria-derived signals that promote insulin secretion. Using mass spectrometry-based phosphoproteo-mics to search for downstream effectors of glucose-dependent signal tran ...

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

Background: Overexpression of the transsulfuration enzyme cystathionine-beta-synthase (CBS), and overproduction of its product, hydrogen sulfide (H2S) are recognized as potential pathogenetic factors in Down syndrome (DS). The purpose of the study was to d ...

This thesis investigates the effects of aluminates, sulfates, and heterogeneous substrates on the nucleation and growth of synthetic calcium-silicate-hydrates (C-S-H) produced by dropwise precipitation. The use of synthetic C-S-H, separate from other cemen ...

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Dynamical potentials appear in many advanced electronic-structure methods, including self-energies from many-body perturbation theory, dynamical mean-field theory, electronic-transport formulations, and many embedding approaches. Here, we propose a novel t ...

Nanofabrication is key to many technological advances, especially the challenge of merging nanophotonics with electronics. Here, we investigate the fabrication process of plasmonic interdigitated gold electrodes having a very high aspect ratio (i.e. long a ...

Modeling of uncertainties in biochemical reactions

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Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Unique corrosion behavior of an archaeological Roman iron ring: Microchemical characterization and thermodynamic considerations

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Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

Modeling, analysis, and design of complex biological networks

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Individual and combined benefits of different nonequilibrium proofreading mechanisms

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

Influence of temperature on phase assemblages of belite-ye'elimite cement

Reinforcement learning approach to control an inverted pendulum: A general framework for educational purposes

Optimized numerical solutions of SIRDVW multiage model controlling SARS-CoV-2 vaccine roll out: An application to the Italian scenario

SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin-secreting cells

Computational tools and resources for designing new pathways to small molecules

Role of the cystathionine beta-synthase / H2S pathway in the development of cellular metabolic dysfunction and pseudohypoxia in down syndrome

Precipitation, Characterization, Kinetic, and Thermodynamic Modelling of Synthetic C-S-H Systems (C-S-H, CASH, CSH+$)

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Unified Green's function approach for spectral and thermodynamic properties from algorithmic inversion of dynamical potentials

Controlling surface effects in extremely high aspect ratio gold plasmonic electrodes