A5073464886- Protein Structure and Dynamics
- Enzyme Structure and Function
- Forest Insect Ecology and Management
- Plant and animal studies
- Advanced Chemical Physics Studies
- Pesticide Residue Analysis and Safety
- Quantum, superfluid, helium dynamics
- Ecology and Vegetation Dynamics Studies
- Machine Learning in Materials Science
- High-Energy Particle Collisions Research
- Microbial Metabolic Engineering and Bioproduction
- Inorganic Fluorides and Related Compounds
- Insect-Plant Interactions and Control
- Molecular Junctions and Nanostructures
- Contact Dermatitis and Allergies
- RNA and protein synthesis mechanisms
- Advanced NMR Techniques and Applications
- Insect and Pesticide Research
- Nuclear physics research studies
- Cold Atom Physics and Bose-Einstein Condensates
Bayer (Germany)
2022-2024
University of Freiburg
2015-2018
Karlsruhe Institute of Technology
2012
University of Stuttgart
2009
To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal e.g., backbone dihedral angles or various kinds distances, may be used input data in PCA. Adopting two well-known model problems, folding villin headpiece the functional BPTI, study PCA using distance-based measures is presented which employs...
We present a systematic approach to reduce the dimensionality of complex molecular system. Starting with data set coordinates (obtained from experiment or simulation) and an associated metastable conformational states clustering data), supervised machine learning model is trained assign unknown structures states. In this way, learns determine features that are most important discriminate Using new algorithm exploits feature importance via iterative exclusion principle, we identify essential...
While adequately chosen reaction coordinates are expected to reveal the mechanism of a dynamical process, it proves be notoriously difficult model complex structural rearrangements macromolecule by low-dimensional collective coordinate. Adopting hinge-bending motion T4 lysozyme (T4L) as prominent example and performing 50 μs long unbiased molecular dynamics (MD) simulation T4L, general strategy identify protein functional is developed. As systematic method reduce dimensionality dynamics,...
Short-range DFT/long-range ab initio methods allow for a combination of the weak basis-set dependency DFT with an accurate treatment long-range effects like van der Waals interaction. In order to improve existing short-range LDA and GGA density functionals, we developed TPSS-like meta-GGA exchange-correlation functional checked its performance in CCSD(T) calculations thermodynamical properties G2 set molecules.
Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family Monte Carlo techniques has taken a backseat dynamics based methods, which is also reflected in number available packages. Here, we report development generic, versatile package for stochastic simulations demonstrate its application protein conformational change, protein-protein association, small-molecule docking, growth clusters organic molecules....
An in silico model for predicting skin penetration of active ingredients formulated plant protection products (PPP) has been developed using random forests (machine learning technique) that were trained with data from vitro human studies taken the EFSA dermal absorption database and in-house Bayer. In addition to applied dose, various physicochemical properties considered as parameters. The linked a novel percentile approach order make results usable regulatory purposes. Application an...
The decline of insects is a global concern, yet identifying the factors behind it remains challenging due to complexity potential drivers and underlying processes, lack quantitative historical data on insect populations. This study assesses 92 in West Germany, where significant declines have been observed. Using from federal statistical offices market surveys, traces changes landscape structure agricultural practices over 33 years. Over years, region underwent major changes, including...
Quantum Molecular Dynamics (QMD) calculations of central collisions between heavy nuclei are used to study fragment production and the creation collective flow. It is shown that final phase space distributions compatible with expectations from a thermally equilibrated source, which in addition exhibits transverse expansion. However, microscopic analyses transient states intermediate reaction stages show event shapes more complex equilibrium reached only very special cases but not samples...