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A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes \textit{extracellular} process elements such as the bioreactor design and mode of operation,…
Petri-nets are a simple formalism for modeling concurrent computation. Recently, they have emerged as a powerful tool for the modeling and analysis of biochemical reaction networks, bridging the gap between purely qualitative and…
Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
Most neural-operator surrogates for PDEs inherit from DeepONet-style formulations the requirement that the input function be sampled at a fixed, ordered set of sensors. This assumption limits applicability to problems with variable sensor…
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…
Nested Petri nets have been applied for modeling interaction protocols, mobility, adaptive systems and interorganizational workflows. However, few results have been reported on the use of automated tools for analyzing the behavior of these…
Recent developments in next generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical…
Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately…
Protein-protein interaction networks provide a graph-level view of cellular organization, yet their functional modules are overlapping, noisy, and difficult to interpret from cluster assignments alone. Existing community-detection methods…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
Petri nets are a well-known model of concurrency and provide an ideal setting for the study of fundamental aspects in concurrent systems. Despite their simplicity, they still lack a satisfactory causally reversible semantics. We develop…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present…
Maintaining an acceptable level of quality of service in modern complex systems is challenging, particularly in the presence of various forms of uncertainty caused by changing execution context, unpredicted events, etc. Although…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular…