The 10 most recently published documents
The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem.
Existing planning approaches for onshore wind farm siting and grid integration often do not meet minimum cost solutions or social and environmental considerations. In this paper, we develop an exact approach for the integrated layout and cable routing problem of onshore wind farm planning using the Quota Steiner tree problem. Applying a novel transformation on a known directed cut formulation, reduction techniques, and heuristics, we design an exact solver that makes large problem instances solvable and outperforms generic MIP solvers. In selected regions of Germany, the trade-offs between minimizing costs and landscape impact of onshore wind farm siting are investigated. Although our case studies show large trade-offs between the objective criteria of cost and landscape impact, small burdens on one criterion can significantly improve the other criteria. In addition, we demonstrate that contrary to many approaches for exclusive turbine siting, grid integration must be simultaneously optimized to avoid excessive costs or landscape impacts in the course of a wind farm project. Our novel problem formulation and the developed solver can assist planners in decision-making and help optimize wind farms in large regions in the future.
AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor
(2024)
Protein–protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.
We present a heuristic solution approach for the rolling stock rotation problem with predictive maintenance (RSRP-PdM). The task of this problem is to assign a sequence of trips to each of the vehicles and to schedule their maintenance such that all trips can be operated. Here, the health states of the vehicles are considered to be random variables distributed by a family of probability distribution functions, and the maintenance services should be scheduled based on the failure probability of the vehicles. The proposed algorithm first generates a solution by solving an integer linear program and then heuristically improves this solution by applying a local search procedure. For this purpose, the trips assigned to the vehicles are split up and recombined, whereby additional deadhead trips can be inserted between the partial assignments. Subsequently, the maintenance is scheduled by solving a shortest path problem in a state-expanded version of a space-time graph restricted to the trips of the individual vehicles. The solution approach is tested and evaluated on a set of test instances based on real-world timetables.
An Iterative Refinement Approach for the Rolling Stock Rotation Problem with Predictive Maintenance
(2024)
The rolling stock rotation problem with predictive maintenance (RSRP-PdM) involves the assignment of trips to a fleet of vehicles with integrated maintenance scheduling based on the predicted failure probability of the vehicles. These probabilities are determined by the health states of the vehicles, which are considered to be random variables distributed by a parameterized family of probability distribution functions. During the operation of the trips, the corresponding parameters get updated. In this article, we present a dual solution approach for RSRP-PdM and generalize a linear programming based lower bound for this problem to families of probability distribution functions with more than one parameter. For this purpose, we define a rounding function that allows for a consistent underestimation of the parameters and model the problem by a state-expanded event-graph in which the possible states are restricted to a discrete set. This induces a flow problem that is solved by an integer linear program. We show that the iterative refinement of the underlying discretization leads to solutions that converge from below to an optimal solution of the original instance. Thus, the linear relaxation of the considered integer linear program results in a lower bound for RSRP-PdM. Finally, we report on the results of computational experiments conducted on a library of test instances.