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A Context-Aware Cutting Plane Selection Algorithm for Mixed-Integer Programming
No full textThe current cut selection algorithm used in mixed-integer programming solvers has remained largely unchanged since its creation. In this paper, we propose a set of new cut scoring measures, cut filtering techniques, and stopping criteria, extending the current state-of-the-art algorithm and obtaining a 5\% performance improvement for SCIP over the MIPLIB 2017 benchmark set
Explicit modeling of antibody levels for infectious disease simulations in the context of SARS-CoV-2
No full textMeasurable levels of immunoglobulin G antibodies develop after infections with and vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These antibody levels are dynamic: due to waning, antibody levels will drop over time. During the COVID-19 pandemic, multiple models predicting infection dynamics were used by policymakers to support the planning of public health policies. Explicitly integrating antibody and waning effects into the models is crucial for reliable calculations of individual infection risk. However, only few approaches have been suggested that explicitly treat these effects. This paper presents a methodology that explicitly models antibody levels and the resulting protection against infection for individuals within an agent-based model. The model was developed in response to the complexity of different immunization sequences and types and is based on neutralization titer studies. This approach allows complex population studies with explicit antibody and waning effects. We demonstrate the usefulness of our model in two use cases
Gaining Cross-Platform Parallelism for HAL’s Molecular Dynamics Package using SYCL
No full textMolecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of HAL’s MD package that has been successfully migrated from CUDA to SYCL. We describe the different strategies that we followed in the process of porting the code. Following these strategies, we achieved code portability across major GPU vendors. Depending on the actual kernels, both significant performance improvements and regressions are observed. As a side effect of the migration process, we obtained impressing speedups also for execution on CPUs
Introducing TimPassLib – A Library for Integrated Periodic Timetabling and Passenger Routing
No full textClassic models to derive a timetable for public transport often face a chicken-and-egg situation: A good timetable should offer passengers routes with small travel times, but the route choice of passengers depends on the timetable. While models that fix passenger routes were frequently considered in the literature, integrated models that simultaneously optimize timetables and passenger routes have seen increasing attention lately. This creates a growing need for a set of instances that allows to test and compare new algorithmic developments for the integrated problem. Our paper addresses this requirement by presenting TimPassLib, a new benchmark library of instances for integrated periodic timetabling and passenger routing
Modeling the transition of the multimodal pan-European energy system including an integrated analysis of electricity and gas transport
No full textMost recently, the European energy system has undergone a fundamental transformation to meet decarbonization targets without compromising the security of the energy supply. The transition involves several energy-generating and consuming sectors emphasizing sector coupling. The increase in the share of renewable energy sources has revealed the need for flexibility in supporting the electricity grid to cope with the resulting high degree of uncertainty. The new technologies accompanying the energy system transition and the recent political crisis in Europe threatening the security of the energy supply have invalidated the experience from the past by drastically changing the conventional scenarios. Hence, supporting strategic planning tools with detailed operational energy network models with appropriate mathematical precision has become more important than ever to understand the impacts of these disruptive changes. In this paper, we propose a workflow to investigate optimal energy transition pathways considering sector coupling. This workflow involves an integrated operational analysis of the electricity market, its transmission grid, and the gas grid in high spatio-temporal resolution. Thus, the workflow enables decision-makers to evaluate the reliability of high-level models even in case of disruptive events. We demonstrate the capabilities of the proposed workflow using results from a pan-European case study. The case study, spanning 2020-2050, illustrates that feasible potential pathways to carbon neutrality are heavily influenced by political and technological constraints. Through integrated operational analysis, we identify scenarios where strategic decisions become costly or infeasible given the existing electricity and gas networks
Machine learning coarse-grained potentials of protein thermodynamics
No full textA generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics
Continuity of Microscopic Cardiac Conduction in a Computational Cell-by-Cell Model
No full textConduction velocity in cardiac tissue is a crucial electrophysiological parameter for arrhythmia vulnerability. Pathologically reduced conduction velocity facilitates arrhythmogenesis because such conduction velocities decrease the wavelength with which re-entry may occur. Computational studies on CV and how it changes regionally in models at spatial scales multiple times larger than actual cardiac cells exist. However, microscopic conduction within cells and between them have been studied less in simulations. In this work, we study the relation of microscopic conduction patterns and clinically observable macroscopic conduction using an extracellular-membrane-intracellular model which represents cardiac tissue with these subdomains at subcellular resolution. By considering cell arrangement and non-uniform gap junction distribution, it yields anisotropic excitation propagation. This novel kind of model can for example be used to understand how discontinuous conduction on the microscopic level affects fractionation of electrograms in healthy and fibrotic tissue. Along the membrane of a cell, we observed a continuously propagating activation wavefront. When transitioning from one cell to the neighbouring one, jumps in local activation times occurred, which led to lower global conduction velocities than locally within each cell