Browsing by Author "Stamm, Benjamin"

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Open Access
ddX : polarizable continuum solvation from small molecules to proteins
(2024) Nottoli, Michele; Herbst, Michael F.; Mikhalev, Aleksandr; Jha, Abhinav; Lipparini, Filippo; Stamm, Benjamin
Polarizable continuum solvation models are popular in both, quantum chemistry and in biophysics, though typically with different requirements for the numerical methods. However, the recent trend of multiscale modeling can be expected to blur field‐specific differences. In this regard, numerical methods based on domain decomposition (dd) have been demonstrated to be sufficiently flexible to be applied all across these levels of theory while remaining systematically accurate and efficient. In this contribution, we present ddX , an open‐source implementation of dd‐methods for various solvation models, which features a uniform interface with classical as well as quantum descriptions of the solute, or any hybrid versions thereof. We explain the key concepts of the library design and its application program interface, and demonstrate the use of ddX for integrating into standard chemistry packages. Numerical tests illustrate the performance of ddX and its interfaces. This article is categorized under: Software > Quantum Chemistry Software > Simulation Methods
Open Access
Molecular mechanics of disordered solids
(2023) Bamer, Franz; Ebrahem, Firaz; Markert, Bernd; Stamm, Benjamin
Disordered solids are ubiquitous in engineering and everyday use. Although research has made considerable progress in the last decades, our understanding of the mechanics of these materials is, at best, in an embryonic state. Since the nature of disorder complicates the realization of physically meaningful continuum-mechanical models, particle-based molecular descriptions provide a powerful alternative. This paper reviews the numerical realization of classical molecular dynamics from an engineer’s perspective, starting with selecting potential functions, boundary conditions, time integration, and thermodynamic ensembles. Then, we discuss the concept of the potential energy landscape and the computational realization of the most suitable minimization methods. Subsequently, we discuss the algorithms necessary to numerically generate disordered materials, considering their thermodynamic properties and structural identification. We comprehensively and critically review computational methods and strategies available to mimic disordered materials on a molecular level and discuss some intriguing phenomena that are, to date, mostly ignored when applying models based on continuum-mechanical frameworks. We present the crucial difference between the shear response of a crystalline and a disordered structure. In this context, we elaborate on why it is beneficial to use an overdamped, athermal description to disentangle the complex deformation mechanics of disordered solids and comprehensively discuss the theory of the mechanics of disordered materials, including the problems of prediction and reversibility. Furthermore, we examine the fracture process on the nanoscale and investigate the response behavior to more complex deformation protocols. Finally, we provide critical conclusions, including challenges and future perspectives for engineers.