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Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…
The recent decades have seen various attempts at accelerating the process of developing materials targeted towards specific applications. The performance required for a particular application leads to the choice of a particular material…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
The metabolism of an organism is regulated at the cellular level, yet is strongly influenced by its environment. The precise metabolomic study of living organisms is currently hampered by measurement sensitivity: most metabolomic…
Large-Scale Multi-Agent Systems (LS-MAS) consist of several autonomous components, interacting in a non-trivial way, so that the emerging behaviour of the ensemble depends on the individual dynamics of the components and their reciprocal…
Simulation is a well established what-if scenario analysis tool in Operational Research (OR). While traditionally Discrete Event Simulation (DES) and System Dynamics Simulation (SDS) are the predominant simulation techniques in OR, a new…
This volume contains the proceedings of MARS 2024, the sixth workshop on Models for Formal Analysis of Real Systems, held as part of ETAPS 2024, the European Joint Conferences on Theory and Practice of Software. The MARS workshops bring…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
In our current era, numerical simulations have become indispensable theoretical and experimental tools for use in daily research activities, particularly in the materials science fields. However, the installation processes for such…
As recommendation systems become increasingly standard for online platforms, simulations provide an avenue for understanding the impacts of these systems on individuals and society. When constructing a recommendation system simulation,…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The design and analysis of systems that combine computational behaviour with physical processes' continuous dynamics - such as movement, velocity, and voltage - is a famous, challenging task. Several theoretical results from programming…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
Machine learning (ML) components are being added to more and more critical and impactful software systems, but the software development process of real-world production systems from prototyped ML models remains challenging with additional…