There are many different areas of research and technology where MBN Explorer can be applied. These areas are briefly introduced below, and the key themes, subfields and representative case studies in each area are outlined. This brief description is not exhaustive and can be extended to other topics.

Crystals, liquids, gases, and plasmas
- Crystalline structures
- Liquids and soft matter
- Gaseous systems and plasmas
- Thermodynamics and kinetics of matter
- Extreme states of matter
- Characterisation of different states of matter
- Multiscale phenomena

Molecules, atomic and molecular clusters, nanoparticles
- Molecules
- Atomic clusters
- Molecular clusters
- Finite nanosystems: fullerenes, endohedral atoms, nanoparticles, coated and functionalised nanoparticles, etc.
- Structure and dynamics of clusters and nanosystems
- Clusters and nanoparticles deposited on surfaces and embedded in the environment

Biomolecular systems
- Structure of biomolecules and macromolecules
- Biomolecular complexes and biosystems
- Bio-nano systems
- Dynamics of DNA, RNA, proteins, etc.
- Structural, chemical and radiation-induced transformations, biomolecular processes
- Multiscale modelling of the above-mentioned systems

Materials and their interfaces
- Structure of materials and their interfaces
- Elastic and plastic deformations
- Defects and dislocations
- Phase, structural, chemical and radiation-induced transformations
- Materials at extreme conditions
- Thermo-mechanical properties
- Tribological properties of interacting surfaces: nanoindentation, scratching, wear, lubrication, etc.
- Functional surface coatings

Nanostructured materials
- Metallic, (in)organic, composite nanomaterials
- Crystalline superlattices
- Nanotubes, nanowires, nanofractals, nanofilms, graphene, functional nanoparticles, etc.
- Nanoscale chemical, phase, structural and irradiation-driven transformations
- Self-assembly and growth
- Irradiation-driven nanofabrication

Chemical research
- Molecular association, dissociation, chemical reactions
- Fission, fusion, and fragmentation processes
- Thermodynamics and chemical kinetics
- Soft matter chemistry
- Vapour deposition processes and surface chemistry
- Collision-induced chemical transformations
- Chemistry in exotic conditions and environments
- Multiscale modelling in chemical research

Radiation research
- Interaction of radiation with MBN systems
- Propagation of charged particles (including relativistic particles) through a medium and Photon emission processes
- Collision-induced medium effects
- Radiation damage to materials
- Irradiation-induced chemistry
- Radiobiological effects
- Radiation-driven nanofabrication
- Multiscale modelling in radiation research

Multiscale phenomena
- Biomolecular systems
- Nanostructured materials
- Materials and their interfaces
- Chemical research
- Radiation research
- Technological and medical applications

Technology and medicine
- Nanotechnologies
- Bio and chemical technologies
- Material technologies
- Radiation technologies
- Plasma technologies
- Space technologies
- Medicine