computer science

MBN Explorer

MBN Explorer is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand MBN Explorer rather than just read about it. In short: MBN Explorer (MesoBioNano Explorer) is a software package for molecular dynamics simulations, structure optimization and kinetic Monte Carlo simulations. It is designed for multiscale computational analysis of structure and dynamics of atomic clusters and nanoparticles, biomolecules and nanosystems, nanostructured materials, different states of matter and various interfaces.

Key takeaways

MBN Explorer belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect MBN Explorer to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of MBN Explorer from memory before moving on to harder problems.

Reference excerpt

MBN Explorer (MesoBioNano Explorer) is a software package for molecular dynamics simulations, structure optimization and kinetic Monte Carlo simulations. It is designed for multiscale computational analysis of structure and dynamics of atomic clusters and nanoparticles, biomolecules and nanosystems, nanostructured materials, different states of matter and various interfaces. The software has been developed by MBN Research Center.

History MBN Explorer inherited the experience obtained on the development of the software package Cluster Searcher. It started around 2000 as a classical molecular dynamics code for simulating many-body systems interacting via the Morse and the Lennard-Jones potentials. A variety of interatomic potentials and the possibility to combine a group of atoms into rigid blocks were introduced in 2005–2007. The first version of MBN Explorer was released in 2012 as a multipurpose computer code allowing to model different molecular systems of varied level of complexity.

Features MBN Explorer allows for the multiscale description of molecular systems by means of kinetic Monte Carlo approach and the irradiation-driven molecular dynamics. By means of the Monte Carlo approach, the software allows to simulate diffusion-drive processes involving molecular systems on much larger time scales that can be reached in conventional molecular dynamics simulations. The software allows to combine different types of interatomic potentials to specify more than one interaction to a particular atom or a group of atoms. MBN Explorer supports several standard atomic trajectory formats, such as XYZ (text format), DCD (binary format) and DCD+XYZ (hybrid format). It also supports the Protein Data Bank (pdb) file format for describing the three-dimensional structures of biomolecules. Advanced features of the program include:

flexible coarse graining and the possibility to simulate dynamics of rigid bodies, the possibility to perform relativistic molecular dynamics simulations of ultra-relativistic particles in crystalline media, simulation of irradiation-induced chemical transformations by means of irradiation-driven molecular dynamics.

MBN Studio MBN Explorer is complemented with MBN Studio - a multi-task program for molecular modeling and design, as well as for visualization and analysis of results of the simulations performed with MBN Explorer. The built-in molecular modeler can be used to construct isolated and solvated biomolecules, condensed molecular materials, carbon nanotubes and graphene sheets, nanoparticles and crystalline samples.

Projects and collaborations MBN Explorer has been utilized in different research projects in the fields of materials science, nanotechnology and radiation damage:

ARGENT - Advanced Radiotherapy, Generated by Exploiting Nanoprocesses and TechnologiesThis is a multidisciplinary network project involving different research groups, academic and industrial partners. It is financed by the Seventh Framework Programme (FP7) of the EU. PEARL - Periodically Bent Crystals for Crystalline UndulatorsThis is an international project supported by the Horizon 2020 Programme (H2020) of the EU. Nano-IBCT - Nanoscale Insights into Ion-Beam Cancer Therapy VINAT - Theoretical analysis, design and virtual testing of biocompatibility and mechanical properties of titanium-based nanomaterials

See also Comparison of software for molecular mechanics modeling List of software for nanostructures modeling NAMD GROMACS LAMMPS

References

External links MBN Research Center website

Worked examples

Example 1 — a first encounter with MBN Explorer

Start with the simplest possible case. Write down what MBN Explorer claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to MBN Explorer before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about MBN Explorer ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of MBN Explorer

In research: MBN Explorer appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses MBN Explorer in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: MBN Explorer is common in secondary-school and first-year university syllabi. It links to neighbouring topics Computational chemistry, Molecular dynamics software, Molecular modelling software, so understanding it makes those chapters shorter.
In everyday life: Look for MBN Explorer outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study MBN Explorer in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what MBN Explorer means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain MBN Explorer out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is MBN Explorer in simple terms?

Why does MBN Explorer matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study MBN Explorer?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on MBN Explorer.