Simulations are models of phenomena running on computers. According to "The 2020 Science" report ,
- "Computer science is poised to become as fundamental to biology as mathematics has become to physics."
Many types of simulations are used in modern design - aerodynamics, mechanical stress, electronics, radio wave propogation... almost everything can be simulated today. Perhaps the most complex simulations are of nuclear explosions and of planetary climate or weather.
- Computer games may contain simplified simulations, in the form of 'physics engines'. The 'ray tracing' in such games is also a form of simulation, a simulation of how light rays act.
- Simulations of molecular machines with thousands of atoms can be done with software such as NanoEngineer-1.
Simulating life is particularly important.
- Proteinomics aims to simulate the formation and activity of protein molecules on the atomic level. A ribosome was simulated in 2005 (2.6 mln atoms) .
- Scientists have managed to simulate with atomic precision the satellite tobacco mosaic virus (more than 1 million atoms).   (Rus)
- Powered with modern supercomputers scientists have embarked on a quest to simulate bacteria such as E-coli  in minute details.
- In a few decades it will become possible to make an accurate universal cell simulation that can run with arbitrary genome and gene markers. This models may be based on universal cell models for a species and then expanded to similar organisms.
- In the Blue Brain project   scientists aim to simulate the neocortical column, the building block of the human brain. Scientists have already simulated the activity of individual neurons as well as smaller neural networks. See also ArtificialHippocampus
- A group of neuroengineers at Stanford plan to use special-purpose hardware to perform real-time simulations of 1 million neurons 
These simulations will be quite detailed, often simulating the activity of individual molecules. Such models make it possible to better formulate the rules that govern the system on higher levels, making less detailed simulations almost as accurate.
Given progress so far, eventually it will be possible to produce a multi-level simulation of a human being, including a functional brain and a conscious human mind running on it. Transhumanists believe it will also be possible to perform an uploading of a biological human into such a simulation.
For atomic-level simulations data about real objects must be obtained using some form of microscopy. Currently, resolution in virus studies is about 1 nm. Detailed, but not accurate at atomic level, 3D models of viruses can be built after such scanning  .
Multi Level Simulation
- World Integrative Research Initiative BSMH realisation :
Researches of laboratory and clinical observations are accumulated and made accessible to all those who can use them to develop or to validate new hypotheses; it is necessary that the knowledge we have on a sub-system, a certain dimensional scale, or a certain biophysical aspect can be formalised and interconnected to others that are being developed on contiguous sub-systems, scales, domains. We call this new approach Integrative Biomedical Research.
- Virtual Physiological Human - about an integrated human model.
- Yearly check-up: 15-05-2017 - a vision of future human modelling tech applications.
- Integrative Biology - multi-level simulations
- An interesting multi-level simulation, albeit in a game is the game 'Spore' by the designer of SimCity.
Multi level simulations are also important in engineering. In simulating a new processor at the level of voltages and currents, it may be necessary to model the environment it is in at a thermal level, and a logic level, and maybe simulate some parts of the design taking account of statistical quantum effects.
- Social simulations, e.g. pandemic spread 
- Simulation of the whole UK population 
- Climate simulations
- Universe simulations 
- The Encyclopedia of Life is an unprecedented worldwide effort to document the 1.8 million known species of animals, plants and other organisms on the planet.