Computational science

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Not to be confused with computer science.

Computational science (also scientific computing or scientific computation (SC)) is a rapidly

growing multidisciplinary field that uses advanced computing capabilities to understand and
solve complex problems. It is an area of science which spans many disciplines, but at its core it
involves the development of models and simulations to understand natural systems.

 Algorithms (numerical and non-numerical): mathematical models, computational models,

and computer simulations developed to solve science (e.g., biological, physical, and
social), engineering, and humanities problems
 Computer and information science that develops and optimizes the advanced system
hardware, software, networking, and data management components needed to solve
computationally demanding problems
 The computing infrastructure that supports both the science and engineering problem
solving and the developmental computer and information science

In practical use, it is typically the application of computer simulation and other forms of
computation from numerical analysis and theoretical computer science to solve problems in
various scientific disciplines. The field is different from theory and laboratory experiment which
are the traditional forms of science and engineering. The scientific computing approach is to gain
understanding, mainly through the analysis of mathematical models implemented on computers.
Scientists and engineers develop computer programs, application software, that model systems
being studied and run these programs with various sets of input parameters. The essence of
computational science is the application of numerical algorithms[1] and/or computational
mathematics. In some cases, these models require massive amounts of calculations (usually
floating-point) and are often executed on supercomputers or distributed computing platforms.
Actually the science which deals with the Computer Modeling and Simulation of any physical
objects and phenomena by high programming language and software and hardware is known as
Computer Simulation.

Contents
 1 The computational scientist
 2 Applications of computational science
o 2.1 Urban complex systems
o 2.2 Computational finance
o 2.3 Computational biology
o 2.4 Complex systems theory
o 2.5 Computational science in engineering
  3 Methods and algorithms
 4 Conferences and journals
 5 Education
 6 Related fields
 7 See also
 8 References
 9 Additional sources
 10 External links

The computational scientist

Ways to study a system

The term computational scientist is used to describe someone skilled in scientific computing.
This person is usually a scientist, an engineer or an applied mathematician who applies high-
performance computing in different ways to advance the state-of-the-art in their respective
applied disciplines in physics, chemistry or engineering.

Computational science is now commonly considered a third mode of science, complementing

and adding to experimentation/observation and theory (see image on the right).[2] Here, we
define a system as a potential source of data,[3] an experiment as a process of extracting data
from a system by exerting it through its inputs[4] and a model (M) for a system (S) and an
experiment (E) as anything to which E can be applied in order to answer questions about S.[5] A
computational scientist should be capable of:

 recognizing complex problems

 adequately conceptualise the system containing these problems
 design a framework of algorithms suitable for studying this system: the simulation
 choose a suitable computing infrastructure (parallel computing/grid
computing/supercomputers)
 hereby, maximizing the computational power of the simulation
 assessing to what level the output of the simulation resembles the systems: the model is
validated
 adjust the conceptualization of the system accordingly
 repeat cycle until a suitable level of validation is obtained: the computational scientists
trusts that the simulation generates adequately realistic results for the system, under the
studied conditions
In fact, substantial effort in computational sciences has been devoted to the development of
algorithms, the efficient implementation in programming languages, and validation of
computational results. A collection of problems and solutions in computational science can be
found in Steeb, Hardy, Hardy and Stoop (2004).[6]

Philosophers of science addressed the question to what degree computational science qualifies as
science, among them Humphreys[7] and Gelfert.[8] They address the general question of
epistemology: how do we gain insight from such computational science approaches. Tolk[9] uses
these insights to show the epistemological constraints of computer-based simulation research. As
computational science uses mathematical models representing the underlying theory in
executable form, in essence they apply modeling (theory building) and simulation
(implementation and execution). While simulation and computational science are our most
sophisticated way to express our knowledge and understanding, they also come with all
constraints and limits already known for computational solutions.

Applications of computational science

Problem domains for computational science/scientific computing include:

Urban complex systems

In 2015, over half the world’s population live in cities. By the middle of the 21st century, it is
estimated that 75% of the world's population will be urban. This urban growth is focused in the
urban populations of developing countries where cities dwellers will more than double,
increasing from 2.5 billion in 2009 to almost 5.2 billion in 2050. Cities are massive complex
systems created by humans, made up of humans and governed by humans. Trying to predict,
understand and somehow shape the development of cities in the future requires complex
thinking, and requires computational models and simulations to help mitigate challenges and
possible disasters. The focus of research in urban complex systems is, through modelling and
simulation, to build greater understanding of city dynamics and help prepare for the coming
urbanisation.

Computational finance

Main article: Computational finance

In today's financial markets huge volumes of interdependent assets are traded by a large number
of interacting market participants in different locations and time zones. Their behavior is of
unprecedented complexity and the characterization and measurement of the risk inherent to these
highly diverse set of instruments is typically based on complicated mathematical and
computational models. Solving these models exactly in closed form, even at a single instrument
level, is typically not possible, and therefore we have to look for efficient numerical algorithms.
This has become even more urgent and complex recently, as the credit crisis has clearly
demonstrated the role of cascading effects going from single instruments through portfolios of
single institutions to even the interconnected trading network. Understanding this requires a
multi-scale and holistic approach where interdependent risk factors such as market, credit and
liquidity risk are modelled simultaneously and at different interconnected scales.

Computational biology

Main article: Computational biology

Exciting new developments in biotechnology are now revolutionizing biology and biomedical
research. Examples of these techniques are high-throughput sequencing, high-throughput
quantitative PCR, intra-cellular imaging, in-situ hybridization of gene expression, three-
dimensional imaging techniques like Light Sheet Fluorescence Microscopy and Optical
Projection, (micro)-Computer Tomography. Given the massive amounts of complicated data that
is generated by these techniques, their meaningful interpretation, and even their storage, form
major challenges calling for new approaches. Going beyond current bioinformatics approaches,
computational biology needs to develop new methods to discover meaningful patterns in these
large data sets. Model-based reconstruction of gene networks can be used to organize the gene
expression data in systematic way and to guide future data collection. A major challenge here is
to understand how gene regulation is controlling fundamental biological processes like
biomineralisation and embryogenesis. The sub-processes like gene regulation, organic molecules
interacting with the mineral deposition process, cellular processes, physiology and other
processes at the tissue and environmental levels are linked. Rather than being directed by a
central control mechanism, biomineralisation and embryogenesis can be viewed as an emergent
behavior resulting from a complex system in which several sub-processes on very different
temporal and spatial scales (ranging from nanometer and nanoseconds to meters and years) are
connected into a multi-scale system. One of the few available options to understand such systems
is by developing a multi-scale model of the system.

Complex systems theory

Main article: Complex systems

Using information theory, non-equilibrium dynamics and explicit simulations computational

systems theory tries to uncover the true nature of complex adaptive systems.

Computational science in engineering

Main article: Computational engineering

Computational science and engineering (CSE) is a relatively new discipline that deals with the
development and application of computational models and simulations, often coupled with high-
performance computing, to solve complex physical problems arising in engineering analysis and
design (computational engineering) as well as natural phenomena (computational science). CSE
has been described as the "third mode of discovery" (next to theory and experimentation).[10] In
many fields, computer simulation is integral and therefore essential to business and research.
Computer simulation provides the capability to enter fields that are either inaccessible to
traditional experimentation or where carrying out traditional empirical inquiries is prohibitively
expensive. CSE should neither be confused with pure computer science, nor with computer
engineering, although a wide domain in the former is used in CSE (e.g., certain algorithms, data
structures, parallel programming, high performance computing) and some problems in the latter
can be modeled and solved with CSE methods (as an application area).

Methods and algorithms

Algorithms and mathematical methods used in computational science are varied. Commonly
applied methods include:

 Computer algebra, including symbolic computation in fields such as statistics, equation

solving, algebra, calculus, geometry, linear algebra, tensor analysis (multi-linear algebra),
optimization
 Numerical analysis, including Computing derivatives by finite differences
o Application of Taylor series as convergent and asymptotic series
o Computing derivatives by Automatic differentiation (AD)
o Finite element method for solving PDEs
o High order difference approximations via Taylor series and Richardson
extrapolation
o Methods of integration on a uniform mesh: rectangle rule (also called midpoint
rule), trapezoid rule, Simpson's rule
o Runge–Kutta methods for solving ordinary differential equations
o Newton's method
 Discrete Fourier transform
 Monte Carlo methods
 Numerical linear algebra, including decompositions
 Linear programming
 Branch and cut
 Branch and bound
 Molecular dynamics, Car–Parrinello molecular dynamics
 Space mapping
 Time stepping methods for dynamical systems

Both historically and today, Fortran remains popular for most applications of scientific
computing.[11][12] Other programming languages and computer algebra systems commonly used
for the more mathematical aspects of scientific computing applications include GNU Octave,
Haskell,[11] Julia,[11] Maple,[12] Mathematica,[13] MATLAB, Python (with third-party SciPy
library), Perl (with third-party PDL library),[citation needed] R, Scilab, and TK Solver. The more
computationally intensive aspects of scientific computing will often use some variation of C or
Fortran and optimized algebra libraries such as BLAS or LAPACK.

Computational science application programs often model real-world changing conditions, such
as weather, air flow around a plane, automobile body distortions in a crash, the motion of stars in
a galaxy, an explosive device, etc. Such programs might create a 'logical mesh' in computer
memory where each item corresponds to an area in space and contains information about that
space relevant to the model. For example, in weather models, each item might be a square
kilometer; with land elevation, current wind direction, humidity, temperature, pressure, etc. The
program would calculate the likely next state based on the current state, in simulated time steps,
solving equations that describe how the system operates; and then repeat the process to calculate
the next state.

Conferences and journals

In the year 2001, the International Conference on Computational Science (ICCS) was first
organized. Since then it has been organized yearly. ICCS is an A-rank conference in CORE
classification.

The international Journal of Computational Science published its first issue in May
2010.[14][15][16] A new initiative was launched in 2012, the Journal of Open Research Software.[17]
In 2015, ReScience[18] dedicated to the replication of computational results has been started on
GitHub.

Education
At some institutions a specialization in scientific computation can be earned as a "minor" within
another program (which may be at varying levels). However, there are increasingly many
bachelor's, master's and doctoral programs in computational science. The joint degree
programme master program computational science at the University of Amsterdam and the Vrije
Universiteit in computational science was first offered in 2004. In this programme, students:

 learn to build computational models from real-life observations;

 develop skills in turning these models into computational structures and in performing
large-scale simulations;
 learn theory that will give a firm basis for the analysis of complex systems;
 learn to analyze the results of simulations in a virtual laboratory using advanced
numerical algorithms.

George Mason University was one of the early pioneers first offering a multidisciplinary
doctorate Ph.D. program in Computational Sciences and Informatics in 1992 that focused on a
number of specialty areas including bioinformatics, computational chemistry, earth systems and
global changes, computational mathematics, computational physics, space sciences, and
computational statistics

Related fields
 Bioinformatics
 Car–Parrinello molecular dynamics
 Cheminformatics
 Chemometrics
 Computational archaeology
 Computational biology
  Computational chemistry
 Computational materials science
 Computational economics
 Computational electromagnetics
 Computational engineering
 Computational finance
 Computational fluid dynamics
 Computational forensics
 Computational geophysics
 Computational history
 Computational informatics
 Computational intelligence
 Computational law
 Computational linguistics
 Computational mathematics
 Computational mechanics
 Computational neuroscience
 Computational particle physics
 Computational physics
 Computational sociology
 Computational statistics
 Computational sustainability
 Computer algebra
 Computer simulation
 Financial modeling
 Geographic information system (GIS)
 High-performance computing
 Machine learning
 Network analysis
 Neuroinformatics
 Numerical linear algebra
 Numerical weather prediction
 Pattern recognition
 Scientific visualization
 Simulation

See also

 Science portal

 Mathematics portal

 Computer simulations in science

 Computational science and engineering
 Comparison of computer algebra systems
  List of molecular modeling software
 List of numerical analysis software
 List of statistical packages
 Timeline of scientific computing
 Simulated reality
 Extensions for Scientific Computation (XSC)

References
1.

 Nonweiler T. R., 1986. Computational Mathematics: An Introduction to Numerical

Approximation, John Wiley and Sons
  Graduate Education for Computational Science and Engineering.Siam.org, Society for
Industrial and Applied Mathematics (SIAM) website; accessed Feb 2013.
  Siegler, Bernard (1976). Theory of Modeling and Simulation.
  Cellier, François (1990). Continuous System Modelling.
  Minski, Marvin (1965). Models,Minds, Machines.
  Steeb W.-H., Hardy Y., Hardy A. and Stoop R., 2004. Problems and Solutions in Scientific
Computing with C++ and Java Simulations, World Scientific Publishing. ISBN 981-256-112-9
  Humphreys, Paul. Extending ourselves: Computational science, empiricism, and scientific
method. Oxford University Press, 2004.
  Gelfert, Axel. 2016. How to do science with models: A philosophical primer. Cham:
Springer.
  Tolk, Andreas. "Learning Something Right from Models That Are Wrong: Epistemology of
Simulation." In Concepts and Methodologies for Modeling and Simulation, edited by L. Yilmaz,
pp. 87-106, Cham: Springer International Publishing, 2015.
  "Computational Science and Engineering Program: Graduate Student Handbook" (PDF).
cseprograms.gatech.edu. September 2009. Archived from the original (PDF) on 2014-10-14.
Retrieved 2017-08-26.
  Phillips, Lee (2014-05-07). "Scientific computing's future: Can any coding language top a
1950s behemoth?". Ars Technica. Retrieved 2016-03-08.
  Landau, Rubin (2014-05-07). "A First Course in Scientific Computing" (PDF). Princeton
University. Retrieved 2016-03-08.
  Mathematica 6 Scientific Computing World, May 2007
  Sloot, Peter; Coveney, Peter; Dongarra, Jack (2010). "Redirecting". Journal of
Computational Science. 1 (1): 3–4. doi:10.1016/j.jocs.2010.04.003.
  Seidel, Edward; Wing, Jeannette M. (2010). "Redirecting". Journal of Computational
Science. 1 (1): 1–2. doi:10.1016/j.jocs.2010.04.004.
  Sloot, Peter M.A. (2010). "Computational science: A kaleidoscopic view into science".
Journal of Computational Science. 1 (4): 189. doi:10.1016/j.jocs.2010.11.001.
  The Journal of Open Research Software ; announced at software.ac.uk/blog/2012-03-23-
announcing-journal-open-research-software-software-metajournal
 18.  Rougier, Nicolas P.; Hinsen, Konrad; Alexandre, Frédéric; Arildsen, Thomas; Barba,
Lorena A.; Benureau, Fabien C.Y.; Brown, C. Titus; Buyl, Pierre de; Caglayan, Ozan;
Davison, Andrew P.; Delsuc, Marc-André; Detorakis, Georgios; Diem, Alexandra K.;
Drix, Damien; Enel, Pierre; Girard, Benoît; Guest, Olivia; Hall, Matt G.; Henriques,
Rafael N.; Hinaut, Xavier; Jaron, Kamil S.; Khamassi, Mehdi; Klein, Almar; Manninen,
Tiina; Marchesi, Pietro; McGlinn, Daniel; Metzner, Christoph; Petchey, Owen; Plesser,
Hans Ekkehard; Poisot, Timothée; Ram, Karthik; Ram, Yoav; Roesch, Etienne; Rossant,
Cyrille; Rostami, Vahid; Shifman, Aaron; Stachelek, Joseph; Stimberg, Marcel;
Stollmeier, Frank; Vaggi, Federico; Viejo, Guillaume; Vitay, Julien; Vostinar, Anya E.;
Yurchak, Roman; Zito, Tiziano (December 2017). "Sustainable computational science:
the ReScience initiative". PeerJ Comp Sci. 3. e142. arXiv:1707.04393.
doi:10.7717/peerj-cs.142.

Additional sources
 E. Gallopoulos and A. Sameh, "CSE: Content and Product". IEEE Computational
Science and Engineering Magazine, 4(2):39–43 (1997)
 G. Hager and G. Wellein, Introduction to High Performance Computing for Scientists
and Engineers, Chapman and Hall (2010)
 A.K. Hartmann, Practical Guide to Computer Simulations, World Scientific (2009)
 Journal Computational Methods in Science and Technology (open access), Polish
Academy of Sciences
 Journal Computational Science and Discovery, Institute of Physics
 R.H. Landau, C.C. Bordeianu, and M. Jose Paez, A Survey of Computational Physics:
Introductory Computational Science, Princeton University Press (2008)

External links

Wikiversity has learning resources about Scientific computing

Wikimedia Commons has media related to Computational science.

 John von Neumann-Institut for Computing (NIC) at Juelich (Germany)

 The National Center for Computational Science at Oak Ridge National Laboratory
 Center for Simulation and Modeling at George Mason University
 Educational Materials for Undergraduate Computational Studies
 Computational Science at the National Laboratories
 Bachelor in Computational Science, University of Medellin, Colombia, South America
 Simulation Optimization Systems (SOS) Research Laboratory, McMaster University,
Hamilton, ON
 Computational Sciences and Informatics, Ph.D Program, George Mason University