Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Numerical methods for ordinary differential equationsNumerical methods for ordinary differential equations are methods used to find numerical approximations to the solutions of ordinary differential equations (ODEs). Their use is also known as "numerical integration", although this term can also refer to the computation of integrals. Many differential equations cannot be solved exactly. For practical purposes, however – such as in engineering – a numeric approximation to the solution is often sufficient. The algorithms studied here can be used to compute such an approximation.
Project JupyterProject Jupyter (ˈdʒuːpɪtər) is a project to develop open-source software, open standards, and services for interactive computing across multiple programming languages. It was spun off from IPython in 2014 by Fernando Pérez and Brian Granger. Project Jupyter's name is a reference to the three core programming languages supported by Jupyter, which are Julia, Python and R. Its name and logo are an homage to Galileo's discovery of the moons of Jupiter, as documented in notebooks attributed to Galileo.
TemperatureTemperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied on various reference points and thermometric substances for definition. The most common scales are the Celsius scale with the unit symbol °C (formerly called centigrade), the Fahrenheit scale (°F), and the Kelvin scale (K), the latter being used predominantly for scientific purposes.
IPythonIPython (Interactive Python) is a command shell for interactive computing in multiple programming languages, originally developed for the Python programming language, that offers introspection, rich media, shell syntax, tab completion, and history. IPython provides the following features: Interactive shells (terminal and Qt-based). A browser-based notebook interface with support for code, text, mathematical expressions, inline plots and other media. Support for interactive data visualization and use of GUI toolkits.
Euler methodIn mathematics and computational science, the Euler method (also called the forward Euler method) is a first-order numerical procedure for solving ordinary differential equations (ODEs) with a given initial value. It is the most basic explicit method for numerical integration of ordinary differential equations and is the simplest Runge–Kutta method. The Euler method is named after Leonhard Euler, who first proposed it in his book Institutionum calculi integralis (published 1768–1870).
Notebook interfaceA notebook interface or computational notebook is a virtual notebook environment used for literate programming, a method of writing computer programs. Some notebooks are WYSIWYG environments including executable calculations embedded in formatted documents; others separate calculations and text into separate sections. Notebooks share some goals and features with spreadsheets and word processors but go beyond their limited data models. Modular notebooks may connect to a variety of computational back ends, called "kernels".
CythonCython (ˈsaɪθɒn) is a superset of the programming language Python, which allows developers to write Python code (with optional, C-inspired syntax extensions) that yields performance comparable to that of C. Cython is a compiled language that is typically used to generate CPython extension modules. Annotated Python-like code is compiled to C (also usable from e.g. C++) and then automatically wrapped in interface code, producing extension modules that can be loaded and used by regular Python code using the import statement, but with significantly less computational overhead at run time.
Verlet integrationVerlet integration (vɛʁˈlɛ) is a numerical method used to integrate Newton's equations of motion. It is frequently used to calculate trajectories of particles in molecular dynamics simulations and computer graphics. The algorithm was first used in 1791 by Jean Baptiste Delambre and has been rediscovered many times since then, most recently by Loup Verlet in the 1960s for use in molecular dynamics. It was also used by P. H. Cowell and A. C. C.
Numerical analysisNumerical analysis is the study of algorithms that use numerical approximation (as opposed to symbolic manipulations) for the problems of mathematical analysis (as distinguished from discrete mathematics). It is the study of numerical methods that attempt at finding approximate solutions of problems rather than the exact ones. Numerical analysis finds application in all fields of engineering and the physical sciences, and in the 21st century also the life and social sciences, medicine, business and even the arts.
Symplectic integratorIn mathematics, a symplectic integrator (SI) is a numerical integration scheme for Hamiltonian systems. Symplectic integrators form the subclass of geometric integrators which, by definition, are canonical transformations. They are widely used in nonlinear dynamics, molecular dynamics, discrete element methods, accelerator physics, plasma physics, quantum physics, and celestial mechanics. Symplectic integrators are designed for the numerical solution of Hamilton's equations, which read where denotes the position coordinates, the momentum coordinates, and is the Hamiltonian.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Kinetic energyIn physics, the kinetic energy of an object is the form of energy that it possesses due to its motion. It is defined as the work needed to accelerate a body of a given mass from rest to its stated velocity. Having gained this energy during its acceleration, the body maintains this kinetic energy unless its speed changes. The same amount of work is done by the body when decelerating from its current speed to a state of rest.
Numerical methods for partial differential equationsNumerical methods for partial differential equations is the branch of numerical analysis that studies the numerical solution of partial differential equations (PDEs). In principle, specialized methods for hyperbolic, parabolic or elliptic partial differential equations exist. Finite difference method In this method, functions are represented by their values at certain grid points and derivatives are approximated through differences in these values.
Numerical integrationIn analysis, numerical integration comprises a broad family of algorithms for calculating the numerical value of a definite integral, and by extension, the term is also sometimes used to describe the numerical solution of differential equations. This article focuses on calculation of definite integrals. The term numerical quadrature (often abbreviated to quadrature) is more or less a synonym for numerical integration, especially as applied to one-dimensional integrals.
Numerical stabilityIn the mathematical subfield of numerical analysis, numerical stability is a generally desirable property of numerical algorithms. The precise definition of stability depends on the context. One is numerical linear algebra and the other is algorithms for solving ordinary and partial differential equations by discrete approximation. In numerical linear algebra, the principal concern is instabilities caused by proximity to singularities of various kinds, such as very small or nearly colliding eigenvalues.
Numerical methods for linear least squaresNumerical methods for linear least squares entails the numerical analysis of linear least squares problems. A general approach to the least squares problem can be described as follows. Suppose that we can find an n by m matrix S such that XS is an orthogonal projection onto the image of X. Then a solution to our minimization problem is given by simply because is exactly a sought for orthogonal projection of onto an image of X (see the picture below and note that as explained in the next section the image of X is just a subspace generated by column vectors of X).
Statistical mechanicsIn physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. It does not assume or postulate any natural laws, but explains the macroscopic behavior of nature from the behavior of such ensembles. Sometimes called statistical physics or statistical thermodynamics, its applications include many problems in the fields of physics, biology, chemistry, and neuroscience.
R (programming language)R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. The core R language is augmented by a large number of extension packages containing reusable code and documentation. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages in data mining.
Projectile motionProjectile motion is a form of motion experienced by an object or particle (a projectile) that is projected in a gravitational field, such as from Earth's surface, and moves along a curved path under the action of gravity only. In the particular case of projectile motion on Earth, most calculations assume the effects of air resistance are passive and negligible. The curved path of objects in projectile motion was shown by Galileo to be a parabola, but may also be a straight line in the special case when it is thrown directly upward or downward.
