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Cell lists (also sometimes referred to as cell linked-lists) is a data structure in molecular dynamics simulations to find all atom pairs within a given cut-off distance of each other. These pairs are needed to compute the short-range non-bonded interactions in a system, such as Van der Waals forces or the short-range part of the electrostatic ...
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MATLAB (an abbreviation of "MATrix LABoratory" [22]) is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks.MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.
Both binaries and source code are available for SageMath from the download page. If SageMath is built from source code, many of the included libraries such as OpenBLAS, FLINT, GAP (computer algebra system), and NTL will be tuned and optimized for that computer, taking into account the number of processors, the size of their caches, whether there is hardware support for SSE instructions, etc.
Octave programs consist of a list of function calls or a script. The syntax is matrix-based and provides various functions for matrix operations. It supports various data structures and allows object-oriented programming. [26] Its syntax is very similar to MATLAB, and careful programming of a script will allow it to run on both Octave and ...
A model consists of the equations used to capture the behavior of a system. By contrast, computer simulation is the actual running of the program that perform algorithms which solve those equations, often in an approximate manner.
It supports DIA-based profiling of PTMs, such as phosphorylation and ubiquitination, new technologies such as Scanning SWATH [36] and dia-PASEF, [37] and can perform library-free analyses (acts as a database search engine). [38] FlashLFQ Open source: FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. [39]
A Verlet list (named after Loup Verlet) is a data structure in molecular dynamics simulations to efficiently maintain a list of all particles within a given cut-off distance of each other. [1] This method may easily be applied to Monte Carlo simulations. For short-range interactions, a cut-off radius is typically used, beyond which particle ...