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.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Molecular mechanicsMolecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
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.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
SupercomputerA supercomputer is a computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second (FLOPS) instead of million instructions per second (MIPS). Since 2017, there have existed supercomputers which can perform over 1017 FLOPS (a hundred quadrillion FLOPS, 100 petaFLOPS or 100 PFLOPS). For comparison, a desktop computer has performance in the range of hundreds of gigaFLOPS (1011) to tens of teraFLOPS (1013).
Multi-core processorA multi-core processor is a microprocessor on a single integrated circuit with two or more separate processing units, called cores, each of which reads and executes program instructions. The instructions are ordinary CPU instructions (such as add, move data, and branch) but the single processor can run instructions on separate cores at the same time, increasing overall speed for programs that support multithreading or other parallel computing techniques.
Parallel computingParallel computing is a type of computation in which many calculations or processes are carried out simultaneously. Large problems can often be divided into smaller ones, which can then be solved at the same time. There are several different forms of parallel computing: bit-level, instruction-level, data, and task parallelism. Parallelism has long been employed in high-performance computing, but has gained broader interest due to the physical constraints preventing frequency scaling.
Communication protocolA communication protocol is a system of rules that allows two or more entities of a communications system to transmit information via any variation of a physical quantity. The protocol defines the rules, syntax, semantics, and synchronization of communication and possible error recovery methods. Protocols may be implemented by hardware, software, or a combination of both. Communicating systems use well-defined formats for exchanging various messages.
Application layerAn application layer is an abstraction layer that specifies the shared communications protocols and interface methods used by hosts in a communications network. An application layer abstraction is specified in both the Internet Protocol Suite (TCP/IP) and the OSI model. Although both models use the same term for their respective highest-level layer, the detailed definitions and purposes are different. In the Internet protocol suite, the application layer contains the communications protocols and interface methods used in process-to-process communications across an Internet Protocol (IP) computer network.
Vector processorIn computing, a vector processor or array processor is a central processing unit (CPU) that implements an instruction set where its instructions are designed to operate efficiently and effectively on large one-dimensional arrays of data called vectors. This is in contrast to scalar processors, whose instructions operate on single data items only, and in contrast to some of those same scalar processors having additional single instruction, multiple data (SIMD) or SWAR Arithmetic Units.
Transport layerIn computer networking, the transport layer is a conceptual division of methods in the layered architecture of protocols in the network stack in the Internet protocol suite and the OSI model. The protocols of this layer provide end-to-end communication services for applications. It provides services such as connection-oriented communication, reliability, flow control, and multiplexing. The details of implementation and semantics of the transport layer of the Internet protocol suite, which is the foundation of the Internet, and the OSI model of general networking are different.
Massively parallelMassively parallel is the term for using a large number of computer processors (or separate computers) to simultaneously perform a set of coordinated computations in parallel. GPUs are massively parallel architecture with tens of thousands of threads. One approach is grid computing, where the processing power of many computers in distributed, diverse administrative domains is opportunistically used whenever a computer is available. An example is BOINC, a volunteer-based, opportunistic grid system, whereby the grid provides power only on a best effort basis.
Multiple instruction, multiple dataIn computing, multiple instruction, multiple data (MIMD) is a technique employed to achieve parallelism. Machines using MIMD have a number of processors that function asynchronously and independently. At any time, different processors may be executing different instructions on different pieces of data. MIMD architectures may be used in a number of application areas such as computer-aided design/computer-aided manufacturing, simulation, modeling, and as communication switches.
Titan (supercomputer)Titan or OLCF-3 was a supercomputer built by Cray at Oak Ridge National Laboratory for use in a variety of science projects. Titan was an upgrade of Jaguar, a previous supercomputer at Oak Ridge, that uses graphics processing units (GPUs) in addition to conventional central processing units (CPUs). Titan was the first such hybrid to perform over 10 petaFLOPS. The upgrade began in October 2011, commenced stability testing in October 2012 and it became available to researchers in early 2013.
LinuxLinux (ˈlɪnʊks ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the use and importance of GNU software in many distributions, causing some controversy.
Linux distributionA Linux distribution (often abbreviated as distro) is an operating system made from a software collection that includes the Linux kernel, and often a package management system. Linux users usually obtain their operating system by downloading one of the Linux distributions, which are available for a wide variety of systems ranging from embedded devices (for example, OpenWrt) and personal computers (for example, Linux Mint) to powerful supercomputers (for example, Rocks Cluster Distribution).
Classical mechanicsClassical mechanics is a physical theory describing the motion of macroscopic objects, from projectiles to parts of machinery and astronomical objects, such as spacecraft, planets, stars, and galaxies. For objects governed by classical mechanics, if the present state is known, it is possible to predict how it will move in the future (determinism), and how it has moved in the past (reversibility). The "classical" in "classical mechanics" does not refer classical antiquity, as it might in, say, classical architecture.
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.
NanomechanicsNanomechanics is a branch of nanoscience studying fundamental mechanical (elastic, thermal and kinetic) properties of physical systems at the nanometer scale. Nanomechanics has emerged on the crossroads of biophysics, classical mechanics, solid-state physics, statistical mechanics, materials science, and quantum chemistry. As an area of nanoscience, nanomechanics provides a scientific foundation of nanotechnology.
