Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
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 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.
Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
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.
GROMACSGROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.
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.
Single instruction, multiple dataSingle instruction, multiple data (SIMD) is a type of parallel processing in Flynn's taxonomy. SIMD can be internal (part of the hardware design) and it can be directly accessible through an instruction set architecture (ISA), but it should not be confused with an ISA. SIMD describes computers with multiple processing elements that perform the same operation on multiple data points simultaneously. Such machines exploit data level parallelism, but not concurrency: there are simultaneous (parallel) computations, but each unit performs the exact same instruction at any given moment (just with different data).
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.
CorrelationIn statistics, correlation or dependence is any statistical relationship, whether causal or not, between two random variables or bivariate data. Although in the broadest sense, "correlation" may indicate any type of association, in statistics it usually refers to the degree to which a pair of variables are linearly related. Familiar examples of dependent phenomena include the correlation between the height of parents and their offspring, and the correlation between the price of a good and the quantity the consumers are willing to purchase, as it is depicted in the so-called demand curve.
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.
Cross-correlationIn signal processing, cross-correlation is a measure of similarity of two series as a function of the displacement of one relative to the other. This is also known as a sliding dot product or sliding inner-product. It is commonly used for searching a long signal for a shorter, known feature. It has applications in pattern recognition, single particle analysis, electron tomography, averaging, cryptanalysis, and neurophysiology. The cross-correlation is similar in nature to the convolution of two functions.
Single instruction, multiple threadsSingle instruction, multiple threads (SIMT) is an execution model used in parallel computing where single instruction, multiple data (SIMD) is combined with multithreading. It is different from SPMD in that all instructions in all "threads" are executed in lock-step. The SIMT execution model has been implemented on several GPUs and is relevant for general-purpose computing on graphics processing units (GPGPU), e.g. some supercomputers combine CPUs with GPUs. The processors, say a number p of them, seem to execute many more than p tasks.
Hybrid vehicleA hybrid vehicle is one that uses two or more distinct types of power, such as submarines that use diesel when surfaced and batteries when submerged. Other means to store energy include pressurized fluid in hydraulic hybrids. Hybrid powertrains are designed to switch from one power source to another to maximize both fuel efficiency and energy efficiency. In hybrid electric vehicles, for instance, the electric motor is more efficient at producing torque, or turning power, while the combustion engine is better for maintaining high speed.
False memoryIn psychology, a false memory is a phenomenon where someone recalls something that did not actually happen or recalls it differently from the way it actually happened. Suggestibility, activation of associated information, the incorporation of misinformation, and source misattribution have been suggested to be several mechanisms underlying a variety of types of false memory. The false memory phenomenon was initially investigated by psychological pioneers Pierre Janet and Sigmund Freud.
Manycore processorManycore processors are special kinds of multi-core processors designed for a high degree of parallel processing, containing numerous simpler, independent processor cores (from a few tens of cores to thousands or more). Manycore processors are used extensively in embedded computers and high-performance computing. Manycore processors are distinct from multi-core processors in being optimized from the outset for a higher degree of explicit parallelism, and for higher throughput (or lower power consumption) at the expense of latency and lower single-thread performance.
Folding@homeFolding@home (FAH or F@h) is a distributed computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations run on volunteers' personal computers. Folding@home is currently based at the University of Pennsylvania and led by Greg Bowman, a former student of Vijay Pande.
Working memoryWorking memory is a cognitive system with a limited capacity that can hold information temporarily. It is important for reasoning and the guidance of decision-making and behavior. Working memory is often used synonymously with short-term memory, but some theorists consider the two forms of memory distinct, assuming that working memory allows for the manipulation of stored information, whereas short-term memory only refers to the short-term storage of information.
Hybrid vehicle drivetrainHybrid vehicle drivetrains transmit power to the driving wheels for hybrid vehicles. A hybrid vehicle has multiple forms of motive power. Hybrids come in many configurations. For example, a hybrid may receive its energy by burning gasoline, but switch between an electric motor and a combustion engine. Electrical vehicles have a long history combining internal combustion and electrical transmission - as in a diesel–electric power-train - although they have mostly been used for rail locomotives.
Scaled correlationIn statistics, scaled correlation is a form of a coefficient of correlation applicable to data that have a temporal component such as time series. It is the average short-term correlation. If the signals have multiple components (slow and fast), scaled coefficient of correlation can be computed only for the fast components of the signals, ignoring the contributions of the slow components. This filtering-like operation has the advantages of not having to make assumptions about the sinusoidal nature of the signals.
