Implicit solvationImplicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Computational complexityIn computer science, the computational complexity or simply complexity of an algorithm is the amount of resources required to run it. Particular focus is given to computation time (generally measured by the number of needed elementary operations) and memory storage requirements. The complexity of a problem is the complexity of the best algorithms that allow solving the problem. The study of the complexity of explicitly given algorithms is called analysis of algorithms, while the study of the complexity of problems is called computational complexity theory.
Computational neuroscienceComputational neuroscience (also known as theoretical neuroscience or mathematical neuroscience) is a branch of neuroscience which employs mathematical models, computer simulations, theoretical analysis and abstractions of the brain to understand the principles that govern the development, structure, physiology and cognitive abilities of the nervous system. Computational neuroscience employs computational simulations to validate and solve mathematical models, and so can be seen as a sub-field of theoretical neuroscience; however, the two fields are often synonymous.
Duplicate codeIn computer programming, duplicate code is a sequence of source code that occurs more than once, either within a program or across different programs owned or maintained by the same entity. Duplicate code is generally considered undesirable for a number of reasons. A minimum requirement is usually applied to the quantity of code that must appear in a sequence for it to be considered duplicate rather than coincidentally similar.
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.
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 engineeringComputational Engineering is an emerging discipline that deals with the development and application of computational models for engineering, known as Computational Engineering Models or CEM. At this time, various different approaches are summarized under the term Computational Engineering, including using computational geometry and virtual design for engineering tasks, often coupled with a simulation-driven approach In Computational Engineering, algorithms solve mathematical and logical models that describe engineering challenges, sometimes coupled with some aspect of AI, specifically Reinforcement Learning.
Code refactoringIn computer programming and software design, code refactoring is the process of restructuring existing computer code—changing the factoring—without changing its external behavior. Refactoring is intended to improve the design, structure, and/or implementation of the software (its non-functional attributes), while preserving its functionality. Potential advantages of refactoring may include improved code readability and reduced complexity; these can improve the source codes maintainability and create a simpler, cleaner, or more expressive internal architecture or object model to improve extensibility.
HypothesisA hypothesis (: hypotheses) is a proposed explanation for a phenomenon. For a hypothesis to be a scientific hypothesis, the scientific method requires that one can test it. Scientists generally base scientific hypotheses on previous observations that cannot satisfactorily be explained with the available scientific theories. Even though the words "hypothesis" and "theory" are often used interchangeably, a scientific hypothesis is not the same as a scientific theory.
CurveIn mathematics, a curve (also called a curved line in older texts) is an object similar to a line, but that does not have to be straight. Intuitively, a curve may be thought of as the trace left by a moving point. This is the definition that appeared more than 2000 years ago in Euclid's Elements: "The [curved] line is [...] the first species of quantity, which has only one dimension, namely length, without any width nor depth, and is nothing else than the flow or run of the point which [...
