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.
ConcreteConcrete is a composite material composed of aggregate bonded together with a fluid cement that cures over time. Concrete is the second-most-used substance in the world after water, and is the most widely used building material. Its usage worldwide, ton for ton, is twice that of steel, wood, plastics, and aluminium combined. When aggregate is mixed with dry Portland cement and water, the mixture forms a fluid slurry that is easily poured and molded into shape.
Conformational changeProtein dynamics In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change. Factors that may induce such changes include temperature, pH, voltage, light in chromophores, concentration of ions, phosphorylation, or the binding of a ligand.
Reinforced concreteReinforced concrete, also called ferroconcrete, is a composite material in which concrete's relatively low tensile strength and ductility are compensated for by the inclusion of reinforcement having higher tensile strength or ductility. The reinforcement is usually, though not necessarily, steel bars (rebar) and is usually embedded passively in the concrete before the concrete sets. However, post-tensioning is also employed as a technique to reinforce the concrete. In terms of volume used annually, it is one of the most common engineering materials.
Types of concreteConcrete is produced in a variety of compositions, finishes and performance characteristics to meet a wide range of needs. Modern concrete mix designs can be complex. The choice of a concrete mix depends on the need of the project both in terms of strength and appearance and in relation to local legislation and building codes. The design begins by determining the requirements of the concrete. These requirements take into consideration the weather conditions that the concrete will be exposed to in service, and the required design strength.
Precast concretePrecast concrete is a construction product produced by casting concrete in a reusable mold or "form" which is then cured in a controlled environment, transported to the construction site and maneuvered into place; examples include precast beams, and wall panels for tilt up construction. In contrast, cast-in-place concrete is poured into site-specific forms and cured on site. Recently lightweight expanded polystyrene foam is being used as the cores of precast wall panels, saving weight and increasing thermal insulation.
Protein dynamicsProteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.
Prestressed concretePrestressed concrete is a form of concrete used in construction. It is substantially "prestressed" (compressed) during production, in a manner that strengthens it against tensile forces which will exist when in service. This compression is produced by the tensioning of high-strength "tendons" located within or adjacent to the concrete and is done to improve the performance of the concrete in service. Tendons may consist of single wires, multi-wire strands or threaded bars that are most commonly made from high-tensile steels, carbon fiber or aramid fiber.
Fluid dynamicsIn physics, physical chemistry and engineering, fluid dynamics is a subdiscipline of fluid mechanics that describes the flow of fluids—liquids and gases. It has several subdisciplines, including aerodynamics (the study of air and other gases in motion) and hydrodynamics (the study of liquids in motion). Fluid dynamics has a wide range of applications, including calculating forces and moments on aircraft, determining the mass flow rate of petroleum through pipelines, predicting weather patterns, understanding nebulae in interstellar space and modelling fission weapon detonation.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
ThermodynamicsThermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics which convey a quantitative description using measurable macroscopic physical quantities, but may be explained in terms of microscopic constituents by statistical mechanics.
Flow velocityIn continuum mechanics the flow velocity in fluid dynamics, also macroscopic velocity in statistical mechanics, or drift velocity in electromagnetism, is a vector field used to mathematically describe the motion of a continuum. The length of the flow velocity vector is the flow speed and is a scalar. It is also called velocity field; when evaluated along a line, it is called a velocity profile (as in, e.g., law of the wall).
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.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Large eddy simulationLarge eddy simulation (LES) is a mathematical model for turbulence used in computational fluid dynamics. It was initially proposed in 1963 by Joseph Smagorinsky to simulate atmospheric air currents, and first explored by Deardorff (1970). LES is currently applied in a wide variety of engineering applications, including combustion, acoustics, and simulations of the atmospheric boundary layer. The simulation of turbulent flows by numerically solving the Navier–Stokes equations requires resolving a very wide range of time and length scales, all of which affect the flow field.
