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.
Non-equilibrium thermodynamicsNon-equilibrium thermodynamics is a branch of thermodynamics that deals with physical systems that are not in thermodynamic equilibrium but can be described in terms of macroscopic quantities (non-equilibrium state variables) that represent an extrapolation of the variables used to specify the system in thermodynamic equilibrium. Non-equilibrium thermodynamics is concerned with transport processes and with the rates of chemical reactions.
TemperatureTemperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied on various reference points and thermometric substances for definition. The most common scales are the Celsius scale with the unit symbol °C (formerly called centigrade), the Fahrenheit scale (°F), and the Kelvin scale (K), the latter being used predominantly for scientific purposes.
Thermodynamic temperatureThermodynamic temperature is a quantity defined in thermodynamics as distinct from kinetic theory or statistical mechanics. Historically, thermodynamic temperature was defined by Lord Kelvin in terms of a macroscopic relation between thermodynamic work and heat transfer as defined in thermodynamics, but the kelvin was redefined by international agreement in 2019 in terms of phenomena that are now understood as manifestations of the kinetic energy of free motion of microscopic particles such as atoms, molecules, and electrons.
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.
Negative temperatureCertain systems can achieve negative thermodynamic temperature; that is, their temperature can be expressed as a negative quantity on the Kelvin or Rankine scales. This should be distinguished from temperatures expressed as negative numbers on non-thermodynamic Celsius or Fahrenheit scales, which are nevertheless higher than absolute zero. The absolute temperature (Kelvin) scale can be understood loosely as a measure of average kinetic energy. Usually, system temperatures are positive.
Onsager reciprocal relationsIn thermodynamics, the Onsager reciprocal relations express the equality of certain ratios between flows and forces in thermodynamic systems out of equilibrium, but where a notion of local equilibrium exists. "Reciprocal relations" occur between different pairs of forces and flows in a variety of physical systems. For example, consider fluid systems described in terms of temperature, matter density, and pressure.
DiffusionDiffusion is the net movement of anything (for example, atoms, ions, molecules, energy) generally from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in Gibbs free energy or chemical potential. It is possible to diffuse "uphill" from a region of lower concentration to a region of higher concentration, like in spinodal decomposition. Diffusion is a stochastic process due to the inherent randomness of the diffusing entity and can be used to model many real-life stochastic scenarios.
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.
Thermal conductionConduction is the process by which heat is transferred from the hotter end to the colder end of an object. The ability of the object to conduct heat is known as its thermal conductivity, and is denoted k. Heat spontaneously flows along a temperature gradient (i.e. from a hotter body to a colder body). For example, heat is conducted from the hotplate of an electric stove to the bottom of a saucepan in contact with it.
Temperature gradientA temperature gradient is a physical quantity that describes in which direction and at what rate the temperature changes the most rapidly around a particular location. The temperature gradient is a dimensional quantity expressed in units of degrees (on a particular temperature scale) per unit length. The SI unit is kelvin per meter (K/m). Temperature gradients in the atmosphere are important in the atmospheric sciences (meteorology, climatology and related fields). Assuming that the temperature T is an intensive quantity, i.
Color temperatureColor temperature is a parameter describing the color of a visible light source by comparing it to the color of light emitted by an idealized opaque, non-reflective body. The temperature of the ideal emitter that matches the color most closely is defined as the color temperature of the original visible light source. Color temperature is usually measured in kelvins. The color temperature scale describes only the color of light emitted by a light source, which may actually be at a different (and often much lower) temperature.
MixtureIn chemistry, a mixture is a material made up of two or more different chemical substances which are not chemically bonded. A mixture is the physical combination of two or more substances in which the identities are retained and are mixed in the form of solutions, suspensions and colloids. Mixtures are one product of mechanically blending or mixing chemical substances such as elements and compounds, without chemical bonding or other chemical change, so that each ingredient substance retains its own chemical properties and makeup.
Mixture modelIn statistics, a mixture model is a probabilistic model for representing the presence of subpopulations within an overall population, without requiring that an observed data set should identify the sub-population to which an individual observation belongs. Formally a mixture model corresponds to the mixture distribution that represents the probability distribution of observations in the overall population.
Thermal resistanceThermal resistance is a heat property and a measurement of a temperature difference by which an object or material resists a heat flow. Thermal resistance is the reciprocal of thermal conductance. (Absolute) thermal resistance R in kelvins per watt (K/W) is a property of a particular component. For example, a characteristic of a heat sink. Specific thermal resistance or thermal resistivity Rλ in kelvin–metres per watt (K⋅m/W), is a material constant.
Convection–diffusion equationThe convection–diffusion equation is a combination of the diffusion and convection (advection) equations, and describes physical phenomena where particles, energy, or other physical quantities are transferred inside a physical system due to two processes: diffusion and convection. Depending on context, the same equation can be called the advection–diffusion equation, drift–diffusion equation, or (generic) scalar transport equation.
Molecular machineMolecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes.
Thermal conductivityThe thermal conductivity of a material is a measure of its ability to conduct heat. It is commonly denoted by , , or . Heat transfer occurs at a lower rate in materials of low thermal conductivity than in materials of high thermal conductivity. For instance, metals typically have high thermal conductivity and are very efficient at conducting heat, while the opposite is true for insulating materials like mineral wool or Styrofoam.
Computational scienceComputational science, also known as scientific computing, technical computing or scientific computation (SC), is a division of science that uses advanced computing capabilities to understand and solve complex physical problems. This includes Algorithms (numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve sciences (e.
GasGas is one of the four fundamental states of matter. The others are solid, liquid, and plasma. A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or compound molecules made from a variety of atoms (e.g. carbon dioxide). A gas mixture, such as air, contains a variety of pure gases. What distinguishes a gas from liquids and solids is the vast separation of the individual gas particles.
