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Multi-particle Collision Dynamics
Multi-particle collision dynamics (MPC), also known as stochastic rotation dynamics (SRD), is a particle-based mesoscale simulation technique for complex fluids which fully incorporates thermal fluctuations and hydrodynamic interactions. Coupling of embedded particles to the coarse-grained solvent is achieved through molecular dynamics. Method of simulation The solvent is modelled as a set of N point particles of mass m with continuous coordinates \vec_ and velocities \vec_. The simulation consists of streaming and collision steps. During the streaming step, the coordinates of the particles are updated according to \vec_(t+\delta t_) = \vec_(t) + \vec_(t) \delta t_ where \delta t_ is a chosen simulation time step which is typically much larger than a molecular dynamics time step. After the streaming step, interactions between the solvent particles are modelled in the collision step. The particles are sorted into collision cells with a lateral size a. Particle velocities within ea ...
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Molecular Dynamics
Molecular 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. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ...
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Rotation Matrix
In linear algebra, a rotation matrix is a transformation matrix that is used to perform a rotation in Euclidean space. For example, using the convention below, the matrix :R = \begin \cos \theta & -\sin \theta \\ \sin \theta & \cos \theta \end rotates points in the plane counterclockwise through an angle with respect to the positive axis about the origin of a two-dimensional Cartesian coordinate system. To perform the rotation on a plane point with standard coordinates , it should be written as a column vector, and multiplied by the matrix : : R\mathbf = \begin \cos \theta & -\sin \theta \\ \sin \theta & \cos \theta \end \begin x \\ y \end = \begin x\cos\theta-y\sin\theta \\ x\sin\theta+y\cos\theta \end. If and are the endpoint coordinates of a vector, where is cosine and is sine, then the above equations become the trigonometric summation angle formulae. Indeed, a rotation matrix can be seen as the trigonometric summation angle formulae in matrix form. One w ...
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Galilean Invariance
Galilean invariance or Galilean relativity states that the laws of motion are the same in all inertial frames of reference. Galileo Galilei first described this principle in 1632 in his ''Dialogue Concerning the Two Chief World Systems'' using the example of a ship travelling at constant velocity, without rocking, on a smooth sea; any observer below the deck would not be able to tell whether the ship was moving or stationary. The young Albert Einstein "was engrossed in analyzing Galileo's principle of inertia (Galilean relativity)". Formulation Specifically, the term ''Galilean invariance'' today usually refers to this principle as applied to Newtonian mechanics, that is, Newton's laws of motion hold in all frames related to one another by a Galilean transformation. In other words, all frames related to one another by such a transformation are inertial (meaning, Newton's equation of motion is valid in these frames). In this context it is sometimes called ''Newtonian relativity''. ...
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Diffusion Coefficient
Diffusivity, mass diffusivity or diffusion coefficient is a proportionality constant between the molar flux due to molecular diffusion and the gradient in the concentration of the species (or the driving force for diffusion). Diffusivity is encountered in Fick's law and numerous other equations of physical chemistry. The diffusivity is generally prescribed for a given pair of species and pairwise for a multi-species system. The higher the diffusivity (of one substance with respect to another), the faster they diffuse into each other. Typically, a compound's diffusion coefficient is ~10,000× as great in air as in water. Carbon dioxide in air has a diffusion coefficient of 16 mm2/s, and in water its diffusion coefficient is 0.0016 mm2/s. Diffusivity has dimensions of length2 / time, or m2/s in SI units and cm2/s in CGS units. Temperature dependence of the diffusion coefficient Solids The diffusion coefficient in solids at different temperatures is generally found ...
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Viscosity
The viscosity of a fluid is a measure of its resistance to deformation at a given rate. For liquids, it corresponds to the informal concept of "thickness": for example, syrup has a higher viscosity than water. Viscosity quantifies the internal frictional force between adjacent layers of fluid that are in relative motion. For instance, when a viscous fluid is forced through a tube, it flows more quickly near the tube's axis than near its walls. Experiments show that some stress (such as a pressure difference between the two ends of the tube) is needed to sustain the flow. This is because a force is required to overcome the friction between the layers of the fluid which are in relative motion. For a tube with a constant rate of flow, the strength of the compensating force is proportional to the fluid's viscosity. In general, viscosity depends on a fluid's state, such as its temperature, pressure, and rate of deformation. However, the dependence on some of these properties is ...
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KT (energy)
{, class="wikitable" style="float: right;" ! Approximate values of ''kT'' at 298 K ! Units , - , ''kT'' = , , J , - , ''kT'' = , , pN⋅nm , - , ''kT'' = , , cal , - , ''kT'' = , , meV , - , ''kT'' = {{val, kT=-174 , , dBm/Hz , - ! colspan=2, {{center, Related quantities (also at 298 K) , - , ''kT/hc'' ≈ {{val, 207 {{cite web , title=Google Unit Converter , url=https://www.google.ca/search?ei=VzDnW4mbLOfMjwS694DYCw&q=k*298Kelvin%2Fh%2Fc+in+cm%5E-1&oq=k*298Kelvin%2Fh%2Fc+in+cm%5E-1&gs_l=psy-ab.3...2293.2598.0.3103.2.2.0.0.0.0.125.214.1j1.2.0....0...1.1.64.psy-ab..0.0.0....0.gYQvcs3LZis , accessdate=10 November 2018 , , cm−1 , - , ''kT''/''e'' = 25.7 , , mV , - , ''RT'' = ''kT'' ⋅ ''N''A = {{val, 2.479 , , kJ⋅mol−1 , - , ''RT'' = 0.593 , , kcal⋅mol−1 , - , ''h''/''kT'' = 0.16 , , ps ''kT'' (also written as ''k''B''T'') is the product of the Boltzmann constant, ''k'' (or ''k''B), and the temperature, ''T''. This product is used in ...
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Mean Free Path
In physics, mean free path is the average distance over which a moving particle (such as an atom, a molecule, or a photon) travels before substantially changing its direction or energy (or, in a specific context, other properties), typically as a result of one or more successive collisions with other particles. Scattering theory Imagine a beam of particles being shot through a target, and consider an infinitesimally thin slab of the target (see the figure). The atoms (or particles) that might stop a beam particle are shown in red. The magnitude of the mean free path depends on the characteristics of the system. Assuming that all the target particles are at rest but only the beam particle is moving, that gives an expression for the mean free path: :\ell = (\sigma n)^, where is the mean free path, is the number of target particles per unit volume, and is the effective cross-sectional area for collision. The area of the slab is , and its volume is . The typical number of st ...
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Shear Viscosity
The viscosity of a fluid is a measure of its resistance to deformation at a given rate. For liquids, it corresponds to the informal concept of "thickness": for example, syrup has a higher viscosity than water. Viscosity quantifies the internal frictional force between adjacent layers of fluid that are in relative motion. For instance, when a viscous fluid is forced through a tube, it flows more quickly near the tube's axis than near its walls. Experiments show that some stress (such as a pressure difference between the two ends of the tube) is needed to sustain the flow. This is because a force is required to overcome the friction between the layers of the fluid which are in relative motion. For a tube with a constant rate of flow, the strength of the compensating force is proportional to the fluid's viscosity. In general, viscosity depends on a fluid's state, such as its temperature, pressure, and rate of deformation. However, the dependence on some of these properties is n ...
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Thermal Diffusivity
In heat transfer analysis, thermal diffusivity is the thermal conductivity divided by density and specific heat capacity at constant pressure. It measures the rate of transfer of heat of a material from the hot end to the cold end. It has the SI derived unit of m2/s. Thermal diffusivity is usually denoted by lowercase alpha (), but , , ( kappa), , and are also used. The formula is: :\alpha = \frac where * is thermal conductivity (W/(m·K)) * is specific heat capacity (J/(kg·K)) * is density (kg/m3) Together, can be considered the volumetric heat capacity (J/(m3·K)). As seen in the heat equation, :\frac = \alpha \nabla^2 T, one way to view thermal diffusivity is as the ratio of the time derivative of temperature to its curvature, quantifying the rate at which temperature concavity is "smoothed out". In a sense, thermal diffusivity is a contrasting measure to thermal inertia. In a substance with high thermal diffusivity, heat moves rapidly through it because the substa ...
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Colloid
A colloid is a mixture in which one substance consisting of microscopically dispersed insoluble particles is suspended throughout another substance. Some definitions specify that the particles must be dispersed in a liquid, while others extend the definition to include substances like aerosols and gels. The term colloidal suspension refers unambiguously to the overall mixture (although a narrower sense of the word ''suspension'' is distinguished from colloids by larger particle size). A colloid has a dispersed phase (the suspended particles) and a continuous phase (the medium of suspension). The dispersed phase particles have a diameter of approximately 1 nanometre to 1 micrometre. Some colloids are translucent because of the Tyndall effect, which is the scattering of light by particles in the colloid. Other colloids may be opaque or have a slight color. Colloidal suspensions are the subject of interface and colloid science. This field of study was introduced in 1845 by Itali ...
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Polymer
A polymer (; Greek '' poly-'', "many" + ''-mer'', "part") is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass, relative to small molecule compounds, produces unique physical properties including toughness, high elasticity, viscoelasticity, and a tendency to form amorphous and semicrystalline structures rather than crystals. The term "polymer" derives from the Greek word πολύς (''polus'', meaning "many, much") and μέρος (''meros'' ...
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