Chemical structureA chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together and can be represented using structural formulae and by molecular models; complete electronic structure descriptions include specifying the occupation of a molecule's molecular orbitals.
Kinetic theory of gasesThe kinetic theory of gases is a simple, historically significant classical model of the thermodynamic behavior of gases, with which many principal concepts of thermodynamics were established. The model describes a gas as a large number of identical submicroscopic particles (atoms or molecules), all of which are in constant, rapid, random motion. Their size is assumed to be much smaller than the average distance between the particles. The particles undergo random elastic collisions between themselves and with the enclosing walls of the container.
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.
Nucleic acid structure determinationExperimental approaches of determining the structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysical and biochemical methods. Biophysical methods use the fundamental physical properties of molecules for structure determination, including X-ray crystallography, NMR and cryo-EM. Biochemical methods exploit the chemical properties of nucleic acids using specific reagents and conditions to assay the structure of nucleic acids.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Reaction coordinateIn chemistry, a reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. It is usually a geometric parameter that changes during the conversion of one or more molecular entities. In molecular dynamics simulations, a reaction coordinate is called collective variable. These coordinates can sometimes represent a real coordinate system (such as bond length, bond angle...), although, for more complex reactions especially, this can be difficult (and non geometric parameters are used, e.
MetastabilityIn chemistry and physics, metastability denotes an intermediate energetic state within a dynamical system other than the system's state of least energy. A ball resting in a hollow on a slope is a simple example of metastability. If the ball is only slightly pushed, it will settle back into its hollow, but a stronger push may start the ball rolling down the slope. Bowling pins show similar metastability by either merely wobbling for a moment or tipping over completely. A common example of metastability in science is isomerisation.
Computational physicsComputational physics is the study and implementation of numerical analysis to solve problems in physics. Historically, computational physics was the first application of modern computers in science, and is now a subset of computational science. It is sometimes regarded as a subdiscipline (or offshoot) of theoretical physics, but others consider it an intermediate branch between theoretical and experimental physics - an area of study which supplements both theory and experiment.
Representation theoryRepresentation theory is a branch of mathematics that studies abstract algebraic structures by representing their elements as linear transformations of vector spaces, and studies modules over these abstract algebraic structures. In essence, a representation makes an abstract algebraic object more concrete by describing its elements by matrices and their algebraic operations (for example, matrix addition, matrix multiplication).
Relaxation (physics)In the physical sciences, relaxation usually means the return of a perturbed system into equilibrium. Each relaxation process can be categorized by a relaxation time τ. The simplest theoretical description of relaxation as function of time t is an exponential law exp(−t/τ) (exponential decay). Let the homogeneous differential equation: model damped unforced oscillations of a weight on a spring. The displacement will then be of the form . The constant T () is called the relaxation time of the system and the constant μ is the quasi-frequency.
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.
Energy densityIn physics, energy density is the amount of energy stored in a given system or region of space per unit volume. It is sometimes confused with energy per unit mass which is properly called specific energy or . Often only the useful or extractable energy is measured, which is to say that inaccessible energy (such as rest mass energy) is ignored. In cosmological and other general relativistic contexts, however, the energy densities considered are those that correspond to the elements of the stress-energy tensor and therefore do include mass energy as well as energy densities associated with pressure.
