Table 1 Primer of terminology relevant to mesoscale cell biology

Active matter

Matter that is consuming energy, such that its dynamics or structure changes significantly if the energy supply is removed.

Aggregate

Many molecules adhering together into a body or cluster, often in an undesirable, non-functional, or poorly characterised state. This can involve strong interactions resulting in a body that is not in dynamic equilibrium with the surroundings, so molecules are not able to continuously leave and be replaced. Aggregate can also refer to the process of formation of the body of molecules.

Assembly

Bodies or clusters of many proteins and other biomolecules in cells that are assumed or known to be related to function. Assembly can also refer to the process of formation of these bodies or clusters, as in self-assembly (see below).

Ballistic motion

Motion in a straight line at constant speed. The term ballistic motion can be misleading for dynamics inside a cell because inertia is irrelevant at these sizes, and a cellular component only moves at a constant speed if a force is continuously applied that exactly matches the drag experienced by it.

Cell cortex

Organisation of inner plasma membrane and underlying cytoskeleton creating a layer capable of contraction. The cortex controls cell morphology and facilitates movement.

Chromosome territory

A volume of the nucleus inhabited by a single chromosome, with relatively little overlap with the volumes occupied by other chromosomes. This contrasts with an intermingled chaotic mixture.

Colloid

Molecules or polymolecular particles dispersed in a liquid, where the particles have a dimension of 1 nm to 1 μm in at least one direction.

Cytoplasmic body

A liquid-like droplet in the cytoplasm that is strongly enriched in a set of biomolecules, at least some of which are in dynamic equilibrium with the cytoplasm. Cytoplasmic bodies may deform and flow as viscoelastic liquids under force, but unlike liquids their the size and number are limited. These bodies are referred to by a variety of terms including assemblies, granules, clusters and aggregates, or named for their function. They are not membrane bound.

Cytoskeleton

Scaffold of molecular filaments in eukaryotic cells including microfilaments (actin), microtubules (tubulin) and intermediate filaments (keratin, lamin). This scaffold is not static and is constantly being dynamically remodeled.

Euchromatin and heterochromatin

Linear regions of open (euchromatin) or compacted (heterochromatin) nucleosomes along interphase chromosomes. They may come together in the nucleus and be identifiable by light microscopy via characteristic histone modifications or accessory proteins. Histones are proteins that bind DNA in eukaryotes to form structures called nucleosomes that are around 10 nm in diameter.

HiC methodology

A type of chromosome conformational capture (3C) that enables unbiased sampling of the close association of any site in the genome with every other site. It uses chemical crosslinking of DNAs, enzymatic cleavage and re-ligation of DNA, followed by massively parallel sequencing of ligated DNA pairs.

Mean-field theory

A class of theory where fluctuations around a mean value are ignored. For example, the concentration of a cell signaling molecule may be fluctuating around a steady state value, but a mean field theory neglects these fluctuations and uses a constant steady-state estimate.

Mesoscale

A length scale larger than molecular scales of 1 to 10 nm but no larger than the size of the cell. In a cell, mesoscales are approximately 100 nm to the typical 10 μm cell diameter.

Multiscale systems

Systems with important structure and dynamics at multiple length and time scales. For example, the mitotic spindle has dynamics for tubulin joining a growing microtubule as well as for whole chromosomes.

Non-equilibrium phenomena

Phenomena characteristic of systems where any of the following are true: The system is consuming energy; external forces are acting on the system; the system has not yet reached its final equilibrium state.

ODE, PDE

An ordinary differential equation (ODE) is an equation with differentiation in only one variable, often time. A partial differential equation (PDE) has 2 or more variables, often time and one or more of the 3 spatial dimensions x, y and z.

Phase diagram

Typically a plot in which axes represent control parameters (e.g. temperature, concentration), and where in the plot there are areas of two or more distinctive behaviours such as molecules clustering into bodies or spread uniformly. A transition line separates these areas, and denotes the conditions where the system switches between the behaviours.

Phase separation

Separation of any fluid spontaneously into two or more distinct fluids without an energy consuming process, e.g. as oil and water separate. Neither phase is pure so some molecules remain dissolved in the complementary phase. Although phase separation may start with small droplets of one phase in the other, these droplets grow until one liquid layers on top of the other at equilibrium.

Self-assembly

The process of spontaneous formation of structures driven by intermolecular interactions without a requirement for energy consumption. For example, surfactant micelles and clathrin lattices.

Self-organisation

Formation of structure or coordination that occurs spontaneously in a system such as a cell. The organisation arises due to processes inside the cell and is not externally imposed. In cells it arises due to intermolecular interactions or energy-consuming processes. Self-organisation is more general and larger in scope than self-assembly.

Soft-matter physics

The physics of matter that is mostly either liquids, or soft solids that can be made to stretch or flow under relatively small forces. Soft matter also conventionally includes polymers, even though these may not always readily flow.

Transcription factory

Putative multi-protein enzyme structure including RNA polymerases. These transcribe multiple RNA molecules such as messenger RNA precursors, from multiple genes, and these genes may move to the factory to be transcribed. This movement of genes to factories contrasts with textbook models of RNA polymerase moving to assemble and translocate along a static DNA template.

Viscoelasticity

Viscoelastic liquids such as the cytoplasm and nucleoplasm are liquids intermediate in behaviour between simple liquids and solids. Unlike solids they do flow when forces are applied, but unlike simple liquids the speed at which they flow is not simply proportional to the force exerted. Applying the same force rapidly or slowly may have different effects.