Glossary and abbreviations
The following glossary is intended to be a helpful list of definitions for terms that are frequently used in quantum biology, for researchers across a range of disciplines. If you would like to suggest additional terms, or to comment on the definitions, please contact us.
3D three-dimensional
ADP adenosine diphosphate
AlkB alkylation B
AMP adenosine monophosphate
ARDS acute respiratory distress syndrome
ATP adenosine triphosphate
BBO Barium Borate
CALI chromophore-assisted light-inactivation
CASSCF complete active space self-consistent field
CDT chemodynamic therapy
CI configuration interaction
CICR calcium-induced calcium release
CISS chirality-induced spin selectivity
cQED cavity QED
CT-QMC continuous time quantum Monte Carlo
DFT density functional theory
DL Delayed Luminesce
DMFT dynamical mean-field theory
DMRG density matrix renormalization group
DNA deoxyribonucleic acid
ECM extracellular matrix
EDT electrodynamic therapy
ELF extremely low frequency
EMCCD Electron-Multiplying Charged Coupled Device
EMF Electromagnetic field
EPR electron paramagnetic resonance
EPTA Entangled two photon absorption
ET electron transfer
ETC electron transport chain
ETF electron transfer flavoprotein
FAD flavin adenine dinucleotide
FDA Food and Drug Administration
FeS iron-sulfur
FMO Fenna–Matthews–Olson
GDP guanosine 5’-diphosphate
GGA generalized gradient approximation
GMF geomagnetic field
GTP guanosine 5’-triphosphate
HER2 human epidermal growth factor receptor 2
HF Hartree-Fock
HIF hypoxia inducible factor
HMF hypomagnetic field
HPD hematoporphyrin derivative
HSP heat shock protein
ICH intracerebral hemorrhage
IR infrared
ISC intersystem crossing
LDA local density approximation
LED light-emitting diode
LHCII light-harvesting complex II
LHN light-harvesting nanotube
LLLT low level light therapy
MCF7* Michigan Cancer Foundation 7
MCF10A* Michigan Cancer Foundation 10A
MFEs magnetic field effects
ML machine learning
MM molecular mechanics
MO molecular orbital
MR multi-reference
MSC mesenchymal stromal cell
NADPH nicotinamide adenine dinucleotide phosphate
NIR near-infrared light
NISQ noisy intermediate-scale quantum
NMR nuclear magnetic resonance
NOX NADPH oxidase
OXPHOS oxidative phosphorylation
PBM photobiomodulation
PCET proton-coupled electron transfer
PDT photodynamic therapy
PEG polyethylene glycol
PEMF pulsed electromagnetic field
PMT Photomultiplier Tube
PSII photosystem II
PTT photothermal therapy
QA quantum annealing
QED quantum electrodynamics
QM quantum mechanical
QM/MM quantum mechanics / molecular mechanics
RDT radiodynamic therapy
RET resonance energy transfer
RIRR ROS-induced ROS release
RNA ribonucleic acid
ROS reactive oxygen species
RPM radical pair mechanism
SCC-DFTB self-consistent charge density-functional tight-binding
SCF self-consistent field
SD Standard deviation
SDT sonodynamic therapy
SFG Sum Frequency Generation
SR stochastic resonance
STM scanning tunneling microscopy
THz terahertz
TRIM tissue resonance interaction method
Trp tryptophan
UPE ultraweak photon emissions
UV ultraviolet
UVR8 UV resistance locus 8
WMF weak magnetic field
With thanks to Nathan Babcock.
Read Nathan's book, Physical Principles of Quantum Biology, here.
Biophotons are infrared-to-ultraviolet photonic emissions from biological material. They are often called ultraweak emissions due to the comparably low number of photons emitted. They appear to be associated with stressed metabolic states and the balance of reactive oxygen species. These emissions may be distinct from enzymatic bioluminescence and delayed luminescence.
A chromophore is a light-sensitive molecule that absorbs and emits light at various specific wavelengths. This light sensitivity is due to the specific molecular structure of the chromophore. Examples of chromophores are retinal (visual pigment), tryptophan (aromatic amino acid), and chlorophyll (photosynthetic pigment). It is thought that chromophores in biological material were recruited by the need to dissipate or channel the energy of absorbed sunlight, particularly the high-energy and potentially damaging ultraviolet rays. Other important light-sensitive molecules are NADH and FADH.
Coherence, and its counterpart decoherence, is an integral concept in quantum biology. Coherence quantifies to what degree quantum systems preserve observable properties such as superposition and entanglement. Decoherence, on the other hand, describes the loss of such quantum effects, which can be brought about when a quantum system interacts with its (much larger) surrounding environment. The term coherence is used in a number of different contexts, not all of which refer to quantum coherence. Both in the classical and quantum sense coherence can be understood as following from a wave description, where coherence measures how “in phase” two waves are and their corresponding propensity for interference. Because of quantum superposition, however, interference can arise between two classically non-interfering states a and b, describable in the way that (a+b)2 = a2 + b2 + 2ab produces a “coherent” interference term (2ab).
An electrochemical gradient or membrane potential is a difference in proton or ion concentration across a biological membrane, which results in an electric voltage potential that charged particles experience as a force. This membrane potential is achieved in various ways, including through electron transport chains, proton pumps such as ATPase or ion channels.
Electromagnetism is the branch of physics that deals with interactions between charged particles with electric and magnetic fields, and their field unification as light. These interactions are mediated by photons, the quanta (discrete packets) of light, which manifest the particulate nature of the electromagnetic wave.
Entanglement is the strongest form of quantum correlation, which Schrödinger called “the characteristic trait of quantum mechanics, the one that enforces its entire departure from classical lines of thought,” and describes an inseparable whole quantum state whose constituent sub-systems cannot be described independently of the state of any other entangled sub-system in the whole, no matter how far apart they may be. Entanglement has been used as a resource in cryptography for secure communication. In biological systems, entanglement might play a number of roles, for example in information processing and transmission. It could also contribute to more efficient, super resolution imaging of these systems through sensitive techniques using quantum light sources, which are weaker than classical sources but use strong correlations between photons to infer information.
Mitochondria are double membrane-bound organelles found in most eukaryotic cells. They are thought to have evolved from bacteria. Electron transport chains in mitochondrial membranes generate proton gradients that drive the production of adenosine triphosphate (ATP), whose energy-rich bonds fuel most cellular processes. It was thought their primary purpose was purely respiration, which is the process of extracting energy via electron transport from food to oxygen. However, they are now known to be key in generating precursor molecules for growth and suppression of oxidative stress, as well as acting as signalling hubs via ROS and calcium manipulation, and they play key roles in immunity and inflammation, and thus ageing.
A distinction is often made between “trivial” and “non-trivial” quantum effects in biology. Put simply, this is the distinction between the fact that biological matter consists of atoms and, like all atoms, can be described using the quantum model of the atom formalised by Bohr. Non-trivial quantum effects, on the other hand, implicate quantum phenomena such as superposition, coherence, tunnelling and entanglement in giving rise to emergent properties at the mesoscopic and even macroscopic scale.
Light has classically been described as an electromagnetic wave. Einstein’s explanation of the photoelectric effect suggested that light, in addition to behaving like a wave, also comes in discrete packets, behaving as a particle with a minimum “quantum” of energy. These particles of light came to be named photons.
A quantum model is a way of describing, using mathematics, what happens to a state over time, for instance, how does it change empirically. Newton’s equations are often used to model classical systems. In quantum mechanics the most common way to model a system is to use Schrödinger’s equation. Whereas classical models are often described as strictly deterministic, giving an arbitrarily precise measurement of all observables for a physical system, quantum models describe both deterministic (Schrödinger equation) and non-deterministic (measurement “state reduction”) processes, using probabilities and uncertainty relations to describe the properties of physical systems. The famous quantum measurement problem emerges from this distinction.
A “state” describes a property of a system. This might refer to the state of a person’s health, for instance, or the state of a vehicle’s velocity. A quantum state refers to a property of the quantum system under study. This might be the energy, the position, the spin or some other property of interest. What is interesting about quantum physics is that for two quantum states describing a system, a linear combination of their states also describes the system. This is known as the superposition principle, made famous by the Schrödinger’s-cat thought experiment.
A quantum system refers to an object with observable properties of its state, which can be calculated as probability distributions from its wavefunction(s), and which are discretised according to the observable’s spectrum.
Quantum theory describes the discrete, granular nature of wave-particles, such as atoms, electrons, protons and photons, and their aggregates. It was developed out of the need to better describe anomalous experimental observations and is to be distinguished from classical mechanics, which presumes a continuum for all measurements. In particular, classical theory could not accurately and completely explain blackbody radiation. This “ultraviolet catastrophe” led Planck to hypothesise that energy is quantised, or comes in discrete amounts, which was further consolidated by Einstein’s explanation of the photoelectric effect. The result of this is what is often called the “wave-particle” duality of quantum mechanics, where light (and matter) behaves both as a wave and a particle.
The quantum property of spin plays a role in chemical reactions, where electrons that occupy the same orbitals must have opposite spin states, due to the Pauli exclusion principle. Spin chemistry is a field that emerged to explain the effects that magnetic fields, and thus magneto-sensitive spin states, have on chemical reactions. One of the models developed in this field is the radical pair mechanism, which subsequently was applied to chemical reactions in biological systems, namely bird migration and other organismal orientation to the Earth’s magnetic field. The radical pair mechanism involves absorption of a photon by a bound electron, resulting in a spatially separated but spin-correlated pair. Interaction with the electrons’ physical surroundings, including the Earth’s magnetic field, causes the resulting quantum state to oscillate configuration between “singlet” and “triplet” states, where singlet and triplet indicate a different relative orientation of the two spins. These spin states determine distinct (bio)chemical outcomes, which can in principle be sensed by the organism.
Reduction-oxidation (redox) reactions, or the transfer of charged particles like electrons and protons between molecules, are central to the efficient function of biological systems. During aerobic metabolism, by-products known as reactive oxygen species (ROS) are generated. Reactive oxygen species, which include singlet oxygen, superoxide, peroxide, and others, are important signalling molecules in biological systems and are required during normal metabolic processing. Due to their energetic and reactive nature, however, they can emit packets of light to stabilise, and in pathological situations they can exceed normal bounds and cause cellular damage, inflammation and even death.
Spin (more formally, spin angular momentum) describes the quantised response of a physical system to a magnetic field, which is not describable by its orbital angular momentum. Spin is not due to any spinning motion of the particles in question. Rather, spin is an intrinsic quantum property, for instance the quantum counterpart of light polarization for photons. Other intrinsic properties of matter are mass and charge. Mass describes how matter will respond to a gravitational field, charge describes how matter will respond to an electric field, and spin describes how quantum systems such as electrons and protons will respond to a magnetic field. Spin also plays a role in chemical reactions, where electrons that occupy the same orbitals must have opposite spin states (the so-called Pauli exclusion principle). Spin also dictates the magnetic properties of certain materials, for instance paramagnetic materials which have unpaired spins, and diamagnetic materials where all the spins are paired.
The formal description of a quantum state by a state vector (or wavefunction) allows for the possibility that, for two quantum states describing potential outcomes for an observable of a physical system, a linear combination of their states can also describe the system. This is often heuristically exemplified as a (quantum) switch or bit being both “on” and “off” at the same time.
Thermodynamics is the branch of physics that deals with phenomena governing temperature, heat, work, energy, and entropy. As a discipline, it was advanced considerably by the invention and refinement of the steam engine. The laws of thermodynamics describe macroscopic “coarse-grained” properties of physical systems in terms of statistical probabilities of arrangements of their microscopic components. Thermodynamics is now essential to our understanding of chemical and biological systems, both in and out of equilibrium. Thermodynamics has also been expanded to include ideas around information for classical and quantum systems, and the energy costs of their manipulation for computing tasks.
The phenomenon of tunnelling follows from quantum systems’ wave-particle duality and describes how particles can penetrate classically forbidden energy barriers. The likelihood of this tunnelling can be predicted by the Schrödinger equation and depends on the object’s energy and mass, and the width and height of the barrier. This makes tunnelling more likely for very light particles like electrons and protons, but less so for heavier objects, all else being equal.
During oxidative phosphorylation, the movement of electrons through electron transport chains is coupled to proton pumping across the mitochondrial inner membrane. The resultant proton gradient then powers the synthesis of adenosine triphosphate (ATP). Electron leakage from this chain can result in the formation of potentially harmful reactive oxygen species. One way in which this can be mitigated is through uncoupling, which allows proton leak through the membrane without ATP production. Uncoupling is controlled by several different types of protein, and is a key mechanism in homeostasis and signalling.