Molecular machine
Encyclopedia
A molecular machine, or nanomachine, is any discrete number of molecular components that produce quasi-mechanical movements (output) in response to specific stimuli (input). The expression is often more generally applied to molecules that simply mimic functions that occur at the macroscopic level. The term is also common in nanotechnology
where a number of highly complex molecular machines have been proposed that are aimed at the goal of constructing a molecular assembler
. Molecular machines can be divided into two broad categories; synthetic and biological.
Molecular systems capable of shifting a chemical or mechanical process away from equilibrium represent a potentially important branch of chemistry
and nanotechnology
. As the gradient generated from this process is able to perform useful work these types of systems, by definition, are examples of molecular machinery.
and Feynman's Ratchet (or Brownian ratchet
). Maxwell's Demon is well described elsewhere, and a slightly different interpretation of Richard Feynman
's ratchet is given here.
Imagine a very small system (seen below) of two paddles or gears connected by a rigid axle and that it is possible to keep these two paddles at two different temperatures. One of the gears (at T2) has a pawl that is rectifying the system motion, and therefore, the axle can only move in a clockwise rotation, and in doing so, it could lift a weight (m) upward upon ratcheting. Now imagine if the paddle in box T1 was in a much hotter environment than the gear in box T2; it would be expected that the kinetic energy of the gas molecules (red circles) hitting the paddle in T1 would be much higher than the gas molecules hitting the gear at T2. Therefore, with lower kinetic energy of the gases in T2, there would be very little resistance from the molecules on colliding with the gear in the statistically opposite direction. Further, the ratcheting would allow for directionality, and slowly over time, the axle would rotate and ratchet, lifting the weight (m).
As described, this system may seem like a perpetual motion machine; however, the key ingredient is the heat gradient within the system. This ratchet does not threaten the second law of thermodynamics
, because this temperature gradient must be maintained by some external means. Brownian motion
of the gas particles provides the power to the machine, and the temperature gradient allows the machine to drive the system cyclically away from equilibrium. In Feynman's ratchet, random Brownian motion is not fought against, but instead, harnessed and rectified. Unfortunately, temperature gradients cannot be maintained over molecular scale distances because of molecular vibration
redistributing the energy to other parts of the molecule. Furthermore, despite Feynman's machine doing useful work in lifting the mass, using Brownian motion to power a molecular level machine does not provide any insight on how that power (or potential energy of the lifted weight, m) can be used to perform nanoscale tasks.
), and as such, harnessing molecular motion is a far more difficult process. At the macroscopic level, many machines operate in the gas phase, and often, air resistance is neglected, as it is insignificant, but analogously for a molecular system in a Brownian environment, molecular motion is similar "to walking in a hurricane, or swimming in molasses." The phenomenon of Brownian motion (observed by Robert Brown (botanist)
, 1827) was later explained by Albert Einstein
in 1905. Einstein found that Brownian motion is a consequence of scale and not the nature of the surroundings. As long as thermal energy is applied to a molecule, it will undergo Brownian motion with the kinetic energy appropriate to that temperature. Therefore, like Feynman's strategy, when designing a molecular machine, it seems sensible to utilize Brownian motion rather than attempt to fight against it.
Like macroscopic machines, molecular machines typically have movable parts. However, while everyday macroscopic machines may provide inspiration for molecular machines, it is misleading to draw analogies between their design strategy; the dynamics of large and small length scales are simply too different. Harnessing Brownian motion and making molecular level machines is regulated by the second law of thermodynamics
, with its often counter-intuitive consequences, and as such, we need another inspiration.
Although it is a challenging process to harness Brownian motion, nature has provided us with several blueprints for molecular motion performing useful work. Nature has created many useful structures for compartmentalizing molecular systems, hence creating distinct non-equilibrium distributions; the cell membrane
is an excellent example. Lipophilic barriers make use of a number of different mechanisms to power motion from one compartment to another.
, such as rotaxane
s and catenane
s.
The most complex molecular machines are found within cells. These include motor proteins, such as myosin
, which is responsible for muscle contraction, kinesin
, which moves cargo inside cells away from the nucleus along microtubules, and dynein
, which produces the axonemal beating of motile cilia and flagella. These proteins and their nanoscale dynamics are far more complex than any molecular machines that have yet been artificially constructed.
The detailed mechanism of ciliary motility has been described by Satir in a 2008 review article. A high-level-abstraction summary is that, "[i]n effect, the [motile cilium] is a nanomachine composed of perhaps over 600 proteins in molecular complexes, many of which also function independently as nanomachines."
s, have been designed, although experimental studies of these molecules are inhibited by the lack of methods to construct these molecules. These complex molecular machines form the basis of areas of nanotechnology
, including molecular assembler
.
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
where a number of highly complex molecular machines have been proposed that are aimed at the goal of constructing a molecular assembler
Molecular assembler
A molecular assembler, as defined by K. Eric Drexler, is a "proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision". Some biological molecules such as ribosomes fit this definition. This is because they receive instructions from messenger RNA and...
. Molecular machines can be divided into two broad categories; synthetic and biological.
Molecular systems capable of shifting a chemical or mechanical process away from equilibrium represent a potentially important branch of chemistry
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
and nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
. As the gradient generated from this process is able to perform useful work these types of systems, by definition, are examples of molecular machinery.
Historical Insight and Studies
There are two thought experiments that form the historical basis for molecular machines: Maxwell's demonMaxwell's demon
In the philosophy of thermal and statistical physics, Maxwell's demon is a thought experiment created by the Scottish physicist James Clerk Maxwell to "show that the Second Law of Thermodynamics has only a statistical certainty." It demonstrates Maxwell's point by hypothetically describing how to...
and Feynman's Ratchet (or Brownian ratchet
Brownian ratchet
In the philosophy of thermal and statistical physics, the Brownian ratchet, or Feynman-Smoluchowski ratchet is a thought experiment about an apparent perpetual motion machine first analysed in 1912 by Polish physicist Marian Smoluchowski and popularised by American Nobel laureate physicist Richard...
). Maxwell's Demon is well described elsewhere, and a slightly different interpretation of Richard Feynman
Richard Feynman
Richard Phillips Feynman was an American physicist known for his work in the path integral formulation of quantum mechanics, the theory of quantum electrodynamics and the physics of the superfluidity of supercooled liquid helium, as well as in particle physics...
's ratchet is given here.
Imagine a very small system (seen below) of two paddles or gears connected by a rigid axle and that it is possible to keep these two paddles at two different temperatures. One of the gears (at T2) has a pawl that is rectifying the system motion, and therefore, the axle can only move in a clockwise rotation, and in doing so, it could lift a weight (m) upward upon ratcheting. Now imagine if the paddle in box T1 was in a much hotter environment than the gear in box T2; it would be expected that the kinetic energy of the gas molecules (red circles) hitting the paddle in T1 would be much higher than the gas molecules hitting the gear at T2. Therefore, with lower kinetic energy of the gases in T2, there would be very little resistance from the molecules on colliding with the gear in the statistically opposite direction. Further, the ratcheting would allow for directionality, and slowly over time, the axle would rotate and ratchet, lifting the weight (m).
Second law of thermodynamics
The second law of thermodynamics is an expression of the tendency that over time, differences in temperature, pressure, and chemical potential equilibrate in an isolated physical system. From the state of thermodynamic equilibrium, the law deduced the principle of the increase of entropy and...
, because this temperature gradient must be maintained by some external means. Brownian motion
Brownian motion
Brownian motion or pedesis is the presumably random drifting of particles suspended in a fluid or the mathematical model used to describe such random movements, which is often called a particle theory.The mathematical model of Brownian motion has several real-world applications...
of the gas particles provides the power to the machine, and the temperature gradient allows the machine to drive the system cyclically away from equilibrium. In Feynman's ratchet, random Brownian motion is not fought against, but instead, harnessed and rectified. Unfortunately, temperature gradients cannot be maintained over molecular scale distances because of molecular vibration
Molecular vibration
A molecular vibration occurs when atoms in a molecule are in periodic motion while the molecule as a whole has constant translational and rotational motion...
redistributing the energy to other parts of the molecule. Furthermore, despite Feynman's machine doing useful work in lifting the mass, using Brownian motion to power a molecular level machine does not provide any insight on how that power (or potential energy of the lifted weight, m) can be used to perform nanoscale tasks.
Modern Insights and Studies
Unlike macroscopic motion, molecular systems are constantly undergoing significant dynamic motions subject to the laws of Brownian mechanics (or Brownian motionBrownian motion
Brownian motion or pedesis is the presumably random drifting of particles suspended in a fluid or the mathematical model used to describe such random movements, which is often called a particle theory.The mathematical model of Brownian motion has several real-world applications...
), and as such, harnessing molecular motion is a far more difficult process. At the macroscopic level, many machines operate in the gas phase, and often, air resistance is neglected, as it is insignificant, but analogously for a molecular system in a Brownian environment, molecular motion is similar "to walking in a hurricane, or swimming in molasses." The phenomenon of Brownian motion (observed by Robert Brown (botanist)
Robert Brown (botanist)
Robert Brown was a Scottish botanist and palaeobotanist who made important contributions to botany largely through his pioneering use of the microscope...
, 1827) was later explained by Albert Einstein
Albert Einstein
Albert Einstein was a German-born theoretical physicist who developed the theory of general relativity, effecting a revolution in physics. For this achievement, Einstein is often regarded as the father of modern physics and one of the most prolific intellects in human history...
in 1905. Einstein found that Brownian motion is a consequence of scale and not the nature of the surroundings. As long as thermal energy is applied to a molecule, it will undergo Brownian motion with the kinetic energy appropriate to that temperature. Therefore, like Feynman's strategy, when designing a molecular machine, it seems sensible to utilize Brownian motion rather than attempt to fight against it.
Like macroscopic machines, molecular machines typically have movable parts. However, while everyday macroscopic machines may provide inspiration for molecular machines, it is misleading to draw analogies between their design strategy; the dynamics of large and small length scales are simply too different. Harnessing Brownian motion and making molecular level machines is regulated by the second law of thermodynamics
Second law of thermodynamics
The second law of thermodynamics is an expression of the tendency that over time, differences in temperature, pressure, and chemical potential equilibrate in an isolated physical system. From the state of thermodynamic equilibrium, the law deduced the principle of the increase of entropy and...
, with its often counter-intuitive consequences, and as such, we need another inspiration.
Although it is a challenging process to harness Brownian motion, nature has provided us with several blueprints for molecular motion performing useful work. Nature has created many useful structures for compartmentalizing molecular systems, hence creating distinct non-equilibrium distributions; the cell membrane
Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...
is an excellent example. Lipophilic barriers make use of a number of different mechanisms to power motion from one compartment to another.
Examples of molecular machines
From a synthetic perspective, there are two important types of molecular machines: molecular switches (or shuttles) and molecular motors. The major difference between the two systems is that a switch influences a system as a function of state, whereas a motor influences a system as function of trajectory. A switch (or shuttle) may appear to undergo translational motion, but returning a switch to its original position undoes any mechanical effect and liberates energy to the system. Furthermore, switches cannot use chemical energy to repetitively and progressively drive a system away from equilibrium where a motor can.Synthetic
A wide variety of rather simple molecular machines have been synthesized by chemists. They can consist of a single molecule; however, they are often constructed for mechanically-interlocked molecular architecturesMechanically-interlocked molecular architectures
Mechanically interlocked molecular architectures are connections of molecules not through traditional bonds, but instead as a consequence of their topology. This connection of molecules is analogous to keys on a key chain loop. The keys are not directly connected to the key chain loop but they...
, such as rotaxane
Rotaxane
A rotaxane is a mechanically-interlocked molecular architecture consisting of a "dumbbell shaped molecule" which is threaded through a "macrocycle" . The name is derived from the Latin for wheel and axle...
s and catenane
Catenane
A catenane is a mechanically-interlocked molecular architecture consisting of two or more interlocked macrocycles. The interlocked rings cannot be separated without breaking the covalent bonds of the macrocycles. Catenane is derived from the Latin catena meaning "chain"...
s.
- Molecular motorsSynthetic molecular motorsSynthetic molecular motors are molecular machines capable of rotation under energy input. Although the term "molecular motor" has traditionally referred to a naturally occurring protein that induces motion , some groups also use the term when referring to non-biological, non-peptide synthetic...
are molecules that are capable of unidirectional rotation motion powered by external energy input. A number of molecular machines have been synthesized powered by light or reaction with other molecules.
- A molecular propellerMolecular propellerMolecular propeller is a molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers : it has several molecular-scale blades attached at a certain pitch angle around the circumference of a shaft, aligned along the rotational...
is a molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers. It has several molecular-scale blades attached at a certain pitch angle around the circumference of a nanoscale shaft.
- A molecular switchMolecular switchA molecular switch is a molecule that can be reversibly shifted between two or more stable states. The molecules may be shifted between the states in response to changes in e.g. pH, light, temperature, an electrical current, microenvironment, or the presence of a ligand. In some cases, a...
is a molecule that can be reversibly shifted between two or more stable states. The molecules may be shifted between the states in response to changes in e.g. pH, light, temperature, an electrical current, microenvironment, or the presence of a ligand.
- A molecular shuttleMolecular shuttleA molecular shuttle in supramolecular chemistry is a special type of molecular machine capable of shuttling molecules or ions from one location to another. This field is of relevance to nanotechnology in its quest for nanoscale electronic components and also to biology where many biochemical...
is a molecule capable of shuttling molecules or ions from one location to another. A common molecular shuttle consists of a rotaxane where the macrocycle can move between two sites or stations along the dumbbell backbone.
- Molecular tweezers are host molecules capable of holding items between its two arms. The open cavity of the molecular tweezers binds items using non-covalent bonding including hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, and/or electrostatic effects. Examples of molecular tweezers have been reported that are constructed from DNA and are considered DNA machineDNA machineA DNA machine is a molecular machine constructed from DNA. Research into DNA machines was pioneered in the late 1980s by Nadrian Seeman and co-workers from New York University...
s.
- A molecular sensorMolecular sensorA molecular sensor or chemosensor is a molecule that interacts with an analyte to produce a detectable change. Molecular sensors combine molecular recognition with some form of reporter so the presence of the guest can be observed...
is a molecule that interacts with an analyte to produce a detectable change. Molecular sensors combine molecular recognition with some form of reporter, so the presence of the item can be observed.
- A molecular logic gateMolecular logic gateA molecular logic gate is a molecule that performs a logical operation on one or more logic inputs and produces a single logic output. Much academic research is dedicated to the development of these systems and several prototypes now exist...
is a molecule that performs a logical operation on one or more logic inputs and produces a single logic output. Unlike a molecular sensor, the molecular logic gate will only output when a particular combination of inputs are present.
Biological
Myosin
Myosins comprise a family of ATP-dependent motor proteins and are best known for their role in muscle contraction and their involvement in a wide range of other eukaryotic motility processes. They are responsible for actin-based motility. The term was originally used to describe a group of similar...
, which is responsible for muscle contraction, kinesin
Kinesin
A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule filaments, and are powered by the hydrolysis of ATP . The active movement of kinesins supports several cellular functions including mitosis, meiosis and transport of cellular...
, which moves cargo inside cells away from the nucleus along microtubules, and dynein
Dynein
Dynein is a motor protein in cells which converts the chemical energy contained in ATP into the mechanical energy of movement. Dynein transports various cellular cargo by "walking" along cytoskeletal microtubules towards the minus-end of the microtubule, which is usually oriented towards the cell...
, which produces the axonemal beating of motile cilia and flagella. These proteins and their nanoscale dynamics are far more complex than any molecular machines that have yet been artificially constructed.
The detailed mechanism of ciliary motility has been described by Satir in a 2008 review article. A high-level-abstraction summary is that, "[i]n effect, the [motile cilium] is a nanomachine composed of perhaps over 600 proteins in molecular complexes, many of which also function independently as nanomachines."
Theoretical
The construction of more complex molecular machines is an active area of theoretical research. A number of molecules, such as molecular propellerMolecular propeller
Molecular propeller is a molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers : it has several molecular-scale blades attached at a certain pitch angle around the circumference of a shaft, aligned along the rotational...
s, have been designed, although experimental studies of these molecules are inhibited by the lack of methods to construct these molecules. These complex molecular machines form the basis of areas of nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
, including molecular assembler
Molecular assembler
A molecular assembler, as defined by K. Eric Drexler, is a "proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision". Some biological molecules such as ribosomes fit this definition. This is because they receive instructions from messenger RNA and...
.
See also
- DNA machineDNA machineA DNA machine is a molecular machine constructed from DNA. Research into DNA machines was pioneered in the late 1980s by Nadrian Seeman and co-workers from New York University...
- Nanoelectromechanical systemsNanoelectromechanical systemsNanoelectromechanical systems are devices integrating electrical and mechanical functionality on the nanoscale. NEMS form the logical next miniaturization step from so-called microelectromechanical systems, or MEMS devices...
- NanomechanicsNanomechanicsNanomechanics is a branch of nanoscience studying fundamental mechanical properties of physical systems at the nanometer scale. Nanomechanics has emerged on the crossroads of classical mechanics, solid-state physics, statistical mechanics, materials science, and quantum chemistry...
- NanosensorNanosensorNanosensors are any biological, chemical, or surgical sensory points used to convey information about nanoparticles to the macroscopic world. Their use mainly include various medicinal purposes and as gateways to building other nanoproducts, such as computer chips that work at the nanoscale and...
- Protein dynamics
- Nano brainNano brainA nano brain is a conceptual device that executes massively parallel computing following the information processing principles of human brain. This machine assembly would serve as an intelligent decision making unit for the nano-robots, and could be programmed to execute particular operation for...