Molecular machine in the context of Molecular logic gate

A machine is a thermodynamic system that uses power to apply forces and control movement to perform an action. The term is commonly applied to artificial devices, such as those employing engines or motors, but also to natural biological macromolecules, such as molecular machines. Machines can be driven by animals and people, by natural forces such as wind and water, and by chemical, thermal, or electrical power, and include a system of mechanisms that shape the actuator input to achieve a specific application of output forces and movement. They can also include computers and sensors that monitor performance and plan movement, often called mechanical systems.

Renaissance natural philosophers identified six simple machines which were the elementary devices that put a load into motion, and calculated the ratio of output force to input force, known today as mechanical advantage.

ATP synthase is an enzyme that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (P_i). ATP synthase is a molecular machine. The overall reaction catalyzed by ATP synthase is:

• ADP + P_i + 2H_out ⇌ ATP + H₂O + 2H_in

ATP synthase lies across a cellular membrane and forms an aperture that protons can cross from areas of high concentration to areas of low concentration, imparting energy for the synthesis of ATP. This electrochemical gradient is generated by the electron transport chain and allows cells to store energy in ATP for later use. In prokaryotic cells ATP synthase lies across the plasma membrane, while in eukaryotic cells it lies across the inner mitochondrial membrane. Organisms capable of photosynthesis also have ATP synthase across the thylakoid membrane, which in plants is located in the chloroplast and in cyanobacteria is located in the cytoplasm.

Nanoid robotics, or for short, nanorobotics or nanobotics, is an emerging technology field creating machines or robots, which are called nanorobots or simply nanobots, whose components are at or near the scale of a nanometer (10 meters). More specifically, nanorobotics (as opposed to microrobotics) refers to the nanotechnology engineering discipline of designing and building nanorobots with devices ranging in size from 0.1 to 10 micrometres and constructed of nanoscale or molecular components. The terms nanobot, nanoid, nanite, nanomachine and nanomite have also been used to describe such devices currently under research and development.

Nanomachines are largely in the research and development phase, but some primitive molecular machines and nanomotors have been tested. An example is a sensor having a switch approximately 1.5 nanometers across, able to count specific molecules in the chemical sample. The first useful applications of nanomachines may be in nanomedicine. For example, biological machines could be used to identify and destroy cancer cells. Another potential application is the detection of toxic chemicals, and the measurement of their concentrations, in the environment. Rice University has demonstrated a single-molecule car developed by a chemical process and including Buckminsterfullerenes (buckyballs) for wheels. It is actuated by controlling the environmental temperature and by positioning a scanning tunneling microscope tip.

DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, and functional devices such as molecular machines and DNA computers. The field is beginning to be used as a tool to solve basic science problems in structural biology and biophysics, including applications in X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins to determine structures. Potential applications in molecular scale electronics and nanomedicine are also being investigated.

The conceptual foundation for DNA nanotechnology was first laid out by Nadrian Seeman in the early 1980s, and the field began to attract widespread interest in the mid-2000s. This use of nucleic acids is enabled by their strict base pairing rules, which cause only portions of strands with complementary base sequences to bind together to form strong, rigid double helix structures. This allows for the rational design of base sequences that will selectively assemble to form complex target structures with precisely controlled nanoscale features. Several assembly methods are used to make these structures, including tile-based structures that assemble from smaller structures, folding structures using the DNA origami method, and dynamically reconfigurable structures using strand displacement methods. The field's name specifically references DNA, but the same principles have been used with other types of nucleic acids as well, leading to the occasional use of the alternative name nucleic acid nanotechnology.

Molecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work. In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors. One important difference between molecular motors and macroscopic motors is that molecular motors operate in the thermal bath, an environment in which the fluctuations due to thermal noise are significant.

A rotaxane (from Latin rota 'wheel' and axis 'axle') is a mechanically interlocked molecular architecture consisting of a dumbbell-shaped molecule which is threaded through a macrocycle (see graphical representation). The two components of a rotaxane are kinetically trapped since the ends of the dumbbell (often called stoppers) are larger than the internal diameter of the ring and prevent dissociation (unthreading) of the components since this would require significant distortion of the covalent bonds.

Much of the research concerning rotaxanes and other mechanically interlocked molecular architectures, such as catenanes, has been focused on their efficient synthesis or their utilization as artificial molecular machines. However, examples of rotaxane substructure have been found in naturally occurring peptides, including: cystine knot peptides, cyclotides or lasso-peptides such as microcin J25.

Sir James Fraser Stoddart, FRS FRSE HonFRSC (24 May 1942 – 30 December 2024) was a British-American chemist who was Chair Professor in Chemistry at the University of Hong Kong. He was the Board of Trustees Professor of Chemistry and head of the Stoddart Mechanostereochemistry Group in the Department of Chemistry at Northwestern University in the United States. He worked in the area of supramolecular chemistry and nanotechnology. Stoddart developed highly efficient syntheses of mechanically-interlocked molecular architectures such as molecular Borromean rings, catenanes and rotaxanes utilising molecular recognition and molecular self-assembly processes. He demonstrated that these topologies can be employed as molecular switches. His group has even applied these structures in the fabrication of nanoelectronic devices and nanoelectromechanical systems (NEMS). His efforts were recognized by numerous awards, including the 2007 King Faisal International Prize in Science. He shared the Nobel Prize in Chemistry together with Ben Feringa and Jean-Pierre Sauvage in 2016 for the design and synthesis of molecular machines.

Molecular nanotechnology (MNT) is a technology based on the ability to build structures to complex, atomic specifications by means of mechanosynthesis. This is distinct from nanoscale materials.

Based on Richard Feynman's vision of miniature factories using nanomachines to build complex products (including additional nanomachines), this advanced form of nanotechnology (or molecular manufacturing) would make use of positionally-controlled mechanosynthesis guided by molecular machine systems.

Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context.

Proteins rarely act alone as their functions tend to be regulated. Many molecular processes within a cell are carried out by molecular machines that are built from numerous protein components organized by their PPIs. These physiological interactions make up the so-called interactomics of the organism, while aberrant PPIs are the basis of multiple aggregation-related diseases, such as Creutzfeldt–Jakob and Alzheimer's diseases.

The U4 small nuclear Ribo-Nucleic Acid (U4 snRNA) is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA (pre-mRNA). It forms a duplex with U6, and with each splicing round, it is displaced from the U6 snRNA (and the spliceosome) in an ATP-dependent manner, allowing U6 to re-fold and create the active site for splicing catalysis. A recycling process involving protein Brr2 releases U4 from U6, while protein Prp24 re-anneals U4 and U6. The crystal structure of a 5′ stem-loop of U4 in complex with a binding protein has been solved.

Hard determinism (or metaphysical determinism) is a view on free will which holds that determinism is true, that it is incompatible with free will, and therefore that free will does not exist. Although hard determinism generally refers to nomological determinism, it can also be a position taken with respect to other forms of determinism that necessitate the future in its entirety.

Hard determinism is contrasted with soft determinism, which is a compatibilist form of determinism, holding that free will may exist despite determinism. It is also contrasted with metaphysical libertarianism, the other major form of incompatibilism which holds that free will exists and determinism is false.