Molecular machine

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Molecular_machine

Bacterial flagellar motor assembly: Shown here is the C-ring at the base with FliG in red, FliM in yellow, and FliN in shades of purple; the MS-ring in blue; the MotAB in brown; the LP-ring in pink; and the rod in gray.

Molecular 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. Multiple examples of molecular machinery and their components are found in the Protein Data Bank. For the last several decades, scientists have attempted, with varying degrees of success, to miniaturize machines found in the macroscopic world.

The first example of an artificial molecular machine (AMM) was reported in 1994, featuring a rotaxane with a ring and two different possible binding sites. In 2016 the Nobel Prize in Chemistry was awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart, and Bernard L. Feringa for the design and synthesis of molecular machines. A major point is to exploit existing motion in proteins, such as rotation about single bonds or cis-trans isomerization. Different AMMs are produced by introducing various functionalities, such as the introduction of bistability to create switches. A broad range of AMMs has been designed, featuring different properties and applications; some of these include molecular motors, switches, and logic gates. A wide range of applications have been demonstrated for AMMs, including those integrated into polymeric, liquid crystal, and crystalline systems for varied functions (such as materials research, homogenous catalysis and surface chemistry).

Terminology

Several definitions describe a "molecular machine" as 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. The expression is often more generally applied to molecules that simply mimic functions that occur at the macroscopic level. A few prime requirements for a molecule to be considered a "molecular machine" are: the presence of moving parts, the ability to consume energy, and the ability to perform a task. Molecular machines differ from other stimuli-responsive compounds that can produce motion (such as cis-trans isomers) in their relatively larger amplitude of movement (potentially due to chemical reactions) and the presence of a clear external stimulus to regulate the movements (as compared to random thermal motion). Piezoelectric, magnetostrictive, and other materials that produce a movement due to external stimuli on a macro-scale are generally not included, since despite the molecular origin of the motion the effects are not useable on the molecular scale.

This definition generally applies to synthetic molecular machines, which have historically gained inspiration from the naturally occurring biological molecular machines (also referred to as "nanomachines"). Biological machines are considered to be nanoscale devices (such as molecular proteins) in a living system that convert various forms of energy to mechanical work in order to drive crucial biological processes such as intracellular transport, muscle contractions, ATP generation and cell division.

History

What would be the utility of such machines? Who knows? I cannot see exactly what would happen, but I can hardly doubt that when we have some control of the arrangement of things on a molecular scale we will get an enormously greater range of possible properties that substances can have, and of the different things we can do.

— Richard Feynman, There's Plenty of Room at the Bottom

Biological molecular machines have been known and studied for decades given their vital role in sustaining life, and have served as inspiration for synthetically designed systems with similar useful functionality. The advent of conformational analysis, or the study of conformers to analyze complex chemical structures, in the 1950s gave rise to the idea of understanding and controlling relative motion within molecular components for further applications. This led to the design of "proto-molecular machines" featuring conformational changes such as cog-wheeling of the aromatic rings in triptycenes. By 1980, scientists could achieve desired conformations using external stimuli and utilize this for different applications. A major example is the design of a photoresponsive crown ether containing an azobenzene unit, which could switch between cis and trans isomers on exposure to light and hence tune the cation-binding properties of the ether. In his seminal 1959 lecture There's Plenty of Room at the Bottom, Richard Feynman alluded to the idea and applications of molecular devices designed artificially by manipulating matter at the atomic level. This was further substantiated by Eric Drexler during the 1970s, who developed ideas based on molecular nanotechnology such as nanoscale "assemblers", though their feasibility was disputed.

The first example of an artificial molecular machine (a switchable molecular shuttle). The positively charged ring (blue) is initially positioned over the benzidine unit (green), but shifts to the biphenol unit (red) when the benzidine gets protonated (purple) as a result of electrochemical oxidation or lowering of the pH.

Though these events served as inspiration for the field, the actual breakthrough in practical approaches to synthesize artificial molecular machines (AMMs) took place in 1991 with the invention of a "molecular shuttle" by Sir Fraser Stoddart. Building upon the assembly of mechanically linked molecules such as catenanes and rotaxanes as developed by Jean-Pierre Sauvage in the early 1980s, this shuttle features a rotaxane with a ring that can move across an "axle" between two ends or possible binding sites (hydroquinone units). This design realized the well-defined motion of a molecular unit across the length of the molecule for the first time. In 1994, an improved design allowed control over the motion of the ring by pH variation or electrochemical methods, making it the first example of an AMM. Here the two binding sites are a benzidine and a biphenol unit; the cationic ring typically prefers staying over the benzidine ring, but moves over to the biphenol group when the benzidine gets protonated at low pH or if it gets electrochemically oxidized. In 1998, a study could capture the rotary motion of a decacyclene molecule on a copper-base metallic surface using a scanning tunneling microscope. Over the following decade, a broad variety of AMMs responding to various stimuli were invented for different applications. In 2016, the Nobel Prize in Chemistry was awarded to Sauvage, Stoddart, and Bernard L. Feringa for the design and synthesis of molecular machines.

Artificial molecular machines

Main article: Synthetic molecular motor

Over the past few decades, AMMs have diversified rapidly and their design principles, properties, and characterization methods have been outlined more clearly. A major starting point for the design of AMMs is to exploit the existing modes of motion in molecules. For instance, single bonds can be visualized as axes of rotation, as can be metallocene complexes. Bending or V-like shapes can be achieved by incorporating double bonds, that can undergo cis-trans isomerization in response to certain stimuli (typically irradiation with a suitable wavelength), as seen in numerous designs consisting of stilbene and azobenzene units. Similarly, ring-opening and -closing reactions such as those seen for spiropyran and diarylethene can also produce curved shapes. Another common mode of movement is the circumrotation of rings relative to one another as observed in mechanically interlocked molecules (primarily catenanes). While this type of rotation can not be accessed beyond the molecule itself (because the rings are confined within one another), rotaxanes can overcome this as the rings can undergo translational movements along a dumbbell-like axis. Another line of AMMs consists of biomolecules such as DNA and proteins as part of their design, making use of phenomena like protein folding and unfolding.

Some common types of motion seen in some simple components of artificial molecular machines. a) Rotation around single bonds and in sandwich-like metallocenes. b) Bending due to cis-trans isomerization. c) Translational motion of a ring (blue) between two possible binding sites (red) along the dumbbell-like rotaxane axis (purple). d) Rotation of interlocked rings (depicted as blue and red rectangles) in a catenane.

AMM designs have diversified significantly since the early days of the field. A major route is the introduction of bistability to produce molecular switches, featuring two distinct configurations for the molecule to convert between. This has been perceived as a step forward from the original molecular shuttle which consisted of two identical sites for the ring to move between without any preference, in a manner analogous to the ring flip in an unsubstituted cyclohexane. If these two sites are different from each other in terms of features like electron density, this can give rise to weak or strong recognition sites as in biological systems — such AMMs have found applications in catalysis and drug delivery. This switching behavior has been further optimized to acquire useful work that gets lost when a typical switch returns to its original state. Inspired by the use of kinetic control to produce work in natural processes, molecular motors are designed to have a continuous energy influx to keep them away from equilibrium to deliver work.

Various energy sources are employed to drive molecular machines today, but this was not the case during the early years of AMM development. Though the movements in AMMs were regulated relative to the random thermal motion generally seen in molecules, they could not be controlled or manipulated as desired. This led to the addition of stimuli-responsive moieties in AMM design, so that externally applied non-thermal sources of energy could drive molecular motion and hence allow control over the properties. Chemical energy (or "chemical fuels") was an attractive option at the beginning, given the broad array of reversible chemical reactions (heavily based on acid-base chemistry) to switch molecules between different states. However, this comes with the issue of practically regulating the delivery of the chemical fuel and the removal of waste generated to maintain the efficiency of the machine as in biological systems. Though some AMMs have found ways to circumvent this, more recently waste-free reactions such based on electron transfers or isomerization have gained attention (such as redox-responsive viologens). Eventually, several different forms of energy (electric, magnetic, optical and so on) have become the primary energy sources used to power AMMs, even producing autonomous systems such as light-driven motors.

Types

Various AMMs are tabulated below along with indicative images:

Type	Details	Image
Molecular balance	A molecule that can interconvert between two or more conformational or configurational states in response to the dynamic of multiple intra- and intermolecular driving forces, such as hydrogen bonding, solvophobic or hydrophobic effects, π interactions, and steric and dispersion interactions. The distinct conformers of a molecular balance can show different interactions with the same molecule, such that analyzing the ratio of the conformers and the energies for these interactions can enable quantification of different properties (such as CH-π or arene-arene interactions, see image).
Molecular hinge	A molecular hinge is a molecule that can typically rotate in a crank-like motion around a rigid axis, such as a double bond or aromatic ring, to switch between reversible configurations. Such configurations must have distinguishable geometries; for instance, azobenzene groups in a linear molecule may undergo cis-trans isomerization when irradiated with ultraviolet light, triggering a reversible transition to a bent or V-shaped conformation (see image). Molecular hinges have been adapted for applications such as nucleobase recognition, peptide modifications, and visualizing molecular motion.
Molecular logic gate	A molecule that performs a logical operation on one or more logic inputs and produces a single logic output. Modelled on logic gates, these molecules have slowly replaced the conventional silicon-based machinery. Several applications have come forth, such as water quality examination, food safety examination, metal ion detection, and pharmaceutical studies. The first example of a molecular logic gate was reported in 1993, featuring a receptor (see image) where the emission intensity could be treated as a tunable output if the concentrations of protons and sodium ions were to be considered as inputs.
Molecular motor	A molecule that is capable of directional rotary motion around a single or double bond and produce useful work as a result (as depicted in the image). Carbon nanotube nanomotors have also been produced. Single bond rotary motors are generally activated by chemical reactions whereas double bond rotary motors are generally fueled by light. The rotation speed of the motor can also be tuned by careful molecular design.
Molecular necklace	A class of mechanically interlocked molecules derived from catenanes where a large macrocycle backbone connects at least three small rings in the shape of a necklace (see image for example). A molecular necklace consisting of a large macrocycle threaded by n-1 rings (hence comprising n rings) is represented as [n]MN. The first molecular necklace was synthesized in 1992, featuring several α-cyclodextrins on a single polyethylene glycol chain backbone; the authors connected this to the idea of a "molecular abacus" proposed by Stoddart and coworkers around the same time. Several interesting applications have emerged for these molecules, such as antibacterial activity, desulfurization of fuels, and piezoelectricity.
Molecular propeller	A molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers (see schematic image on right). It has several molecular-scale blades attached at a certain pitch angle around the circumference of a nanoscale shaft. Propellers have been shown to have interesting properties, such as variations in pumping rates for hydrophilic and hydrophobic fluids.
Molecular shuttle	A molecule capable of shuttling molecules or ions from one location to another. This is schematically depicted in the image on the right, where a ring (in green) can bind to either one of the yellow sites on the blue macrocyclic backbone. A common molecular shuttle consists of a rotaxane where the macrocycle can move between two sites or stations along the dumbbell backbone; controlling the properties of either site and by regulating conditions like pH can enable control over which site is selected for binding. This has led to novel applications in catalysis and drug delivery.
Molecular switch	A molecule that can be reversibly shifted between two or more stable states in response to certain stimuli. This change of states influences the properties of the molecule according to the state it occupies at the moment. Unlike a molecular motor, any mechanical work done due to the motion in a switch is generally undone once the molecule returns to its original state unless it is part of a larger motor-like system. The image on the right shows a hydrazone-based switch that switches in response to pH changes.
Molecular tweezers	Host molecules capable of holding items between their 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 interactions, or electrostatic effects. For instance, the image on the right depicts tweezers formed by corannulene pincers clasping a C60 fullerene molecule, termed "buckycatcher". Examples of molecular tweezers have been reported that are constructed from DNA and are considered DNA machines.
Nanocar	Single-molecule vehicles that resemble macroscopic automobiles and are important for understanding how to control molecular diffusion on surfaces. The image on the right shows an example with wheels made of fullerene molecules. The first nanocars were synthesized by James M. Tour in 2005. They had an H-shaped chassis and 4 molecular wheels (fullerenes) attached to the four corners. In 2011, Feringa and co-workers synthesized the first motorized nanocar which had molecular motors attached to the chassis as rotating wheels. The authors were able to demonstrate directional motion of the nanocar on a copper surface by providing energy from a scanning tunneling microscope tip. Later, in 2017, the world's first-ever nanocar race took place in Toulouse.

Biological molecular machines

Main article: Protein domain dynamics

A ribosome performing the elongation and membrane targeting stages of protein translation. The ribosome is green and yellow, the tRNAs are dark blue, and the other proteins involved are light blue. The produced peptide is released into the endoplasmic reticulum. Protein domain dynamics can now be seen by neutron spin echo spectroscopy.

Many macromolecular machines are found within cells, often in the form of multi-protein complexes. Examples of biological machines 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 moves cargo inside cells towards the nucleus and produces the axonemal beating of motile cilia and flagella. "[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 ... Flexible linkers allow the mobile protein domains connected by them to recruit their binding partners and induce long-range allostery via protein domain dynamics." Other biological machines are responsible for energy production, for example ATP synthase which harnesses energy from proton gradients across membranes to drive a turbine-like motion used to synthesise ATP, the energy currency of a cell. Still other machines are responsible for gene expression, including DNA polymerases for replicating DNA, RNA polymerases for producing mRNA, the spliceosome for removing introns, and the ribosome for synthesising proteins. These machines and their nanoscale dynamics are far more complex than any molecular machines that have yet been artificially constructed.

Biological machines have potential applications in nanomedicine. For example, they could be used to identify and destroy cancer cells. Molecular nanotechnology is a speculative subfield of nanotechnology regarding the possibility of engineering molecular assemblers, biological machines which could re-order matter at a molecular or atomic scale. Nanomedicine would make use of these nanorobots, introduced into the body, to repair or detect damages and infections, but these are considered to be far beyond current capabilities.

Research and applications

Advances in this area are inhibited by the lack of synthetic methods. In this context, theoretical modeling has emerged as a pivotal tool to understand the self-assembly or -disassembly processes in these systems.

Possible applications have been demonstrated for AMMs, including those integrated into polymeric, liquid crystal, and crystalline systems for varied functions. Homogenous catalysis is a prominent example, especially in areas like asymmetric synthesis, utilizing noncovalent interactions and biomimetic allosteric catalysis. AMMs have been pivotal in the design of several stimuli-responsive smart materials, such as 2D and 3D self-assembled materials and nanoparticle-based systems, for versatile applications ranging from 3D printing to drug delivery.

AMMs are gradually moving from the conventional solution-phase chemistry to surfaces and interfaces. For instance, AMM-immobilized surfaces (AMMISs) are a novel class of functional materials consisting of AMMs attached to inorganic surfaces forming features like self-assembled monolayers; this gives rise to tunable properties such as fluorescence, aggregation and drug-release activity.

Most of these "applications" remain at the proof-of-concept level. Challenges in streamlining macroscale applications include autonomous operation, the complexity of the machines, stability in the synthesis of the machines and the working conditions.

Biomining

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Biomining

Biomining refers to processes that use organisms to extract metals from ores and other solid materials. The largest application currently being used is the treatment of mining waste containing iron, copper, zinc, and gold. It may also be useful in maximizing the yields of increasingly low grade ore deposits. Biomining has been proposed as a relatively environmentally friendly alternative and/or supplementation to traditional mining. Current methods of biomining are modified leach mining processes. These aptly named bioleaching processes most commonly includes the inoculation of extracted rock with bacteria and acidic solution, with the leachate salvaged and processed for the metals of value. Aspirational applications include space biomining, fungal bioleaching and biomining with hybrid biomaterials.

Biomining is related to biohydrometallurgy, a subset or specialized form of hydrometallurgy, which refers to the use of aqueous solutions for metal extraction through a series of chemical reactions. In biohydrometallurgy, the aqueous solutions contain biological agents (bacteria), which assist in the recovery of metals. Bioleaching is closely related to biohydrometallurgy. It focuses on extraction or liberation of metals from their ores through the use of living organisms. Relative to traditional forms of metallurgy, biohydrometallurgy or bioleaching is slow but in principle low cost. These techniques are mainly applied to recovery of copper and gold from low-grade ores. These techniques have been proposed to the extraction of uranium, nickel, and other metals.

History

The possibility of using microorganisms in biomining applications was realized after the 1951 paper by Kenneth Temple and Arthur Colmer. In the paper the authors presented evidence that the bacteria Acidithiobacillus ferrooxidans (basonym Thiobacillus ferrooxidans) is an iron oxidizer that thrive in iron, copper and magnesium-rich environments. In the experiment, A. ferrooxidans was inoculated into media containing between 2,000 and 26,000 ppm ferrous iron, finding that the bacteria grew faster and were more motile in the high iron concentrations. The byproducts of the bacterial growth caused the media to turn very acidic, in which the microorganisms still thrived. Following this experiment, the potential to use fungi to leach metals from their environment and use microorganisms to take up radioactive elements like uranium and thorium have also been explored.

While the 1960s was when industrial biomining got its start, humans have been unknowingly using biomining practices for hundreds of years. In western Europe the practice of extracting copper from metallic iron by placing it into drainage streams, used to be considered an act of alchemy. However, today we know that it is a fairly simple chemical reaction.

Cu²⁺ + Fe⁰ → Cu⁰ + Fe²⁺

In the Middle Ages in Portugal, Spain and Wales, miners unknowingly used this reaction to their advantage when they discovered that when flooding deep mine shafts for a period with some leftover iron they were able to obtain copper.

In China, the use of biomining techniques has been documented as early as 6th-7th century BC. The relationship between water and ore to produce copper was well documented, and during the Tang dynasty and Song dynasty copper was produced using hydrometallurgical techniques. Though the mechanism of oxidation via bacteria was not understood, the unintended use of biomining allowed copper production in China to reach 1000 Tons per year.

Biomining was first used more than 300 years ago to recover copper. Early work on copper bioleaching was carried out at the mines of Chuquicamata and Lo Aguirre in Chile.

Mechanism

A Simplified scheme illustrating bioleaching of copper from its ore chalcopyrite

The processes often involve the use ferric ions (Fe³⁺) for oxidation of sulfide minerals. The organisms that promote these reactions tolerate high metal concentrations and low pH:

CuFeS₂+4H⁺+O₂ → Cu²⁺+Fe²⁺+2S⁰+2H₂O

4Fe²⁺ + 4H⁺ + O₂ → 4Fe³⁺ + 2H₂O

2S⁰ + 3O₂+2H₂O → 2 SO^2-₄ + 4H⁺,

CuFeS₂ + 4Fe³⁺ → Cu²⁺ + 2 S⁰ + 5 Fe²⁺

Bioleaching technologies

Direct vs indirect leaching

Biohydrometallurgy can be productively implemented in two ways: direct and indirect leaching. Direct leaching entails physical contact between the ore and the microbe. The sulfide ore serves as an electron donor, which supplies energy to the organisms when coupled to the reduction of oxygen. Many sulfide ores are susceptible to direct leaching: covelite (CuS), chalcocite (Cu₂S), galena (PbS), molybdenite (MoS₂), and more. The energy producing conversion can be represented:

MS + 2 O₂ → MSO₄

"Indirect leaching" requires no physical contact between the organism and the sulfide mineral. Here, the bacteria produce Fe³⁺ (ferric) ions, which can be viewed as the lixiviant. Ferric ions attack the sulfide (usually) ore. The general equation for the solubilization of a metal sulfide ore is:

MS + Fe₂(SO₄)₃ + O₂ → 2 FeSO₄ +MSO₄ + S

Here the target of the biomining is M, often copper. The bacteria can then promote the re-oxidation of ferrous by air and the oxidation of sulfur-containing products to sulfuric acid.

The oxidation of the pyrite is of particular interest in gold recovery for gold-containing pyrite (and related "pyritic" minerals). The goal here is to solubilize pyrite using air:

FeS₂ + O₂ + 2 H₂O → FeSO₄ + 2 H₂SO₄

In terms of mechanism, an early step entails oxidation of pyrite to thiosulfate by ferric ion (Fe³⁺), which in turn is reduced to give ferrous ion (Fe²⁺). Thiosulfate is also oxidized by air to give sulfate:

S₂O2−3 + 2 O₂ + H₂O → 2HSO−4

The oxidation of the ferrous ion by air is promoted by bacteria:

4 FeSO₄ + O₂ + 2 H₂SO₄ → 2Fe₂(SO₄)₃ + 2 H₂O

Thus the roles of the bacteria are the oxidations of the ferrous and thiosulfate. As a practical matter, the bacteria require nutrients such as ammonium and phosphate.

The sulfate salts are metal aquo complexes, not anhydrous as depicted.

Similar reactions apply to the proposed leaching of nickel ions from pentlandite ores and uranium from UO2-containing ores.

Heap or dump leaching

Bioleaching was one of the first widely used applications of biomining. It is practiced in two broad venues:

• rock is treated with an extractant (lixiviant), which percolates through the solid and the metals are recovered from the leachate.
  • Dump bioleaching, waste rock is piled into mounds (>100m tall) and saturated with sulfuric acid to encourage mineral oxidation from native bacteria. Inoculation of the rock with bacteria is often not performed in dump bioleaching which instead relies on the bacteria already present in the rock.
  • Heap bioleaching is a newer take on dump leaching. The process includes more processing in which the rocks are ground into a finer grain size. This finer grain is then stacked only 2 – 10 m high and is well irrigated allowing for plenty of oxygen and carbon dioxide to reach the bacteria. The mounds are also often inoculated with bacteria. The liquid coming out at the bottom of the pile, called leachate, is rich in the processed mineral. The heaps reside on non-porous platforms which catch the leachate for processing. Once collected the leachate is transported to a precipitation plant where the metal is reprecipitated and purified. The waste liquid, now void of the valuable minerals, can be pumped back to the top of the pile and the cycle is repeated.

The temperature inside the leach dump often rises spontaneously as a result of microbial activities. Thus, thermophilic iron-oxidizing chemolithotrophs such as thermophilic Acidithiobacillus species and Leptospirillum and at even higher temperatures the thermoacidophilic archaeon Sulfolobus (Metallosphaera sedula) may become important in the leaching process above 40 °C.

In situ copper biomining of and electro-winning for recovery from Kupferschiefer deposits

Stirred tank

A major alternative to heap or dump leaching is continuously stirred tank reactor (STR). Alternatives include the airlift reactor (ALR) or pneumatic reactor (PR) of the Pachuca type to extract the low concentration mineral resources efficiently.

In situ biomining

In situ biomining involves the flooding and inoculation of fractured ore bodies that have yet to be removed from the ground. Once the bacteria are introduced to the ore deposits, they begin leaching the precious metals, which can then be extracted as leachate with a recovery well. In-situ mining also shows promise for applications in cost-effective deep subsurface extraction of metals.

In situ biomining, is the one current method utilizing bioleaching that serves as an effective and viable replacement for traditional mining. Because in-situ biomining, negates the need for the extraction of the ore bodies, this method stops the need for hauling or smelting of the ore. This would mean there would be no waste rocks or mineral tailings that contaminate the surface. In-situ biomining poses environmental challenges, such as the contamination of ground water.

Applications

Gold

Bioleaching from pyritic ores (pyrite, marcasite, arsenopyrite) utilize iron- and sulfur-oxidizing bacteria, including Acidithiobacillus ferrooxidans (formerly known as Thiobacillus ferrooxidans) and Acidithiobacillus thiooxidans (formerly known as Thiobacillus thiooxidans). There is no interest in obtaining iron salts from this kind of treatment. Rather, traces of precious metals such as gold may be liberated in the process since tiny particles of gold are often associated with pyrite. Sulfuric acid is produced in the processing of these pyritic ores, using indirect leaching. Plants for biooxidation of gold-bearing concentrates have been operated at 40 °C with mixed cultures of Leptospirillum ferrooxidans or of the genera Acidithiobacillus. Gold is frequently found in nature associated with arsenopyrite and pyrite. In the microbial leaching process Acidithiobacillus ferrooxidans, etc. dissolve these minerals, exposing trapped gold (Au). The following reaction summarizes the process:

2 FeAsS[Au] + 7 O₂ + 2 H₂O + H₂SO₄ → Fe₂(SO₄)₃ + 2 H₃AsO₄ + [Au]

Copper ores

One of the largest applications of these leaching methods is in the mining of copper. Acidithiobacillus ferrooxidans has the ability to solubilize copper from its sulfidic ores. The acidophilic archaea Sulfolobus metallicus and Metallosphaera sedula can tolerate up to 4% of copper. The main application is for extraction from low grade ores using Thiobacillus thiooxidans. – an important consideration in the face of the depletion of high grade ores.

The copper can then be recovered from the solution by plating it out on scrap iron or electrowinning.

Fe⁰ + Cu²⁺ → Cu⁰ + Fe²⁺

The main copper mineral chalcopyrite (CuFeS₂) is not leached very efficiently. Instead, the dominant technology remains flotation. The leaching of CuFeS₂ proceeds according the route indicated for indirect leaching above.

Uranium

Bioleaching of non-sulfidic ores such as pitchblende also uses ferric iron as an oxidant (e.g., UO₂ + 2 Fe³⁺ ==> UO₂²⁺ + 2 Fe²⁺). In this case, the purpose of the bacterial step is the regeneration of Fe³⁺. Sulfidic iron ores can be added to speed up the process and provide a source of iron. Bioleaching of non-sulfidic ores by layering of waste sulfides and elemental sulfur, colonized by Acidithiobacillus spp., has been demonstrated, which provides a strategy for accelerated leaching of materials that do not contain sulfide minerals.

Biomining was used in Canada in the 1970s to extract additional uranium out of exploited mines. As in the biomining of copper, Acidithiobacillus ferrooxidans can oxidize U⁴⁺ to U⁶⁺ with O₂ as electron acceptor. However, it is likely that the uranium leaching process depends more on the chemical oxidation of uranium by Fe³⁺, with At. ferrooxidans contributing mainly through the reoxidation of Fe²⁺ to Fe³⁺.

UO₂ + Fe₂(SO₄)₃ → UO₂SO₄ + 2 FeSO₄

Aspirational themes

Additional capabilities, of current bioleaching technologies include the bioleaching of metals from sulfide ores, phosphate ores, and concentrating of metals from solution. For example, the bioleaching of cobalt mine tailings has been investigated using stirred tanks.

Illustration of the process of uranium heap leaching. In bioleaching, the heap would have been inoculated with the process specific microbe.

Coal desulfurization

Biological methods have shown some promise for the removal of sulfur from coal, giving a cleaner-burning fuel. This concept has not progressed beyond demonstration phase, however.

Biomining in space

Theoretical map of space biomining/bioleaching based biological life support system (BLSS)

Microorganisms could be employed to mine extraterrestrially.

Space biomining is at the conceptual stage. Bioleaching in space also shows promise for application in building biological life support systems (BLSS). BLSS do not usually contain biological component, however, the use of microorganisms to breakdown waste and regolith, while being able to capture their byproducts like nitrates and methane would theoretically allow for a cyclical system of regenerative life support.

The experimental unit of the experiment

 

S. desiccabilis is a microorganisms that showed high efficacy

Fungi in biomining

Fungi and plants (phytoextraction also known as phytomining) may also be used. Species of filamentous fungi, specifically those in the genera of Aspergillus and Penicillium have been shown as effective bioleaching agents. Fungi have the ability to solubilize metals through acidolysis, redoxolysis and chelation reactions. Like bacteria, fungi have been studied for their ability to extract rare earth elements and to process low grade ore. But their most promising and studied usage is in the breakdown of E-waste and the recovery of valuable metals from it, like gold. Despite the promise of fungal bioleaching, there has been no industrial applications of it as it does not out compete its bacterial counterparts.

Fungi can be grown on many substrates, such as electronic scrap, catalytic converters, and fly ash from municipal waste incineration. Experiments have shown that two fungal strains (Aspergillus niger, Penicillium simplicissimum) were able to mobilize Cu and Sn by 65%, and Al, Ni, Pb, and Zn by more than 95%. Aspergillus niger can produce some organic acids such as citric acid. This form of leaching does not rely on microbial oxidation of metal but rather uses microbial metabolism as source of acids that directly dissolve the metal.

Economic feasibility and potential drawbacks

As a complement to traditional mining, biomining allows for extraction of some low-grade ore and mine tailings. The approach is environmentally appealing, however the Finnish Talvivaara project proved to be environmentally and economically disastrous.

Cyberspace

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Cyberspace

Nightscape in Chongqing, China. Artificial landscapes and "city lights at night" were some of the first metaphors used by the genre for cyberspace (in Neuromancer by William Gibson).

Cyberspace is an interconnected digital environment. It is a type of virtual world popularized with the rise of the Internet. The term entered popular culture from science fiction and the arts but is now used by technology strategists, security professionals, governments, military and industry leaders and entrepreneurs to describe the domain of the global technology environment, commonly defined as standing for the global network of interdependent information technology infrastructures, telecommunications networks and computer processing systems. Others consider cyberspace to be just a notional environment in which communication over computer networks occurs. The word became popular in the 1990s when the use of the Internet, networking, and digital communication were all growing dramatically; the term cyberspace was able to represent the many new ideas and phenomena that were emerging. As a social experience, individuals can interact, exchange ideas, share information, provide social support, conduct business, direct actions, create artistic media, play games, engage in political discussion, and so on, using this global network. Cyberspace users are sometimes referred to as "cybernauts".

The term cyberspace has become a conventional means to describe anything associated with general computing, the Internet and the diverse Internet culture. The U.S. government recognizes the interdependent network of information technology infrastructures and cyber-physical systems operating across this medium as part of the US national critical infrastructure. Amongst individuals on cyberspace, there is believed to be a code of shared rules and ethics mutually beneficial for all to follow, referred to as cyberethics. Many view the right to privacy as most important to a functional code of cyberethics. Such moral responsibilities go hand in hand when working online with global networks, specifically when opinions are involved with online social experiences.

According to Chip Morningstar and F. Randall Farmer, cyberspace is defined more by the social interactions involved rather than its technical implementation. In their view, the computational medium in cyberspace is an augmentation of the communication channel between real people; the core characteristic of cyberspace is that it offers an environment that consists of many participants with the ability to affect and influence each other. They derive this concept from the observation that people seek richness, complexity, and depth within a virtual world.

Etymology

The term cyberspace first appeared in the visual arts in the late 1960s, when Danish artist Susanne Ussing (1940–1998) and her partner architect Carsten Hoff (b. 1934) constituted themselves as Atelier Cyberspace. Under this name the two made a series of installations and images entitled "sensory spaces" that were based on the principle of open systems adaptable to various influences, such as human movement and envisioned urban planning architectures.

Atelier Cyberspace worked at a time when the Internet did not exist and computers were more or less off-limit to artists and creative engagement. In a 2015 interview with Scandinavian art magazine Kunstkritikk, Carsten Hoff recollects that although Atelier Cyberspace did try to implement computers, they had no interest in the virtual space as such:

To us, "cyberspace" was simply about managing spaces. There was nothing esoteric about it. Nothing digital, either. It was just a tool. The space was concrete, physical.

In the same interview, Hoff continues:

Our shared point of departure was that we were working with physical settings, and we were both frustrated and displeased with the architecture from the period, particularly when it came to spaces for living. We felt that there was a need to loosen up the rigid confines of urban planning, giving back the gift of creativity to individual human beings and allowing them to shape and design their houses or dwellings themselves – instead of having some clever architect pop up, telling you how you should live. We were thinking in terms of open-ended systems where things could grow and evolve as required. For instance, we imagined a kind of mobile production unit, but unfortunately the drawings have been lost. It was a kind of truck with a nozzle at the back. Like a bee building its hive. The nozzle would emit and apply material that grew to form amorphous mushrooms or whatever you might imagine. It was supposed to be computer-controlled, allowing you to create interesting shapes and sequences of spaces. It was a merging of organic and technological systems, a new way of structuring the world. And a response that counteracted industrial uniformity. We had this idea that sophisticated software might enable us to mimic the way in which nature creates products – where things that belong to the same family can take different forms. All oak trees are oak trees, but no two oak trees are exactly alike. And then a whole new material – polystyrene foam – arrived on the scene. It behaved like nature in the sense that it grew when its two component parts were mixed. Almost like a fungal growth. This made it an obvious choice for our work in Atelier Cyberspace.

The works of Atelier Cyberspace were originally shown at a number of Copenhagen venues and have later been exhibited at The National Gallery of Denmark in Copenhagen as part of the exhibition "What's Happening?"

The term cyberspace first appeared in fiction in the 1980s in the work of cyberpunk science fiction author William Gibson, first in his 1982 short story "Burning Chrome" and later in his 1984 novel Neuromancer. In the next few years, the word became prominently identified with online computer networks. The portion of Neuromancer cited in this respect is usually the following:

Cyberspace. A consensual hallucination experienced daily by billions of legitimate operators, in every nation, by children being taught mathematical concepts... A graphic representation of data abstracted from the banks of every computer in the human system. Unthinkable complexity. Lines of light ranged in the nonspace of the mind, clusters and constellations of data. Like city lights, receding.

Now widely used, the term has since been criticized by Gibson, who commented on the origin of the term in the 2000 documentary No Maps for These Territories:

All I knew about the word "cyberspace" when I coined it, was that it seemed like an effective buzzword. It seemed evocative and essentially meaningless. It was suggestive of something, but had no real semantic meaning, even for me, as I saw it emerge on the page.

Metaphorical

Don Slater uses a metaphor to define cyberspace, describing the "sense of a social setting that exists purely within a space of representation and communication ... it exists entirely within a computer space, distributed across increasingly complex and fluid networks." The term cyberspace started to become a de facto synonym for the Internet, and later the World Wide Web, during the 1990s, especially in academic circles and activist communities. Author Bruce Sterling, who popularized this meaning, credits John Perry Barlow as the first to use it to refer to "the present-day nexus of computer and telecommunications networks". Barlow describes it thus in his essay to announce the formation of the Electronic Frontier Foundation (note the spatial metaphor) in June 1990:

In this silent world, all conversation is typed. To enter it, one forsakes both body and place and becomes a thing of words alone. You can see what your neighbors are saying (or recently said), but not what either they or their physical surroundings look like. Town meetings are continuous and discussions rage on everything from sexual kinks to depreciation schedules. Whether by one telephonic tendril or millions, they are all connected to one another. Collectively, they form what their inhabitants call the Net. It extends across that immense region of electron states, microwaves, magnetic fields, light pulses and thought which sci-fi writer William Gibson named Cyberspace.

— John Perry Barlow, "Crime and Puzzlement", 1990-06-08

As Barlow and the EFF continued public education efforts to promote the idea of "digital rights", the term was increasingly used during the Internet boom of the late 1990s.

Virtual environments

Although in the present-day, loose use of the term cyberspace no longer implies or suggests immersion in a virtual reality, current technology allows the integration of a number of capabilities (sensors, signals, connections, transmissions, processors, and controllers) sufficient to generate a virtual interactive experience that is accessible regardless of a geographic location. It is for these reasons cyberspace has been described as the ultimate tax haven.

In 1989, Autodesk, an American multinational corporation that focuses on 2D and 3D design software, developed a virtual design system called Cyberspace.

Recent definitions of Cyberspace

Although several definitions of cyberspace can be found both in scientific literature and in official governmental sources, there is no fully agreed official definition yet. According to F. D. Kramer, there are 28 different definitions of the term cyberspace.

The most recent draft definition is the following:

Cyberspace is a global and dynamic domain (subject to constant change) characterized by the combined use of electrons and the electromagnetic spectrum, whose purpose is to create, store, modify, exchange, share, and extract, use, eliminate information and disrupt physical resources. Cyberspace includes: a) physical infrastructures and telecommunications devices that allow for the connection of technological and communication system networks, understood in the broadest sense (SCADA devices, smartphones/tablets, computers, servers, etc.); b) computer systems (see point a) and the related (sometimes embedded) software that guarantee the domain's basic operational functioning and connectivity; c) networks between computer systems; d) networks of networks that connect computer systems (the distinction between networks and networks of networks is mainly organizational); e) the access nodes of users and intermediaries routing nodes; f) constituent data (or resident data). Often, in common parlance (and sometimes in commercial language), networks of networks are called the Internet (with a lowercase i), while networks between computers are called intranet. Internet (with a capital I, in journalistic language sometimes called the Net) can be considered a part of the system a). A distinctive and constitutive feature of cyberspace is that no central entity exercises control over all the networks that make up this new domain. Just as in the real world there is no world government, cyberspace lacks an institutionally predefined hierarchical center. To cyberspace, a domain without a hierarchical ordering principle, we can, therefore, extend the definition of international politics coined by Kenneth Waltz: as being "with no system of law enforceable." This does not mean that the dimension of power in cyberspace is absent, nor that power is dispersed and scattered into a thousand invisible streams, nor that it is evenly spread across myriad people and organizations, as some scholars had predicted. On the contrary, cyberspace is characterized by a precise structuring of hierarchies of power.

The Joint Chiefs of Staff of the United States Department of Defense define cyberspace as one of five interdependent domains, the remaining four being land, air, maritime, and space. See United States Cyber Command

Cyberspace as an Internet metaphor

See also: Internet metaphors and Internet-related prefixes

While cyberspace should not be confused with the Internet, the term is often used to refer to objects and identities that exist largely within the communication network itself, so that a website, for example, might be metaphorically said to "exist in cyberspace". According to this interpretation, events taking place on the Internet are not happening in the locations where participants or servers are physically located, but "in cyberspace". The philosopher Michel Foucault used the term heterotopias to describe such spaces which are simultaneously physical and mental.

Firstly, cyberspace describes the flow of digital data through the network of interconnected computers: it is at once not "real"—since one could not spatially locate it as a tangible object—and clearly "real" in its effects. There have been several attempts to create a concise model about how cyberspace works since it is not a physical thing that can be looked at. Secondly, cyberspace is the site of computer-mediated communication (CMC), in which online relationships and alternative forms of online identity are enacted, raising important questions about the social psychology of Internet use, the relationship between "online" and "offline" forms of life and interaction, and the relationship between the "real" and the virtual. Cyberspace draws attention to the remediation of culture through new media technologies: it is not just a communication tool, but a social destination, and is culturally significant in its own right. Finally, cyberspace can be seen as providing new opportunities to reshape society and culture through "hidden" identities, or it can be seen as borderless communication and culture.

Cyberspace is the "place" where a telephone conversation appears to occur. Not inside your actual phone, the plastic device on your desk. Not inside the other person's phone, in some other city. The place between the phones. [...] in the past twenty years, this electrical "space," which was once thin and dark and one-dimensional—little more than a narrow speaking-tube, stretching from phone to phone—has flung itself open like a gigantic jack-in-the-box. Light has flooded upon it, the eerie light of the glowing computer screen. This dark electric netherworld has become a vast flowering electronic landscape. Since the 1960s, the world of the telephone has cross-bred itself with computers and television, and though there is still no substance to cyberspace, nothing you can handle, it has a strange kind of physicality now. It makes good sense today to talk of cyberspace as a place all its own.

— Bruce Sterling, Introduction to The Hacker Crackdown

The "space" in cyberspace has more in common with the abstract, mathematical meanings of the term (see space) than physical space. It does not have the duality of positive and negative volume (while in physical space, for example, a room has the negative volume of usable space delineated by positive volume of walls, Internet users cannot enter the screen and explore the unknown part of the Internet as an extension of the space they are in), but spatial meaning can be attributed to the relationship between different pages (of books as well as web servers), considering the unturned pages to be somewhere "out there." The concept of cyberspace, therefore, refers not to the content being presented to the surfer, but rather to the possibility of surfing among different sites, with feedback loops between the user and the rest of the system creating the potential to always encounter something unknown or unexpected.

Video games differ from text-based communication in that on-screen images are meant to be figures that actually occupy a space and the animation shows the movement of those figures. Images are supposed to form the positive volume that delineates the empty space. A game adopts the cyberspace metaphor by engaging more players in the game, and then figuratively representing them on the screen as avatars. Games do not have to stop at the avatar-player level, but current implementations aiming for more immersive playing space (i.e. Laser tag) take the form of augmented reality rather than cyberspace, fully immersive virtual realities remaining impractical.

Although the more radical consequences of the global communication network predicted by some cyberspace proponents (i.e. the diminishing of state influence envisioned by John Perry Barlow) failed to materialize and the word lost some of its novelty appeal, it remains current as of 2006.

Some virtual communities explicitly refer to the concept of cyberspace—for example, Linden Lab calling their customers "Residents" of Second Life—while all such communities can be positioned "in cyberspace" for explanatory and comparative purposes (as did Sterling in The Hacker Crackdown, followed by many journalists), integrating the metaphor into a wider cyber-culture.

The metaphor has been useful in helping a new generation of thought leaders to reason through new military strategies around the world, led largely by the US Department of Defense (DoD). The use of cyberspace as a metaphor has had its limits, however, especially in areas where the metaphor becomes confused with physical infrastructure. It has also been critiqued as being unhelpful for falsely employing a spatial metaphor to describe what is inherently a network.

Alternate realities in philosophy and art

Predating computers

A forerunner of the modern ideas of cyberspace is the Cartesian notion that people might be deceived by an evil demon that feeds them a false reality. This argument is the direct predecessor of modern ideas of a brain in a vat and many popular conceptions of cyberspace take Descartes's ideas as their starting point.

Visual arts have a tradition, stretching back to antiquity, of artifacts meant to fool the eye and be mistaken for reality. This questioning of reality occasionally led some philosophers and especially theologians to distrust art as deceiving people into entering a world which was not real (see Aniconism). The artistic challenge was resurrected with increasing ambition as art became more and more realistic with the invention of photography, film (see Arrival of a Train at La Ciotat), and immersive computer simulations.

Influenced by computers

Philosophy

American counterculture exponents like William S. Burroughs (whose literary influence on Gibson and cyberpunk in general is widely acknowledged) and Timothy Leary were among the first to extol the potential of computers and computer networks for individual empowerment.

Some contemporary philosophers and scientists (e.g. David Deutsch in The Fabric of Reality) employ virtual reality in various thought experiments. For example, Philip Zhai in Get Real: A Philosophical Adventure in Virtual Reality connects cyberspace to the Platonic tradition:

Let us imagine a nation in which everyone is hooked up to a network of VR infrastructure. They have been so hooked up since they left their mother's wombs. Immersed in cyberspace and maintaining their life by teleoperation, they have never imagined that life could be any different from that. The first person that thinks of the possibility of an alternative world like ours would be ridiculed by the majority of these citizens, just like the few enlightened ones in Plato's allegory of the cave.

Note that this brain-in-a-vat argument conflates cyberspace with reality, while the more common descriptions of cyberspace contrast it with the "real world".

Cyber-geography

The "Geography of Notopia" (Papadimitriou, 2006) theorizes about the complex interplay of cyber-cultures and the geographical space. This interplay has several philosophical and psychological facets (Papadimitriou, 2009).

A new communication model

The technological convergence of the mass media is the result of a long adaptation process of their communicative resources to the evolutionary changes of each historical moment. Thus, the new media became an extension of the traditional media in cyberspace, allowing the public access to information in a wide range of digital devices. In other words, it is a cultural virtualization of human reality as a result of the migration from physical to virtual space (mediated by the ICTs), ruled by codes, signs and particular social relationships. Forwards, arise instant ways of communication, interaction and possible quick access to information, in which we are no longer mere senders, but also producers, reproducers, co-workers and providers. New technologies also help to "connect" people from different cultures outside the virtual space, which was unthinkable fifty years ago. In this giant relationships web, we mutually absorb each other's beliefs, customs, values, laws and habits, cultural legacies perpetuated by a physical-virtual dynamics in constant metamorphosis (ibidem). In this sense, Professor Doctor Marcelo Mendonça Teixeira created, in 2013, a new model of communication to the virtual universe, based in Claude Elwood Shannon (1948) article "A Mathematical Theory of Communication".

Art

Main article: New media art

Having originated among writers, the concept of cyberspace remains most popular in literature and film. Although artists working with other media have expressed interest in the concept, such as Roy Ascott, "cyberspace" in digital art is mostly used as a synonym for immersive virtual reality and remains more discussed than enacted.

Computer crime

Main article: Computer crime

Cyberspace also brings together every service and facility imaginable to expedite money laundering. One can purchase anonymous credit cards, bank accounts, encrypted global mobile telephones, and false passports. From there one can pay professional advisors to set up IBCs (International Business Corporations, or corporations with anonymous ownership) or similar structures in OFCs (Offshore Financial Centers). Such advisors are loath to ask any penetrating questions about the wealth and activities of their clients, since the average fees criminals pay them to launder their money can be as much as 20 percent.

5-level model

In 2010, a five-level model was designed in France. According to this model, cyberspace is composed of five layers based on information discoveries: 1) language, 2) writing, 3) printing, 4) Internet, 5) Etc., i.e. the rest, e.g. noosphere, artificial life, artificial intelligence, etc., etc. This original model links the world of information to telecommunication technologies.