Image of atom under microscope

Observing Atom Under Microscope

Atoms are really tiny. Even with the most powerful of microscopes, it’s impossible to view one with the naked eye, since they’re so small. But wouldn’t it be amazing to observe an atom under a microscope?

Essentially, an atom is a chemical element that still has the characteristics of the original element (iron, copper, carbon, and so on). As a result of this division, its components (electrons, protons, and neutrons) do not retain the characteristics of the element.

Before we proceed with microscopy, let us know more about atoms. The name atom comes from the Greek word “atomos” for “uncuttable/indivisible.”  In the early 1800s, John Dalton proposed that atoms were the smallest particles of elements that could exist. He also said that atoms of the same element are identical, but atoms of different elements can be different.

Dalton’s atomic theory was modified over the years and is now called the “Standard Model” of particle physics.


Atoms are tiny, measuring about 1 x 10-10 meters in diameter. Because of their diminutive size, a light microscope would be ineffective. While it is not feasible to view an atom using a regular light microscope, several techniques have been developed for doing so.

Here are some of the methods:

Electron Microscopy


Researchers and materials scientists are continuously working on improving electron microscopes in order to be able to examine electrons at the atomic scale.

According to one of the studies in Vienna University of Technology, researchers using energy-filtered transmission electron microscopy (EFTEM) discovered that it is feasible to see pictures of individual electrons in their orbit under specific circumstances.

In addition, a new scanning transmission electron microscopes was unveiled in the UK and is capable of resolving details down to the atomic level. According to scientists, the instrument can see things that are a million times smaller than human hair.

STEM approaches have performed well thus far.

STEM Depth

This approach has been utilized to view interfacial atoms that exist between metal nanoparticles and supports. In 2015, a team of scientists used STEM depth sectioning to look at gold atoms on titanium dioxide directly. This technique was chosen because gold exhibits high catalytic activity on Titanium dioxide.

The following steps were used in the procedure:

  • Gold is deposited on Titania support in order to prepare the gold catalyst.
  • The calcination of the solution in the air (or reduction) at high temperatures in the presence of hydrogen (H2)

The sample was examined with the aberration-corrected scanning transmission electron microscopes after it was prepared.

The researchers were able to locate the atoms in three dimensions by using this approach, which was capable of detecting particles that were brighter than Titanium atoms. The scientists were able to see the atoms by recording the focal series of Z-contrast photos from the fold nanocrystal’s interface regions.

Annular Bright-Field Scanning Transmission Electron Microscopy

Researchers had encountered problems, but it became clear that using the annular bright-field scanning transmission electron microscope, lithium atoms could be observed. To observe lithium ions using this electron microscope model, such material as Lithium manganese oxide (LiMn2O4) was used.

When the researchers examined this compound/stone using a microscope, they were able to distinguish the various atoms (Li, Mn, and O) and thus identify the lithium atoms on their own. However, only with a scanning transmission electron microscope at a resolution of 0.1 nm or lower with corrected spherical aberration could they do so.

A single, drifting individual atom (strontium atom) was also photographed recently using a regular camera by a student from the University of Oxford.

The Scanning Tunneling Microscope

Another method that can be used to observe individual atoms is through the scanning tunneling microscope.

Main parts of the scanning tunneling microscope:

Sharp metallic tip – This is the section that is brought near to the sample (conductor)

Scanning control, distance control – The distance between the tip and sample surface is adjusted by this knob. It regulates scanning.

A computer for data processing and display – The channel through which information is passed. The piezoelectric tube is also controlled by the computer.

A piezoelectric controlled probe – The Piezoelectric element responds to varying voltage, causing the scanning tip’s horizontal and height positions to change during operation.

Scanning tunneling microscopy (STM) is one of the methods invented in Switzerland in the early 1980s by Gerd Binnig and Heinrich Rohrer.

The technique of atomic force microscopy (AFM) works by sending an electronic wave over the surface of the sample (element). The transmission of electrons on the sample’s surface makes it possible to position and detect atoms.

How it Works:

A scanning tunneling microscope’s tiny sharp/pointed metal tip is brought right up against the sample’s surface. The distance between the pointed metal tip and the sample is incredibly small, almost touching (about 1 nm).

A small voltage is applied between the two, which allows a tunneling current to flow when the tip is very close to the surface of the sample. The surface is scanned using current flowing between the two to provide a three-dimensional image of the surface and thus an overall view of atoms on the surface of the sample.

The point of this approach is that electrons may only flow from the pointed metal’s tip to the sample or vice versa. The scanner moves (the tip) the current swiftly across the surface of the sample since it comes from the metal tip.

The computer then takes over and applies the charge to the atom that has been detected by the metal tip. When the metal point locates an atom at the sample’s surface, electrons flow between them, and the computer records this shift. The position of the tip as it moved and identified more points of atom locations was recorded in x-y coordinates.

The surface of the material contains numerous points, each representing individual atoms. These spots on the surface represent atoms that may be scanned and examined. As a result, it is possible to determine their structure.

Electron Microscope Tunneling

According to quantum physics, electrons should be unable to go through such barriers (such as air). When they can do so, however, they generate what is known as a tunneling current. This allows atoms of various materials to be studied at the atomic level/scale.

The scanning tunneling electron microscope is a device that uses the tip of a sharp metal needle to scan over surfaces of materials at extremely close range. When the scanning tunneling microscope’s metallic tip is brought very near to the surface of the sample (conductor), a small space is left between them. Electrons can tunnel through this gap and generate a current as they move from the metal tip to the sample surface.

The distance between the scanning tunneling microscope’s probe and the sample is adjustable, which allows for different resolution images to be taken. This instrument can image materials with resolutions down to a single atom!

By altering the voltage applied to the probe, it is possible to move the scanning tunneling microscope tip across the surface of the sample. As the probe moves, it detects changes in the current (and voltage) that occur as it passes over individual atoms on the surface of the material.

As the metallic tip is dragged across the sample material, the current generated varies with changes in surface texture (surface profile), allowing for specific atoms to be identified.

The scanning tunneling electron microscope, unlike the light microscope, utilizes electrons to find and position atoms. Thus it works even without visible light. Furthermore, rather than acting like particles, electrons in this process act like a wave, allowing them to penetrate the barrier.

How Electron Microscopes Tunneling Works

When looking at the surface of sample material with the scanning tunneling microscope, there are two primary modes of operation. The constant current mode and the constant height mode are examples of these.

Constant Current Mode

The amount of current that flows between the metallic sharp tip and the sample surface varies depending on the surface profile (peaks and depths) if the distance between the tip and the surface is greater, there will be less current. On the other hand, more distance will result in more/high electricity.

In the constant current mode, the tip is moved up and down to maintain the same height as it moves across the sample surface, thus maintaining a consistent current level. Given that the surface contours across the sample change, altering the tip upward and downward allows for a constant current.

By detecting the change in position of the metallic tip (as it vertically rises and falls), atoms may be located and positioned.

 Constant Height Mode

The tip’s height does not fluctuate while it travels over the sample in this mode, allowing only the current to vary. As a result, only the present changes depending on the surface features of the sample.

The method described above, in which atoms are tracked and positioned by the changing current, is referred to as AC-DC recording.

clear image of atom under microscope

Atomic Force Microscopy

Another microscopy method that can be used to observe atoms is atomic force microscopy. It is a type of scanning probe microscope that functions by recording the specimen height, friction, and magnetism.

With a probe, it is feasible to acquire an image of a certain surface area. This method was developed with the goal of overcoming the scanning tunneling microscope’s limits when employing atomic force microscopy to examine non-conductive substances like proteins (the scanning tunneling microscope is only used to study conductive material).

Main parts of the Atomic Force Microscope

  • Sharp tip (Probe) -probe scans the surface of the sample with a scanning motion.
  • Optical lever – Allow for measurements to be taken by evaluating cantilever deflections.
  • The piezoelectric scanner – The purpose of the diamond rod is to slide the sharp tip over the surface of the sample.
  • Cantilever – the soft girder on which the tip is fastened

How Does the Atomic Force Microscope Work

The atomic force microscope probe (produced through micro-fabrication) is extremely sensitive and makes contact with the sample.

The instrument sends out a very fine probe, which is then drawn across the surface of the sample by capillary action. It does not need light or electrons to examine the surface of the specimen. One of this method’s biggest advantages is that it allows for higher resolution and efficiency.

When the AFM tip approaches the sample surface, the attractive force between the surface of the sample and the tip causes the cantilever to bend toward that surface. When the tip is near to but still away from the sample, however, deflection is caused by repulsive forces, causing the cantilever to bend the other way.

While the z-scanner lifts and lowers the cantilever, the x-y scanner reciprocates the sample back and forth. These movements allow you to scan the whole surface area of the sample. In addition, a position detector/sensor (optical lever) installed in place records the cantilever’s bending.

The beam changes that are reflected off the top of the cantilever are detected by the position sensor. There are also variations in the beams as the cantilever moves, which all get recorded. The topography of the sample surface is documented to provide a precise replica as a result of these adjustments.

A laser diode generates a laser beam, which is reflected off the flat back of the cantilever and detected by a photodetector as the sharp tip moves across the surface. As the sharp point travels over the surface, it raises and lowers the cantilever, which in turn causes changes in the deflected beam. This beam change is converted into an image of the sample surface.

The movement of the AFM tip is usually controlled by a scanner made up of piezoelectric material, so the piezoelectric scanner. This sort of material (piezoelectric material) is widely utilized in both AFM and STM since it moves the tip along precise x, y, z axes.

For such small offsets as the tip moves across the sample surface, this material provides excellent reproducibility.

Two Modes of Operation

There are two modes of atomic force microscopy: contact mode and non-contact mode.

Contact Mode

In contact mode, the probe/tip comes into touch with the sample surface and is dragged lightly over its features. The cantilever deflects as the probe travels across the surface in contact, allowing for laser scanning of the surface.

This technique has several drawbacks, including the fact that it is difficult to use due to its simple setup and that it might harm the sample as well as the probe. Dragging the end across the surface gouges it, which may have an impact on the quality of your finished picture.

When using a scratch sample, it is essential to consider the scratches on the surface. Scratches are intentionally made in this case since they can provide insight into other areas of interest. Here’s another example: some researchers scratch the sample surface with their fingers to deposit additional samples in the scarred area.

The same case can be observed in some types of electroplating. The technique is also applied for measuring friction at the nanoscale. It mostly involves scratching the surface by pulling the tip of the cantilever across the sample surface.

Non-contact Mode

The non-contact mode of atomic force microscopy is called dynamic force microscopy. It’s also sometimes called the tapping mode because the probe makes contact with the sample surface and then lifts off again. The goal of this is to move it over a surface area without actually dragging the probe on the sample surface.

This mode is used to measure the stiffness of a sample, which is the measure of how much force it takes to deform a material. In this way, you can determine things like Young’s modulus and shear modulus.

When scanning the sample, the cantilever swings just above it. A precise high-speed loop ensures that the cantilever, and thus the tip, does not hit against the surface of the sample.

The cantilever’s resonance frequency is reduced as a result of the tip being near to the surface, which is aided by the feedback loop and maintains a constant vibration.

The tip of the instrument scans as it revolves and traces across the surface of the sample, creating a three-dimensional image of the surface.

This approach has several advantages: The tip’s sharpness is maintained while the sample is unharmed. Because the tip is protected from harm, it may be utilized repeatedly while producing high-quality pictures of the specimen’s surface.

Tapping Mode

The tapping mode involves allowing the cantilever to just touch the sample surface for a brief period. This approach helps prevent sample-induced lateral force and dragging problems caused by the workpiece’s breadth.

The cantilever tip vibrates at a greater amplitude (20-100 nm), allowing the deflection signal to be large enough for the control circuit. This method is frequently used to scan damaged samples since it lowers the high resolution.

The Structure of an Atom

An atom is composed of a nucleus, which is made up of protons and neutrons, and electrons that orbit around it. The number of protons in an atom’s nucleus determines what element it is. For example, an atom with six protons in its nucleus is oxygen, while an atom with two protons is hydrogen.

The electrons orbit the nucleus in shells. The farther away the electron is from the nucleus, the higher its energy level.

The atomic number is the sum of protons in an atom, whereas the electronic structure is determined by the arrangement of electrons. Hydrogen differs from other elements in that it doesn’t have any neutrons.

It is truly amazing to observe an atom in its magnified image. The use of electron microscopes and scanning tunneling microscopes have allowed researchers to get a detailed look at the atomic level. The pictures produced from these instruments are stunning, and give us a greater understanding of the world on a quantum level.


Observing an atom under a microscope opens up a world of wonder. It is not easy to accomplish because you will need sophisticated equipment to see it. Even with the most powerful microscope, it will still be a struggle to finally observe it.  Some equipments to use for observing atoms are the electron microscope and the atomic force microscope.

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