In this work we briefly describe the most relevant features of WSXM, a freeware scanning probe microscopy software based on MS-Windows. The article is structured in three different sections: The introduction is a perspective on the importance of software on scanning probe microscopy. The second section is devoted to describe the general structure of the application; in this section the capabilities of WSXM to read third party files are stressed. Finally, a detailed discussion of some relevant procedures of the software is carried out.

https://nanoed.tul.cz/pluginfile.php/1608/mod_resource/content/1/view.pdf

WSXM: a software for scanning probe microscopy and a tool for nanotechnology.

'Bottom-up fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).

/pdf/folding-dna-to-create-nanoscale-shapes-and-patterns-1liv7u73y0.pdf

Folding DNA to create nanoscale shapes and patterns

Meeting the Universe Halfway is an ambitious book with far-reaching implications for numerous fields in the natural sciences, social sciences, and humanities. In this volume, Karen Barad, theoretical physicist and feminist theorist, elaborates her theory of agential realism. Offering an account of the world as a whole rather than as composed of separate natural and social realms, agential realism is at once a new epistemology, ontology, and ethics. The starting point for Barad’s analysis is the philosophical framework of quantum physicist Niels Bohr. Barad extends and partially revises Bohr’s philosophical views in light of current scholarship in physics, science studies, and the philosophy of science as well as feminist, poststructuralist, and other critical social theories. In the process, she significantly reworks understandings of space, time, matter, causality, agency, subjectivity, and objectivity.

In an agential realist account, the world is made of entanglements of “social” and “natural” agencies, where the distinction between the two emerges out of specific intra-actions. Intra-activity is an inexhaustible dynamism that configures and reconfigures relations of space-time-matter. In explaining intra-activity, Barad reveals questions about how nature and culture interact and change over time to be fundamentally misguided. And she reframes understanding of the nature of scientific and political practices and their “interrelationship.” Thus she pays particular attention to the responsible practice of science, and she emphasizes changes in the understanding of political practices, critically reworking Judith Butler’s influential theory of performativity. Finally, Barad uses agential realism to produce a new interpretation of quantum physics, demonstrating that agential realism is more than a means of reflecting on science; it can be used to actually do science.

Meeting the Universe Halfway: Quantum Physics and the Entanglement of Matter and Meaning

The semiconductor industry has seen a remarkable miniaturization trend, driven by many scientific and technological innovations. But if this trend is to continue, and provide ever faster and cheaper computers, the size of microelectronic circuit components will soon need to reach the scale of atoms or molecules—a goal that will require conceptually new device structures. The idea that a few molecules, or even a single molecule, could be embedded between electrodes and perform the basic functions of digital electronics—rectification, amplification and storage—was first put forward in the mid-1970s. The concept is now realized for individual components, but the economic fabrication of complete circuits at the molecular level remains challenging because of the difficulty of connecting molecules to one another. A possible solution to this problem is ‘mono-molecular’ electronics, in which a single molecule will integrate the elementary functions and interconnections required for computation.

Electronics using hybrid-molecular and mono-molecular devices

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

SINCE its invention in the early 1980s by Binnig and Rohrer1,2, the scanning tunnelling microscope (STM) has provided images of surfaces and adsorbed atoms and molecules with unprecedented resolution The STM has also been used to modify surfaces, for example by locally pinning molecules to a surface3 and by transfer of an atom from the STM tip to the surface4 Here we report the use of the STM at low temperatures (4 K) to position individual xenon atoms on a single-crystal nickel surface with atomic pre-cision This capacity has allowed us to fabricate rudimentary structures of our own design, atom by atom The processes we describe are in principle applicable to molecules also In view of the device-like characteristics reported for single atoms on surfaces5,6, the possibilities for perhaps the ultimate in device miniaturization are evident

Positioning single atoms with a scanning tunnelling microscope

A method for confining electrons to artificial structures at the nanometer lengthscale is presented. Surface state electrons on a copper(111) surface were confined to closed structures (corrals) defined by barriers built from iron adatoms. The barriers were assembled by individually positioning iron adatoms with the tip of a 4-kelvin scanning tunneling microscope (STM). A circular corral of radius 71.3 A was constructed in this way out of 48 iron adatoms. Tunneling spectroscopy performed inside of the corral revealed a series of discrete resonances, providing evidence for size quantization. STM images show that the corral's interior local density of states is dominated by the eigenstate density expected for an electron trapped in a round two-dimensional box.

https://science.sciencemag.org/content/sci/262/5131/218.full.pdf

Confinement of electrons to quantum corrals on a metal surface.

Image projection relies on classical wave mechanics and the use of natural or engineered structures such as lenses or resonant cavities. Well-known examples include the bending of light to create mirages in the atmosphere, and the focusing of sound by whispering galleries. However, the observation of analogous phenomena in condensed matter systems is a more recent development, facilitated by advances in nanofabrication. Here we report the projection of the electronic structure surrounding a magnetic Co atom to a remote location on the surface of a Cu crystal; electron partial waves scattered from the real Co atom are coherently refocused to form a spectral image or 'quantum mirage'. The focusing device is an elliptical quantum corral, assembled on the Cu surface. The corral acts as a quantum mechanical resonator, while the two-dimensional Cu surface-state electrons form the projection medium. When placed on the surface, Co atoms display a distinctive spectroscopic signature, known as the many-particle Kondo resonance, which arises from their magnetic moment. By positioning a Co atom at one focus of the ellipse, we detect a strong Kondo signature not only at the atom, but also at the empty focus. This behaviour contrasts with the usual spatially-decreasing response of an electron gas to a localized perturbation.

Quantum mirages formed by coherent projection of electronic structure

THE scanning tunnelling microscope1 (STM) has been employed in recent years in attempts to develop atomic-scale electronic devices, both by examining device-like characteristics in preexisting structures2,3 and by creating new structures by the precise manipulation of atoms and molecules with the STM tip4–6. Here we report the operation of a bistable switch that derives its function from the motion of a single atom. A xenon atom is moved reversibly between stable positions on each of two stationary conducting 'leads', corresponding to the STM tip and a nickel surface. The state of the switch is set (that is, the xenon atom is moved to the desired location) by the application of a voltage pulse of the appropriate sign across the leads. The state of the switch is identified by measuring the conductance across the leads. This switch is a prototype of a new class of potentially very small electronic devices which we will call atom switches.

An atomic switch realized with the scanning tunnelling microscope

We have obtained images of individual Xe atoms absorbed on a Ni(110) surface using a low-temperature scanning tunneling microscope (STM). The atom-on-jellium model has been used to calculate the apparent height of a Xe atom as imaged with the STM and the result is found to be in good agreement with experiment. We conclude that the Xe 6s resonance, although lying close to the vacuum level, is the origin of the Fermi-level local state density which renders Xe «visible» in the STM

D. M. Eigler

Papers

Positioning single atoms with a scanning tunnelling microscope

Confinement of electrons to quantum corrals on a metal surface.

Quantum mirages formed by coherent projection of electronic structure

An atomic switch realized with the scanning tunnelling microscope

Imaging Xe with a low-temperature scanning tunneling microscope.