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Archive for the 'Computational nanotechnology' Category

Precisely removing individual atoms with microscope creates novel molecule

Posted by Jim Lewis on March 3rd, 2017

A molecule with two unpaired electrons too unstable to be made by chemical synthesis was fabricated using a scanning probe microscope to remove two hydrogen atoms from a single molecule adsorbed to a copper surface at ultra low temperature and ultra high vacuum.

From de novo protein design to molecular machine systems

Posted by Jim Lewis on January 30th, 2017

A review from the group leading recent rapid progress in de novo protein design describes the successes, identifies the remaining challenges, and heralds the advance “from the Stone Age to the Iron Age” in protein design.

Two-component, 120-subunit icosahedral cage extends protein nanotechnology

Posted by Jim Lewis on January 28th, 2017

Ten designs spanning three types of icosahedral architectures produce atomically precise multi-megadalton protein cages to deliver biological cargo or serve as scaffolds for organizing various molecular functions.

Cleanly placing atomically precise graphene nanoribbons

Posted by Jim Lewis on January 23rd, 2017

Atomically precise chevron-shaped graphene nanoribbons were purified after solution synthesis, cleanly placed by dry contact transfer on a hydrogen-passivated Si surface, imaged and manipulated by scanning tunneling microscopy, and covalently bonded to depassivated surface positions.

Designing novel protein backbones through digital evolution

Posted by Jim Lewis on January 17th, 2017

Computational recombination of small elements of structure from known protein structures generates a vast library of designs that balance protein stability with the potential for new functions and novel interactions.

Assembling a large, stable, icosahedral protein molecular cage

Posted by Jim Lewis on September 9th, 2016

A trimeric protein was designed to self assemble into a 60 unit icosahedron with a roomy interior that might find use to ferry molecular cargo into cells or as a chemical reactor.

Rational improvement of DNA nanodevice function

Posted by Jim Lewis on August 13th, 2016

Recent research documents a structure-based rational design strategy combining molecular dynamics and single molecule imaging to improve the performance of a DNA tweezers that accurately positions an enzyme and its cofactor.

Atomically precise location of dopants a step toward quantum computers

Posted by Jim Lewis on August 4th, 2016

Precise matching of STM images and theoretical calculations provides exact lattice locations of dopant atoms, advancing the prospects for silicon-based quantum computers.

Watching individual chemical bonds during a reaction

Posted by Jim Lewis on August 2nd, 2016

Combining computational nanotechnology with a noncontact-atomic force microscope probe tipped by a single CO molecule allowed researchers to visualize the dance of individual chemical bonds during a complex organic reaction on a silver surface.

Peptoid nanosheets assemble by different design rule

Posted by Jim Lewis on July 31st, 2016

Chains of monomers joined by non-biological peptoid bonds follow different rules of self-assembly and form structures not found in chains joined by the peptide bonds used to form proteins.

Engineered protein assembles molecules into atomically precise lattice

Posted by Jim Lewis on July 30th, 2016

An engineered protein controls the assembly of C60 fullerene molecules into an atomically precise lattice that conducts electricity while neither component alone would.

Simulation of quantum entanglement with subsurface dopant atoms

Posted by Jim Lewis on June 9th, 2016

Atomic resolution measurement of quasi-particle tunneling maps of spin-resolved states reveals interference processes that allow simulation of processes important for developing quantum computers based on atomically precise doping of silicon.

Protein design provides a novel metabolic path for carbon fixation

Posted by Jim Lewis on June 8th, 2016

Computational design of an enzyme that carboligates three one-carbon molecules to form one three-carbon molecule, an activity that does not exist in nature, provides proof-of-principle for a novel metabolic pathway for carbon fixation.

Crowd-sourced RNA structure design uncovers new insights

Posted by Jim Lewis on March 12th, 2016

Thousands of amateurs playing the online RNA folding game Eterna, backed up by a real-world automated lab testing their predictions, have provided insights to improve the algorithms computers use to design RNA molecules.

Multiple advances in de novo protein design and prediction

Posted by Jim Lewis on February 14th, 2016

New families of protein structures, barrel proteins for positioning small molecules, self-assembling protein arrays, and precision sculpting of protein architectures highlight de novo protein design advances.

Rational design of protein architectures not found in nature

Posted by Jim Lewis on February 11th, 2016

Computational design of proteins satisfying predetermined geometric constraints produced stable proteins with the designed structure that are not found in nature.

De novo protein design space extends far beyond biology

Posted by Jim Lewis on February 3rd, 2016

A fully automated design protocol generates dozens of designs for proteins based on helix-loop-helix-loop repeat units that are very stable, have crystal structures that match the design, have very different overall shapes, and are unrelated to any natural protein.

Conference video: Nanoscale Materials, Devices, and Processing Predicted from First Principles

Posted by Jim Lewis on January 15th, 2016

Prof. William Goddard presented four advances from his research group that enable going from first principles quantum mechanics calculations to realistic nanosystems of interest with millions or billions of atoms.

Conference video: Mythbusting Knowledge Transfer Mechanisms through Science Gateways

Posted by Jim Lewis on January 14th, 2016

Prof. Gerhard Klimeck described the success of, a science and engineering gateway providing online simulations through a web browser for nanotechnology research and education.

Electron tomography reveals precise positions of individual atoms in aperiodic material

Posted by Jim Lewis on January 11th, 2016

The positions of 3769 tungsten atoms in a tungsten needle segment were determined to a precision of 19 pm (0.019 nm), including the position of a single atom defect in the interior of the sample, by using aberration-corrected scanning transmission electron microscopy and computerized tomography.