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This paper introduces SiQAD, a computer-aided design tool enabling the rapid design and simulation of atomic silicon dangling bond quantum dot patterns capable of computational logic. Several simulation tools are included, each able to inform the designer on various aspects of their designs: a ground-state electron configuration finder, a non-equilibrium electron dynamics simulator, and an electric potential landscape solver with clocking electrode support. Simulations have been compared against past experimental results to inform the electron population estimation and dynamic behavior. New logic gates suitable for this platform have been designed and simulated, and a clocked wire has been demonstrated. This work paves the way for the exploration of the vast and fertile design space of atomic silicon dangling bond quantum dot circuits.

With nanoelectronics reaching the limit of atom-sized devices, it has become critical to examine how irregularities in the local environment can affect device functionality. Here, we characterize the influence of charged atomic species on the electrostatic potential of a semiconductor surface at the subnanometer scale. Using noncontact atomic force microscopy, two-dimensional maps of the contact potential difference are used to show the spatially varying electrostatic potential on the (100) surface of hydrogen-terminated highly doped silicon. Three types of charged species, one on the surface and two within the bulk, are examined. An electric field sensitive spectroscopic signature of a single probe atom reports on nearby charged species. The identity of one of the near-surface species has been uncertain in the literature, and we suggest that its character is more consistent with either a negatively charged interstitial hydrogen or a hydrogen vacancy complex.

Using a noncontact atomic force microscope, we track and manipulate the position of single electrons confined to atomic structures engineered from silicon dangling bonds on the hydrogen terminated silicon surface. An attractive tip surface interaction mechanically manipulates the equilibrium position of a surface silicon atom, causing rehybridization that stabilizes a negative charge at the dangling bond. This is applied to controllably switch the charge state of individual dangling bonds. Because this mechanism is based on short range interactions and can be performed without applied bias voltage, we maintain both site-specific selectivity and single-electron control. We extract the short range forces involved with this mechanism by subtracting the long range forces acquired on a dimer vacancy site. As a result of relaxation of the silicon lattice to accommodate negatively charged dangling bonds, we observe charge configurations of dangling bond structures that remain stable for many seconds at 4.5 K. Subsequently, we use charge manipulation to directly prepare the ground state and metastable charge configurations of dangling bond structures composed of up to six atoms.

It has been proposed that miniature circuitry will ultimately be crafted from single atoms. Despite many advances in the study of atoms and molecules on surfaces using scanning probe microscopes, challenges with patterning and limited thermal structural stability have remained. Here we demonstrate rudimentary circuit elements through the patterning of dangling bonds on a hydrogen-terminated silicon surface. Dangling bonds sequester electrons both spatially and energetically in the bulk bandgap, circumventing short-circuiting by the substrate. We deploy paired dangling bonds occupied by one moveable electron to form a binary electronic building block. Inspired by earlier quantum dot-based approaches, binary information is encoded in the electron position, allowing demonstration of a binary wire and an OR gate. Rudimentary circuit elements, including a binary wire and an OR gate, can be created through the patterning of dangling bonds on a hydrogen-terminated silicon surface.

We report the study of single dangling bonds (DB) on the hydrogen terminated silicon (100) surface using a low temperature scanning tunneling microscope (LT-STM). By investigating samples prepared with different annealing temperatures, we establish the critical role of subsurface arsenic dopants on the DB electronic properties. We show that when the near surface concentration of dopants is depleted as a result of $1250{\deg}C$ flash anneals, a single DB exhibits a sharp conduction step in its I(V) spectroscopy that is not due to a density of states effect but rather corresponds to a DB charge state transition. The voltage position of this transition is perfectly correlated with bias dependent changes in STM images of the DB at different charge states. Density functional theory (DFT) calculations further highlight the role of subsurface dopants on DB properties by showing the influence of the DB-dopant distance on the DB state. We discuss possible theoretical models of electronic transport through the DB that could account for our experimental observations., Comment: 21 pages, 6 figures

We envision and theoretically investigate a novel behavior of a functionalized nanoparticle designed to translocate through a liquidlike membrane. We develop a statistical-mechanical approach to such a system. We predict a new mechanism for the opening of a circular energy-dominated pore on the membrane by a nanoparticle functionalized with a peptide aggregate. Following fluctuations in the position and orientation of the nanoparticle, the peptide aggregate incorporates into the membrane and locally destabilizes it. The nucleation of a pore centered at the peptide aggregate attached to the particle is a precursor to particle translocation. The subsequent opening of the pore is assisted by adhesion of the membrane to the particle. We determine the conditions in which thermal fluctuations in the membrane shape and the pore size can induce translocation of the particle. For different system parameters quantities such as the free energy, entropy, pore size, degree of particle wrapping, and the probability of spontaneous translocation are obtained.

We construct a statistical mechanical model for a polymer brush in θ-solvent. The model is exactly solvable for realistic polymer models (e.g. the freely rotating chain and the rotational isomeric state models) and it readily accounts for inhomogeneities of the brush with respect to the plane parallel to the grafting surface. The interactions between neighboring chains is mimicked by the presence of a confinement potential centered on the grafting point of each chain. We explore the model to calculate the equilibrium and kinetic properties of the polymer brush. We find that the variations of the brush free energy and height with the coverage depend strongly on the stiffness of the polymer chain (bond angle) and on the severity of the chain confinement. The results for the growth kinetics of the brush are compared with recent measurements on the formation of a PEG2000 brush from solution.

Single n-alkane molecules in θ-conditions with lengths up to 200 monomers have been studied using realistic polymer models beginning with the RIS model. We show that the generalization to the continuous rotational potential model is essential for a quantitative description. Both models are solved (exactly and numerically efficiently) with an adaptation of the transfer matrix method to obtain the chain end distribution function, force-extension curve, structure factor and Kratky plot, mean square radius of gyration, and characteristic ratio. We test the results by using different sets of geometric and energetic parameters from the literature. We compare our results to other theoretical and also to experimental data. We also extract the Kuhn length using the Gibbs ensemble.

Here we report the direct observation of single electron charging of a single atomic dangling bond (DB) on the H-Si(100)-2×1 surface. The tip of a scanning tunneling microscope is placed adjacent to the DB to serve as a single-electron sensitive charge detector. Three distinct charge states of the dangling bond--positive, neutral, and negative--are discerned. Charge state probabilities are extracted from the data, and analysis of current traces reveals the characteristic single-electron charging dynamics. Filling rates are found to decay exponentially with increasing tip-DB separation, but are not a function of sample bias, while emptying rates show a very weak dependence on tip position, but a strong dependence on sample bias, consistent with the notion of an atomic quantum dot tunnel coupled to the tip on one side and the bulk silicon on the other.

Here we report the direct observation of single electron charging of a single atomic dangling bond (DB) on the H-Si(100)-2×1 surface. The tip of a scanning tunneling microscope is placed adjacent to the DB to serve as a single-electron sensitive charge detector. Three distinct charge states of the dangling bond--positive, neutral, and negative--are discerned. Charge state probabilities are extracted from the data, and analysis of current traces reveals the characteristic single-electron charging dynamics. Filling rates are found to decay exponentially with increasing tip-DB separation, but are not a function of sample bias, while emptying rates show a very weak dependence on tip position, but a strong dependence on sample bias, consistent with the notion of an atomic quantum dot tunnel coupled to the tip on one side and the bulk silicon on the other.

We review our recent efforts in building atom-scale quantum-dot cellular automata circuits on a silicon surface. Our building block consists of silicon dangling bond on a H-Si(001) surface, which has been shown to act as a quantum dot. First the fabrication, experimental imaging, and charging character of the dangling bond are discussed. We then show how precise assemblies of such dots can be created to form artificial molecules. Such complex structures can be used as systems with custom optical properties, circuit elements for quantum-dot cellular automata, and quantum computing. Considerations on macro-to-atom connections are discussed., 2013 Workshop on Field-Coupled Nanocomputing (FCN 2013), February 7-8, 2013, Tampa, Florida, USA, Series: Lecture Notes in Computer Science; no. 8280

The Si(111) - 7 x 7 surface is one of the most interesting semiconductor surfaces because of its complex reconstruction and fascinating electronic properties. While it is known that the Si - 7 x 7 is a conducting surface, the exact surface conductivity has eluded consensus for decades as measured values differ by 7 orders of magnitude. Here we report a combined STM and transport measurement with ultra-high spatial resolution and minimal interaction with the sample, and quantitatively determine the intrinsic conductivity of the Si - 7 x 7 surface. This is made possible by the capability of measuring transport properties with or without a single atomic step between the measuring probes: we found that even a single step can reduce the surface conductivity by two orders of magnitude. Our first principles quantum transport calculations confirm and lend insight to the experimental observation., 7 pages (main text+EPAPS), 5 figures

Motivated by the need for less destructive imaging of nanostructures, we pursue point-source in-line holography (also known as point projection microscopy, or PPM) with very low energy electrons (-100 eV). This technique exploits the recent creation of ultrasharp and robust nanotips, which can field emit electrons from a single atom at their apex, thus creating a path to an extremely coherent source of electrons for holography. Our method has the potential to achieve atom resolved images of nanostructures including biological molecules. We demonstrate a further advantage of PPM emerging from the fact that the very low energy electrons employed experience a large elastic scattering cross section relative to many-keV electrons. Moreover, the variation of scattering factors as a function of atom type allows for enhanced elemental contrast. Low energy electrons arguably offer the further advantage of causing minimum damage to most materials. Model results for small molecules and adatoms on graphene substrates, where very small damage is expected, indicate that a phase contrast is obtainable between elements with significantly different Z-numbers. For example, for typical setup parameters, atoms such as C and P are discernible, while C and N are not., 15 pages, 5 figures

We study both experimentally and theoretically the electronic behavior of dangling bonds (DBs) at a hydrogen terminated Si(100)-2×1 surface. Dangling bonds behave as quantum dots and, depending on their separation, can be tunnel coupled with each other or completely isolated. On n-type highly doped silicon, the latter have a net charge of -1e, while coupled DBs exhibit altered but predictable filling behavior derived from an interplay between interdot tunneling and Coulomb repulsion. We found good correlation between many scanning tunneling micrographs of dangling bond structures and our theoretical results of a corresponding extended Hubbard model. We also demonstrated chemical methods to prevent tunnel coupling and isolate charge on a single dangling bond. © 2011 American Institute of Physics.

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009

It is demonstrated that the silicon atom dangling bond (DB) state serves as a quantum dot. Coulomb repulsion causes DBs separated by $\ensuremath{\lesssim}2\text{ }\text{ }\mathrm{nm}$ to exhibit reduced localized charge, which enables electron tunnel coupling of DBs. Scanning tunneling microscopy measurements and theoretical modeling reveal that fabrication geometry of multi-DB assemblies determines net occupation and tunnel coupling strength among dots. Electron occupation of DB assemblies can be controlled at room temperature. Electrostatic control over charge distribution within assemblies is demonstrated.

It is now a well-known fact that the phase of electron waves is altered by external magnetic fields via the Aharonov-Bohm effect. This implies that any electron interference effects will be to some degree affected by the presence of such fields. In this study we examine the distortion effects of external (constant and variable) magnetic fields on electron interference and holography. For digital holography, the reconstruction of the object is done via numerical calculations and this leaves the door open for correcting phase distortions in the hologram reconstruction. We design and quantitatively assess such correction schemes, which decidedly depend on our knowledge of the magnetic field values in the holographic recording process. For constant fields of known value we are able to correct for magnetic distortions to a great extent. We find that variable fields are more destructive to the holographic process than constant fields. We define two criteria, related respectively to global and local contrast of the hologram to establish the maximum allowed external field which does not significantly hinder the accuracy of in-line holographic microscopy with electrons.

We investigate the interaction between a nanoparticle and an oil-water interface with particular emphasis on the particle crossing through the interface. The formation of a three-phase contact line is investigated in two cases, namely in the presence and in the absence of surface forces. We carefully examine the interplay between capillary and surface forces in such systems. Two instabilities of the interface (snap-in/snap-out) as the particle is moved through the interface are identified and quantitatively described. While the snap-in instability was observed in some AFM studies, the precise interface position and configuration relative to the particle at the instability depends on the nature of the surface forces present in the system. After the snap-in, the particle is adsorbed and must overcome an energy barrier due to the interface deformation in order to cross-over to the other liquid. We make quantitative predictions on the interface configuration at the instabilities and the free energy barrier height. The roles of particle size and different interaction parameters characterizing the system in determining the magnitude of the energy barrier for crossing and in the formation of a three-phase contact line are discussed. Ultimately, this study will enable us to make quantitative predictions on capillary effects in nanoparticle-microemulsions mixtures and other colloidal systems. For particles in the micrometer range and larger the capillary forces dominate over the surface forces and dictate how the snap-in occurs. However, the situation becomes different for particle sizes smaller than about 100 nm. The presence of surface forces modifies the interface configuration and the free energy jump at the snap-in instability.

We propose a self-consistent molecular theory of conformational properties of flexible polymers in melts and solutions. The method employs the polymer reference interaction site model for the intermolecular correlations and the Green function technique for the intramolecular correlations. We demonstrate this method on n-alkane molecules in different environments: water, hexane, and in melt, corresponding to poor, good, and theta condition, respectively. The numerical results of the intramolecular correlation function, the radius of gyration, and the characteristic ratio of a polymer chain are indicative of conformational changes from one environment to another and are in agreement with other findings in the literature. Scaling laws for the chain size with respect to the number of monomers are discussed. We show results for the intra- and intermolecular correlation functions and the medium-induced potential. We also extract the Kuhn length and the characteristic ratio for the infinite chain limit for melts. The latter is compared to the experimental results and computer simulation. The conformational free energy per monomer in different solvents is calculated. Our treatment can be generalized readily to other polymer-solvent systems, for example, those containing branched copolymers and polar solvents.

We propose a self-consistent molecular theory of conformational properties of flexible polymers in solution. It is applied to the collapse of a hydrophobic polymer chain in water, and can be readily generalized to any polymer-solvent system (e.g., copolymers with high complexity). We stress the potential of this method for a variety of problems, such as protein folding.

Two closely spaced dangling bonds positioned on a silicon surface and sharing an excess electron are revealed to be a strong candidate for a charge qubit. Based on our study of the coherent dynamics of this qubit, its extremely high tunneling rate ~ 10^14 1/s greatly exceeds the expected decoherence rates for a silicon-based system, thereby overcoming a critical obstacle of charge qubit quantum computing. We investigate possible configurations of dangling bond qubits for quantum computing devices. A first-order analysis of coherent dynamics of dangling bonds shows promise in this respect., 17 pages, 3 EPS figures, 1 table

A lensless holographic in-line point source microscope was envisioned more than half a century ago, but its realization with electron waves has come short due to not only difficulties inherent in Fresnel-type reconstruction methods, but also to the lack of an adequate (spatially and temporally coherent) point source. With the recent creation of ultrasharp nanotips, which can field emit electrons from a single atom at their apex, an extremely coherent electron source is available that provides a great boost to the holographic method. The spatial coherence of such nanotips is a few A, while their temporal coherence is characterized by a value of energy dispersion (FWHM) as low as 0.1 eV. In this work we ascertain the use of such a microscope in the imaging of nanoscale structures and interfaces. The method is suitable for two- and three- dimensional imaging of solid nanoparticles, thin crystals, and surfaces, but also for biological entities. We show how improvements in the reconstruction method can be made by applying the rigorous Fresnel-Kirchhoff diffraction theory adapted to Electron Optics. Sub-nanometer resolution is achievable for beam energy between 100–200 eV.