3,868 research outputs found
Euclidean distance geometry and applications
Euclidean distance geometry is the study of Euclidean geometry based on the
concept of distance. This is useful in several applications where the input
data consists of an incomplete set of distances, and the output is a set of
points in Euclidean space that realizes the given distances. We survey some of
the theory of Euclidean distance geometry and some of the most important
applications: molecular conformation, localization of sensor networks and
statics.Comment: 64 pages, 21 figure
The octet rule in chemical space: Generating virtual molecules
We present a generator of virtual molecules that selects valid chemistry on
the basis of the octet rule. Also, we introduce a mesomer group key that allows
a fast detection of duplicates in the generated structures.
Compared to existing approaches, our model is simpler and faster, generates
new chemistry and avoids invalid chemistry. Its versatility is illustrated by
the correct generation of molecules containing third-row elements and a
surprisingly adept handling of complex boron chemistry.
Without any empirical parameters, our model is designed to be valid also in
unexplored regions of chemical space. One first unexpected finding is the high
prevalence of dipolar structures among generated molecules.Comment: 24 pages, 10 figure
Molecular Realization of a Quantum NAND Tree
The negative-AND (NAND) gate is universal for classical computation making it
an important target for development. A seminal quantum computing algorithm by
Farhi, Goldstone and Gutmann has demonstrated its realization by means of
quantum scattering yielding a quantum algorithm that evaluates the output
faster than any classical algorithm. Here, we derive the NAND outputs
analytically from scattering theory using a tight-binding (TB) model and show
the restrictions on the TB parameters in order to still maintain the NAND gate
function. We map the quantum NAND tree onto a conjugated molecular system, and
compare the NAND output with non-equilibrium Green's function (NEGF) transport
calculations using density functional theory (DFT) and TB Hamiltonians for the
electronic structure. Further, we extend our molecular platform to show other
classical gates that can be realized for quantum computing by scattering on
graphs.Comment: 17 pages, 6 figures, 1 tabl
Silicon Atomic Quantum Dots Enable Beyond-CMOS Electronics
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.Comment: 28 pages, 19 figure
Efficient mining of discriminative molecular fragments
Frequent pattern discovery in structured data is receiving
an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset
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