Quantum vertex model for reversible classical computing.

Mappings of classical computation onto statistical mechanics models have led to remarkable successes in addressing some complex computational problems. However, such mappings display thermodynamic phase transitions that may prevent reaching solution even for easy problems known to be solvable in polynomial time. Here we map universal reversible classical computations onto a planar vertex model that exhibits no bulk classical thermodynamic phase transition, independent of the computational circuit. Within our approach the solution of the computation is encoded in the ground state of the vertex model and its complexity is reflected in the dynamics of the relaxation of the system to its ground state. We use thermal annealing with and without 'learning' to explore typical computational problems. We also construct a mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating an approach to reversible classical computation based on state-of-the-art implementations of quantum annealing.

A tight-binding model for MoS2 monolayers.

We propose an accurate tight-binding parametrization for the band structure of MoS2 monolayers near the main energy gap. We introduce a generic and straightforward derivation for the band energies equations that could be employed for other monolayer dichalcogenides. A parametrization that includes spin-orbit coupling is also provided. The proposed set of model parameters reproduce both the correct orbital compositions and location of valence and conductance band in comparison with ab initio calculations. The model gives a suitable starting point for realistic large-scale atomistic electronic transport calculations.

Single-electron transport in a three-ion magnetic molecule modulated by a transverse field.

We study single-electron transport in a three-ion molecule with strong uniaxial anisotropy and in the presence of a transverse magnetic field. Two magnetic ions are connected to each other through a third, nonmagnetic ion. The magnetic ions are coupled to ideal metallic leads and a back gate voltage is applied to the molecule, forming a field-effect transistor. The microscopic Hamiltonian describing this system includes inter-ion hopping, on-site repulsions and magnetic anisotropies. For a range of values of the parameters of the Hamiltonian, we obtain an energy spectrum similar to that of single-molecule magnets in the giant spin approximation where the two states with maximum spin projection along the uniaxial anisotropy axis are well separated from other states. In addition, upon applying an external in-plane magnetic field, the energy gap between the ground and first excited states of the molecule oscillates, going to zero at certain special values of the field, analogous to the diabolical points resulting from Berry phase interference in the giant spin model. Thus, our microscopic model provides the same phenomenological behavior expected from the giant spin model of a single-molecule magnet but with direct access to the internal structure of the molecule, thus making it more appropriate for realistic electronic transport studies. To illustrate this point, the nonlinear electronic transport in the sequential tunneling regime is evaluated for values of the field near these degeneracy points. We show that the existence of these points has a clear signature in the I-V characteristics of the molecule, most notably the modulation of excitation lines in the differential conductance.

Disorder and electronic transport in graphene.

In this review, we provide an account of the recent progress in understanding electronic transport in disordered graphene systems. Starting from a theoretical description that emphasizes the role played by band structure properties and lattice symmetries, we describe the nature of disorder in these systems and its relation to transport properties. While the focus is primarily on theoretical and conceptual aspects, connections to experiments are also included. Issues such as short- versus long-range disorder, localization (strong and weak), the carrier density dependence of the conductivity, and conductance fluctuations are considered and some open problems are pointed out.

Critical metal phase at the Anderson metal-insulator transition with Kondo impurities.

It is well known that magnetic impurities can change the symmetry class of disordered metallic systems by breaking spin and time-reversal symmetry. At low temperature, these symmetries can be restored by Kondo screening. It is also known that at the Anderson metal-insulator transition, wave functions develop multifractal fluctuations with power-law correlations. Here, we consider the interplay of these two effects. We show that multifractal correlations open local pseudogaps at the Fermi energy at some random positions in space. When dilute magnetic impurities are at these locations, Kondo screening is strongly suppressed. When the exchange coupling J is smaller than a certain value J;{*}, the metal-insulator transition point extends to a critical region in the disorder strength parameter and to a band of critical states.

Nonperturbative scaling theory of free magnetic moment phases in disordered metals.

The crossover between a free magnetic moment phase and a Kondo phase in low-dimensional disordered metals with dilute magnetic impurities is studied. We perform a finite-size scaling analysis of the distribution of the Kondo temperature obtained from a numerical renormalization group calculation of the local magnetic susceptibility for a fixed disorder realization and from the solution of the self-consistent Nagaoka-Suhl equation. We find a sizable fraction of free (unscreened) magnetic moments when the exchange coupling falls below a critical value Jc. Between the free moment phase due to Anderson localization and the Kondo-screened phase we find a phase where free moments occur due to the appearance of random local pseudogaps at the Fermi energy whose width and power scale with the elastic scattering rate 1/tau.

Measuring the Lyapunov exponent using quantum mechanics.

We study the time evolution of two wave packets prepared at the same initial state, but evolving under slightly different Hamiltonians. For chaotic systems, we determine the circumstances that lead to an exponential decay with time of the wave packet overlap function. We show that for sufficiently weak perturbations, the exponential decay follows a Fermi golden rule, while by making the difference between the two Hamiltonians larger, the characteristic exponential decay time becomes the Lyapunov exponent of the classical system. We illustrate our theoretical findings by investigating numerically the overlap decay function of a two-dimensional dynamical system.

Late onset of CAD gene amplification in unamplified PALA resistant Chinese hamster mutants.

In rodent cells, resistance to PALA (N-phosphonacetyl-L-aspartate) has always been found associated with amplification of the CAD gene (carbamyl-P synthetase, aspartate transcarbamylase, dihydro-orotase). We describe two PALA resistant Chinese hamster mutant cell lines in which amplification of the CAD gene was not present. The PALA resistant phenotype was stable when the cells were grown in non-selective medium. However, after prolonged growth in the presence of the same drug concentration used for selection, cells with increased CAD gene copy number and higher levels of resistance overrode the original population. In these cell populations, a heterogeneous organization of the CAD genes was revealed by fluorescence in situ hybridization on mitotic chromosomes indicating that the additional copies of the gene were generated in several ways, such as non-disjunction and breakage-fusion-bridge cycles. The clastogenic effect of PALA, evidenced as chromosomal aberrations in the cells grown in the presence of the drug, could have favored the late onset of the amplified mutants. It is tempting to speculate that, during the expansion of tumor populations, different drug resistance mechanisms, including gene amplification, could occur in succession and lead to the generation of cells highly resistant to chemotherapeutic agents.

Nonperturbative saddle point for the effective action of disordered and interacting electrons in 2D.

We find a nonperturbative saddle-point solution for the nonlinear sigma model proposed by Finkelstein for interacting and disordered electronic systems. Spin rotation symmetry, present in the original saddle-point solution, is spontaneously broken at one loop, as in the Coleman-Weinberg mechanism. The new solution is singular in both the disorder and triplet interaction strengths, and it also explicitly demonstrates that a nontrivial ferromagnetic state appears in a theory where the disorder average is carried out from the outset.

Different genome organization in two new cell lines established from human gastric carcinoma.

Two gastric cancer cell lines, AKG and GK2, were established from a pleural and an ascitic effusion, respectively. GK2 cells have a pseudodiploid karyotype with an add(6)(q27) chromosome in all metaphases examined. The karyotype of AKG cells is highly rearranged: FISH analysis with painting probes has shown that DNA sequences derived from single chromosomes are scattered on several (as many as eight) markers. In this cell line, the C-MYC and the K-RAS oncogenes are amplified. The organization and the copy number of the C-MYC-amplified units are different from the K-RAS units, suggesting that the two oncogenes were amplified independently. The presence of a few marker chromosomes carrying both C-MYC and K-RAS could be due to translocation events that followed the amplification.

Fluorescence in situ hybridization with a synthetic (T2AG3)n polynucleotide detects several intrachromosomal telomere-like repeats on human chromosomes.

(T2AG3) repeats comprise the telomeres of human chromosomes and also are present at interstitial locations. Using a long synthetic (T2AG3)n probe, we have localized telomere-like repeats at several internal sites on human chromosomes.

Selection of N-(phosphonacetyl)-L-aspartate resistant Chinese hamster mutants in the presence of the uridine uptake inhibitor dipyridamole.

In mammalian cells selected in culture for resistance to PALA the CAD gene is amplified and these cells are a widely used model system to study gene amplification. Selection of resistant mutants is routinely performed in medium supplemented with dialyzed serum, because the cytotoxic effect of PALA is reversed by uridine, which is contained in serum. We have shown that in Chinese hamster cells dipyridamole reduced uridine uptake to less than 5% with limited effect on cell survival. Moreover, in medium supplemented with complete serum and 10 microM dipyridamole the toxicity of PALA was similar to that obtained in medium containing dialyzed serum. We then used 10 microM dipyridamole to inhibit uridine uptake during selection of PALA resistant colonies and found that both the frequency and the type of mutants were as those obtained in the presence of dialyzed serum. In particular, in the five mutants tested, the mechanism of resistance to PALA was amplification of the CAD gene.

Telomeric and nontelomeric (TTAGGG)n sequences in gene amplification and chromosome stability.

We have isolated eight PALA-resistant mutants from CHO-PV cells and have shown that the CAD gene was amplified. We then localized the CAD genes with fluorescence in situ hybridization followed by G-banding and identified 10 different marker chromosomes carrying amplified DNA. TTAGGG repetitions, which normally map to the telomeres and centromeres, have also been localized on the 10 marker chromosomes. The organization of amplified genes and of TTAGGG sequences suggests that dicentrics were formed during amplification and that breakage-fusion-bridge cycles may have generated 7 marker chromosomes. One isochromosome was probably derived from abnormal centromere segregation at anaphase. The most striking observation was that TTAGGG sequences of centromeric origin surrounded the amplified regions and were always localized at the telomeres of the chromosome arms carrying amplified DNA. These results indicate that the recombination events that accompanied gene amplification frequently involved centromeric DNA. Moreover, breakage within centromeric TTAGGG repeats may produce telomere-like structures that stabilize the ends of rearranged chromosomes.

Variation of minisatellites in chemically induced mutagenesis and in gene amplification.

A mutation assay in cultured mammalian cells was developed based on direct analysis of minisatellite DNA. Chinese hamster cells (V79) were mutagenized with nitrosoguanidine and independent colonies were isolated and expanded. DNA fingerprints were then obtained after digestion with HinfI or HaeIII and hybridization with 33.15 and 33.6 probes (Jeffreys et al., 1985). 12 colonies from untreated cells were also analyzed. Digestion with HaeIII and hybridization with 33.15 probe detected the highest frequency of induced variants. The results suggest that minisatellite sequences are hypermutable sites that can be used to monitor the mutagenic effect of chemical agents. We have also analyzed the DNA fingerprints of 17 independent Chinese hamster (CHO) cell lines carrying amplification of the CAD gene. The DNA fingerprint analysis showed a variation in minisatellite regions in 3 lines while no variation was observed in independent colonies from the CHO parental cell line. The results suggest that these sequences may be hot spots for recombination during gene amplification.