A. R. Bishop

Los Alamos National Laboratory, Лос-Аламос, California, United States

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Publications (949)2392.15 Total impact

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    ABSTRACT: Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.
    Scientific Reports 03/2015; 5. DOI:10.1038/srep09037 · 5.08 Impact Factor
  • Physical Review E 01/2015; 91(1). DOI:10.1103/PhysRevE.91.012905 · 2.33 Impact Factor
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    ABSTRACT: A stability criterion for solitons of the driven nonlinear Schrödinger equation (NLSE) has been conjectured. The criterion states that p^{'}(v)<0 is a sufficient condition for instability, while p^{'}(v)>0 is a necessary condition for stability; here, v is the soliton velocity and p=P/N, where P and N are the soliton momentum and norm, respectively. To date, the curve p(v) was calculated approximately by a collective coordinate theory, and the criterion was confirmed by simulations. The goal of this paper is to calculate p(v) exactly for several classes and cases of the generalized NLSE: a soliton moving in a real potential, in particular a time-dependent ramp potential, and a time-dependent confining quadratic potential, where the nonlinearity in the NLSE also has a time-dependent coefficient. Moreover, we investigate a logarithmic and a cubic NLSE with a time-independent quadratic potential well. In the latter case, there is a bisoliton solution that consists of two solitons with asymmetric shapes, forming a bound state in which the shapes and the separation distance oscillate. Finally, we consider a cubic NLSE with parametric driving. In all cases, the p(v) curve is calculated either analytically or numerically, and the stability criterion is confirmed.
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    ABSTRACT: We consider a two-dimensional (2D) generalization of a recently proposed model [Phys. Rev. E 88, 032905 (2013)], which gives rise to bright discrete solitons supported by the defocusing nonlinearity whose local strength grows from the center to the periphery. We explore the 2D model starting from the anti-continuum (AC) limit of vanishing coupling. In this limit, we can construct a wide variety of solutions including not only single-site excitations, but also dipole and quadrupole ones. Additionally, two separate families of solutions are explored: the usual "extended" unstaggered bright solitons, in which all sites are excited in the AC limit, with the same sign across the lattice (they represent the most robust states supported by the lattice, their 1D counterparts being what was considered as 1D bright solitons in the above-mentioned work), and the vortex cross, which is specific to the 2D setting. For all the existing states, we explore their stability (analytically, whenever possible). Typical scenarios of instability development are exhibited through direct simulations.
    Physical Review E 12/2014; 91(4). DOI:10.1103/PhysRevE.91.043201 · 2.33 Impact Factor
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    ABSTRACT: Schizophrenia (SZ) genome-wide association studies (GWASs) have identified common risk variants in >100 susceptibility loci; however, the contribution of rare variants at these loci remains largely unexplored. One of the strongly associated loci spans MIR137 (miR137) and MIR2682 (miR2682), two microRNA genes important for neuronal function. We sequenced ∼6.9 kb MIR137/MIR2682 and upstream regulatory sequences in 2,610 SZ cases and 2,611 controls of European ancestry. We identified 133 rare variants with minor allele frequency (MAF) <0.5%. The rare variant burden in promoters and enhancers, but not insulators, was associated with SZ (p = 0.021 for MAF < 0.5%, p = 0.003 for MAF < 0.1%). A rare enhancer SNP, 1:g.98515539A>T, presented exclusively in 11 SZ cases (nominal p = 4.8 × 10(-4)). We further identified its risk allele T in 2 of 2,434 additional SZ cases, 11 of 4,339 bipolar (BP) cases, and 3 of 3,572 SZ/BP study controls and 1,688 population controls; yielding combined p values of 0.0007, 0.0013, and 0.0001 for SZ, BP, and SZ/BP, respectively. The risk allele T of 1:g.98515539A>T reduced enhancer activity of its flanking sequence by >50% in human neuroblastoma cells, predicting lower expression of MIR137/MIR2682. Both empirical and computational analyses showed weaker transcription factor (YY1) binding by the risk allele. Chromatin conformation capture (3C) assay further indicated that 1:g.98515539A>T influenced MIR137/MIR2682, but not the nearby DPYD or LOC729987. Our results suggest that rare noncoding risk variants are associated with SZ and BP at MIR137/MIR2682 locus, with risk alleles decreasing MIR137/MIR2682 expression. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
    The American Journal of Human Genetics 11/2014; 95(6). DOI:10.1016/j.ajhg.2014.11.001 · 10.99 Impact Factor
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    Cristiano Nisoli, A. R. Bishop
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    ABSTRACT: We show that a mesoscale model, with a minimal number of parameters, can describe well the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures for denaturation under torque and stretch, phase diagrams for stable DNA, probe/response profiles under mechanical loads, and the density of dsDNA as a function of stretch and twist. We find strong agreement with available single molecule manipulation experiments.
    The Journal of Chemical Physics 06/2014; 141(11). DOI:10.1063/1.4895724 · 3.12 Impact Factor
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    Cristiano Nisoli, A R Bishop
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    ABSTRACT: The inverse square potential arises in a variety of different quantum phenomena, yet notoriously it must be handled with care: it suffers from pathologies rooted in the mathematical foundations of quantum mechanics. We show that its recently studied conformality breaking corresponds to an infinitely smooth winding-unwinding topological transition for the classical statistical mechanics of a one-dimensional system: this describes the tangling or untangling of floppy polymers under a biasing torque. When the ratio between torque and temperature exceeds a critical value the polymer undergoes tangled oscillations, with an extensive winding number. At lower torque or higher temperature the winding number per unit length is zero. Approaching criticality, the correlation length of the order parameter-the extensive winding number-follows a Kosterlitz-Thouless-type law. The model is described by the Wilson line of a (0+1) U(1) gauge theory, and applies to the tangling or untangling of floppy polymers and to the winding or diffusing kinetics in diffusion-convection reactions.
    Physical Review Letters 02/2014; 112(7):070401. DOI:10.1103/PhysRevLett.112.070401 · 7.73 Impact Factor
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    ABSTRACT: A non-Hermitian quantum optimization algorithm is created and used to find the ground state of an antiferromagnetic Ising chain. We demonstrate analytically and numerically (for up to N=1024 spins) that our approach leads to a significant reduction of the annealing time that is proportional to $\ln N$, which is much less than the time (proportional to $N^2$) required for the quantum annealing based on the corresponding Hermitian algorithm. We propose to use this approach to achieve similar speed-up for NP-complete problems by using classical computers in combination with quantum algorithms.
    Quantum Information Processing 02/2014; 13:371–389. DOI:10.1007/s11128-013-0656-z · 2.96 Impact Factor
  • K. H. Ahn, T. F. Seman, T. Lookman, A. R. Bishop
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    ABSTRACT: We analyze the essential role played by complex energy landscapes in the nanometer- to micron-scale inhomogeneities observed in perovskite manganites using a model expressed in terms of symmetrized atomic-scale lattice distortion modes. We also examine the stability of large metal and insulator domains in the absence of defects. Our results demonstrate that an intrinsic mechanism, which involves long-range interactions between strain fields, the Peierls-Nabarro energy barrier, and complex energy landscapes with multiple metastable states, rather than an extrinsic mechanism such as chemical randomness, is responsible for the inhomogeneity in perovskite manganites.
    Physical Review B 10/2013; 88(14). DOI:10.1103/PhysRevB.88.144415 · 3.66 Impact Factor
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    ABSTRACT: We study the stable states of the wave equation with d-spatial and 1-time dimensions and with space-time periodic potential. The dispersed stable states spectrum of such -periodic wave equation is due to the incommensurability of the speed of light and the ratio of space and time periods. A Bloch-Floquet analysis leads to a -cube as a reduced Brillouin zone, but because of the speed incommensurability the stable states in this cube may form a spectrum of sets with a reduced dimensionality. For electromagnetic waves in photonic crystals the medium may amplify some waves with lengths fitting the crystal lattice. The energy from the external field can be pumped to the waves via the dipole moment oscillations.
    EPL (Europhysics Letters) 09/2013; 103(5):50001. DOI:10.1209/0295-5075/103/50001 · 2.27 Impact Factor
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    ABSTRACT: X-ray pair distribution function (pdf) and U L 3 extended x-ray absorption fine structure (EXAFS) and neutron pdf measurements that give identical results for UO 2 show U(VI)-oxo moieties with x rays for mixed valence U 4 O 9 and U 3 O 7 , in contrast to the neutron data that indicate only U(V) sites with no short U-O bonds as well as other differences. In addition, although the EXAFS spectra of UO 2 are essentially identical at 30, 100, and 200 K, those of the UO 2+x compounds exhibit different nearest-neighbor U-O distributions at each temperature. Further tunneling polaron-type behavior is found in the broadening of the features of the O K-edge x-ray absorption spectra (XAS) of the UO 2+x compounds. Raman spectra of powders also show a large increase in scattering cross section with increasing O content that would originate in a change in the electronic structure that increases the overall polarizability. The XAS and Raman also show that U 4 O 9 does not behave as a linear combination of the UO 2 and U 3 O 7 fluorite endpoints. The properties induced by mobile rather than static charged quasiparticles were explored by optical pumping of the metal-to-metal charge-transfer transition. The temperature dependence of 4.71 eV pump–1.57 eV probe reflectivity on UO 2 that initially populates the U 6d-dominated portion of the upper Hubbard band (UHB) shows a sharp 28-μsec lifetime peak at 25 K that may be associated with the fluctuations of its antiferromagnetic transition. Pumping at 3.14 eV into the 5f -dominated portion of the UHB shows an analogous 2.8-μsec peak but also a plateau bracketing this peak that ends in a cusp at 50–60 K and an abrupt change in the hardening rate of a novel 12–15 GHz phonon that is the signature for the quasiparticle quantum phase. The different results for the different excitation channels indicate a highly specific nonthermal relaxation mechanism. These results constitute the first observation of a distinct phase of photoinduced quasiparticles that is sufficiently coupled to the lattice to undergo a gap-opening transition. When the intragap state is probed with a terahertz time domain spectroscopy (TTDS) measurement 33 psec after a 3.14 excitation pulse, it shows increased absorption in the 0.5–1.1 THz range with a decrease in temperature from ∼30 to 10 K instead of the expected decrease, a result consistent with the presence of a condensate. These results are too extreme to originate in the dynamical, nonadiabatic, coupled charge-transfer–phonon/tunneling polaron scenario previously used for doped Mott-Hubbard insulators with intermediate electron-phonon coupling and therefore indicate novel physics. One possibility that could cause all of these behaviors is that a collective, dynamical, charge transfer-coupled Peierls distortion involving the 2 U(V) ↔ U(IV) + U(VI)-oxo excitation occurs coherently over an entire domain to cause the atoms in this domain to condense into a system with Bose-Einstein or Bose-Einstein-Hubbard properties.
    Physical Review B 09/2013; 88(11):115135. DOI:10.1103/PhysRevB.88.115135 · 3.66 Impact Factor
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    ABSTRACT: Exotic vortex states with long range attraction and short range repulsion have recently been proposed to arise in certain superconducting hybrid structures such as type-I/type-II layered systems as well as multi-band superconductors. In previous work it has been shown that such systems can form clump or phase separated states, but little is known about how they behave in the presence of pinning and under an applied drive. Using large scale simulations we examine the static and dynamic properties of such vortex states interacting with random and periodic pinning. In the absence of pinning this system does not form patterns but instead undergoes complete phase separation. When pinning is present there is a transition from inhomogeneous to homogeneous vortex configurations similar to a wetting phenomenon. Under an applied drive, a dynamical dewetting process can occur from a strongly pinned homogeneous state into pattern forming states, such as moving stripes that are aligned with the direction of drive or moving labyrinth or clump phases. We show that a signature of the exotic vortex interactions observable with transport measurements is a robust double peak feature in the differential resistance curves. Our results should be valuable for determining whether such vortex interactions are occurring in these systems and also for addressing the general problem of systems with competing interactions in the presence of random and periodic pinning.
    Journal of Physics Condensed Matter 08/2013; 25(34):345703. DOI:10.1088/0953-8984/25/34/345703 · 2.22 Impact Factor
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    ABSTRACT: Sparse matrix-vector multiplication (spMVM) is the most time-consuming kernel in many numerical algorithms and has been studied extensively on all modern processor and accelerator architectures. However, the optimal sparse matrix data storage format is highly hardware-specific, which could become an obstacle when using heterogeneous systems. Also, it is as yet unclear how the wide single instruction multiple data (SIMD) units in current multi- and many-core processors should be used most efficiently if there is no structure in the sparsity pattern of the matrix. We suggest SELL-C-sigma, a variant of Sliced ELLPACK, as a SIMD-friendly data format which combines long-standing ideas from General Purpose Graphics Processing Units (GPGPUs) and vector computer programming. We discuss the advantages of SELL-C-sigma compared to established formats like Compressed Row Storage (CRS) and ELLPACK, and show its suitability on a variety of hardware platforms (Intel Sandy Bridge, Intel Xeon Phi and Nvidia Tesla K20) for a wide range of test matrices from different application areas. Using appropriate performance models we develop deep insight into the data transfer properties of the SELL-C-sigma spMVM kernel. SELL-C-sigma comes with two tuning parameters whose performance impact across the range of test matrices is studied and for which reasonable choices are proposed. This leads to a hardware-independent ("catch-all") sparse matrix format, which achieves very high efficiency for all test matrices across all hardware platforms.
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    Jian-Huang She, A R Bishop
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    ABSTRACT: We study the RKKY interaction in non-Fermi-liquid metals. We find that the RKKY interaction mediated by some non-Fermi-liquid metals can be of much longer range than for a Fermi liquid. The oscillatory nature of the RKKY interaction thus becomes more important in such non-Fermi liquids, and gives rise to enhanced frustration when the spins form a lattice. Frustration suppresses the magnetic ordering temperature of the lattice spin system. Furthermore, we find that the spin system with a longer range RKKY interaction can be described by the Brazovskii model, where the ordering wave vector lies on a higher dimensional manifold. Strong fluctuations in such a model lead to a first-order phase transition and/or glassy phase. This may explain some recent experiments where glassy behavior was observed in stoichiometric heavy fermion material close to a ferromagnetic quantum critical point.
    Physical Review Letters 07/2013; 111(1):017001. DOI:10.1103/PhysRevLett.111.017001 · 7.73 Impact Factor
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    ABSTRACT: We numerically examine vortex matter with repulsive interactions at short range and attractive interactions at long range in the presence of periodic pinning arrays. Such competing vortex interactions are predicted to occur in multiband superconductors or type-I and type-II hybrid materials. For weak pinning, the vortices form cluster states, while for strong pinning, the vortices form uniform states in which flux is evenly distributed among the pinning sites. As a function of external drive, the weak pinning system exhibits clump depinning with no structure changes, while the strong pinning system depins into a disordered fluctuating state followed by a transition to a partially aligned stripe state. For weak pinning, there is a single peak in the differential conductivity, while for strong pinning there are two peaks, indicating that transport curves could be used to distinguish between vortex systems with purely repulsive interactions and those with additional long range attractive interactions.
    Journal of Superconductivity and Novel Magnetism 05/2013; 26(5). DOI:10.1007/s10948-012-2096-x · 0.93 Impact Factor
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    ABSTRACT: We address the question of the origin of the recently discovered chiral property of the charge-density-wave phase in 1$T$-TiSe$_2$ which so far lacks a microscopic understanding. We argue that the lattice degrees of freedom seems to be crucial for this novel phenomenon. We motivate a theoretical model that takes into account one valence and three conduction bands, a strongly screened Coulomb interaction between the electrons, as well as the coupling of the electrons to a transverse optical phonon mode. The Falicov-Kimball model extended in this way possesses a charge-density-wave state at low temperatures, which is accompanied by a periodic lattice distortion. The charge ordering is driven by a lattice deformation and electron-hole pairing (excitonic) instability in combination. We show that both electron-phonon interaction and phonon-phonon interaction must be taken into account at least up to quartic order in the lattice displacement to achieve a stable chiral charge order. The chiral property is exhibited in the ionic displacements. Furthermore, we provide the ground-state phase diagram of the model and give an estimate of the electron-electron and electron-phonon interaction constants for 1$T$-TiSe$_2$.
    Physical Review B 04/2013; 88(7). DOI:10.1103/PhysRevB.88.075138 · 3.66 Impact Factor
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    ABSTRACT: We model the quantum electron transfer (ET) in the photosynthetic reaction center (RC), using a non-Hermitian Hamiltonian approach. Our model includes (i) two protein cofactors, donor and acceptor, with discrete energy levels and (ii) a third protein pigment (sink) which has a continuous energy spectrum. Interactions are introduced between the donor and acceptor, and between the acceptor and the sink, with noise acting between the donor and acceptor. The noise is considered classically (as an external random force), and it is described by an ensemble of two-level systems (random fluctuators). Each fluctuator has two independent parameters, an amplitude and a switching rate. We represent the noise by a set of fluctuators with fitting parameters (boundaries of switching rates), which allows us to build a desired spectral density of noise in a wide range of frequencies. We analyze the quantum dynamics and the efficiency of the ET as a function of (i) the energy gap between the donor and acceptor, (ii) the strength of the interaction with the continuum, and (iii) noise parameters. As an example, numerical results are presented for the ET through the active pathway in a quinone-type photosystem II RC.
    Fortschritte der Physik 04/2013; 61(2-3):95 - 110. DOI:10.1002/prop.201200069 · 1.23 Impact Factor
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    ABSTRACT: We investigate the dynamics of solitons of the cubic nonlinear Schrödinger equation with an external time-independent force of the form f(x)=rexp(−iKx). Here the solitons travel with an oscillating velocity and all other characteristics of the solitons (amplitude, width, momentum, and phase) also oscillate. This behavior was predicted by a collective variable theory and confirmed by simulations. However, the reason for these oscillations remains unclear. Moreover, the spectrum of the oscillations exhibits a second strong peak, in addition to the intrinsic soliton peak. We show that the additional frequency belongs to a certain extended linear mode (which we refer to as a phonon for short) close to the lower band edge of the phonon continuum. Initially the soliton is at rest. When it starts to move it is deformed, begins to oscillate, and excites the above phonon mode such that the total momentum in a certain moving frame is conserved. In this frame the phonon does not move. However, not only does the soliton move in the homogeneous, time-periodic field of the phonon, but it also oscillates.
    Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 03/2013; 87(3). DOI:10.1103/PhysRevE.87.032917 · 2.33 Impact Factor
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    ABSTRACT: High-temperature superconducting copper oxides display a variety of both long-range and local lattice anomalies which are related to the onset of the pseudogap phase and / or the onset of superconductivity. Here we show that these anomalies demonstrate polaron formation where specifically the local character of the polarons plays an important role. We predict that unconventional isotope effects will appear in both the long-wavelength and local lattice effects.
    EPL (Europhysics Letters) 03/2013; 101(4):47004. DOI:10.1209/0295-5075/101/47004 · 2.27 Impact Factor
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    ABSTRACT: We report that terahertz (THz) irradiation of mouse mesenchymal stem cells (mMSCs) with a single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source results in irradiation specific heterogenic changes in gene expression. The THz effect depends on irradiation parameters such as the duration and type of THz source, and on the degree of stem cell differentiation. Our microarray survey and RT-PCR experiments demonstrate that prolonged broadband THz irradiation drives mMSCs toward differentiation, while 2-hour irradiation (regardless of THz sources) affects genes transcriptionally active in pluripotent stem cells. The strictly controlled experimental environment indicates minimal temperature changes and the absence of any discernable response to heat shock and cellular stress genes imply a non-thermal response. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression.
    Scientific Reports 01/2013; 3:1184. DOI:10.1038/srep01184 · 5.08 Impact Factor

Publication Stats

17k Citations
2,392.15 Total Impact Points

Institutions

  • 1970–2015
    • Los Alamos National Laboratory
      • • Center for Nonlinear Studies
      • • Theoretical Division
      • • Applied Physics Division
      Лос-Аламос, California, United States
  • 2004–2012
    • Beth Israel Deaconess Medical Center
      • Department of Medicine
      Boston, MA, United States
  • 2007
    • McGill University
      • Department of Physics
      Montréal, Quebec, Canada
    • University of Washington Seattle
      • Department of Chemistry
      Seattle, Washington, United States
  • 2006
    • Université Paris-Sud 11
      Orsay, Île-de-France, France
    • Università degli Studi di Trento
      Trient, Trentino-Alto Adige, Italy
  • 2003
    • Abdus Salam International Centre for Theoretical Physics
      Trst, Friuli Venezia Giulia, Italy
  • 2001
    • Boston University
      • Department of Physics
      Boston, Massachusetts, United States
  • 2000
    • Xerox Research Center Webster
      Webster, New York, United States
    • Rutgers, The State University of New Jersey
      • Department Physics and Astronomy
      New Brunswick, New Jersey, United States
    • University of California, Riverside
      Riverside, California, United States
  • 1992–2000
    • University of Bayreuth
      • Institute of Physics
      Bayreuth, Bavaria, Germany
    • Scuola Internazionale Superiore di Studi Avanzati di Trieste
      Trst, Friuli Venezia Giulia, Italy
    • Stanford University
      Palo Alto, California, United States
    • Complutense University of Madrid
      Madrid, Madrid, Spain
  • 1999
    • Université de Mons
      Mons, Walloon, Belgium
  • 1998
    • University of Bristol
      • Department of Engineering Mathematics
      Bristol, England, United Kingdom
  • 1994–1998
    • University Carlos III de Madrid
      • High Technical College
      Getafe, Madrid, Spain
    • University of Rome Tor Vergata
      Roma, Latium, Italy
    • Tel Aviv University
      Tell Afif, Tel Aviv, Israel
  • 1997
    • Ukrainian Academy of Agrarian Sciences
      Kievo, Kyiv City, Ukraine
    • Fudan University
      Shanghai, Shanghai Shi, China
  • 1996
    • McMaster University
      • Department of Physics and Astronomy
      Hamilton, Ontario, Canada
  • 1995
    • University of Hyderabad
      Bhaganagar, Telangana, India
    • Universidad Autónoma de San Luis Potosí
      San Luis, San Luis Potosí, Mexico
  • 1993–1995
    • University of Zagreb
      Zagrabia, Grad Zagreb, Croatia
    • Institute of Physics, Zagreb
      Zagrabia, Grad Zagreb, Croatia
  • 1991
    • Universidad Autónoma de Madrid
      Madrid, Madrid, Spain
    • Argonne National Laboratory
      • Division of Materials Science
      Lemont, Illinois, United States
  • 1990
    • City College of New York
      • Department of Physics
      New York, New York, United States
    • Kansas State University
      • Department of Physics
      Манхэттен, Kansas, United States
  • 1988–1990
    • The Ohio State University
      • Department of Mathematics
      Columbus, Ohio, United States
  • 1975–1988
    • Cornell University
      • Laboratory of Atomic and Solid State Physics
      Итак, New York, United States
    • University of Pennsylvania
      Filadelfia, Pennsylvania, United States
  • 1986
    • Fukuoka Institute of Technology
      Hukuoka, Fukuoka, Japan
  • 1982
    • Okayama University
      • Department of Physics
      Okayama, Okayama, Japan
  • 1980
    • IBM
      Armonk, New York, United States
  • 1979–1980
    • Queen Mary, University of London
      Londinium, England, United Kingdom