| 1. |
- Konopik, Michael, et al.
(författare)
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Solving the subset sum problem with a nonideal biological computer
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:9
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Tidskriftsartikel (refereegranskat)abstract
- We consider the solution of the subset sum problem based on a parallel computer consisting of self-propelled biological agents moving in a nanostructured network that encodes the computing task in its geometry. We develop an approximate analytical method to analyze the effects of small errors in the nonideal junctions composing the computing network by using a Gaussian confidence interval approximation of the multinomial distribution. We concretely evaluate the probability distribution for error-induced paths and determine the minimal number of agents required to obtain a proper solution. We finally validate our theoretical results with exact numerical simulations of the subset sum problem for different set sizes and error probabilities, and discuss the scalability of the nonideal problem using realistic experimental error probabilities.
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| 2. |
- Dorsch, Sven, et al.
(författare)
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Characterization of electrostatically defined bottom-heated InAs nanowire quantum dot systems
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:12
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Tidskriftsartikel (refereegranskat)abstract
- Conversion of temperature gradients to charge currents in quantum dot systems enables probing various concepts from highly efficient energy harvesting and fundamental thermodynamics to spectroscopic possibilities complementary to conventional bias device characterization. In this work, we present a proof-of-concept study of a device architecture where bottom-gates are capacitively coupled to an InAs nanowire and double function as local joule heaters. The device design combines the ability to heat locally at different locations on the device with the electrostatic definition of various quantum dot and barrier configurations. We demonstrate the versatility of this combined gating- and heating approach by studying, as a function of the heater location and bias, the Seebeck effect across the barrier-free nanowire, fit thermocurrents through quantum dots for thermometry and detect the phonon energy using a serial double quantum dot. The results indicate symmetric heating effects when the device is heated with different gates and we present detection schemes for the electronic and phononic heat transfer contribution across the nanowire. Based on this proof-of-principle work, we propose a variety of future experiments.
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| 3. |
- Dzhigaev, D, et al.
(författare)
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Three-dimensional coherent x-ray diffraction imaging of ferroelastic domains in single CsPbBr3 perovskite nanoparticles
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:6
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Tidskriftsartikel (refereegranskat)abstract
- Metal halide perovskites attract significant interest due to their remarkable performance in optoelectronic devices. However, the gap in understanding the relationship between their nanoscale structure and properties limits their application towards novel devices. In this work, twinned ferroelastic domains in single 500 nm CsPbBr3 particles are studied with 3D Bragg coherent x-ray diffraction imaging. A preferential double-domain structure is revealed in four identical particles, with one domain oriented along the [110] and the other along the [002] direction. The particles exhibit similar scattering volume ratios of 0.12 0.026 between twin phases, suggesting the possibility of a deterministic formation process. The domains exhibit a difference in lattice tilt of 0.59 degrees, in excellent agreement with calculations of the lattice mismatch at the (112) twin boundary. These results provide important insights both for the fundamental understanding of ferroelastic nanoscale materials and for the performance improvement of perovskite-based devices. Moreover, this work paves the way towards real-time imaging of the domain dynamics in ferroic systems.
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| 4. |
- Gower, Artur, et al.
(författare)
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Effective waves for random three-dimensional particulate materials
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:6
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Tidskriftsartikel (refereegranskat)abstract
- How do you take a reliable measurement of a material whose microstructure is random? When using wave scattering, the answer is often to take an ensemble average (average over time or space). By ensemble averaging we can calculate the average scattered wave and the effective wavenumber. To date, the literature has focused on calculating the effective wavenumber for a plate filled with particles. One clear unanswered question was how to extend this approach to a material of any geometry and for any source. For example, does the effective wavenumber depend on only the microstructure, or also on the material geometry? In this work, we demonstrate that the effective wavenumbers depend on only microstructure, though beyond the long wavelength limit there are multiple effective wavenumbers for one fixed incident frequency. We show how to calculate the average wave scattered from a random particulate material of any shape, and for broad frequency ranges. As an example, we show how to calculate the average wave scattered from a sphere filled with particles.
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| 5. |
- Gustafsson, Mats, et al.
(författare)
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Upper bounds on absorption and scattering
- 2020
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 22:7
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Tidskriftsartikel (refereegranskat)abstract
- A general framework for determining fundamental bounds in nanophotonics is introduced in this paper. The theory is based on convex optimization of dual problems constructed from operators generated by electromagnetic integral equations. The optimized variable is a contrast current defined within a prescribed region of a given material constitutive relations. Two power conservation constraints analogous to the optical theorem are utilized to tighten the bounds and to prescribe either losses or material properties. Thanks to the utilization of matrix rank-1 updates, modal decompositions, and model order reduction techniques, the optimization procedure is computationally efficient even for complicated scenarios. No dual gaps are observed. The method is well-suited to accommodate material anisotropy and inhomogeneity. To demonstrate the validity of the method, bounds on scattering, absorption, and extinction cross sections are derived first and evaluated for several canonical regions. The tightness of the bounds is verified by comparison to optimized spherical nanoparticles and shells. The next metric investigated is bi-directional scattering studied closely on a particular example of an electrically thin slab. Finally, the bounds are established for Purcell's factor and local field enhancement where a dimer is used as a practical example.
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| 6. |
- Korten, Till, et al.
(författare)
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Design of network-based biocomputation circuits for the exact cover problem
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:8
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Tidskriftsartikel (refereegranskat)abstract
- Exact cover is a non-deterministic polynomial time (NP)-complete problem that is central to optimization challenges such as airline fleet planning and allocation of cloud computing resources. Solving exact cover requires the exploration of a solution space that increases exponentially with cardinality. Hence, it is time- and energy consuming to solve large instances of exact cover by serial computers. One approach to address these challenges is to utilize the inherent parallelism and high energy efficiency of biological systems in a network-based biocomputation (NBC) device. NBC is a parallel computing paradigm in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. The network is then explored in parallel using a large number of biological agents, such as molecular-motor-propelled protein filaments. The answer to the combinatorial problem can then be inferred by measuring the positions through which the agents exit the network. Here, we (i) show how exact cover can be encoded and solved in an NBC device, (ii) define a formalization that allows to prove the correctness of our approach and provides a mathematical basis for further studying NBC, and (iii) demonstrate various optimizations that significantly improve the computing performance of NBC. This work lays the ground for fabricating and scaling NBC devices to solve significantly larger combinatorial problems than have been demonstrated so far.
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| 7. |
- Maroju, P. K., et al.
(författare)
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Analysis of two-color photoelectron spectroscopy for attosecond metrology at seeded free-electron lasers
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:4
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Tidskriftsartikel (refereegranskat)abstract
- The generation of attosecond pulse trains at free-electron lasers opens new opportunities in ultrafast science, as it gives access, for the first time, to reproducible, programmable, extreme ultraviolet (XUV) waveforms with high intensity. In this work, we present a detailed analysis of the theoretical model underlying the temporal characterization of the attosecond pulse trains recently generated at the free-electron laser FERMI. In particular, the validity of the approximations used for the correlated analysis of the photoelectron spectra generated in the two-color photoionization experiments are thoroughly discussed. The ranges of validity of the assumptions, in connection with the main experimental parameters, are derived.
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| 8. |
- Miranda, M. Sanchez, et al.
(författare)
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Prospects for single-molecule electrostatic detection in molecular motor gliding motility assays
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:6
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Tidskriftsartikel (refereegranskat)abstract
- Molecular motor gliding motility assays based on myosin/actin or kinesin/microtubules are of interest for nanotechnology applications ranging from cargo-trafficking in lab-on-a-chip devices to novel biocomputation strategies. Prototype systems are typically monitored by expensive and bulky fluorescence microscopy systems. The development of integrated, direct electric detection of single filaments would strongly benefit applications and scale-up. We present estimates for the viability of such a detector by calculating the electrostatic potential change generated at a carbon nanotube transistor by a motile actin filament or microtubule under realistic gliding assay conditions. We combine this with detection limits based on previous state-of-the-art experiments using carbon nanotube transistors to detect catalysis by a bound lysozyme molecule and melting of a bound short-strand DNA molecule. Our results show that detection should be possible for both actin and microtubules using existing low ionic strength buffers given good device design, e.g., by raising the transistor slightly above the guiding channel floor. We perform studies as a function of buffer ionic strength, height of the transistor above the guiding channel floor, presence/absence of the casein surface passivation layer for microtubule assays and the linear charge density of the actin filaments/microtubules. We show that detection of microtubules is a more likely prospect given their smaller height of travel above the surface, higher negative charge density and the casein passivation, and may possibly be achieved with the nanoscale transistor sitting directly on the guiding channel floor.
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| 9. |
- Potts, Patrick, et al.
(författare)
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A thermodynamically consistent Markovian master equation beyond the secular approximation
- 2021
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- Markovian master equations provide a versatile tool for describing open quantum systems whenmemory effects of the environment may be neglected. As these equations are of an approximatenature, they often do not respect the laws of thermodynamics when no secular approximation isperformed in their derivation. Here we introduce a Markovian master equation that isthermodynamically consistent and provides an accurate description whenever memory effects canbe neglected. The thermodynamic consistency is obtained through a rescaled Hamiltonian for thethermodynamic bookkeeping, exploiting the fact that a Markovian description implies a limitedresolution for heat. Our results enable a thermodynamically consistent description of a variety ofsystems where the secular approximation breaks down.
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| 10. |
- Reuther, Cordula, et al.
(författare)
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Molecular motor-driven filament transport across three-dimensional, polymeric micro-junctions
- 2021
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Ingår i: New Journal of Physics. - : Institute of Physics Publishing (IOPP). - 1367-2630. ; 23:12
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Tidskriftsartikel (refereegranskat)abstract
- Molecular motor-driven filament systems have been extensively explored for biomedical and nanotechnological applications such as lab-on-chip molecular detection or network-based biocomputation. In these applications, filament transport conventionally occurs in two dimensions (2D), often guided along open, topographically and/or chemically structured channels which are coated by molecular motors. However, at crossing points of different channels the filament direction is less well determined and, though crucial to many applications, reliable guiding across the junction can often not be guaranteed. We here present a three-dimensional (3D) approach that eliminates the possibility for filaments to take wrong turns at junctions by spatially separating the channels crossing each other. Specifically, 3D junctions with tunnels and overpasses were manufactured on glass substrates by two-photon polymerization, a 3D fabrication technology where a tightly focused, femtosecond-pulsed laser is scanned in a layer-to-layer fashion across a photo-polymerizable inorganic-organic hybrid polymer (ORMOCER(R)) with mu m resolution. Solidification of the polymer was confined to the focal volume, enabling the manufacturing of arbitrary 3D microstructures according to computer-aided design data. Successful realization of the 3D junction design was verified by optical and electron microscopy. Most importantly, we demonstrated the reliable transport of filaments, namely microtubules propelled by kinesin-1 motors, across these 3D junctions without junction errors. Our results open up new possibilities for 3D functional elements in biomolecular transport systems, in particular their implementation in biocomputational networks.
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