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Khorsandmanesh, Y., Björnson, E., Jaldén, J. & Lindoff, B. (2024). Beam Coherence Time Analysis for Mobile Wideband mmWave Point-to-Point MIMO Channels. IEEE Wireless Communications Letters, 13(6), 1546-1550
Open this publication in new window or tab >>Beam Coherence Time Analysis for Mobile Wideband mmWave Point-to-Point MIMO Channels
2024 (English)In: IEEE Wireless Communications Letters, ISSN 2162-2337, E-ISSN 2162-2345, Vol. 13, no 6, p. 1546-1550Article in journal (Refereed) Published
Abstract [en]

Multi-Gbps data rates are achievable in millimeter-wave (mmWave) bands, but a prominent issue is the tiny wavelength that results in rapid fading variations and significant pilot signaling for channel estimation. In this letter, we recognize that the angles of scattering clusters seen from the UE vary slowly compared to the small-scale fading. We characterize the beam coherence time, which quantifies how frequently the UE must update its downlink receive combining matrix. The exact beam coherence time is derived in the single-cluster case, and an achievable lower bound is proposed for the multi-cluster case. These values are determined so that at least half of the received signal gain is maintained in between the combining updates. We demonstrate how the beam coherence time can be hundreds of times larger than the channel coherence time of the small-scale fading.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2024
Keywords
Coherence time, Millimeter wave communication, Fading channels, Scattering, OFDM, MIMO communication, Array signal processing, Millimeter wave (mmWave), beam coherence time, half-power beamwidth, user mobility
National Category
Telecommunications
Identifiers
urn:nbn:se:kth:diva-349619 (URN)10.1109/LWC.2024.3381434 (DOI)001246583100047 ()2-s2.0-85189303602 (Scopus ID)
Note

QC 20240702

Available from: 2024-07-02 Created: 2024-07-02 Last updated: 2024-07-02Bibliographically approved
Raja, S. N., Jain, S., Kipen, J., Jaldén, J., Stemme, G., Herland, A. & Niklaus, F. (2024). Electromigrated Gold Nanogap Tunnel Junction Arrays: Fabrication and Electrical Behavior in Liquid and Gaseous Media. ACS Applied Materials and Interfaces
Open this publication in new window or tab >>Electromigrated Gold Nanogap Tunnel Junction Arrays: Fabrication and Electrical Behavior in Liquid and Gaseous Media
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2024 (English)In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252Article in journal (Refereed) Epub ahead of print
Abstract [en]

Tunnel junctions have been suggested as high-throughput electronic single molecule sensors in liquids with several seminal experiments conducted using break junctions with reconfigurable gaps. For practical single molecule sensing applications, arrays of on-chip integrated fixed-gap tunnel junctions that can be built into compact systems are preferable. Fabricating nanogaps by electromigration is one of the most promising approaches to realize on-chip integrated tunnel junction sensors. However, the electrical behavior of fixed-gap tunnel junctions immersed in liquid media has not been systematically studied to date, and the formation of electromigrated nanogap tunnel junctions in liquid media has not yet been demonstrated. In this work, we perform a comparative study of the formation and electrical behavior of arrays of gold nanogap tunnel junctions made by feedback-controlled electromigration immersed in various liquid and gaseous media (deionized water, mesitylene, ethanol, nitrogen, and air). We demonstrate that tunnel junctions can be obtained from microfabricated gold nanoconstrictions inside liquid media. Electromigration of junctions in air produces the highest yield (61–67%), electromigration in deionized water and mesitylene results in a lower yield than in air (44–48%), whereas electromigration in ethanol fails to produce viable tunnel junctions due to interfering electrochemical processes. We map out the stability of the conductance characteristics of the resulting tunnel junctions and identify medium-specific operational conditions that have an impact on the yield of forming stable junctions. Furthermore, we highlight the unique challenges associated with working with arrays of large numbers of tunnel junctions in batches. Our findings will inform future efforts to build single molecule sensors using on-chip integrated tunnel junctions.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
Keywords
nanogap, electromigration, tunnel junction, single molecule sensing, nanofabrication
National Category
Nano Technology Electrical Engineering, Electronic Engineering, Information Engineering Physical Sciences
Research subject
Electrical Engineering; Electrical Engineering
Identifiers
urn:nbn:se:kth:diva-350025 (URN)10.1021/acsami.4c03282 (DOI)
Funder
Swedish Research Council, 2018-06169KTH Royal Institute of TechnologySwedish Foundation for Strategic Research, ITM17-0049
Note

QC 20240705

Available from: 2024-07-05 Created: 2024-07-05 Last updated: 2024-07-05Bibliographically approved
Raja, S. N., Jain, S., Kipen, J., Jaldén, J., Stemme, G., Herland, A. & Niklaus, F. (2024). High-bandwidth low-current measurement system for automated and scalable probing of tunnel junctions in liquids. Review of Scientific Instruments, 95(7), Article ID 074710.
Open this publication in new window or tab >>High-bandwidth low-current measurement system for automated and scalable probing of tunnel junctions in liquids
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2024 (English)In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 95, no 7, article id 074710Article in journal (Refereed) Published
Abstract [en]

Tunnel junctions have long been used to immobilize and study the electronic transport properties of single molecules. The sensitivity of tunneling currents to entities in the tunneling gap has generated interest in developing electronic biosensors with single molecule resolution. Tunnel junctions can, for example, be used for sensing bound or unbound DNA, RNA, amino acids, and proteins in liquids. However, manufacturing technologies for on-chip integrated arrays of tunnel junction sensors are still in their infancy, and scalable measurement strategies that allow the measurement of large numbers of tunneling junctions are required to facilitate progress. Here, we describe an experimental setup to perform scalable, high-bandwidth (>10 kHz) measurements of low currents (pA–nA) in arrays of on-chip integrated tunnel junctions immersed in various liquid media. Leveraging a commercially available compact 100 kHz bandwidth low-current measurement instrument, we developed a custom two-terminal probe on which the amplifier is directly mounted to decrease parasitic probe capacitances to sub-pF levels. We also integrated a motorized three-axis stage, which could be powered down using software control, inside the Faraday cage of the setup. This enabled automated data acquisition on arrays of tunnel junctions without worsening the noise floor despite being inside the Faraday cage. A deliberately positioned air gap in the fluidic path ensured liquid perfusion to the chip from outside the Faraday cage without coupling in additional noise. We demonstrate the performance of our setup using rapid current switching observed in electromigrated gold tunnel junctions immersed in deionized water.

Place, publisher, year, edition, pages
AIP Publishing, 2024
National Category
Nano Technology Electrical Engineering, Electronic Engineering, Information Engineering
Research subject
Electrical Engineering; Electrical Engineering
Identifiers
urn:nbn:se:kth:diva-350909 (URN)10.1063/5.0204188 (DOI)
Funder
Swedish Research Council, 2018-06169Swedish Foundation for Strategic Research, ITM17-0049Swedish Foundation for Strategic Research, STP19-0065
Note

QC 20240724

Available from: 2024-07-23 Created: 2024-07-23 Last updated: 2024-07-24Bibliographically approved
Xu, X. & Jaldén, J. (2024). Marginalized Beam Search Algorithms for Hierarchical HMMs. IEEE Transactions on Signal Processing, 72, 3013-3027
Open this publication in new window or tab >>Marginalized Beam Search Algorithms for Hierarchical HMMs
2024 (English)In: IEEE Transactions on Signal Processing, ISSN 1053-587X, E-ISSN 1941-0476, Vol. 72, p. 3013-3027Article in journal (Refereed) Published
Abstract [en]

Inferring a state sequence from a sequence of measurements is a fundamental problem in bioinformatics and natural language processing. The Viterbi and the Beam Search (BS) algorithms are popular inference methods, but they have limitations when applied to Hierarchical Hidden Markov Models (HHMMs), when the primary interest lies in the outer state sequence. The Viterbi algorithm can not infer outer states without inner states, while the BS algorithm requires marginalization over prohibitively large state spaces. We propose two new algorithms to overcome these limitations: the greedy marginalized BS algorithm and the local focus BS algorithm. We show that they approximate the most likely outer state sequence with higher performance than the Viterbi algorithm, and we evaluate the performance of these algorithms on an explicit duration HMM with simulated and real nanopore base calling data.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2024
Keywords
Signal processing algorithms, Decoding, Hidden Markov models, Viterbi algorithm, Search problems, RNA, Complexity theory, Viterbi, beam search
National Category
Signal Processing
Identifiers
urn:nbn:se:kth:diva-350799 (URN)10.1109/TSP.2024.3415468 (DOI)001263372000003 ()2-s2.0-85196748675 (Scopus ID)
Note

QC 20240722

Available from: 2024-07-22 Created: 2024-07-22 Last updated: 2024-07-22Bibliographically approved
Kipen, J. & Jaldén, J. (2023). Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data. PloS Computational Biology, 19(11), Article ID e1011345.
Open this publication in new window or tab >>Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data
2023 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 19, no 11, article id e1011345Article in journal (Refereed) Published
Abstract [en]

Next-generation single-molecule protein sequencing technologies have the potential to significantly accelerate biomedical research. These technologies offer sensitivity and scalability for proteomic analysis. One auspicious method is fluorosequencing, which involves: cutting naturalized proteins into peptides, attaching fluorophores to specific amino acids, and observing variations in light intensity as one amino acid is removed at a time. The original peptide is classified from the sequence of light-intensity reads, and proteins can subsequently be recognized with this information. The amino acid step removal is achieved by attaching the peptides to a wall on the C-terminal and using a process called Edman Degradation to remove an amino acid from the N-Terminal. Even though a framework (Whatprot) has been proposed for the peptide classification task, processing times remain restrictive due to the massively parallel data acquisicion system. In this paper, we propose a new beam search decoder with a novel state formulation that obtains considerably lower processing times at the expense of only a slight accuracy drop compared to Whatprot. Furthermore, we explore how our novel state formulation may lead to even faster decoders in the future.

Place, publisher, year, edition, pages
Public Library of Science (PLoS), 2023
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-340116 (URN)10.1371/journal.pcbi.1011345 (DOI)37934778 (PubMedID)2-s2.0-85176315601 (Scopus ID)
Note

QC 20231128

Available from: 2023-11-28 Created: 2023-11-28 Last updated: 2023-12-11Bibliographically approved
Kipen, J., Jaldén, J., Raja, S. N. & Jain, S. (2023). Efficient Implementation of Robust CUSUM Algorithm to Characterize Nanogaps Measurements with Heavy-Tailed Noise. In: ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP): . Paper presented at ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Rhodes, Greece, June 04-June 10, 2023 (pp. 1-5). Institute of Electrical and Electronics Engineers (IEEE)
Open this publication in new window or tab >>Efficient Implementation of Robust CUSUM Algorithm to Characterize Nanogaps Measurements with Heavy-Tailed Noise
2023 (English)In: ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Institute of Electrical and Electronics Engineers (IEEE), 2023, p. 1-5Conference paper, Published paper (Refereed)
Abstract [en]

Detection of bio-molecules through quantum tunneling currents could lead to the next-generation DNA sequencing methods. In order to analyze the stability of these sensitive devices, it is necessary to characterize their conductance switching statistics. This characterization can be realized by denoising the tunneling current signal and clustering the outcomes. The first step can be done with the CUSUM algorithm, which detects abrupt changes and has been used in similar devices. We found heavy-tailed non-Gaussian noise in the measurement setup of the experimental devices. This paper suggests an approximation in the likelihood ratio step of the CUSUM algorithm that is more robust than the simple Gaussian noise assumption and, at the same time, is computationally more efficient than computing the fitted true likelihoods.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2023
National Category
Signal Processing Nano Technology Other Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:kth:diva-333693 (URN)10.1109/ICASSP49357.2023.10096779 (DOI)2-s2.0-85180538433 (Scopus ID)
Conference
ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Rhodes, Greece, June 04-June 10, 2023
Note

QC 20230809

Available from: 2023-08-09 Created: 2023-08-09 Last updated: 2024-01-04Bibliographically approved
Rosén, A., Liedholm Johnson, E. & Jaldén, J. (2023). Evaluating and Enhancing the Status of Sustainability in Engineering Education. In: Proceedings of the 19th International CDIO Conference: . Paper presented at 19th International CDIO Conference, Trondheim, Norway, 26–29 June 2023 (pp. 29-42).
Open this publication in new window or tab >>Evaluating and Enhancing the Status of Sustainability in Engineering Education
2023 (English)In: Proceedings of the 19th International CDIO Conference, 2023, p. 29-42Conference paper, Published paper (Refereed)
Abstract [en]

When the optional CDIO Standard for Sustainable Development was introduced in 2020, the CDIO community was encouraged “to document the work and share their experiences, in particular reflecting on the usefulness of the new standards for future refinement and development”. This paper is a response to that call, providing insights in how this optional Standard has been used for evaluating and enhancing the status of sustainability in the Civil Engineering and Urban Management program and Electrical Engineering program at the KTH Royal Institute of Technology. Details are shared on how sustainability is integrated in the programs, and opportunities and barriers for enhancing the status of sustainability in the two programs, and in engineering education in general, are discussed. The paper concludes that the CDIO Standard for Sustainable Development provides a framework and terminology for dialogue and collaboration, within as well as between programs, that can be used for driving change, from an add-on approach, through integration approaches, towards transformative approaches to sustainability in engineering education.

Series
Proceedings of the International CDIO Conference, ISSN 2002-1593
National Category
Learning
Identifiers
urn:nbn:se:kth:diva-330673 (URN)2-s2.0-85177094753 (Scopus ID)
Conference
19th International CDIO Conference, Trondheim, Norway, 26–29 June 2023
Note

QC 20231206

Part of ISBN 978-823036186-3 

Available from: 2023-06-30 Created: 2023-06-30 Last updated: 2023-12-06Bibliographically approved
Khorsandmanesh, Y., Björnson, E. & Jaldén, J. (2023). Fronthaul Quantization-Aware MU-MIMO Precoding for Sum Rate Maximization. In: ICC 2023 - IEEE International Conference on Communications: Sustainable Communications for Renaissance: . Paper presented at 2023 IEEE International Conference on Communications, ICC 2023, Rome, Italy, May 28 2023 - Jun 1 2023 (pp. 1332-1337). Institute of Electrical and Electronics Engineers (IEEE)
Open this publication in new window or tab >>Fronthaul Quantization-Aware MU-MIMO Precoding for Sum Rate Maximization
2023 (English)In: ICC 2023 - IEEE International Conference on Communications: Sustainable Communications for Renaissance, Institute of Electrical and Electronics Engineers (IEEE) , 2023, p. 1332-1337Conference paper, Published paper (Refereed)
Abstract [en]

This paper considers a multi-user multiple-input multiple-output (MU-MIMO) system where the precoding matrix is selected in a baseband unit (BBU) and then sent over a digital fronthaul to the transmitting antenna array. The fronthaul has a limited bit resolution with a known quantization behavior. We formulate a new sum rate maximization problem where the precoding matrix elements must comply with the quantizer. We solve this non-convex mixed-integer problem to local optimality by a novel iterative algorithm inspired by the classical weighted minimum mean square error (WMMSE) approach. The precoding optimization subproblem becomes an integer least-squares problem, which we solve with a new algorithm using a sphere decoding (SD) approach. We show numerically that the proposed precoding technique vastly outperforms the baseline of optimizing an infinite-resolution precoder and then quantizing it. We also develop a heuristic quantization-aware precoding that outperforms the baseline while having comparable complexity.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2023
Keywords
quantization-aware precoding, Sum rate maximization, weighted minimum mean square error
National Category
Signal Processing Telecommunications Communication Systems
Identifiers
urn:nbn:se:kth:diva-341463 (URN)10.1109/ICC45041.2023.10279822 (DOI)2-s2.0-85178302343 (Scopus ID)
Conference
2023 IEEE International Conference on Communications, ICC 2023, Rome, Italy, May 28 2023 - Jun 1 2023
Note

QC 20240110

Part of ISBN 9781538674628

Available from: 2024-01-10 Created: 2024-01-10 Last updated: 2024-03-18Bibliographically approved
Xu, X., Bhalla, N., Ståhl, P. & Jaldén, J. (2023). Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network. BMC Bioinformatics, 24(1), Article ID 461.
Open this publication in new window or tab >>Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
2023 (English)In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 24, no 1, article id 461Article in journal (Refereed) Published
Abstract [en]

BackgroundBasecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov models (HMMs) that relied on pre-segmenting ion current measurements. However, the CTC-RNN model operates independently of prior biological and physical insights.ResultsWe present a novel basecaller named Lokatt: explicit duration Markov model and residual-LSTM network. It leverages an explicit duration HMM (EDHMM) designed to model the nanopore sequencing processes. Trained on a newly generated library with methylation-free Ecoli samples and MinION R9.4.1 chemistry, the Lokatt basecaller achieves basecalling performances with a median single read identity score of 0.930, a genome coverage ratio of 99.750%, on par with existing state-of-the-art structure when trained on the same datasets.ConclusionOur research underlines the potential of incorporating prior knowledge into the basecalling processes, particularly through integrating HMMs and recurrent neural networks. The Lokatt basecaller showcases the efficacy of a hybrid approach, emphasizing its capacity to achieve high-quality basecalling performance while accommodating the nuances of nanopore sequencing. These outcomes pave the way for advanced basecalling methodologies, with potential implications for enhancing the accuracy and efficiency of nanopore-based DNA sequencing protocols.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
Basecalling, HMM, LSTM, Nanopore sequencing
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:kth:diva-341527 (URN)10.1186/s12859-023-05580-x (DOI)001115621100003 ()38062356 (PubMedID)2-s2.0-85178887529 (Scopus ID)
Note

QC 20231222

Available from: 2023-12-22 Created: 2023-12-22 Last updated: 2024-05-01Bibliographically approved
Xu, X. & Jaldén, J. (2023). Marginalized Beam Search Algorithms for Hierarchical HMMs.
Open this publication in new window or tab >>Marginalized Beam Search Algorithms for Hierarchical HMMs
2023 (English)Other (Other academic)
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:kth:diva-346020 (URN)
Available from: 2024-04-29 Created: 2024-04-29 Last updated: 2024-05-01Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6630-243X

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