publications

2025

1. SimMS: A GPU-Accelerated Cosine Similarity implementation for Tandem Mass Spectrometry

   Onoprishvili, Tornike, Yuan, Jui-Hung, Petrov, Kamen, Ingalalli, Vijay, Khederlarian, Lila, Leuchtenmuller, Niklas, Chandra, Sona, Duarte, Aurelien, Bender, Andreas, and Gloaguen, Yoann

   Bioinformatics Feb 2025

   Abs

   Untargeted metabolomics involves a large-scale comparison of the fragmentation pattern of a mass spectrum against a database containing known spectra. Given the number of comparisons involved, this step can be time-consuming.In this work, we present a GPU-accelerated cosine similarity implementation for Tandem Mass Spectrometry (MS), with an approximately 1000-fold speedup compared to the MatchMS reference implementation, without any loss of accuracy. This improvement enables repository-scale spectral library matching for compound identification without the need for large compute clusters. This impact extends to any spectral comparison-based methods such as molecular networking approaches and analogue search.All code, results, and notebooks supporting are freely available under the MIT license at https://github.com/pangeAI/simms/.

2020

1. Functional all-optical logic gates for true time-domain signal processing in nonlinear photonic crystal waveguides

   Jandieri, Vakhtang, Khomeriki, Ramaz,  Onoprishvili, Tornike, Werner, Douglas H, Berakdar, Jamal, and Erni, Daniel

   Optics Express Feb 2020

   Abs

   We present a conceptual study on the realization of functional and easily scalable all-optical NOT, AND and NAND logic gates using bandgap solitons in coupled photonic crystal waveguides. The underlying structure consists of a planar air-hole type photonic crystal with a hexagonal lattice of air holes in crystalline silicon (c-Si) as the nonlinear background material. The remaining logical operations can be performed using combinations of these three logic gates. A unique feature of the proposed working scheme is that it operates in the true time-domain, enabling temporal solitons to maintain a stable pulse envelope during each logical operation. Hence, multiple concatenated all-optical logic gates can be easily realized, paving the way to multiple-input all-optical logic gates for ultrafast full-optical digital signal processing. In the suggested setup, there is no need to amplify the output signal after each operation, which can be directly used as a new input signal for another logical operation. The feasibility and efficiency of the proposed logic gates as well as their scalability is demonstrated using our original rigorous theoretical formalism together with full-wave computational electromagnetics.

2019

1. Digital signal processing in coupled photonic crystal waveguides and its application to an all-optical AND logic gate

   Jandieri, Vakhtang,  Onoprishvili, Tornike, Khomeriki, Ramaz, Erni, Daniel, and Pistora, Jaromir

   Optical and Quantum Electronics Feb 2019

   Abs

   The realization of all-optical AND logic gates for pulsed signal operation based on the photonic bandgap transmission phenomenon is proposed. We are using realistic planar air-hole type coupled photonic crystal waveguides (C-PCWs) with Kerr-type nonlinear background medium. The novelty of our analysis is that the proposed AND logic gate operates with the temporal solitons, which maintain a stable envelope propagating in the nonlinear C-PCWs, enabling true ultrafast full-optical digital signal processing in the time-domain. The bandgap transmission takes place when the operating frequency is chosen at the very edge of the dispersion curve of one of the supermodes in the C-PCWs. In this regard, our original fast and accurate method is used to efficiently calculate the supermodes of the C-PCW system. The underlying semi-analytical full-wave modal analysis is based on the evaluation of the lattice sums for complex wavenumbers using the transition-matrix method in combination with the generalized reflection-matrix approach. As a proof of concept successful pulse operation of the all-optical AND logic gate is demonstrated in the framework of extensive full-wave finite-difference time-domain electromagnetics analysis.