Olfactorial Perceptronics
External linkThe perceptronics research group works as an interdisciplinary team on topics of perceptive electronics (short:perceptronics) for olfaction.
Dr. Alexander Croy
Dr. Croy's research mainly focuses on computational efforts, especially machine learning techniques and simulations for the development and description of nanomaterials. His research interests also include electronic olfaction and the associated interdisciplinary challenges. He is affiliated with the Chair of Physical and Theoretical Chemistry as Akademischer Rat ("assistant professor/lecturer").
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Image: A. Bierling
Alexander Croy, Dr
Senior Researcher and Lecturer (akad. Rat)
Professorship of Theoretical Chemistry
Filter 30 publications
Highlighted authors are members of the University of Jena.
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Zandpack: A general tool for time-dependent transportsimulation of nanoelectronics
Year of publicationPublished in:Computer physics communications: an international journal devoted to computational physics and computer programs in physicsThe auxiliary mode approach to time-dependent open quantum system calculations is implemented and refined to yield a feasible computational approach to simulate nanostructures far from equilibrium. It is done by a careful diagonalization of the electrode level-width function, and provides an efficient approach which can simulate large, open systems at the level of time-dependent density functional theory. The approach, as given in this work, is implemented in the new open-source code Zandpack. The framework is applied to three systems perturbed by the same THz electromagnetic field pulse-form: 1) A Hubbard model for hydrogen on graphene is used to calculate spin-currents, mutual information, spin-transitions, and a pump-probe setup. 2) An armchair graphene nanoribbon (AGNR) probed by a metal tip showing electrons excited from the valence band of the AGNR into the tip via electron-electron interactions. 3) A gold break-junction is modeled with various gap distances, and displays behavior that is more different from the adiabatic case as the gap widens. In the examples 2 and 3, we develop and use a general linearization scheme for time-dependent open system calculations, which utilizes the DFTB+or SIESTAcodes. Program summary Program Title: Zandpack CPC Library link to program files: (to be added by Technical Editor) Developer's repository link: https://github.com/AleksBL Licensing provisions: MPL-2.0 Programming language: Python Nature of problem: Simulating the evolution of electrons in a device region connected to electrodes that are experiencing a time-dependent and strong bias, while at the same time describing the evolving device electrons accurately at the mean-field level. The electronic structure of the electrodes must also be described accurately in terms of the energy-dependence of its level-width function. This on a practical level requires fitting a set of known functions to a sum of Lorentzians. This fit then fixes the parameters of a coupled system of ODEs, in which the electronic density and Hamiltonian appears. Lastly, this system of ODEs has to be solved numerically. Solution method: A user-friendly routine for fitting the electrode level-width functions is implemented. It can either take input from TBtrans or custom user input and convert it to a sum of Lorentzians. We employ the auxiliary mode expansion (AME) method following Popescu and Croy [New J. Phys. 18, 093,944 (2016)] with a modified version of the diagonalization technique, combined with an effective account for the electrode level-width functions. The code can obtain the initial steady state, and propagate this initial steady state after application of a user-defined voltage bias-pulse applied to the electrodes using an explicit Runge-Kutta solver. Throughout this propagation, a user-defined density-dependence is needed, e.g. by interfacing to an external LCAO-DFT code. Such an interface is available for SIESTA and DFTB+, but can also be written by the user. Additional comments including restrictions and unusual features: The AME method does not have any restrictions on how fast oscillations can be, meaning it is valid for slow (e.g. THz fields) as well as fast (e.g. optical fields) perturbations. Simulations with normal-superconducting-normal type setups are also possible. In the current implementation, phonons cannot be included in the calculation, but the method does in theory allow for such [Y. Zhang, C. Y. Yam, G. Chen, J. Chem. Phys. 138 (16) (2013)].- University Bibliography Jena:
- fsu_mods_00034615External link
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Modeling high-order harmonic generation in quantum dots using a real-space tight-binding approach
Year of publicationPublished in:The Journal of Chemical Physics : JCPRecently, the size-dependence of high-order harmonic generation (HHG) in quantum dots (QDs) has been investigated experimentally. In particular, for longer driving wavelengths and quantum dots smaller than 3 nm, HHG was strongly suppressed; however, there is no computational model capable of describing the strong-field response of such systems. In this work, we introduce a computationally efficient three-dimensional real-space tight-binding model specifically designed for the simulation of HHG in confined systems. The model parameters are meticulously derived from density functional theory calculations for the semiconductor bulk, followed by a process of Wannierization. Our findings demonstrate that the proposed model accurately captures the observed dependency of the HHG yield on the quantum dot size. In addition, we simulate the HHG yield for elliptically polarized pulses for different QD-sizes and driving wavelengths up to 5 μm. The proposed model fills the theoretical void in simulating HHG within medium-sized nanostructures, which cannot be described by methods applied for periodic solids, or small molecules or atoms.- University Bibliography Jena:
- fsu_mods_00034842External link
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Semiconductor Bloch equations in Wannier gauge with well-behaved dephasing
Year of publicationPublished in:Computer physics communications: an international journal devoted to computational physics and computer programs in physicsThe semiconductor Bloch equations (SBEs) with a dephasing operator for the microscopic polarizations are a well established approach to simulate high-harmonic spectra in solids. We discuss the impact of the dephasing operator on the stability of the numerical integration of the SBEs in the Wannier gauge. It is shown that the commonly used phenomenological approach to apply dephasing is ill-defined in the presence of band crossings and leads to artifacts in the carrier distribution. They are caused by rapid changes of the dephasing operator matrix elements in the Wannier gauge, which render the convergence of the simulation in the stationary basis infeasible. In the comoving basis, also called Houston basis, these rapid changes can be resolved, but only at the cost of a largely increased computation time. As a remedy, we propose a modification of the dephasing operator with reduced magnitude in energetically close subspaces. This approach removes the artifacts in the carrier distribution and significantly speeds up the calculations, while affecting the high-harmonic spectrum only marginally. To foster further development, we provide our parallelized source code.- University Bibliography Jena:
- fsu_mods_00029532External link
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Multiscale simulation framework for the electromechanical behavior of large polymer based structures on the example of PEDOT:PSS
Year of publicationPublished in:Computational Materials Science- University Bibliography Jena:
- fsu_mods_00027179External link
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High-Performance Phototransistor Based on a 2D Polybenzimidazole Polymer
Year of publicationPublished in:Advanced Materials- University Bibliography Jena:
- fsu_mods_00025285External link
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Charge carrier mobilities in γ-graphynes: a computational approach
Year of publicationPublished in:NanoscaleGraphynes, a class of two-dimensional carbon allotropes, exhibit exceptional electronic properties, similar to graphene, but with intrinsic band gaps, making them promising for semiconducting applications. The incorporation of acetylene linkages allows for systematic modulation of their properties. However, the theoretical characterization of graphynes remains computationally demanding, particularly for electron-phonon coupling (EPC) analyses. Here, we employ the density functional tight binding method within the DFTBEPHY framework, providing an efficient and accurate approach for computing EPC and transport properties. We investigate the structural, mechanical, electronic, and transport properties of graphynes, comparing transport calculations using the constant relaxation-time approximation and the self-energy relaxation-time approximation (SERTA) alongside analytical models based on parabolic- and Kane-band approximations. For graphyne, the SERTA relaxation time is 0.63 (1.69) ps for holes (electrons). In graphdiyne, the relaxation time is 0.04 (0.14) ps for holes (electrons). While the hole mobilities in graphyne are on the order of 103 cm2 V-1 s-1, the electron mobilities reach up to 104 cm2 V-1 s-1. In graphdiyne, the mobility values for both types of charge carriers are on the order of 102 cm2 V-1 s-1. The phonon-limited mobilities at room temperature in graphyne fall between those of graphene and MoS2, while in graphdiyne, they are comparable to those of MoS2.- University Bibliography Jena:
- fsu_mods_00028741External link
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Monosaccharide-Derived Enantioselectivity in SWCNT Chemoresistive VOC Sensing
Year of publicationPublished in:Chemistry: a European JournalSemiconducting single-walled carbon nanotubes (sc-SWCNTs) are of great potential for vapor sensing. However, sc-SWCNTs lack recognition features for discriminating between sparsely functionalized moieties, molecules with similar structural features, and enantiomer pairs. This becomes a major setback in discriminating between volatile organic compounds (VOCs). Here, we used two galactosides decorated with aromatic groups as a recognition layer in chemoresistive sc-SWCNT sensors to produce chiral preference toward six terpenoid enantiomers. The multichirality and multifunctionality of a monosaccharide scaffold were exploited to maximize the limited interacting features associated with VOCs. The developed system establishes a robust and tunable platform for enantioselective gas sensing.- University Bibliography Jena:
- fsu_mods_00028980External link
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MORE-Q, a dataset for molecular olfactorial receptor engineering by quantum mechanics
Year of publicationPublished in:Scientific dataWe introduce the MORE-Q dataset, a quantum-mechanical (QM) dataset encompassing the structural and electronic data of non-covalent molecular sensors formed by combining 18 mucin-derived olfactorial receptors with 102 body odor volatilome (BOV) molecules. To have a better understanding of their intra- and inter-molecular interactions, we have performed accurate QM calculations in different stages of the sensor design and, accordingly, MORE-Q splits into three subsets: i) MORE-Q-G1: QM data of 18 receptors and 102 BOV molecules, ii) MORE-Q-G2: QM data of 23,838 BOV-receptor configurations, and iii) MORE-Q-G3: QM data of 1,836 BOV-receptor-graphene systems. Each subset involves geometries optimized using GFN2-xTB with D4 dispersion correction and up to 39 physicochemical properties, including global and local properties as well as binding features, all computed at the tightly converged PBE+D3 level of theory. By addressing BOV-receptor-graphene systems from a QM perspective, MORE-Q can serve as a benchmark dataset for state-of-the-art machine learning methods developed to predict binding features. This, in turn, can provide valuable insights for developing the next-generation mucin-derived olfactory receptor sensing devices.- University Bibliography Jena:
- fsu_mods_00022155External link
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A dataset of laymen olfactory perception for 74 mono-molecular odors
Year of publicationPublished in:Scientific dataThe molecular structure of an odor determines whether and how it is perceived by humans. However, the principles of how odorant chemistry links to perceptual patterns remain largely unknown and are primarily studied using odor rating datasets from highly trained olfactory experts, such as perfumers. This limits our knowledge of typical odor perception and its variability over individuals. We provide a dataset featuring free descriptions, evaluative ratings, and qualitative labels for 74 chemically diverse mono-molecular odorants, rated by a large sample of young adults. A total of 1,227 participants described and rated the odors, and completed questionnaires covering their demographic background, personality traits, and the role of olfaction in their daily lives. The dataset offers a valuable foundation for research aimed at understanding the fundamentals of olfactory perception.- University Bibliography Jena:
- fsu_mods_00022143External link
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A standardized lexicon of body odor words crafted from 17 countries
Year of publicationPublished in:Scientific dataBody odors offer a unique window into the physiological and psychological profile of the emitter. This information, broadcast in nonverbal communication, significantly shapes social interactions. However, effectively digitizing body odors requires a precise framework for perceptual operationalization. Previous research has used a very limited number of verbal terms, such as pleasant, intense, or attractive, which fails to adequately capture qualitative differences. To address this gap, we elicited body odor descriptions from 2,607 participants across 17 countries and 13 languages. All these descriptions are presented here in one dataset, together with a condensed list of 25 body odor words (BOW). Those terms reliably differentiated between body states, and were validated in a separate study with a different group of 155 perceivers. The dataset, available as a web application, provides a novel operationalization of body odor impressions, which is a precondition for studying olfaction in human nonverbal communication, for perception-based digitization of body odors and for comparative studies.- University Bibliography Jena:
- fsu_mods_00022154External link
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Investigation Into the Properties of γ-Valerolactone and γ-Butyrolactone Imide-Based Electrolytes for Lithium-Ion Batteries
Year of publicationPublished in:Battery EnergyThis study presents a detailed comparative study of lactone-based electrolytes (γ-valerolactone, GVL and γ-butyrolactone, GBL) combined with lithium imide-based salts, namely lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium bis(fluoromethanesulfonyl)imide (LiFSI). Propylene carbonate is employed as a reference electrolyte solvent. The physicochemical properties of these electrolyte systems are determined experimentally and further calculated using our developed computational model. Besides, in-silico investigations are used to reveal valuable insights into the molecular interactions of the electrolyte components, such as self-diffusion coefficients and radial distribution functions. Furthermore, the suitability of lactone-based electrolytes for electrochemical applications is demonstrated by their promising rate capability and cycling stability over 200 cycles in graphite half-cells, especially with 1 M LiTFSI and 2 wt% vinylene carbonate, together with their favorable performance on lithium iron phosphate. An excellent capacity retention achieved in a full-cell configuration (> 80% after 200 cycles) further validates the potential of lactones as battery solvent alternatives, with GVL standing out due to its bio-based origin.- University Bibliography Jena:
- fsu_mods_00028569External link
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From Local Atomic Environments to Molecular Information Entropy
Year of publicationPublished in:ACS OmegaThe similarity of local atomic environments is an important concept in many machine learning techniques, which find applications in computational chemistry and material science. Here, we present and discuss a connection between the information entropy and the similarity matrix of a molecule. The resulting entropy can be used as a measure of the complexity of a molecule. Exemplarily, we introduce and evaluate two specific choices for defining the similarity: one is based on a SMILES representation of local substructures, and the other is based on the SOAP kernel. By tuning the sensitivity of the latter, we can achieve good agreement between the respective entropies. Finally, we consider the entropy of two molecules in a mixture. The gain of entropy due to the mixing can be used as a similarity measure of the molecules. We compare this measure to the average and best-match kernel. The results indicate a connection between the different approaches and demonstrate the usefulness and broad applicability of the similarity-based entropy approach.- University Bibliography Jena:
- fsu_mods_00012828External link