@article{Blickenstorfer2021,
title = {Quantitative Diffractometric Biosensing},
author = {Yves Blickenstorfer and Markus Müller and Roland Dreyfus and Andreas Michael Reichmuth and Christof Fattinger and Andreas Frutiger},
url = {https://link.aps.org/doi/10.1103/PhysRevApplied.15.034023},
doi = {10.1103/PhysRevApplied.15.034023},
year = {2021},
date = {2021-03-09},
journal = {Physical Review Applied},
volume = {15},
number = {3},
pages = {034023},
abstract = {Diffractometric biosensing is a promising technology to overcome critical limitations of refractometric biosensors, the dominant class of label-free optical transducers. These limitations manifest themselves by higher noise and drifts due to insufficient rejection of refractive index fluctuations caused by variation in temperature, solvent concentration, and, most prominently, nonspecific binding. Diffractometric biosensors overcome these limitations with inherent self-referencing on the submicron scale with no compromise on resolution. Despite this highly promising attribute, the field of diffractometric biosensors has only received limited recognition. A major reason is the lack of a general quantitative analysis. This hinders comparison to other techniques and amongst different diffractometric biosensors. For refractometric biosensors, on the other hand, such a comparison is possible by means of the refractive index unit (RIU). In this paper, we suggest the coherent surface mass density, Γcoh, as a quantity for label-free diffractometric biosensors with the same purpose as the RIU in refractometric sensors. It is easy to translate Γcoh to the total surface mass density Γtot, which is an important parameter for many assays. We provide a generalized framework to determine Γcoh for various diffractometric biosensing arrangements that enables quantitative comparison. Additionally, the formalism can be used to estimate background scattering in order to further optimize sensor configurations. Finally, a practical guide with important experimental considerations is given to enable readers of any background to apply the theory. Therefore, this paper provides a powerful tool for the development of diffractometric biosensors and will help the field to mature and unveil its full potential.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{https://doi.org/10.1021/acssensors.0c02346,
title = {Investigating Complex Samples with Molograms of Low-Affinity Binders},
author = {Andreas M Reichmuth and Katharina Kübrich and Yves Blickenstorfer and Andreas Frutiger and Dmitry Momotenko and Volker Gatterdam and Fridolin Treindl and Christof Fattinger and Janos Vörös},
url = {https://pubs.acs.org/doi/abs/10.1021/acssensors.0c02346},
doi = {10.1021/acssensors.0c02346},
year = {2021},
date = {2021-02-25},
journal = {American Chemical Society},
abstract = {In vitro diagnostics relies on the quantification of minute amounts of a specific biomolecule, called biomarker, from a biological sample. The majority of clinically relevant biomarkers for conditions beyond infectious diseases are detected by means of binding assays, where target biomarkers bind to a solid phase and are detected by biochemical or physical means. Nonspecifically bound biomolecules, the main source of variation in such assays, need to be washed away in a laborious process, restricting the development of widespread point-of-care diagnostics. Here, we show that a diffractometric assay provides a new, label-free possibility to investigate complex samples, such as blood plasma. A coherently arranged sub-micron pattern, that is, a peptide mologram, is created to demonstrate the insensitivity of this diffractometric assay to the unwanted masking effect of nonspecific interactions. In addition, using an array of low-affinity binders, we also demonstrate the feasibility of molecular profiling of blood plasma in real time and show that individual patients can be differentiated based on the binding kinetics of circulating proteins.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{@Article{s21020469,
title = {Ultra-Stable Molecular Sensors by Sub-Micron Referencing and Why They Should Be Interrogated by Optical Diffraction - Part I. The Concept of a Spatial Affinity Lock-in Amplifier},
author = {Frutiger Andreas and Fattinger Christof and Vörös János},
url = {https://www.mdpi.com/1424-8220/21/2/469},
doi = {10.3390/s21020469},
issn = {1424-8220},
year = {2021},
date = {2021-01-11},
journal = {Sensors},
volume = {21},
number = {2},
pages = {469},
abstract = {Label-free optical biosensors, such as surface plasmon resonance, are sensitive and well-established for the characterization of molecular interactions. Yet, these sensors require stabilization and constant conditions even with the use of reference channels. In this paper, we use tools from signal processing to show why these sensors are so cross-sensitive and how to overcome their drawbacks. In particular, we conceptualize the spatial affinity lock-in as a universal design principle for sensitive molecular sensors even in the complete absence of stabilization. The spatial affinity lock-in is analogous to the well-established time-domain lock-in. Instead of a time-domain signal, it modulates the binding signal at a high spatial frequency to separate it from the low spatial frequency environmental noise in Fourier space. In addition, direct sampling of the locked-in sensor’s response in Fourier space enabled by diffraction has advantages over sampling in real space as done by surface plasmon resonance sensors using the distributed reference principle. This paper and part II hint at the potential of spatially locked-in diffractometric biosensors to surpass state-of-the-art temperature-stabilized refractometric biosensors. Even simple, miniaturized and non-stabilized sensors might achieve the performance of bulky lab instruments. This may enable new applications in label-free analysis of molecular binding and point-of-care diagnostics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Article{s21010009,
title = {Ultra Stable Molecular Sensors by Submicron Referencing and Why They Should Be Interrogated by Optical Diffraction—Part II. Experimental Demonstration},
author = {Frutiger, Andreas and Gatterdam, Karl and Blickenstorfer, Yves and Reichmuth, Andreas Michael and Fattinger, Christof and Vörös, János},
url = {https://www.mdpi.com/1424-8220/21/1/9?utm_source=TrendMD&utm_medium=cpc&utm_campaign=Sensors__TrendMD_0},
doi = { https://doi.org/10.3390/s21010009},
issn = {1424-8220},
year = {2020},
date = {2020-12-22},
journal = {Sensors 2021},
volume = {21 (1)},
number = {9},
abstract = {Label-free optical biosensors are an invaluable tool for molecular interaction analysis. Over the past 30 years, refractometric biosensors and, in particular, surface plasmon resonance have matured to the de facto standard of this field despite a significant cross reactivity to environmental and experimental noise sources. In this paper, we demonstrate that sensors that apply the spatial affinity lock-in principle (part I) and perform readout by diffraction overcome the drawbacks of established refractometric biosensors. We show this with a direct comparison of the cover refractive index jump sensitivity as well as the surface mass resolution of an unstabilized diffractometric biosensor with a state-of-the-art Biacore 8k. A combined refractometric diffractometric biosensor demonstrates that a refractometric sensor requires a much higher measurement precision than the diffractometric to achieve the same resolution. In a conceptual and quantitative discussion, we elucidate the physical reasons behind and define the figure of merit of diffractometric biosensors. Because low-precision unstabilized diffractometric devices achieve the same resolution as bulky stabilized refractometric sensors, we believe that label-free optical sensors might soon move beyond the drug discovery lab as miniaturized, mass-produced environmental/medical sensors. In fact, combined with the right surface chemistry and recognition element, they might even bring the senses of smell/taste to our smart devices.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Fattinger2020,
title = {Focal Molography – an optical method for label-free detection of biomolecular interactions},
author = {Fattinger, Christof; Frutiger, Andreas},
url = {https://www.sps.ch/fileadmin/articles-pdf/2020/Mitteilungen_Progress_77.pdf},
year = {2020},
date = {2020-10-01},
journal = {Progress in Physics},
volume = {62},
number = {77},
abstract = {Focal molography is a new method for label-free molecular interaction analysis in crude samples. In contrast to refractometric optical sensors, focal molography is insensitive to nonspecific molecular interactions. This unique property is achieved with a special 2D nanopattern of molecular binding sites on a chip, termed mologram. A mologram is designed such that molecules bound to it diffract light constructively into a focal spot. The intensity of the focused light is measured to quantify the amount of bound molecules. In biological samples, highly abundant off-target molecules readily adsorb to the surface of the sensor. Yet, this process is completely random and the off-target molecules do not bind to the ordered binding sites of the mologram. Thus, their scattering is uniform in all spatial directions and therefore they hardly contribute to the measured light intensity in the narrow solid angle of the focal spot.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Reichmuth2020,
title = {Quantification of Molecular Interactions in Living Cells in Real Time using a Membrane Protein Nanopattern},
author = {Andreas Michael Reichmuth and Mirjam Zimmermann and Florian Wilhelm and Andreas Frutiger and Yves Blickenstorfer and Christof Fattinger and Maria Waldhoer and János Vörös},
doi = {10.1021/acs.analchem.0c00987},
issn = {0003-2700},
year = {2020},
date = {2020-01-01},
journal = {Analytical Chemistry},
abstract = {Molecular processes within cells have traditionally been studied with biochemical methods due to their high degree of specificity and ease of use. In recent years, cell-based assays have gained more and more popularity since they facilitate the extraction of mode of action, phenotypic, and toxicity information. However, to provide specificity, cellular assays rely heavily on biomolecular labels and tags while label-free cell-based assays only offer holistic information about a bulk property of the investigated cells. Here, we introduce a cell-based assay for protein–protein interaction analysis. We achieve specificity by spatially ordering a membrane protein of interest into a coherent pattern of fully functional membrane proteins on the surface of an optical sensor. Thereby, molecular interactions with the coherently ordered membrane proteins become visible in real time, while nonspecific interactions and holistic changes within the living cell remain invisible. Due to its unbiased nature, this new cell-based detection method presents itself as an invaluable tool for cell signaling research and drug discovery.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Frutiger2019,
title = {Principles for Sensitive and Robust Biomolecular Interaction Analysis: The Limits of Detection and Resolution of Diffraction-Limited Focal Molography},
author = {Andreas Frutiger and Yves Blickenstorfer and Silvio Bischof and Csaba Forró and Matthias Lauer and Volker Gatterdam and Christof Fattinger and János Vörös},
doi = {10.1103/physrevapplied.11.014056},
year = {2019},
date = {2019-01-28},
journal = {Physical Review Applied},
volume = {11},
number = {1},
pages = {014056},
abstract = {Label-free biosensors enable the monitoring of biomolecular interactions in real time, which is key to the analysis of the binding characteristics of biomolecules. While refractometric optical biosensors such as surface plasmon resonance (SPR) are sensitive and well-established, they are susceptible to any change of the refractive index in the sensing volume caused by minute variations in composition of the sample buffer, temperature drifts, and most importantly nonspecific binding to the sensor surface in complex fluids such as blood. The limitations arise because refractometric sensors measure the refractive index of the entire sensing volume. Conversely, diffractometric biosensors–for example, focal molography–only detect the diffracted light from a coherent assembly of analyte molecules. Thus any refractive index distribution that is noncoherent with respect to this molecular assembly does not add to the coherent signal. This makes diffractometric biosensors inherently robust and enables sensitive measurements without reference channels or temperature stabilization. The coherent assembly is generated by selective binding of the analyte molecules to a synthetic binding pattern–the mologram. Focal molography has been introduced theoretically [C. Fattinger, Phys. Rev. X 4, 031024 (2014)] and verified experimentally [V. Gatterdam, A. Frutiger, K.-P. Stengele, D. Heindl, T. Lübbes, J. Vörös, and C. Fattinger, Nat. Nanotechnol. 12, 1089 (2017)] in previous papers. However, further understanding of the underlying physics and a diffraction-limited readout is needed to unveil its full potential. This paper introduces refined theoretical models, which can accurately quantify the amount of biological matter bound to the mologram from the diffracted intensity. In addition, it presents measurements of diffraction-limited molographic foci, i.e., Airy discs. These improvements enable us to demonstrate a resolution in real-time binding experiments comparable to the best SPR sensors without the need for temperature stabilization or drift correction and to detect low-molecular-weight compounds label free in an endpoint format. The presented experiments exemplify the robustness and sensitivity of the diffractometric sensor principle.},
note = {test},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Frutiger2018,
title = {Image reversal reactive immersion lithography improves the detection limit of focal molography},
author = {Andreas Frutiger and Cla Duri Tschannen and Yves Blickenstorfer and Andreas M Reichmuth and Christof Fattinger and Janos Vörös},
doi = {10.1364/ol.43.005801},
issn = {0146-9592},
year = {2018},
date = {2018-01-01},
journal = {Optics Letters},
volume = {43},
number = {23},
pages = {5801},
abstract = {Focal molography is a label-free optical biosensing method that relies on a coherent pattern of binding sites for biomolecular interaction analysis. Reactive immersion lithography (RIL) is central to the patterning of molographic chips but has potential for improvements. Here, we show that applying the idea of image reversal to RIL enables the fabrication of coherent binding patterns of increased quality (i.e., higher analyte efficiency). Thereby the detection limit of focal molography in biological assays can be improved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}