Project portfolio

LabVIEW was used to develop a software platform for the integration of a microscope camera, an automated stage, four Thorlabs motors, a Lakeshore temperature controller, and a Horiba Raman spectrometer. The software platform provides an efficient user interface for controlling the experimental setup, as well as a script engine for developing custom experiments. A database using a MySQL server was developed to store experimental data. To complement data analysis, a special GUI was developed in Igor PRO software to extract past experimental data from the MySQL server. The following papers were published using this software integration:

1. Benshalom N, Reuveni G, Korobko R, Yaffe O, and Hellman O. Dielectric response of rock-salt crystals at finite temperatures from first principles. Phys. Rev. Mat. 03/2022
2.  Menahem M, Dai Z, Aharon S, Sharma R, Asher M, Diskin-Posner Y, Korobko R, Rappe AM, Yaffe O. Strongly Anharmonic Octahedral Tilting in Two-Dimensional Hybrid Halide Perovskites. Acs Nano. 05/2021
3.  Asher M, Angerer D, Korobko R, Diskin-Posner Y, Egger DA, Yaffe O. Anharmonic Lattice Vibrations in Small-Molecule Organic Semiconductors. Advanced Materials 01/2020 (Deerfield Beach, Fla.)
4. Sharma R, Dai Z, Gao L, Brenner TM, Yadgarov L, Zhang J, Rakita Y, Korobko R, Rappe AM, Yaffe O. Elucidating the atomistic origin of anharmonicity in tetragonal CH3NH3PbI3 with Raman scattering. Physical Review Materials 09/2020

The photoluminescence (PL) collected by the objective was dispersed using a dichroic mirror and directed to a silicon photomultiplier tube (PMT) sensitive to 750-900 nm light. The electrical signal was amplified and passed to a National Instruments (NI) 6343 card, as well as the microscope pixel and line clocks. The three digitized signals were then passed to a computer and processed by an in-house LabVIEW program that reconstructed the confocal microscopy image. This software-hardware integration led to the development of the following paper:

Self-Healing and Light-Soaking in MAPbI3: The Effect of H2O Ceratti D. R., Tenne R., Bartezzaghi, Cremonesi L., Segev L., Kalchenko V., Oron D., Potenza M.A.C, Hodes G., Cahen D. (2022) Advanced materials (Weinheim)

A micromanager code was integrated with a Nikon microscope to enable real-time imaging of microfluidic devices while they were being operated. This integration allowed for the visualization of the dynamic processes occurring within the microfluidic devices, which led to a better understanding of their behavior. The integration of the micromanager code with the Nikon microscope was published in a paper in Nature Biotechnology:

Fedyuk, V., Erez, N., Furth, N. et al. Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics. Nat Biotechnol (2022).

The origin of life is a complex and challenging question that has been debated by scientists for centuries. One of the most popular theories is that life arose from self-reproducing supramolecular structures, which are large molecules that can make copies of themselves. However, the transition from chaotic chemistry to self-reproducing supramolecular structures is a difficult one, and it is not clear how it could have occurred.

In this study, we investigated the reproduction characteristic of the graded autocatalysis replication domain (GARD) computer-simulated physicochemically rigorous lipid-based model. This model is designed to be compatible with heterogeneous environments, address the network's spatial demarcation, and portray trans-generational compositional information transfer. We found that compositionally reproducing states are extremely rare, suggesting that random roaming would be a vastly inefficient path toward reproduction. However, we also found that all self-reproducing states are also dynamic attractors of the catalytic network. This suggests that self-reproducing supramolecular structures could have arisen spontaneously, and that the transition from chaotic chemistry to self-reproduction is not as difficult as previously thought.

Our findings provide new insights into the origin of life, and they suggest that self-reproducing supramolecular structures may have been the first form of life on Earth.

Amit Kahana, Lior Segev, Doron Lancet, Attractor dynamics drives self-reproduction in protobiological catalytic networks, Cell Reports Physical Science, 2023, 101384

Since thermal infrared cameras calculate an ‘apparent’ 225 temperature of each pixel (Tap) based on a fixed emissivity setting applied to the entire image (here: 226 1), temperatures of each pixel must be corrected using their correct ε and reflected Lin for each 227 pixel. Therefore, we developed an algorithm based on deep learning (Falk et al., 2019) using 228 Python 3.6 with the “OpenCV” library (Bradski, 2000) in order to segment the IR images of the 229 PV field into 3 categories: panels, sun-exposed soil and shaded soil (Figure S7). Using this 230 segmentation, both the fractions of each category in the entire PV field, their temperature 231 (Discussion S1) and the mean emitted thermal radiation were calculated. 

Rafael Stern, Jonathan D Muller, Eyal Rotenberg, Madi Amer, Lior Segev, Dan Yakir, Photovoltaic fields largely outperform afforestation efficiency in global climate change mitigation strategies, PNAS nexus, 2023