Periodic Reporting for period 1 - MIMOSA (4D Microscopy of biological materials by short pulse terahertz sources (MIMOSA))
Okres sprawozdawczy: 2022-09-01 do 2023-08-31
Cryo-electron microscopy and tomography have been among the greatest achievements in biological imaging, but these techniques suffer from insufficient chemical resolution. The EU-funded MIMOSA project aims to provide an alternative to nanoscale tomography with a high chemical resolution for biological and medical applications, based on the tomographic atom probe (TAP). The project aims to develop a prototype of a new TAP triggered by intense stable terahertz (THz) pulses at high repetition rates. Another project goal is to deliver a prototype of an efficient intense THz source based on novel ultrafast high-energy fibre lasers that can be used in nano-tomography for biological and medical applications and as a test platform for commercialisation of the TH-triggered TAP.
Regarding the development of intense THz sources, the project has made excellent progress. The parameters of low-repetition rate source have been well measured in term of polarization, shape and spectrum, by developing original methods for THz pulse characterization. At the same time, for high-repetition-rate single-cycle THz pule generation, the parameters of the THz source driven at 1m have been optimized reaching outstanding performances. Furthermore, progress on the 2 µm fiber laser source has been significant and a prototype has been constructed and tested by the industrial partner. Moreover, to enhance the THz capabilities for TAP analysis we have decided to shape the THz pulses. The THz pulse shaping strategy has been refined and the first structures drawn up.
We have moved forwards the first steps in constructing a prototype for a novel TAP instrument triggered by THz pulses for biological materials. This involved concurrent efforts in two distinct areas: understanding the interaction between the THz pulse and the analyzed sample, both theoretically and experimentally, and developing new protocols for the preparation of biological samples. Here, experimental work is coupled with theoretical calculations to analyze the effect of the matrix on biological samples.
Interaction of intense THz pulses with biocompatible materials is a very new field in materials science. Moreover, ion emission and acceleration by THz pulses has never been studied before. To gain new insights on these processes, we have started investigating the methodological and computational aspects of modeling the effect on electronic and optical properties when applying strong static electric fields and time-dependent radiations, in visible and THz domains. We performed numerical calculations of ions trajectories under the action of the static DC field and the THz transient, studying the effect of the THz pulse characteristics on the ion energy. We have started to compare the prediction of these theoretical work with the results obtained in THz-TAP in terms of success rate and performance by varying operating conditions of the THz pulse.
With regard to specimen preparation, we worked on the preparation of proteins, micelles and liposomes embedded in silica glass. Significant efforts have been directed towards thin films fabrication rather than employing traditional bulk silica glass. Proteins embedded within these films have been labelled with gold nanoparticles. This methodology enables a more efficient mapping of proteins presence and densities. Consequently, it increases the likelihood of locating the target protein within the TAP specimen. However, this surface approach presented notable challenges due to substantial variations in the field of evaporation across layers of disparate materials. To overcome these hurdles, experiments are currently being conducted with higher glass density. By exploring this new avenue, it is anticipated that these operational challenges can be mitigated, paving the way for more consistent and reliable results.
To study the effect of the matrix on biological samples we carried out a thorough computational analysis of the protein-cage interface interaction using classical molecular dynamics. In this way, we have achieved a quantitative understanding of the early onset of the embedding process in order to draw preliminary inferences on the capability of orthosilicic acid to stabilize the dynamics of small biological systems. In this respect, we can draw preliminary inferences on the capability of orthosilicic acid to stabilize the dynamics of small biological systems.
During this first year of the project, we have demonstrated that THz pulses enable evaporation of metallic and non-metallic samples with a significant reduction of the sample heating. This result is crucial because thermal effects will compromise the analysis of biological materials in TAP.
We have moved forwards the first steps in constructing a prototype for a novel TAP instrument triggered by THz pulses for biological materials. This involved concurrent efforts in two distinct areas: understanding the interaction between the THz pulse and the analyzed sample, both theoretically and experimentally, and developing new protocols for the preparation of biological samples. Here, experimental work is coupled with theoretical calculations to analyze the effect of the matrix on biological samples.
Interaction of intense THz pulses with biocompatible materials is a very new field in materials science. Moreover, ion emission and acceleration by THz pulses has never been studied before. To gain new insights on these processes, we have started investigating the methodological and computational aspects of modeling the effect on electronic and optical properties when applying strong static electric fields and time-dependent radiations, in visible and THz domains. We performed numerical calculations of ions trajectories under the action of the static DC field and the THz transient, studying the effect of the THz pulse characteristics on the ion energy. We have started to compare the prediction of these theoretical work with the results obtained in THz-TAP in terms of success rate and performance by varying operating conditions of the THz pulse.
With regard to specimen preparation, we worked on the preparation of proteins, micelles and liposomes embedded in silica glass. Significant efforts have been directed towards thin films fabrication rather than employing traditional bulk silica glass. Proteins embedded within these films have been labelled with gold nanoparticles. This methodology enables a more efficient mapping of proteins presence and densities. Consequently, it increases the likelihood of locating the target protein within the TAP specimen. However, this surface approach presented notable challenges due to substantial variations in the field of evaporation across layers of disparate materials. To overcome these hurdles, experiments are currently being conducted with higher glass density. By exploring this new avenue, it is anticipated that these operational challenges can be mitigated, paving the way for more consistent and reliable results.
To study the effect of the matrix on biological samples we carried out a thorough computational analysis of the protein-cage interface interaction using classical molecular dynamics. In this way, we have achieved a quantitative understanding of the early onset of the embedding process in order to draw preliminary inferences on the capability of orthosilicic acid to stabilize the dynamics of small biological systems. In this respect, we can draw preliminary inferences on the capability of orthosilicic acid to stabilize the dynamics of small biological systems.
During this first year of the project, we have demonstrated that THz pulses enable evaporation of metallic and non-metallic samples with a significant reduction of the sample heating. This result is crucial because thermal effects will compromise the analysis of biological materials in TAP.
The MIMOSA consortium plays a leading role in advancing the science necessary for realizing of revolutionary instrumentation for 4D microscopy of biocompatible materials, including:
• The world’s first demonstration of THz-pulse shape control and efficiency optimization in a two-color plasma generation scheme. Unlike what has been reported in existing literature, the temporal shape of the THz pulse strongly depends on the combination of two factors: chirp and phase-shift
• The world’s first demonstration of the athermal field-ion evaporation using THz-electric field with tailored temporal pulse shape, suggesting that this innovative concept is very appealing for biomaterial analysis.
• The world’s first high-intensity THz-source driven by a femtosecond fiber pump laser and using a reflective echelon mirror scheme, demonstrating the capability of the technology to operate at high-repetition rates with high THz-field strengths.
• The first TAP analysis of bio-compatible materials showing large 3D volume containing several proteins, using deep-UV-TAP. This finding illustrates the potential of deep-UV-TAP for more accurate scientific investigations due to minimized experimental artifacts.
• The development of a 2 µm all-fiber laser system. The novelty of the developed laser design is an all-fiber concept up to the final amplifier, which reduces the free-space sections in the laser system to a minimum, reducing water-vapor absorptions. The technology developed by AFS will provide new capabilities for mid-infrared lasers with high performances in compact and reliable architectures. This would open up new market opportunities in the fields of materials processing and surgery.
• The world’s first demonstration of a simple and accurate method for measuring the arbitrary polarization state of broadband and high-energy THz pulses. Our method enables detection of the full pulse bandwidth and significantly improves measurement time efficiency.
• The major impact of our theoretical and computational analysis of the interaction mechanisms between the silicon-based matrix and the protein, related but not limited to the evaporation of water occurring at the interface, is on the determination of the most suitable material for building the hosting cage.
• The study of the static and THz laser-matter interaction is of paramount importance for the thorough understanding of the dissociation mechanisms at the base of the TAP technique. The ab-initio simulations of realistic systems, starting from the dissociation of orthosilicic acid, will thus enhance our knowledge of TAP and, generally, of the interaction mechanisms between THz laser fields and biomolecular aggregates.
• The world’s first demonstration of THz-pulse shape control and efficiency optimization in a two-color plasma generation scheme. Unlike what has been reported in existing literature, the temporal shape of the THz pulse strongly depends on the combination of two factors: chirp and phase-shift
• The world’s first demonstration of the athermal field-ion evaporation using THz-electric field with tailored temporal pulse shape, suggesting that this innovative concept is very appealing for biomaterial analysis.
• The world’s first high-intensity THz-source driven by a femtosecond fiber pump laser and using a reflective echelon mirror scheme, demonstrating the capability of the technology to operate at high-repetition rates with high THz-field strengths.
• The first TAP analysis of bio-compatible materials showing large 3D volume containing several proteins, using deep-UV-TAP. This finding illustrates the potential of deep-UV-TAP for more accurate scientific investigations due to minimized experimental artifacts.
• The development of a 2 µm all-fiber laser system. The novelty of the developed laser design is an all-fiber concept up to the final amplifier, which reduces the free-space sections in the laser system to a minimum, reducing water-vapor absorptions. The technology developed by AFS will provide new capabilities for mid-infrared lasers with high performances in compact and reliable architectures. This would open up new market opportunities in the fields of materials processing and surgery.
• The world’s first demonstration of a simple and accurate method for measuring the arbitrary polarization state of broadband and high-energy THz pulses. Our method enables detection of the full pulse bandwidth and significantly improves measurement time efficiency.
• The major impact of our theoretical and computational analysis of the interaction mechanisms between the silicon-based matrix and the protein, related but not limited to the evaporation of water occurring at the interface, is on the determination of the most suitable material for building the hosting cage.
• The study of the static and THz laser-matter interaction is of paramount importance for the thorough understanding of the dissociation mechanisms at the base of the TAP technique. The ab-initio simulations of realistic systems, starting from the dissociation of orthosilicic acid, will thus enhance our knowledge of TAP and, generally, of the interaction mechanisms between THz laser fields and biomolecular aggregates.