A team of researchers at Nagoya University in Japan has created a 3-Dimensional computational simulation of the process of genome structure formation in the human cell nucleus. They expect the model to contribute to the understanding of cellular regulatory mechanisms and diseases, such as cancer, that damage the genome.  

The three-dimensional structure of the genome plays a vital role in regulating the DNA functions of animal and plant cells because it affects its reading and replication. Shin Fujishiro and Masaki Sasai, Professor Emeritus of Nagoya University’s Department of Complex Systems Science, Graduate School of Informatics, constructed a 3D model by analyzing the whole genome of human cells. They used this model as a platform to investigate the relationship between the structure, dynamics, and functions of the human genome. 

“The spatial organization of DNA and its dynamic movement in cells are crucial for understanding cell functions,” Professor Sasai explains. “Researchers have devoted considerable effort to explaining DNA organization in cells by developing various experimental methods, including biochemical and microscope technologies, but now a unified picture is required. Our research introduces the first computational model that can quantitatively analyze various data from the full genome of human cells in a consolidated way.” 

To help understand the process, the researchers investigated chromatin. Chromatin is a mixture of DNA with proteins that exist in cells as a way to keep the DNA compact. According to their model, chromatin is unevenly distributed and during the unfolding process that occurs during cell division, repulsive forces among the chromatin chains induce them to separate. This same force also separates chromatin into active and inactive compartments in the nuclei. The researchers found that their proposed mechanism clarified biochemical and microscopic findings of previous studies.  

Professor Sasai adds: “Our model provides an indispensable tool and an original perspective in cell biology. From the computational model developed in this research, we can determine how perturbations in cells affect genome dynamics and organization. We can also investigate how disease cells, including various cancer cells, affect the genome. It allows us to more deeply analyze the relationship between genome structure and transcription regulation. The model developed in this research provides a fundamental tool and a new viewpoint in cell biology.” 

The team of researchers, including Dr. Oleksandr Kyriienko from the University of Exeter, has shown that controlling light can be achieved by inducing and measuring a nonlinear phase shift down to a single polariton level. 

Polaritons are hybrid particles that combine properties of light and matter. They arise in optical structures at strong light-matter coupling, where photons hybridize with underlying particles in the materials – quantum well excitons (bound electron-hole pairs).

The new research, led by the experimental group of Prof D Krizhanovskii from the University of Sheffield, has observed that interaction between polaritons in micropillars leads to a cross-phase-modulation between modes of different polarization.

The change of phase is significant even in the presence of (on average) a single polariton and can be further increased in structures with stronger confinement of light. This brings an opportunity for quantum polaritonic effects that can be used for quantum sensing and supercomputing.

Theoretical analysis, led by Dr. Oleksandr Kyriienko, shows the observed single polariton phase shift can be further increased, and cascading micropillars offer a path toward polaritonic quantum gates.

Quantum effects with weak light beams can in turn help detect chemicals, and gas leakage, and perform computation at largely increased speed.

Dr. Kyriienko said: “The experimental results reveal that quantum effects at a single polariton level can be measured in a single micropillar. From the theory point of view, it is important to increase phase shifts and develop the system into an optically controlled phase gate. We will see more efforts to build quantum polaritonic lattices as a quantum technology platform.”

Polaritons have proven to be an excellent platform for nonlinear optics, where particles enjoy increased coherence due to cavity field and strong nonlinear from exciton-exciton scattering.

Previously, polaritonic experiments led to the observation of polaritonic Bose-Einstein condensation and various macroscopic nonlinear effects, including the formation of solitons and vortices. However, the observation of quantum polaritonic effects in the low occupation limit remains an uncharted field.

The study shows that polaritons can sustain nonlinearity and coherence in extremely small occupations. This triggers a search for polaritonic systems that can further enhance quantum effects and operate as quantum devices.

Dr.. Paul Walker, the corresponding author of the study, explains: “We have used high-quality micropillars from gallium arsenide provided by collaborators from the University of Paris Saclay, France. These pillars confine modes of different polarization that are close in energy. By pumping light into one of the modes (fundamental), we probe a signal sent into another (higher energy) mode, and observe that the presence of a weak (single photon) pulse leads to polarization rotation. This can be seen as a controlled phase rotation.”

The senior author of the study Prof Krizhanovskii concludes: “In the presented experiment we have made a first step to see single-polariton effects. There is certainly a room for improvement. In fact, using cavities of smaller size and optimizing the structure we expect to increase phase shift orders of magnitude. This will establish the state-of-the-art for future polaritonic chips.”