Internal Seminar Series

The OIST Internal Seminar Series is an informal meeting within the OIST community, where students, postdocs, research assistants and professors alike get to share a piece of their daily lives over free pizza/pastry. During a typical seminar, a speaker will introduce their unit or research field, discuss their latest results, or explain plans for future work.

One of the goals of the Internal Seminar Series is to foster an interdisciplinary, cooperative environment within OIST, where we can learn from each other and understand the motivations that drive research in fields we are not familiar with. This is based on the understanding that the activities at OIST are intrinsically interesting and worthwhile to learn about for curiosity's sake. Beyond this, there is the possibility that internal collaborations may spring up in unforeseen areas of research. We value the diversity of speakers: from students to professors, regardless of study field, age, race, and sex.

Seminars are organized every two weeks. Please see the "Calendar" or "Upcoming Events" links on the left for more information about upcoming seminars. Each seminar usually takes place in Lab 3 room C700 and starts at 16:00, after which there will be free pizza and beverages. The refreshment is financially supported by President's office, while they do not influence the topics, speakers, time, and venue of the seminars.

Note on alcohol:
From Fall 2024, we offer beer along the other refreshments. This is paid for privately by generous faculty and executives. Don't ruin it. Don't drink and drive. You can always call e.g. Ishikawa Taxi (098-972-5406) or Agachi Daiko (080-6485-9978).

Interested in speaking at an Internal Seminar? Fill out the form or contact internalseminar@oist.jp

2024 Fall

All seminars this term will be available both on-site and on Zoom.

September 10 (L4E48)

  • Dr. Alec LaGrow, Scientific Imaging Section
  • Dr. Eugene Khaskin, Science and Technology Group

September 24 (C700)

  • Dr. Melissa Matthews, Molecular Cryo-Electron Microscopy Unit

October 8 (C700)

  • David O'Connell, Quantum Gravity Unit

Space, Time and Sliding Doors

In this talk I will cover a few elements of my PhD project, which roughly deals with topology change in a physical context. Starting with an observation surrounding Hollywood's dearest Gwyneth Paltrow, we will slowly walk through the relevant structures required to phrase my PhD research goal. Along the way we will discuss some aspects of topology, geometry and relativity theory, hopefully with a bit of something for everyone.

  • Giulio Foggi Rota, Complex Fluids and Flows Unit

Turbulent flows over flexible canopies

Canopy flows occur when numerous slender elements protruding from a supporting surface interact with a moving fluid. These flows are often found in nature and are particularly interesting from geophysical and biological perspectives. In this work, we begin by examining the dynamics of a flexible fibre clamped in turbulent flow and then extend this understanding to the collective behaviour of flexible canopies. This development provides fundamental physical insights that pave the way for investigating more complex and realistic natural scenarios, such as the swaying of crops in the wind or the agitation of kelp forests by marine currents.

October 22 (C700)

  • Ryo Nakatani, Computational Neuroscience Unit

Astrocytes actively alter electrical membrane potential; How and why

The electrical properties of cellular membranes are the basis for information transfer within the brain. Typically, these processes are done with the intercommunication of neurons via dynamic changes of the electrical membrane potential (hyper-polarization/depolarization). However, recent studies have also observed that astrocytes, non-neuronal supportive cells, also have depolarization, specifically in the periphery where they are in close contact with neurons. Utilizing a computational whole-cell astrocyte model, we explore previous hypotheses on the mechanism of astrocytic depolarization as well as provide a new prediction into how these mechanisms work, and why they are relevant.

  • Hirokazu Maruoka, Nonlinear and Non-equilibrium Physics Unit

Data-driven discovery of self-similarity using neural networks

Physics is the fundamentally a data-driven enterprise based on the experimental data and simulation data. In this seminar, I will talk about our powerful data-driven approach that combines self-similarity and neural networks. By introducing similarity parameters, which are power-law monomials composed of physical parameters, all the data points converge to a single line, which is known as data collapse. This means that all the self-similarity of data points is fully exploited, providing significant insights into the physics. In order to obtain these data collapse relations, the only unknown parameters are their power exponents of the similarity parameters. The general conventional method to obtain power exponents has been dimensional analysis though it is limited to only special cases. Based on this insight of self-similarity, we have succesfully invented a systematic approach to get data collapse using neural network technique. Through this seminar, I would like to demonstrate : what is data-collapse? what is self-similarity? and what is the strategy to get data-collapse from arbitrary data?

November 5 (C700)

  • Dr. Jamila Rodrigues and Dr. Yi Huang, Complexity Science and Evolution Unit

Okinawa coastal fisheries: exploring ideas of climate change and the future of fishing industry

Japan's coastline is characterised by the presence of fishing communities that play a pivotal role in the provision of seafood. These community-based fisheries provide employment for local families while simultaneously embodying cultural heritage. Just like other fishing communities worldwide, Okinawa fishers are confronted with challenges such as the impact of climatic stressors that affect marine ecosystems and the fishing industry. In this seminar, we introduce our project focusing on Okinawa fishers. We have developed a transdisciplinary study in collaboration with scholars, local fishers, and the Okinawa Prefecture Fisheries Cooperative Federation. The objective of our study is to analyse fishers’ perceptions of local climate change, their concerns about the future of the fisheries industry, and their notions of well-being. By incorporating a transdisciplinary approach, our study aims to provide a broader understanding of how local climate change is perceived by local fishers and its impacts on Okinawa fishing communities. We will introduce our research methods and some preliminary findings. We are open to discuss with the audience on how to develop strategies for researchers who are interested in engaging with coastal communities and beyond.

  • Zohreh Shahrabifarahani, Light-Matter Interactions for Quantum Technologies Unit

Two photon generation using optical nanofiber-trapped cold atoms useful for “Heralded single photon” scheme 

We aim to experimentally realize the nonlinear effect of Four-Wave Mixing (FWM) in an atomic system cooled and trapped near an optical nanofiber (ONF) waveguide. This setup enables the generation of pairs of correlated photons, which are beneficial for heralded single-photon source schemes. The optical nanofiber facilitates this process by allowing for significantly lower power requirements and enabling efficient coupling of the generated photons back into the ONF for transmission to any desired destination. The produced atomic-based single photons will exhibit a narrowband spectrum due to the cancellation of the Doppler effect in cold atoms, and compatible with other atomic-based quantum systems, including atomic quantum memories.

November 19 (C700)

  • Lenard Lajos Szantho, Model-Based Evolutionary Genomics Unit

Towards better phylogenetic models of evolution by accounting for compositionally constrained sites

Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from various phylogenetic models. Analyses of empirical datasets have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies, that are strongly supported, e.g. observing long-branch attraction (LBA) artifact. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets.

In my talk I will introduce "compositional constraint analysis" a method to investigate the effect of site-specific constraints on amino acid composition on phylogenetic inference, and "CAT-PMSF", a phylogenetic pipeline to ameliorate the effect of LBA artifacts by accounting for across-site compositional heterogeneity while still running in a feasible amount of time as presented on several empirical datasets including Microsporidia, Nematoda, and Platyhelminthes.

  • Emily Satyadhi, Molecular Neuroscience Unit

Impairment in axonal translation caused by reduction in ATP level during aging in sensory neurons

Axonal translation is an important mechanism which plays a role in maintaining axonal morphology as well as mediating axonal injury and recovery. During axonal translation, mitochondria is thought to be stored along the axon to provide energy required for translation. The decline in mitochondria activity is one of the hallmarks of aging, however, it is still unclear whether the decline in mitochondria activity can be linked to the level of axonal translation in aging neurons. In here, we utilize the microfluidic device to separate the cell body and the axon of the DRG neurons. Using live imaging, we found that there is a significant decrease in the level of axonal translation level as well as the number of translational hotspots in aging neurons. We also showed that supplementing the culture with NMN, which can increase mitochondria activity, was able to increase the level of axonal translation of the aging neurons similar to the level observed in young neurons.

December 3 (C700)

  • Emma Gairin, Marine Eco-Evo-Devo Unit
Decoding the relationship between fish gene expression and the environment
 
A large fraction of the worldwide human population lives within a few kilometers of the oceans, causing unprecedented degradation to coastal habitats. This degradation is often monitored with water parameters or biological community surveys, but these are not directly informative of the compounded impact of stressors on organisms. Transcriptomics may offer an exhaustive method to assess the effects of human activities on organisms by assessing the expression level of all genes, revealing sublethal effects and acclimation to local conditions. However, this is hampered by the versatility of gene expression, which is often considered to hide environmental effects. Here, we obtained the transcriptomes of adult livers and whole-body juveniles of the blue damselfish Chrysiptera cyanea in eighteen coastal locations, from urban bays to isolated reefs, in Okinawa, Japan. We confronted the field data with laboratory-generated transcriptomes of fish exposed to a single stressor. Using pathway reconstruction, we show that the transcriptomic landscapes were influenced by urbanization level and detected a specific signature for marker genes associated with chemical pollution exposure. By comparing the signature of fed and fasted fish in the laboratory with changes in energy metabolism in the various field locations, we were able to retrieve the nutritional status of each fish and identify that urban zones may provide ‘fast food’, with large quantities of low-quality nutrients. Taken together, our results demonstrate that environmental transcriptomics coupled with pathway reconstruction and lab experiments can provide unsuspected information for ecosystem assessment and reveal the profound and long-lasting impact of urbanization on coastal fishes.
 

December 17 (C700)

  • Dr. Florian Pflug, Biological Complexity Unit
Individual growth vs. population growth in E. coli, a problem of optimal resource allocation 
 
In a growing population of bacteria we observe two separate but interlinked exponential growth processes. The first, well-known process is the exponential increase in number of cells, driven by each cell's cycle of genome replication, growth and division. The second is the exponential growth of cell sizes, driven by the self-reproduction of ribosomes. To maximise their fitness, bacteria must find an optimal balance between these two processes. Finding this balance can be framed as the problem of optimal allocation of resources between DNA replication (which is a prerequisite for division) and ribosome production (which drives cellular growth). We present a mathematical model for this problem of resource allocation, and show that can predict the change in growth rate in response to a change resource allocation. To validate this model, we present an experimental method that allows us to precisely measure the timing of replication in E. coli which serves as a stand-in for the amount of resources allocated to this process. We apply this method to different E. coli mutants with perturbed allocation of resources, and show that our model predictions agree reasonably well with experimental observations.
 
  • Dr. Samy Lakhal, Nonlinear and Non-equilibrium Physics Unit

On random fields and the laws of nature

The shapes, forms and textures surrounding us are rich in details. In many physical setups, that richness actually emerges from the taming of noise and fluctuations by the physical laws of nature. By mimicking these laws, scientists, graphic designers and other artists can reproduce complexity at small costs. In this talk, I will introduce some basics of random modeling and their applications to texture synthesis. I will then show direct examples and applications in physics and visual design.
 
 
Current organizers:
  • Yasha Neiman (yaakov.neiman@oist.jp) 
  • Anouk Beraud (a.beraud@oist.jp)
  • Monika Eggenberger (monika.eggenberger2@oist.jp)
  • Aleksandra Gavrilova (aleksandra.gavrilova@oist.jp)
  • Aditya Singh (aditya.singh@oist.jp)

Reach all current organizers at: internalseminar@oist.jp

Special thanks to Akiko Ishimine (President Office) for managing the budget and payment for internal seminars, Tomoko Yoshino (Mitarai Unit) for dealing with paper works for the payment, and Akiko Mizukoshi (University Community Services) for communicating with the cafe to provide refreshment.

Former organizers:

  • Jonathan Ward
  • Yunhui Zheng
  • Amy Shen
  • Eliot Fried
  • Stefan Pommer
  • Carolina Diaz
  • Tina Mularski
  • Oleg Simakov
  • Alexander Badrutdinov 
  • Omar Jáidar 
  • Marco Tsui 
  • Eiji Uchibe 
  • Hiroshi Izumi
  • Jérémie Gillet
  • Mary Ann Price
  • Shao Fang Wang
  • Romanas Chaleckis
  • Bianca Sieveritz
  • Lauren Dembeck
  • Robert Campbell
  • Andreas Thomasen
  • Jason Ball 
  • Maéva Techer 
  • Maggi Mars Brisbin
  • Afshan Jamshaid 
  • Fabien Benureau
  • Nadine Wirkuttis
  • Kamila Mustafina
  • Yuka Suzuki
  • Kun-Lung Li
  • Jigyasa Arora
  • Lewis Ruks
  • Aleksandra Bliznina
  • Ainash Garifullina
  • Thato Mokhothu
  • Mohamed Boubakour
  • Lakshmipriya Swaminathan
  • Munissa Sadykova
  • Charles Whitaker
  • Akira Kawano
  • Marylka Yoe Uusisaari