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Order formation of biomolecules based on
soft matter physics

*This Lab. is not accepting new student.

TAKAGI Lab.
Senior Lecturer:SHIMOKAWA Naofumi

E-mail:
[Research areas]Soft matter physics, Interface chemistry
[Keywords]Lipid membrane, Vesicle, Liposome, Order formation, Phase separation, Phase transition, Self-organization, Simulation

Skills and background we are looking for in prospective students

We do not ask for any special knowledges in advance. Since we study about biomolecules and their behaviors based on physics and chemistry, we hope that your field of study can be utilized in the research. Even if you have not studied physics, chemistry, and biology deeply, we will give guidance carefully.

What you can expect to learn in this laboratory

We want you to learn about physics, chemistry, and biology widely. In addition, you can study how to plan what kind of experiments to perform, how to image what is happening at the molecular level from the obtained experimental results, how to search literatures for unknown tasks, how to prepare the papers and presentations.

【Job category of graduates】
Cosmetics, Chemistry, Food, etc.

Research outline


Fig.1 (top) Spontaneous pore formation in
charged lipid membrane. (bottom) Reproduction
of pore formation by numerical simulation.


Fig.2 (top) Characteristic phase-separated pattern
formation in fatty acid-containing lipid membranes.
(bottom) Spontaneous membrane deformation
in fatty acid-containing lipid membranes.

Polymers, liquid crystals, colloids, amphiphilic molecules, biomolecules, are called “soft matter”, and their basic physical properties and behavior under non-equilibrium conditions have attracted great attention from physics. Since many important molecules and structures in vivo are regarded as soft matter, soft matters physics becomes a powerful tool for understanding biological functions. Phospholipids, which are representative amphiphilic molecules, spontaneously form a lipid bilayer structure in water, and have the same structure as the cell membranes and biological membranes. We aim to reveal the mechanism of spontaneous order formation in lipid bilayer membranes based on physics and chemistry, and lead to the understanding of biological mechanisms in cell membranes and biological membranes.

■ Order formation governed by electrostatic interaction

Negatively charged phospholipids play important roles in the generation of membrane potential, protein adsorption, channel activity, etc. However, it is not sufficient to understand how charged lipids contribute the order formation in lipid membranes. We investigate the phase separation and membrane deformation of negatively charged lipid membranes by experimental, theoretical, and numerical simulation methods. In the experiment, we aim to control the electrostatic repulsion between negatively charged lipids and electrostatic attraction between molecules with positive charge in solution and negatively charged lipids, and to form various ordered structures. Based on the free energy calculation, we consider the influence of electrostatic interaction on phase behavior theoretically. Moreover, using coarse-grained molecular dynamics simulation, we examine the dynamical behavior of charged lipid membranes and the interaction between charged membranes and other charged guest molecules.

■ Order formation governed by additive molecules

We add the various molecules to lipid membranes and clarify the effect of the additive molecules from the change of the order structure. As an example, we observed the phase-separated structures and the membrane deformation when fatty acids such as palmitic acid and oleic acid were added to the lipid membranes. The relationship between fatty acids and various diseases including lifestyle diseases is discussed and, in particular, it is believed to be linked to increase and decrease of the amount of cholesterol. We examine how the interaction between cholesterol and fatty acid plays a role in the formation of order structures.

Key publications

  1. N. Shimokawa, R. Mukai, M. Nagata, M. Takagi, “Formation of modulated phase and domain rigidification in fatty acids-containing lipid membranes” Phys. Chem. Chem. Phys., 19, 13252 (2017).
  2. N. Shimokawa, H. Himeno, T. Hamada, M. Takagi, S. Komura, D. Andelman, “Phase diagrams and ordering in charged membranes: Binary mixtures of charged and neutral lipids” J. Phys. Chem. B, 120, 6358 (2016).
  3. H. Himeno, H. Ito, Y. Higuchi, T. Hamada, N. Shimokawa, M. Takagi, “Coupling between pore formation and phase separation in charged lipid membranes” Phys. Rev. E, 92, 062713 (2015).

Equipment

Confocal laser scanning microscopy
Fluorescent and phase-contrast microscopy
Differential scanning calorimetry
Langmuir monolayer
High performance parallel computers

Teaching policy

We will give guidance on the following three points.

  1. Independence : make a research plan by yourself, provide your original idea, carry out the research responsibly, and disseminate your research by yourself
  2. Objectivity : improve your research objectively with introducing some opinions from professors, other students, and other researchers
  3. Collaborative : share your research results with other students and work hard together

[Website] URL:http://www.jaist.ac.jp/ms/labs/takagi/

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