Life Science Group

Division of Life Science： Biological Function and Information Group

Kenji Shiraishi (University of Tsukuba, CCS 2008-2013 Nagoya University 2013-present)

Yasuteru Shigeta (Osaka Univ. Univ of Tsukuba CCS. 2014.3～） Mitsuo Shoji (University of Tsukuba, CCS) Megumji Kayanuma (University of Tsukuba, CCS)

My activity in Center for Computational Sciences (CCS)

Particle Physics Astrophysics and Nuclear Physics Quantum Condensed Matter Physics

Life Science

Global Enviromental Science

High Performance Computing

Computational Informatics My activity in Center for Computational Sciences (CCS)

Particle Physics

Industry Astrophysics and Nuclear Physics Quantum Condensed Matter Physics Mass production of Devices Life Science

Global Enviromental Science

High Performance Computing

Computational Informatics My activity in Center for Computational Sciences (CCS)

Particle Physics

Industry Astrophysics and Nuclear Physics Quantum Condensed Matter Physics Mass production of Devices Life Science (Prof. Shigeta from next March)

Global Enviromental Science

High Performance Computing

Computational Informatics Contents

1. Overview 2. Interaction with other field 3. Research result summary 4. Future plan

1. Overview of life science group

Life Science Group Collaborates with Computational Computer Science G, Condensed Science Matter G, and Astrophysics G. 1. Overview of life science group

History of Universe Invention of (Extended) Condensed Automobile Matter & so on Evolution Generation Formation Elementary Generation of Heavy Invention of Big Bang Particle of Stars and Birth Elements Computer by Generation Galaxies of Life (Fe, C, Si,..) Human being Birth of Human Computer can even design Being next generation computer itself. eg: Si nanowire device Life Science Group Collaborates with Computational Computer Science G, Condensed Science Matter G, and Astrophysics G. Overview in more details Life Science Group Wants to Cover History of Universe Related to Life Science with Other Groups Main Target of Life Science Group Generation of Stars and Galaxies (Generation of Planet sin Habitable Birth Generation Zone) of Life of Bio-functions

Earth, Mercury Evolution of Living Creature Extrasolar Planet (Existence of Life?)

Generation of Materials

Extended Target of Life Science Group 2.Interaction with Other Fields • Computer Science Group New Computation Algorism (GPU, super parallel computers and so on) • Condensed Matter Group First principles (Ab initio) calculation method which can predict material properties as well as bio-functions • Astrophysics Group Origin of Life ・Origin of Excess of L-Amino Acid in living creature ・Mechanism of habitable planet generation

We believe that astrophysics is very important for life science. (collaborating with Australian University, CNRS (France) as well as Nagoya University and Osaka University and so on)

3. Research Results Summary

1. Microscopic Origin of Bio-functions 1.1 Nitric Oxide Reductase 2. Origin of Life (Collaboration with Condensed Matter G and Astrophysics G) 2.1 Homochirality of Amino Acids in Proteins 2.2 Approaches towards Generation Mechanism of Habitable Planets 1. Method for Bio-function Research

• QM/MM Approaches is used for describing bio-functional proteins. • QM regions are calculated by Ab initio quantum chemical approaches • MM regions are treated by AMBER force fields

1.1 Nitric Oxide Reductase(NOR) (by M. Shoji)

NOR reduces NO to N2O

Systems used for QM/MM calculations. QM regions are enlarged. (A) NOR, (B) topo, (C) TS, and (D) OEC-PSII. 2. Origin of Life 2.1 Homochirality of Amino Acids in Proteins What is Homochirality? Enantiomer (Miror image isomer) Amino Acids have two types of enantisomer.

L-type (Left) D-type (Right)

In Chemial Experiments In living creature L-type D-type L-type D-type 50% 50% over 99%

N O living C creature Story of homochirality generation in the early solar system

4.6PY ago ① Birth of early solar system Early solar system  supernova explosion  Present solar system Cosmic dust UV ② Polarized light is generated by the scattering by cosmic polymer Polarized light dusts ③ Homochiralitiy is generated Homochirality by the circular polarized light emitssion * Amino acid ④ Meteorite with excess L-type meteorite amino acids Radioactive Elements meteorite ⑤ Above meteorites become earth the origin of life on earth

Present *asymmetric carbon Purpose of this work To clarify the mechanism of selective destruction of amino acids. What kind of light can destruct amino acid selectively to generate homochirality Early D-type amino acid 大質solar量星 Cosmic Polarized D型アミノ酸 UV輻射宇宙ダスト system Dust 円偏light光

LL-type型ア aminoミノ酸 acid

Chemical experiments cannot clarify the Computational science detail mechanism of homochirality. approach is powerful

Circular dichroism (CD) is calculated by ab initio calculations CD describes the selective destruction of enantiomer by polarized light Calculated circular dichroism of alanine and isovaline

Alanine Isovaline Wavelength [nm] Wavelength [nm] 600 300 200 150 120 100 90 80 600 300 200 150 120 100 90 80 30000 0.14 30000 0.09

O O 0.08 0.12 25000 s 25000 s

c c 0.07

l 0.10 l

a 20000 a 20000 0.06

o o 0.08

0.05

r ε

15000 ε 15000

S S 0.04

t 0.06 t

e 10000 10000 0.03 e

n 0.04 n

t 0.02 t

h 5000 5000 h

0.02

0.01 0 0.00 0 0.00 60 80 60 50 40

R 60 R 40 40

v 30 v

l 40 l

[ 20 [

20 20 1

20 0

ε ε

e 0 0 0 0 e

Δ Δ

u -10 u

2 -20 2

c -20 -20 c

-20 m -40

2 -30 2

] ]

-40

-60 -40 -60 -80 -60 -50 2 4 6 8 10 12 14 16 2 4 6 8 10 12 14 16 Energy [eV] Energy [eV] Curve 2. (a) L-Alan126.3524ine nm Curve 4. (c) L-Isoval133.0155ine nm

Wave length Alanine 126.4 nm 110nm – 135nm 113.7 nm Valine Vacuum ultraviolet 124.0 nm region Isovaline 133.0 nm Conclusion

Homochirality can be generated by the emission of circular polarized light emission in the early solar system

Vacuum ultra violet circular polarized light can generate homochirality of amino acid in living creature （110-135 nm） Cosmic Filter?? 2.2 Approaches towards Generation Mechanism of Habitable Planets (A Preliminary Result)

Story of planet generation There is a missing link for understanding planet formation from cosmic dusts (living place of living creatures). Collaboration between Astrophysics, Condensed Matter Physics and Life Science is inevitable to overcome this missing link.

• Cosmic dusts get together and formation of planetesimal (very small planet) occurs • Comic dusts essentially obey fluid mechanics. (Physics of continuum can be applied) • However, cosmic dusts occasionally behave as inertial particles, and collision of these cosmic dusts is the origin of generation of planetesimal. Method of numerical simulation of Nervier-Stokes equation

• Incompressible fluid (Future, compressible fluid treatment) • No magnetic field (Future, magnetic hydromechanics (MHD) treatment) • Mesh: 256×256×256 • Time evolution: Runge-Kutta 4th order • Number of Inertial Particles 16×16×16

Equation for inertial particle

Stokes Number

※Neglecting gravity ３ 3. Future plan (by Prof. Shigeta)