LDL vs HDL water Masakazu Matsumoto 2008-07-22 | Supercooled water at ambient pressure (right) and under 3,000 atm (left). Hydrogen bonds are gradated according to their lifetime. Contrary to normal liquid, pressure makes water more mobile.
Osmosis 浸透圧 Revised Masakazu Matsumoto 2023-04-15 | 浸透圧が生じるしくみを説明するためのアニメーションです。青の分子は中央の半透膜を透過できないので、膜の上下で圧力差が生じます。これが浸透圧です。* ソースコード github.com/vitroid/p5js/tree/main/osmosis* 実装 vitroid.github.io/p5js/osmosis
Simulation of a guitar string. Masakazu Matsumoto 2022-11-08 | A string of the guitar is simulated as a chain of mass connected by springs.The motion is counter-intuitive.
Maxwells velocity distribution Masakazu Matsumoto 2021-10-18 | 整列した剛体球の一つにエネルギーを与えたあと、そのエネルギーが全分子に分配されます。x方向とy方向の速度分布がそれぞれの軸上にリアルタイムで表示されます。それらは、短時間の間に正規分布になります。
Benchmark test of three algorithms Masakazu Matsumoto 2021-07-16 | Three algorithms to prepare the hydrogen-disordered ice structures are compared.Rahmans: youtu.be/Wj7kSzckyA8Bushs: youtu.be/feccn_pUov0Ours: youtu.be/5Yy8hY9A63M
GenIce Algorithm Masakazu Matsumoto 2021-07-16 | The algorithm to prepare a hydrogen-disordered ice structure proposed by Matsumoto et al. is illustrated.The algorithm finds the Euler cycle in the ice lattice. It is a linear-time algorithm.
Buchs Algorithm Masakazu Matsumoto 2021-07-16 | The algorithm to prepare a hydrogen-disordered ice structure proposed by Buch et al.is illustrated.The blue dots are defects not having two incoming or two outgoing hydrogen bonds. The algorithm stochastically purges such defects.
Rahmans algorithm Masakazu Matsumoto 2021-07-16 | The algorithm to prepare a hydrogen-disordered ice structure proposed by Rahman and Stillinger is illustrated.Starting from a hydrogen-ordered ice structure, the algorithm introduces randomness by inverting directed cycles randomly.
ペットボトルを振っても圧力は上がらない Masakazu Matsumoto 2021-05-29 | ペットボトルを振る力学エネルギーがすべて熱になったとしても、中の液体の温度はわずかしか上がりません。ペットボトルの中身は、長い時間をかけて平衡状態になっているはずなので、温度がわずかしか上がらなければ、圧力も変わらないはずです。これを実証してみました。ただし、さらに深く考えると、非常に細かい泡が生じた場合には、ラプラス圧によって圧力がわずかに高くなる可能性があります。
Hot ice emerging in the carbon nanobrush Masakazu Matsumoto 2020-11-27 | カーボンナノチューブで作ったナノブラシのすきまに水を入れると、水の結晶構造が変化して、50℃まで融けない氷が作れるかもしれない、という研究です。水分子と水分子をつなぐ水素結合を黒い線で表現しています。The research suggests that filling the gaps in the nanobrushes made of carbon nanotubes with water may change the crystalline structure of the water and produce ice that does not melt until 50°C.doi.org/10.1063/1.5111843
EO hydrate vs THF hydrate Masakazu Matsumoto 2020-11-27 | 左の画像は酸化エチレン(EO)水溶液からI型ハイドレートが成長するシミュレーション、右の画像はテトラヒドロフラン(THF)水溶液からII型ハイドレートが成長するシミュレーションです。圧倒的にEOハイドレートのほうが速く成長することがわかります。なぜでしょうか。EOハイドレートの場合には、すべてのケージにEO分子が入れるので、入り間違いはおこりません。一方、THFハイドレートは大ケージにしか入れないので、誤ってハイドレート表面の小ケージの場所に吸着した場合には、ふたたび表面から離脱するまで結晶成長が止まってしまうからです。この現象を積極的に利用し、ケージに入りたがるのに実際には入れない分子を添加することでハイドレートの結晶成長を抑制する手法もあります。The left image simulates the growth of type I hydrate from ethylene oxide (EO) aqueous solution and the right image simulates the growth of type II hydrate from tetrahydrofuran (THF) aqueous solution.By far, the EO hydrate grows faster than the EO hydrate. Why is this?In the case of EO hydrate, every cage is filled with EO molecules, so there is no chance of misplacement. On the other hand, THF hydrate is only allowed to enter the large cage, and if it is accidentally adsorbed to a small cage on the surface of the hydrate, the crystal growth stops until it leaves the surface again.This phenomenon can be actively exploited by adding molecules that want to enter the cage, but cannot, to inhibit the crystal growth of the hydrate.* http://doi.org/10.1021/acs.jpcc.5b10293* http://doi.org/10.1021/acs.jpcc.6b06498
Icosahedron Masakazu Matsumoto 2020-05-02 | An undistorted icosahedron drawn with an iPad. #PolyhedronChallenge
Dodecahedron Masakazu Matsumoto 2020-05-02 | An undistorted dodecahedron drawn on ProCreate in iPad. #PolyhedronChallenge
Osmosis by a rubber balloon Masakazu Matsumoto 2019-11-15 | Rubber blocks air but passes through CO2 gas. When the bottle is filled with CO2 and capped with a rubber balloon, CO2 leaks through the balloon membrane but the air cannot go in. Consequently, balloon inflates inside and implodes.
Solid-liquid critical behavior of water in a carbon nanotube. Masakazu Matsumoto 2019-07-29 | A demonstration to identify the crystalline order in water in a carbon nanotube. Temperature is 290 K.Mochizuki, K. & Koga, K. Solid-liquid critical behavior of water in nanopores. Proc. Natl. Acad. Sci. U. S. A. 112, 8221–8226 (2015).
Why can they breathe underwater? Masakazu Matsumoto 2019-05-15 | (See the original video by Lindsey Svierk: youtube.com/watch?v=gDwqWAv1RO4 )Because it is super water-repellent!As you can see, the skin is glittering and it seems to be water-repellent. So I made a 3D-printed anole (named Anolis Plasticus) with a variety of coatings and found that the normal water-repellent coating didn't keep a bubble. Therefore, we fabricated a super water-repellent Anole named Anolis Repellentus using Glaco mirror-coat zero super water-repellent coating (for automobile mirror). I finally got a big bubble!A water anole breathes in water by moving air in and out between air bubbles and lungs. Therefore, it is essential to keep the bubble volume as large as possible. When it exhales air, it goes into the bubble and diffuses around the air membrane around the body. It has a very large surface area for exchanging CO2 and O2.I expect that it controls the angle of the head to keep the bubble close to the nostrils. Otherwise, the bubble is very mobile and easily moves to the highest position of the head (for example, the eye lid).It is a research work of Masakazu Matsumoto, Okayama University, Japan.なぜウォーターアノールは水中で呼吸できるのか?なぜなら超撥水性の皮膚を持っているからだ!もとの写真を見ると、皮膚がギラついていて、水を弾いているように見えます。そこで、我々は3Dプリンタで実際にトカゲを作り(Anolis Plasticusと名付けました)、その表皮にいろんなコーティングをして、ウォーターアノールど同じように泡を作れるか試しました。その結果、トカゲの皮膚は単なる撥水性では不十分で、超撥水性でないと泡を保持できないことがわかりました。自動車のミラーに塗る超撥水性コーティングであるガラコミラーコートゼロを塗ったトカゲ(Anolis Repellentusと名付けました)だけが、泡を安定に保持できました。彼らは肺と気泡の間で空気を移動させて呼気の交換を行うので、大きな泡を作る必要があります。吐きだした息は、気泡にたまるだけでなく、体表面を覆う空気膜に拡散していきますから、仮想的にはとても大きな表面積で二酸化炭素と酸素を交換できるはずです。超撥水性表面に生じる泡は、通常の泡とは違いとても動きやすいので、いつも鼻を高く維持し、泡が鼻の穴の近くにくるように制御する必要があります。また、水中に長くとどまるためには、泡をできるだけ失わないよう、肺活量を厳密に制御する必要もあります。なかなか人間には真似できない技ですね。これは岡山大学異分野基礎科学研究所の研究です。今のところ論文にはなっていません。共同研究をご希望の場合はご連絡下さい。
酸化エチレンハイドレートの結晶化の解析 Masakazu Matsumoto 2019-02-26 | 分子シミュレーションしたあと、私たちがどんな風にデータを読むかをデモする映像です。2019年3月2日に秋葉原UDXシアターで開催される、見える化シンポジウム2019用に編集した映像。音楽はnekamiさん(twitter.com/nekami_works )です。
Caustic simulation with Python II Masakazu Matsumoto 2018-12-23 | プールの底のきらめきのシミュレーション。よりスムーズな表現を使用し、128x72個のphotonを追跡しました。質点とバネでできた128x72の格子の運動をLeap frog積分で時間発展させて膜面の運動をシミュレーションします。それで生じた凹凸に従って屈折・集光する光の濃淡を表示しています。ソースは github.com/vitroid/PyCaustics で公開しています。
Caustic simulation with Python Masakazu Matsumoto 2018-12-22 | A combination of numpy membrane simulation and photon simulation. Photon numbers are 128x72.プールの底のきらめきをシミュレーション。
Nucleation of a clathrate hydrate Masakazu Matsumoto 2018-08-16 | Nucleation of ethylene oxide clathrate hydrate is simulated and various topological analyses are applied.酸化エチレン水溶液からハイドレートが核生成する過程をシミュレーションしました。ネットワーク解析の実例として、さまざまな尺度を用いてこの過程を解析し、酸化エチレンのI型水和単結晶が生じていることを確認しました。Yagasaki, T., Matsumoto, M. & Tanaka, H. Formation of Clathrate Hydrates of Water-Soluble Guest Molecules. J. Phys. Chem. C 120, 21512–21521 (2016).
Nucleation of new ice named T2 Masakazu Matsumoto 2018-05-03 | A new high-pressure ice phase of TIP4P/2005 water model identified by computer simulations.
Chirality in the hydrogen bond network of the supercooled liquid water Masakazu Matsumoto 2017-07-27 | In this movie, water molecules are not drawn. Only the polyhedral structure made by hydrogen bonds are drawn. Blue and red regions represent the handednesses of the local structure. Note that ice structures do not possess chirality and therefore are not shown in this representation You can see that polyhedra of the same color aggregates to make a large domain. The domain structure fluctuates thermally, but it yields the heterogeneity in structure.In was published in the Physical Review Letters: doi:10.1103/PhysRevLett.115.197801
Emergence of new ice type T Masakazu Matsumoto 2017-07-19 | Emergence of a new ice, type T, was observed in the molecular dynamics simulation of the coexistence of liquid water and high pressure ice phase VII (7).The ice T appeared at the interface between liquid water (blank area) and ice VII (red dots) quickly fill the liquid region, then it erudes ice VII and finally the whole system is filled with a single crystal of ice T.To cite this video: Hirata, M., Yagasaki, T., Matsumoto, M. & Tanaka, H. Phase diagram of TIP4P/2005 water at high pressure. Langmuir acs.langmuir.7b01764 (2017). doi:10.1021/acs.langmuir.7b01764
Emergence of new ice type R Masakazu Matsumoto 2017-07-19 | Emergence of a new ice, type R, was observed in the molecular dynamics simulation of the coexistence of liquid water and high pressure ice phase VI (6).To cite this video: Hirata, M., Yagasaki, T., Matsumoto, M. & Tanaka, H. Phase diagram of TIP4P/2005 water at high pressure. Langmuir acs.langmuir.7b01764 (2017). doi:10.1021/acs.langmuir.7b01764
Anomalous properties of water Masakazu Matsumoto 2017-02-15 | Based on Martin Chaplin's website.http://www1.lsbu.ac.uk/water/water_anomalies.htmlBGM is not included. Please sing by yourself.
水の異常な性質 Masakazu Matsumoto 2017-02-15 | 英語版もあります。Martin Chaplinのサイトから抜粋加筆しました。http://www1.lsbu.ac.uk/water/water_anomalies.html著作権の都合でBGMは含まれていません．各自で口ずさんで下さい．
Research Institute for Interdisciplinary Science, Okayama University Masakazu Matsumoto 2016-07-30 | A promotion video for RIIS, OU.
Panorama in water Masakazu Matsumoto 2015-08-11 | Another test for YouTube 360 panorama.Swim the sea of water molecules.
Panorama of methane hydrate dissociation Masakazu Matsumoto 2015-08-11 | A test movie for 360 panorama feature of YouTube.
Dissociation of Methane Hydrate in Pure / Salt Waters Masakazu Matsumoto 2015-02-18 | Comparison of the rate of dissociation of methane hydrate in different solvents.
The static aspect of Tokyo Masakazu Matsumoto 2014-11-09 | 動くものの撮影を徹底的に拒むカメラによる撮影。これでも動画です。動いている間は撮影されないので、ワープしているように見えます。Movie taken with the camera that refuses to capture any motion.Processed from the original movie at youtube.com/watch?v=kw3MEiTKbpk .
The dynamic aspect of Tokyo Masakazu Matsumoto 2014-11-09 | 動くものがその残像を残すカメラによる撮影。Movie with the "Persistence of vision" camera.Processed from the original movie at youtube.com/watch?v=kw3MEiTKbpk .
Methane Hydrate in Saltwater Masakazu Matsumoto 2014-09-17 | All the water molecules and methane molecules in aqueous solution are hidden. Methane in the clathrate hydrate is colored according to the altitude from the average sphere surface; Methane molecules in gas phase are drawn as a fused bubble.
Coexistence of ice and liquid water Masakazu Matsumoto 2014-08-27 | Illustrates how molecular motions are different in liquid water and ice.
Planetary Motion Masakazu Matsumoto 2014-08-27 | Planetary motion and interaction in order to explain the molecular dynamics simulations.
Liquid water vs Supercritical fluid water Masakazu Matsumoto 2014-06-04 | Left: supercritical water at 670 K; density is 0.3 g / cm3.Right: normal liquid water at room temperature; T=300 K, 1.0 g / cm3.Molecules in SCW travel like those in gas, but sometimes make a cluster like liquid.超臨界水は、気体のように分子がばらばらになっている部分と、液体のように水素結合でつながってクラスタになっている部分が混在しています。
Emergence of new crystal ice leading to ice VII Masakazu Matsumoto 2014-06-03 | A new type of crystalline ice, "partially plastic ice", was discovered in the course of freezing into ice VII at very high pressure and temperature.3D-printable unit cell of the new crystal is available here: http://www.thingiverse.com/thing:346416See DOI:10.1039/c4cp01616e for detail.
Supercritical fluid water Masakazu Matsumoto 2014-05-07 | Dynamics of the fluid water above its critical point.670 K, 0.3 g/cm. One picosecond is stretched one second in the movie.The hydrogen bond network is shattered but still clusters exist.Free water molecule spins and hugs another.Compare with normal water: http://youtu.be/FtxLih3KeTA
Ice VII, Plastic Ice, and their Critical State Masakazu Matsumoto 2013-11-25 | 超高圧の氷VII(5万気圧)と、プラスチック氷(5万気圧)と、それらの臨界点(18万気圧)での状態を比較したムービーです。前半では、氷VIIに近い結合状態の水分子は赤または青で表現し、どちらとも言えない分子には白を着色しました。氷VIIはほとんど真っ青、プラスチック氷と臨界状態では赤白青の混合状態になっているのがわかります。後半では、立方体形状の結晶の内部の状態まで見えるようにするために、分子を描く代わりに、色の濃さごとの等高面を描いています。プラスチック氷は、赤白青の混合状態のままですが、臨界状態では、全体が真っ青や真っ赤(つまり氷VIIと同じ構造)の状態から、赤白青の混合状態まで、すべての状態がつぎつぎに出現するのがわかります。プラスチック氷相と、その臨界状態は岡山大学理学部化学科理論化学研究室でコンピュータシミュレーションにより予言されました。実験による検証を待っています。Himoto, K., Matsumoto, M. & Tanaka, H. Yet another criticality of water. Phys. Chem. Chem. Phys. -- (2013). http://dx.doi.org/10.1039/c3cp54726dComparison of ice VII, plastic ice, and their critical state.Pressure is 5 GPa for ice VII and plastic ice, and 18 GPa for critical point.Note that the phase transition between ice VII and plastic ice is first-order at low pressure and second-order at higher pressures than 13.3 GPa according to the simulation result.Blue and red color indicate the local order of ice VII. In critical state, you can see the large fluctuation of the order parameter from all-blue to all-red, corresponding to the total flip of the spins in the Ising model.
IceVII, Plastic Ice, and Liquid Water Masakazu Matsumoto 2013-11-20 | Himoto, K., Matsumoto, M. & Tanaka, H. Yet another criticality of water. Phys. Chem. Chem. Phys. -- (2013). http://dx.doi.org/10.1039/c3cp54726dComparison of molecular motion of water at the same pressure.Left: ice VII, in which both translation and rotation are not allowedCenter: the plastic phase of water, in which rotation is allowed but molecules are on the lattice sites.Right: supercritical fluid water, in which water molecules move freely.Molecules in solid phases are colored according to the orientational order parameter.Note that the plastic ice phase is predicted by computer simulation but yet to be discovered by experiments.
Liquid-liquid separation of water followed by ice crystallization Masakazu Matsumoto 2013-10-31 | Molecular dynamics simulation of supercooled liquid water that exibits the liquid-liquid phase separation below the hypothesized second critical point. This is the first simulation evidence that water can separate into two different liquids, that are low- and high-density liquid water.Crystal ice nucleation starts after 500 ns inside the low-density liquid region and it fully crystallizes after 800 ns, when a single crystal of ice spans across the simulation cell.Total volume is fixed constant and therefore the ice cannot finally fill the whole cell and some high-density liquid region remains unfrozen under very high pressure.To cite this: Yagasaki, T., Matsumoto, M. & Tanaka, H. Spontaneous liquid-liquid phase separation of water. Phys. Rev. E 89, 020301 (2014). doi:10.1103/PhysRevE.89.020301
