Masahiko Hara | RIKEN, Wako, Japan (original) (raw)

Papers by Masahiko Hara

Research paper thumbnail of 21aHA-2 Molecular Zippers

Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2011

Research paper thumbnail of Fixation of protein molecules for STM measurement

New deposition technique, ``guest-host anchoring method'', has been developed for scann... more New deposition technique, ``guest-host anchoring method'', has been developed for scanning tunneling microscopy (STM) visualization of biological macromolecules with clear discrimination against artifacts. The electroactive protein (cytochrome c3) molecules were embedded in the liquid crystal matrix, and imaged by STM as a function of applied voltage. Those STM images are encouraging for potential application of this new method to the STM imagings of a wide range of uncoated biological macromolecules.

Research paper thumbnail of Formation and Superlattice of Long-Range-Ordered Self-Assembled Monolayers of Pentafluorobenzenethiols on Au(111)

Research paper thumbnail of Intense Fluorescence from Light-Driven Self-Assembled Aggregates of Nonionic Azobenzene Derivative

Journal of The American Chemical Society, 2005

We describe here the highly fluorescent self-assembled spherical aggregates of an azobenzene mole... more We describe here the highly fluorescent self-assembled spherical aggregates of an azobenzene molecule without a specific ionic component in organic solution under UV light illumination. The first stage of trans-to-cis photoisomerization by UV light at 365 nm was followed by a significant enhancement, up to about 1000 times, of the emission from an azobenzene molecule (CN2Azo) with a long alkyl chain, which is due to the spontaneous formation of spherical organic aggregates. Fluorescence emission was further enhanced in the dark, and the quantum yield increased to about 0.3. We also report the significant size and structural changes of the aggregates, from nanometer-scale micelle-like aggregates to micrometer-scale vesicular aggregates, obtained only from the variation in the concentration of an azobenzene derivative. The light-driven azobenzene aggregates show the size and structure dependences of emission wavelength from violet-blue to green-yellow.

Research paper thumbnail of Amoeba-based emergent computing: combinatorial optimization and autonomous meta-problem solving

International Journal of …, 2009

Research paper thumbnail of Amoeba-Inspired Nanoarchitectonic Computing: Solving Intractable Computational Problems Using Nanoscale Photoexcitation Transfer Dynamics

Langmuir, 2013

Biologically inspired computing devices and architectures are expected to overcome the limitation... more Biologically inspired computing devices and architectures are expected to overcome the limitations of conventional technologies in terms of solving computationally demanding problems, adapting to complex environments, reducing energy consumption, and so on. We previously demonstrated that a primitive single-celled amoeba (a plasmodial slime mold), which exhibits complex spatiotemporal oscillatory dynamics and sophisticated computing capabilities, can be used to search for a solution to a very hard combinatorial optimization problem. We successfully extracted the essential spatiotemporal dynamics by which the amoeba solves the problem. This amoeba-inspired computing paradigm can be implemented by various physical systems that exhibit suitable spatiotemporal dynamics resembling the amoeba's problem-solving process. In this Article, we demonstrate that photoexcitation transfer phenomena in certain quantum nanostructures mediated by optical near-field interactions generate the amoebalike spatiotemporal dynamics and can be used to solve the satisfiability problem (SAT), which is the problem of judging whether a given logical proposition (a Boolean formula) is self-consistent. SAT is related to diverse application problems in artificial intelligence, information security, and bioinformatics and is a crucially important nondeterministic polynomial time (NP)-complete problem, which is believed to become intractable for conventional digital computers when the problem size increases. We show that our amoeba-inspired computing paradigm dramatically outperforms a conventional stochastic search method. These results indicate the potential for developing highly versatile nanoarchitectonic computers that realize powerful solution searching with low energy consumption.

Research paper thumbnail of Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

International journal of molecular sciences, Jan 25, 2018

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, an... more The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The...

Research paper thumbnail of Formation and Annealing Effect of Tolanethioacetate Self-Assembled Monolayers on Au(111)

Bulletin of the Korean Chemical Society

Research paper thumbnail of Surface Potential Change Depending on Molecular Orientation of Hexadecanethiol Self-Assembled Monolayers on Au(111)

Bulletin of the Korean Chemical Society

Research paper thumbnail of Surface Structures and Thermal Desorption Behaviors of Cyclopentanethiol Self-Assembled Monolayers on Au(111)

Bulletin of the Korean Chemical Society

Research paper thumbnail of Direct Observation of the Interaction between the Ferritin Endowed with Ti-binding Peptide and the Target: The Mechanism of Specificity and Selectivity

Research paper thumbnail of Effects of Solvent on the Structure of Octanethiol Self-Assembled Monolayers on Au(111) at a High Solution Temperature

Bulletin of the Korean Chemical Society

Research paper thumbnail of Laser Scanning-Assisted Tip-Enhanced Optical Microscopy for Robust Optical Nanospectroscopy

Applied spectroscopy, Jul 1, 2016

Laser-scanning-assisted tip-enhanced optical microscopy was developed for robust optical nanospec... more Laser-scanning-assisted tip-enhanced optical microscopy was developed for robust optical nanospectroscopy. The laser-scanning system was utilized to automatically set and keep the center of a tight laser-focusing spot in the proximity of a metallic tip with around 10 nm precision. This enabled us to efficiently and stably induce plasmon-coupled field enhancement at the apex of the metallic probe tip. The laser-scanning technique was also applied to tracking and compensating the thermal drift of the metallic tip in the spot. This technique is usable for long-term tip-enhanced optical spectroscopy without any optical degradation.

Research paper thumbnail of Immobilization of molecular tubes on self-assembled monolayers of beta-cyclodextrin and dodecanethiol inclusion complexes

Research paper thumbnail of Hybridization of Polynucleotides Using Self-Assembled Monolayer Containing Pyrenyl Groups

Molecular Crystals and Liquid Crystals Science and Technology Section a Molecular Crystals and Liquid Crystals, 2002

To realize an efficient hybridization of polynucleotides, self-assembled monolayer (SAM) containi... more To realize an efficient hybridization of polynucleotides, self-assembled monolayer (SAM) containing pyrene groups was prepared on a gold substrate because pyrene molecules have an affinity for nucleic acid bases through van der Waals interaction. The SAM was prepared from 11-(1-pyrene)-1-undeacathiol and 11-mercapto-1-undecanol mixed solution. The mixed SAM gave an efficient hybridization of polyadenylic acid and polyuridylic acid observed by surface plasmon resonance.

Research paper thumbnail of Long-Ranged and Short-Ranged Electrostatic Interaction Between Modified Silicon Surfaces and Recombinant Ferritin Molecules

Japanese Journal of Applied Physics, Jul 1, 2005

Research paper thumbnail of Nanorheology measurement on a single polymer chain

Applied Physics Letters, Jul 21, 2002

The mechanical properties of a single chain of a synthesized polystyrene were measured by atomic ... more The mechanical properties of a single chain of a synthesized polystyrene were measured by atomic force microscopy (AFM). In the conventional force-distance curve measurement, the stress-strain behavior of a chain was obtained. We also measured the dynamic sinusoidal ...

Research paper thumbnail of ChemInform Abstract: Selective Aerobic Oxidation of Methanol in the Coexistence of Amines by Nanoporous Gold Catalysts: Highly Efficient Synthesis of Formamides

Research paper thumbnail of Scanning Tunneling Microscopy Investigations on Heteroepitaxially Grown Overlayers of Cu-Phthalocyanine on Au(111) Surfaces

Research paper thumbnail of Origin of Current Enhancement through a Ferrocenylundecanethiol Island Embedded in Alkanethiol SAMs by Using Electrochemical Potential Control

The Journal of Physical Chemistry C, May 9, 2007

Electroactive ferrocenylundecanethiol islands embedded in an n-decanethiol SAM matrix were studie... more Electroactive ferrocenylundecanethiol islands embedded in an n-decanethiol SAM matrix were studied under potential control using in situ scanning tunneling microscopy (STM). Contrary to previous reports, the positive charges on ferrocene moieties are not a ...

Research paper thumbnail of 21aHA-2 Molecular Zippers

Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2011

Research paper thumbnail of Fixation of protein molecules for STM measurement

New deposition technique, ``guest-host anchoring method'', has been developed for scann... more New deposition technique, ``guest-host anchoring method'', has been developed for scanning tunneling microscopy (STM) visualization of biological macromolecules with clear discrimination against artifacts. The electroactive protein (cytochrome c3) molecules were embedded in the liquid crystal matrix, and imaged by STM as a function of applied voltage. Those STM images are encouraging for potential application of this new method to the STM imagings of a wide range of uncoated biological macromolecules.

Research paper thumbnail of Formation and Superlattice of Long-Range-Ordered Self-Assembled Monolayers of Pentafluorobenzenethiols on Au(111)

Research paper thumbnail of Intense Fluorescence from Light-Driven Self-Assembled Aggregates of Nonionic Azobenzene Derivative

Journal of The American Chemical Society, 2005

We describe here the highly fluorescent self-assembled spherical aggregates of an azobenzene mole... more We describe here the highly fluorescent self-assembled spherical aggregates of an azobenzene molecule without a specific ionic component in organic solution under UV light illumination. The first stage of trans-to-cis photoisomerization by UV light at 365 nm was followed by a significant enhancement, up to about 1000 times, of the emission from an azobenzene molecule (CN2Azo) with a long alkyl chain, which is due to the spontaneous formation of spherical organic aggregates. Fluorescence emission was further enhanced in the dark, and the quantum yield increased to about 0.3. We also report the significant size and structural changes of the aggregates, from nanometer-scale micelle-like aggregates to micrometer-scale vesicular aggregates, obtained only from the variation in the concentration of an azobenzene derivative. The light-driven azobenzene aggregates show the size and structure dependences of emission wavelength from violet-blue to green-yellow.

Research paper thumbnail of Amoeba-based emergent computing: combinatorial optimization and autonomous meta-problem solving

International Journal of …, 2009

Research paper thumbnail of Amoeba-Inspired Nanoarchitectonic Computing: Solving Intractable Computational Problems Using Nanoscale Photoexcitation Transfer Dynamics

Langmuir, 2013

Biologically inspired computing devices and architectures are expected to overcome the limitation... more Biologically inspired computing devices and architectures are expected to overcome the limitations of conventional technologies in terms of solving computationally demanding problems, adapting to complex environments, reducing energy consumption, and so on. We previously demonstrated that a primitive single-celled amoeba (a plasmodial slime mold), which exhibits complex spatiotemporal oscillatory dynamics and sophisticated computing capabilities, can be used to search for a solution to a very hard combinatorial optimization problem. We successfully extracted the essential spatiotemporal dynamics by which the amoeba solves the problem. This amoeba-inspired computing paradigm can be implemented by various physical systems that exhibit suitable spatiotemporal dynamics resembling the amoeba's problem-solving process. In this Article, we demonstrate that photoexcitation transfer phenomena in certain quantum nanostructures mediated by optical near-field interactions generate the amoebalike spatiotemporal dynamics and can be used to solve the satisfiability problem (SAT), which is the problem of judging whether a given logical proposition (a Boolean formula) is self-consistent. SAT is related to diverse application problems in artificial intelligence, information security, and bioinformatics and is a crucially important nondeterministic polynomial time (NP)-complete problem, which is believed to become intractable for conventional digital computers when the problem size increases. We show that our amoeba-inspired computing paradigm dramatically outperforms a conventional stochastic search method. These results indicate the potential for developing highly versatile nanoarchitectonic computers that realize powerful solution searching with low energy consumption.

Research paper thumbnail of Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

International journal of molecular sciences, Jan 25, 2018

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, an... more The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The...

Research paper thumbnail of Formation and Annealing Effect of Tolanethioacetate Self-Assembled Monolayers on Au(111)

Bulletin of the Korean Chemical Society

Research paper thumbnail of Surface Potential Change Depending on Molecular Orientation of Hexadecanethiol Self-Assembled Monolayers on Au(111)

Bulletin of the Korean Chemical Society

Research paper thumbnail of Surface Structures and Thermal Desorption Behaviors of Cyclopentanethiol Self-Assembled Monolayers on Au(111)

Bulletin of the Korean Chemical Society

Research paper thumbnail of Direct Observation of the Interaction between the Ferritin Endowed with Ti-binding Peptide and the Target: The Mechanism of Specificity and Selectivity

Research paper thumbnail of Effects of Solvent on the Structure of Octanethiol Self-Assembled Monolayers on Au(111) at a High Solution Temperature

Bulletin of the Korean Chemical Society

Research paper thumbnail of Laser Scanning-Assisted Tip-Enhanced Optical Microscopy for Robust Optical Nanospectroscopy

Applied spectroscopy, Jul 1, 2016

Laser-scanning-assisted tip-enhanced optical microscopy was developed for robust optical nanospec... more Laser-scanning-assisted tip-enhanced optical microscopy was developed for robust optical nanospectroscopy. The laser-scanning system was utilized to automatically set and keep the center of a tight laser-focusing spot in the proximity of a metallic tip with around 10 nm precision. This enabled us to efficiently and stably induce plasmon-coupled field enhancement at the apex of the metallic probe tip. The laser-scanning technique was also applied to tracking and compensating the thermal drift of the metallic tip in the spot. This technique is usable for long-term tip-enhanced optical spectroscopy without any optical degradation.

Research paper thumbnail of Immobilization of molecular tubes on self-assembled monolayers of beta-cyclodextrin and dodecanethiol inclusion complexes

Research paper thumbnail of Hybridization of Polynucleotides Using Self-Assembled Monolayer Containing Pyrenyl Groups

Molecular Crystals and Liquid Crystals Science and Technology Section a Molecular Crystals and Liquid Crystals, 2002

To realize an efficient hybridization of polynucleotides, self-assembled monolayer (SAM) containi... more To realize an efficient hybridization of polynucleotides, self-assembled monolayer (SAM) containing pyrene groups was prepared on a gold substrate because pyrene molecules have an affinity for nucleic acid bases through van der Waals interaction. The SAM was prepared from 11-(1-pyrene)-1-undeacathiol and 11-mercapto-1-undecanol mixed solution. The mixed SAM gave an efficient hybridization of polyadenylic acid and polyuridylic acid observed by surface plasmon resonance.

Research paper thumbnail of Long-Ranged and Short-Ranged Electrostatic Interaction Between Modified Silicon Surfaces and Recombinant Ferritin Molecules

Japanese Journal of Applied Physics, Jul 1, 2005

Research paper thumbnail of Nanorheology measurement on a single polymer chain

Applied Physics Letters, Jul 21, 2002

The mechanical properties of a single chain of a synthesized polystyrene were measured by atomic ... more The mechanical properties of a single chain of a synthesized polystyrene were measured by atomic force microscopy (AFM). In the conventional force-distance curve measurement, the stress-strain behavior of a chain was obtained. We also measured the dynamic sinusoidal ...

Research paper thumbnail of ChemInform Abstract: Selective Aerobic Oxidation of Methanol in the Coexistence of Amines by Nanoporous Gold Catalysts: Highly Efficient Synthesis of Formamides

Research paper thumbnail of Scanning Tunneling Microscopy Investigations on Heteroepitaxially Grown Overlayers of Cu-Phthalocyanine on Au(111) Surfaces

Research paper thumbnail of Origin of Current Enhancement through a Ferrocenylundecanethiol Island Embedded in Alkanethiol SAMs by Using Electrochemical Potential Control

The Journal of Physical Chemistry C, May 9, 2007

Electroactive ferrocenylundecanethiol islands embedded in an n-decanethiol SAM matrix were studie... more Electroactive ferrocenylundecanethiol islands embedded in an n-decanethiol SAM matrix were studied under potential control using in situ scanning tunneling microscopy (STM). Contrary to previous reports, the positive charges on ferrocene moieties are not a ...