Masamitsu Wakabayashi

Amoeba-inspired nanoarchitectonic computing: solving intractable computational problems using nanoscale photoexcitation transfer dynamics.

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 amoebas 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.

New Reaction Model for O–O Bond Formation and O2 Evolution Catalyzed by Dinuclear Manganese Complex

A new mechanism of the oxygen evolving reaction catalyzed by [H(2)O(terpy)Mn(μ-O)(2)Mn(terpy)OH(2)](3+) is proposed by using density functional theory. This proton coupled electron transfer (PCET) model shows reasonable barriers. Because in experiments excess oxidants (OCl(-) or HSO(5)(-)) are required to evolve oxygen from water, we considered the Mn(2) complex neutralized by three counterions. Structure optimization made the coordinated OCl(-) withdraw a H(+) from the water ligand and produces the reaction space for H(2)O(2) formation with the deprotonated OH(-) ligand. The reaction barrier for the H(2)O(2) formation from OH(-) and protonated OCl(-) depends significantly on the system charge and is 14.0 kcal/mol when the system is neutralized. The H(2)O(2) decomposes to O(2) during two PCET processes to the Mn(2) complex, both with barriers lower than 12.0 kcal/mol. In both PCET processes the spin moment of transferred electrons prefers to be parallel to that of Mn 3d electrons because of the exchange interaction. This model thus explains how the triplet O(2) molecule is produced.

Anisotropic Dissymmetry Factor, g: Theoretical Investigation on Single Molecule Chiroptical Spectroscopy

A formula for an anisotropic dissymmetry factor g evaluating the chiroptical response of orientationally fixed molecules is derived. Incorporating zeroth- and first-order multipole expansion terms, it is applied to bridged triarylamine helicene molecules to examine the experimental results of single-molecule chiroptical spectroscopy. The ground- and excited-state wave functions and a series of transition moments required for the evaluation of the anisotropic g value are calculated using time-dependent density functional theory (TDDFT). The probability histograms obtained for simulated g values, uniformly sampled in regard to the direction of light propagation toward the fixed molecule, show that even for a given diastereomer, the dissymmetry factors have positive and negative values and can deviate from their averages to a considerable extent when the angle between the electric dipole transition moment and the propagation vector of the incident light is near 0 or 180°.

Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths

We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called “AmoebaSAT [Aono et al. 2013],” which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], “the satisfiability problem,” and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [http://www.cs.ubc.ca/~hoos/5/benchm.html]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate “AmoebaChem,” which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.

Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism

In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow.

A Nanophotonic Computing Paradigm: Problem-Solving and Decision-Making Systems Using Spatiotemporal Photoexcitation Transfer Dynamics

In contrast to conventional digital computers that operate as instructed by programmers, biological organisms solve problems and make decisions through intrinsic spatiotemporal dynamics in which their dynamic components process environmental information in a self-organized manner. Previously, we formulated two mathematical models of spatiotemporal dynamics by which the single-celled amoeba (a plasmodial slime mold), which exhibits complex spatiotemporal oscillatory dynamics and sophisticated computing capabilities, could solve a problem and make a decision by changing its amorphous shape in dynamic and uncertain environments. These models can also be implemented by various physical systems that exhibit suitable spatiotemporal dynamics resembling the amoeba’s shape-changing capability. Here we demonstrate that the photoexcitation transfer phenomena in certain quantum nanostructures mediated by optical near-field interactions mimic the amoeba-like spatiotemporal dynamics and can be used to solve two highly complex problems; the satisfiability problem, which is one of the most difficult combinatorial optimization problems, to determine whether a given logical proposition is self-consistent, and the multi-armed bandit problem, which is a decision-making problem in finding the most profitable option from among a number of options that provide rewards with different unknown probabilities. Our problem-solving and decision-making models exhibited better performances than conventionally known best algorithms. These demonstrations pave the way for a novel nanophotonic computing paradigm in which both coherent and dissipative processes are exploited for performing powerful solution searching and efficient decision-making with low energy consumption.

A study of QM/Langevin-MD simulation for oxygen-evolving center of photosystem II

We have performed three QM/Langevin-MD simulations for oxygen-evolving complex (OEC) and surrounding residues, which are different configurations of the oxidation numbers on Mn atoms in the Mn4O5Ca cluster. By analyzing these trajectories, we have observed sensitivity of the change to the configuration of Mn oxidation state on O atoms of carboxyl on three amino acids, Glu354, Ala344, and Glu333. The distances from Mn to O atoms in residues contacting with the Mn4O5Ca cluster were analyzed for the three trajectories. We found the good correlation of the distances among the simulations. However, the distances with Glu354, Ala344, and Glu333 have not shown the correlation. These residues can be sensitive index of the changes of Mn oxidation numbers.

Theoretical investigation on single-molecule chiroptical spectroscopy

Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.