Low-dimensional projection of reactivity classes in chemical reaction dynamics using supervised dimensionality reduction.

Transition state theory (TST) provides a framework to estimate the rate of chemical reactions. Despite its great success with many reaction systems, the underlying assumptions such as local equilibrium and nonrecrossing do not necessarily hold in all cases. Although dynamical systems theory can provide the mathematical foundation of reaction tubes existing in phase space that enables us to predict the fate of reactions free from the assumptions of TST, numerical demonstrations for large systems have been yet one of the challenges.

Inferring the roles of individuals in collective systems using information-theoretic measures of influence.

In collective systems, influence of individuals can permeate an entire group through indirect interactionscom-plicating any scheme to understand individual roles from observations. A typical approach to understand an individuals influence on another involves consideration of confounding factors, for example, by conditioning on other individuals outside of the pair. This becomes unfeasible in many cases as the number of individuals increases.

Isolated prosopagnosia caused by damage to the right inferior longitudinal fasciculus: a case report.

Prosopagnosia is a cognitive disorder in which facial recognition is severely impaired despite normal vision and intelligence. Prosopagnosia was first reported in the 1800s, but its cause remains unclear. Although other neurological symptoms are often present, some patients have pure prosopagnosia.

An encompassed representation of timescale hierarchies in first-order reaction network.

Complex networks are pervasive in various fields such as chemistry, biology, and sociology. In chemistry, first-order reaction networks are represented by a set of first-order differential equations, which can be constructed from the underlying energy landscape. However, as the number of nodes increases, it becomes more challenging to understand complex kinetics across different timescales.

Comparison of particle image velocimetry and the underlying agents dynamics in collectively moving self propelled particles.

Collective migration of cells is a fundamental behavior in biology. For the quantitative understanding of collective cell migration, live-cell imaging techniques have been used using e.g.

Dynamically induced conformation depending on excited normal modes of fast oscillation.

We present dynamical effects on conformation in a simple bead-spring model consisting of three beads connected by two stiff springs. The conformation defined by the bending angle between the two springs is determined not only by a given potential energy function depending on the bending angle, but also by fast motion of the springs which constructs the effective potential. A conformation corresponding with a local minimum of the effective potential is hence called the dynamically induced conformation.

Dependence of DNA length on binding affinity between TrpR and trpO of DNA.

We scrutinize the length dependency of the binding affinity of bacterial repressor TrpR protein to trpO (specific site) on DNA. A footprinting experiment shows that the longer the DNA length, the larger the affinity of TrpR to the specific site on DNA. This effect termed "antenna effect" might be interpreted as follows: longer DNA provides higher probability for TrpR to access to the specific site aided by one-dimensional diffusion along the nonspecific sites of DNA.

Flickering of cardiac state before the onset and termination of atrial fibrillation.

Complex dynamical systems can shift abruptly from a stable state to an alternative stable state at a tipping point. Before the critical transition, the system either slows down in its recovery rate or flickers between the basins of attraction of the alternative stable states. Whether the heart critically slows down or flickers before it transitions into and out of paroxysmal atrial fibrillation (PAF) is still an open question.

Mechanism and Experimental Observability of Global Switching Between Reactive and Nonreactive Coordinates at High Total Energies.

We present a mechanism of global reaction coordinate switching, namely, a phenomenon in which the reaction coordinate dynamically switches to another coordinate as the total energy of the system increases. The mechanism is based on global changes in the underlying phase space geometry caused by a switching of dominant unstable modes from the original reactive mode to another nonreactive mode in systems with more than 2 degrees of freedom. We demonstrate an experimental observability to detect a reaction coordinate switching in an ionization reaction of a hydrogen atom in crossed electric and magnetic fields.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model.

A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins.

Measuring dynamical randomness of quantum chaos by statistics of Schmidt eigenvalues.

We study statistics of entanglement generated by quantum chaotic dynamics. Using an ensemble of the very large number (>/~10(7)) of quantum states obtained from the temporally evolving coupled kicked tops, we verify that the estimated one-body distribution of the squared Schmidt eigenvalues for the quantum chaotic dynamics can agree surprisingly well with the analytical one for the universality class of the random matrices described by the fixed trace ensemble (FTE). In order to quantify this agreement, we introduce the L(1) norm of the difference between the one-body distributions for the quantum chaos and FTE and use it as an indicator of the dynamical randomness.

Nanosecond simulations of the dynamics of C60 excited by intense near-infrared laser pulses: impulsive Raman excitation, rearrangement, and fragmentation.

Impulsive Raman excitation of C(60) by single or double pulses of near-infrared wavelength λ = 1800 nm was investigated by using a time-dependent adiabatic state approach combined with the density functional theory method. We confirmed that the vibrational energy stored in a Raman active mode of C(60) is maximized when T(p) ~ T(vib)/2 in the case of a single pulse, where T(p) is the pulse length and T(vib) is the vibrational period of the mode. In the case of a double pulse, mode selective excitation can be achieved by adjusting the pulse interval τ.

Dynamical switching of a reaction coordinate to carry the system through to a different product state at high energies.

Questions of how the nature of a reaction coordinate that dominates the reaction ceases to exist and whether some new features emerge as an increase of total energy of systems are investigated for many degrees of freedom Hamiltonian systems. As a model system, a hydrogen atom in crossed electric and magnetic fields is scrutinized. It is shown that, when the total energy increases, the reaction coordinate no longer dominates the reaction as did at the lower energies.

Bifurcation of no-return transition states in many-body chemical reactions.

A new method is presented to study bifurcation of no-return transition states (TSs) at potential saddles for systems of many degrees of freedom (dof). The method enables us to investigate analytically when and how the no-return TS bifurcates. Our method reveals a new aspect of bifurcation for systems of many dof, i.

Exact formula of the distribution of Schmidt eigenvalues for dynamical formation of entanglement in quantum chaos.

The exact formula of the one-level distribution of the Schmidt eigenvalues is obtained for dynamical formation of entanglement in quantum chaos. The formula is based on the random matrix theory of the fixed-trace ensemble, and is derived using the theory of the holonomic system of differential equations. We confirm that the formula describes the universality of the distribution of the Schmidt eigenvalues in quantum chaos.

Fractional behavior in multidimensional Hamiltonian systems describing reactions.

The fractional behavior is presented for a minimal Hamiltonian system of three degrees of freedom which describes reaction processes. The model has a double-well potential where the Arnold web within the well is nonuniform. The survival probability within the well exhibits power law decay in addition to exponential decay.

Fractional behavior in nonergodic reaction processes of isomerization.

We present numerical evidence of fractional behavior in reactions for a prototype model of three-degree-of-freedom isomerization. The survival probability in the well exhibits two distinct ranges of time scales: one where it decreases with a power law, and the other where it decreases exponentially. Trajectories corresponding to power law decays exhibit 1/f spectra and subdiffusion in action space, and those with exponential decays exhibit Lorentzian spectra and normal diffusion.

Definability of no-return transition states in the high-energy regime above the reaction threshold.

No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used "configuration" TS pass only once, robustly exist up to a moderately high-energy regime above the reaction threshold, even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom starts to lose locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear.

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization.

By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations of molecular motions associated with a straight-through reaction tube in the phase space inside which all reactive trajectories pass from one basin to another, with eliminating recrossing trajectories in the configuration space. This visualization provides us with a chemical intuition of how chemical species "walk along" the reaction-rate slope in the multidimensional phase space compared with the intrinsic reaction path in the configuration space. The distinct nonergodic features in the two different HCN and CNH wells can be easily demonstrated by a section of Poincare surface of section in those potential minima, which predicts in a priori the pattern of trajectories residing in the potential well.