Reproducing the Reaction Route Map on the Shape Space from Its Quotient by the Complete Nuclear Permutation-Inversion Group.

This study develops an algorithm to reproduce reaction route maps (RRMs) in the shape space from the outputs of potential search algorithms. To demonstrate the algorithm, global reaction route mapping is utilized as a potential search algorithm, but the proposed algorithm should work with other potential search algorithms in principle. The proposed algorithm does not require any encoding of the molecular configurations and is thus applicable to complicated realistic molecules for which efficient encoding is not readily available.

Spectral-clustering approach to Lagrangian vortex detection.

One of the ubiquitous features of real-life turbulent flows is the existence and persistence of coherent vortices. Here we show that such coherent vortices can be extracted as clusters of Lagrangian trajectories. We carry out the clustering on a weighted graph, with the weights measuring pairwise distances of fluid trajectories in the extended phase space of positions and time.

Deciphering Time Scale Hierarchy in Reaction Networks.

Markovian dynamics on complex reaction networks are one of the most intriguing subjects in a wide range of research fields including chemical reactions, biological physics, and ecology. To represent the global kinetics from one node (corresponding to a basin on an energy landscape) to another requires information on multiple pathways that directly or indirectly connect these two nodes through the entire network. In this paper we present a scheme to extract a hierarchical set of global transition states (TSs) over a discrete-time Markov chain derived from first-order rate equations.

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.

Local-heterogeneous responses and transient dynamics of cage breaking and formation in colloidal fluids.

Quantifying the interactions in dense colloidal fluids requires a properly designed order parameter. We present a modified bond-orientational order parameter, ψ̄6, to avoid problems of the original definition of bond-orientational order parameter. The original bond-orientational order parameter can change discontinuously in time but our modified order parameter is free from the discontinuity and, thus, it is a suitable measure to quantify the dynamics of the bond-orientational ordering of the local surroundings.

Detecting invariant manifolds as stationary Lagrangian coherent structures in autonomous dynamical systems.

Normally hyperbolic invariant manifolds (NHIMs) are well-known organizing centers of the dynamics in the phase space of a nonlinear system. Locating such manifolds in systems far from symmetric or integrable, however, has been an outstanding challenge. Here, we develop an automated detection method for codimension-one NHIMs in autonomous dynamical systems.

Non-Markovian properties and multiscale hidden Markovian network buried in single molecule time series.

We present a novel scheme to extract a multiscale state space network (SSN) from single-molecule time series. The multiscale SSN is a type of hidden Markov model that takes into account both multiple states buried in the measurement and memory effects in the process of the observable whenever they exist. Most biological systems function in a nonstationary manner across multiple timescales.

Reactivity boundaries for chemical reactions associated with higher-index and multiple saddles.

Reactivity boundaries that divide the origin and destination of trajectories are of crucial importance to reveal the mechanism of reactions, which was recently found to exist robustly even at high energies for index 1 saddles [Phys. Rev. Lett.

Reactivity boundaries to separate the fate of a chemical reaction associated with an index-two saddle.

Reactivity boundaries that divide the destination and the origin of trajectories are of crucial importance to reveal the mechanism of reactions. We investigate whether such reactivity boundaries can be extracted for higher index saddles in terms of a nonlinear canonical transformation successful for index-one saddles by using a model system with an index-two saddle. It is found that the true reactivity boundaries do not coincide with those extracted by the transformation taking into account a nonlinearity in the region of the saddle even for small perturbations, and the discrepancy is more pronounced for the less repulsive direction of the index-two saddle system.

Influence of SigB inactivation on Corynebacterium glutamicum protein secretion.

The non-essential Corynebacterium glutamicum sigma factor, sigB, modulates global gene expression during the transition from exponential growth to the stationary phase. Utilizing a signal peptide derived from C. glutamicum R CgR_0949, a sigB disruption mutant able to secrete 3- to 5-fold more green fluorescence protein (GFP) and α-amylase than the wild type strain was isolated.

Development of a rapid process monitoring method for dry-coated tableting process by using near-infrared spectroscopy.

A nondestructive transmittance near-infrared (NIR) method for detecting off-centered cores in dry-coated (DC) tablets was developed as a monitoring system in the DC tableting process. Caffeine anhydrate was used as a core active pharmaceutical ingredient (API), and DC tablets were made by the direct compression method. NIR spectra were obtained from these intact DC tablets using the transmittance method.

High yield secretion of heterologous proteins in Corynebacterium glutamicum using its own Tat-type signal sequence.

Efficient protein secretion, the basis of large-scale production of many compounds central to the biotechnology industry, is achieved by signal peptide and propeptide optimization in addition to optimizing host factors affecting heterologous protein production. Here, we fused green fluorescent protein (GFP) to the recently identified Tat-type secretory signal peptide of CgR0949 to demonstrate a high-yield protein secretion system of Corynebacterium glutamicum. The resultant secretion vector facilitated effective secretion of active-form GFP (20 mg l(-1)) into C.

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.

How does a choice of Markov partition affect the resultant symbolic dynamics?

The mutual relationship among Markov partitions is investigated for one-dimensional piecewise monotonic map. It is shown that if a Markov partition is regarded as a map-refinement of the other Markov partition, that is, a concept we newly introduce in this article, one can uniquely translate a set of symbolic sequences by one Markov partition to those by the other or vice versa. However, the set of symbolic sequences constructed using Markov partitions is not necessarily translated with each other if there exists no map-refinement relation among them.

Development of a method for nondestructive NIR transmittance spectroscopic analysis of acetaminophen and caffeine anhydrate in intact bilayer tablets.

Calibration models for nondestructive NIR analysis of API (active pharmaceutical ingredient) contents in two separate layers of intact bilayer tablets were established. These models will enable the use of NIR transmittance spectroscopy in bilayer tableting processes for the control of API contents in separate layers. Acetaminophen and caffeine anhydrate were used as APIs, and tablets were made by the direct compression method.

Cytochrome P450 monooxygenases involved in anthracene metabolism by the white-rot basidiomycete Phanerochaete chrysosporium.

Cytochrome P450 monooxygenases (P450s) involved in anthracene metabolism by the white-rot basidiomycete Phanerochaete chrysosporium were identified by comprehensive screening of both catalytic potentials and transcriptomic profiling. Functional screening of P. chrysosporium P450s (PcCYPs) revealed that 14 PcCYP species catalyze stepwise conversion of anthracene to anthraquinone via intermediate formation of anthrone.

Exploring remnants of invariants buried in a deep potential well in chemical reactions.

We revisit the concept of "remnant of invariant manifolds" originally discussed by Shirts and Reinhardt in a two degrees of freedom Henon-Heiles system [J. Chem. Phys.

Probing remnants of invariants to mediate energy exchange in highly chaotic many-dimensional systems.

A technique is presented to scrutinize a piece of remnants of invariants [R. B. Shirts and W.

Local integrals and their globally connected invariant structure in phase space giving rise to a promoting mode of chemical reaction.

We develop a method to extract local integrals, that is, integrals defined locally in the linear regime of an arbitrary point in phase space. The individual integral represents a vibrational mode. We also propose an index that quantifies the extent of connection between neighboring local integrals.

Pick's disease with Pick bodies: an unusual autopsy case showing degeneration of the pontine nucleus, dentate nucleus, Clarke's column, and lower motor neuron.

We report a 51-year-old female with Pick's disease with Pick bodies (PDPB) showing a brainweight of 530 g. This case was considered to be a very rare case of PDPB, in which the lesion developed in the temporal and frontal lobes and later spread to the parietal lobe, occipital lobe, brainstem, cerebellum and spinal cord. This case showed very atypical clinicopathological findings.

A semiclassical theory for nonseparable rovibrational motions in curved space and its application to energy quantization of nonrigid molecules.

The nonseparability of vibrational and rotational motions of a nonrigid molecule placed in the rotationally isotropic space induces several important effects on the dynamics of intramolecular energy flow and chemical reaction. However, most of these studies have been performed within the framework of classical mechanics. We present a semiclassical theory for the motions of such nonrigid molecules and apply to the energy quantization of three body atomic cluster.

Microscopic description of the equality between violation of fluctuation-dissipation relation and energy dissipation.

In systems far from equilibrium, the fluctuation-dissipation relation is violated due to the lack of detailed balance. Recently, for a class of Langevin equations, it has been proved that this violation is related to energy dissipation as an equality [Phys. Rev.

Dynamical and statistical effects of the intrinsic curvature of internal space of molecules.

The Hamilton dynamics of a molecule in a translationally and/or rotationally symmetric field is kept rigorously constrained in its phase space. The relevant dynamical laws should therefore be extracted from these constrained motions. An internal space that is induced by a projection of such a limited phase space onto configuration space is an intrinsically curved space even for a system of zero total angular momentum.

Degradation of 4-nitrophenol by the lignin-degrading basidiomycete Phanerochaete chrysosporium.

The fungal metabolism of 4-nitrophenol (4-NP) was investigated using the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Despite its phenolic feature, 4-NP was not oxidized by extracellular ligninolytic peroxidases. However, 4-NP was converted to 1,2-dimethoxy-4-nitrobenzene via intermediate formation of 4-nitroanisole by the fungus only under ligninolytic conditions.