Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station.

A major incident occurred at the Fukushima Daiichi Nuclear Power Station following the tsunami triggered by the Tohoku-Pacific Ocean Earthquake in March 2011, whereby seawater entered the torus room in the basement of the reactor building. Here, we identify and analyze the bacterial communities in the torus room water and several environmental samples. Samples of the torus room water (1 × 109 Bq137Cs/L) were collected by the Tokyo Electric Power Company Holdings from two sampling points between 30 cm and 1 m from the bottom of the room (TW1) and the bottom layer (TW2). A structural analysis of the bacterial communities based on 16S rRNA amplicon sequencing revealed that the predominant bacterial genera in TW1 and TW2 were similar. TW1 primarily contained the genus Limnobacter, a thiosulfate-oxidizing bacterium. γ-Irradiation tests on Limnobacter thiooxidans, the most closely related phylogenetically found in TW1, indicated that its radiation resistance was similar to ordinary bacteria. TW2 predominantly contained the genus Brevirhabdus, a manganese-oxidizing bacterium. Although bacterial diversity in the torus room water was lower than seawater near Fukushima, ~70% of identified genera were associated with metal corrosion. Latent environment allocation-an analytical technique that estimates habitat distributions and co-detection analyses-revealed that the microbial communities in the torus room water originated from a distinct blend of natural marine microbial and artificial bacterial communities typical of biofilms, sludge, and wastewater. Understanding the specific bacteria linked to metal corrosion in damaged plants is important for advancing decommissioning efforts. IMPORTANCE: In the context of nuclear power station decommissioning, the proliferation of microorganisms within the reactor and piping systems constitutes a formidable challenge. Therefore, the identification of microbial communities in such environments is of paramount importance. In the aftermath of the Fukushima Daiichi Nuclear Power Station accident, microbial community analysis was conducted on environmental samples collected mainly outside the site. However, analyses using samples from on-site areas, including adjacent soil and seawater, were not performed. This study represents the first comprehensive analysis of microbial communities, utilizing meta 16S amplicon sequencing, with a focus on environmental samples collected from the radioactive element-containing water in the torus room, including the surrounding environments. Some of the identified microbial genera are shared with those previously identified in spent nuclear fuel pools in countries such as France and Brazil. Moreover, our discussion in this paper elucidates the correlation of many of these bacteria with metal corrosion.

Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel.

We propose a water pump that actively transports water molecules through nanochannels. Spatially asymmetric noise fluctuations imposed on the channel radius cause unidirectional water flow without osmotic pressure, which can be attributed to hysteresis in the cyclic transition between the wetting/drying states. We show that the water transport depends on fluctuations, such as white, Brownian, and pink noises. Because of the high-frequency components in white noise, fast switching of open and closed states inhibits channel wetting. Conversely, pink and Brownian noises generate high-pass filtered net flow. Brownian fluctuation leads to a faster water transport rate, whereas pink noise has a higher capability to overcome pressure differences in the opposite direction. A trade-off relationship exists between the resonant frequency of the fluctuation and the flow amplification. The proposed pump can be considered as an analogy for the reversed Carnot cycle, which is the upper limit of the energy conversion efficiency.

PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes.

SUMMARY: : Similarity searches of amino acid sequences against the public metagenomic data can provide users insights about the function of sequences based on the environmental distribution of similar sequences. However, a considerable reduction in the amount of data or the accuracy of the result was necessary to conduct sequence similarity searches against public metagenomic data, because of the vast data size more than Terabytes. Here, we present an ultra-fast service for the highly accurate amino acid sequence similarity search, called PZLAST, which can search the user's amino acid sequences to several Terabytes of public metagenomic sequences in ∼10-20 min. PZLAST accomplishes its search speed by using PEZY-SC2, which is a Multiple Instruction Multiple Data many-core processor. Results of PZLAST are summarized by the ontology-based environmental distribution of similar sequences. PZLAST can be used to predict the function of sequences and mine for homologs of functionally important gene sequences. AVAILABILITY AND IMPLEMENTATION: PZLAST is freely accessible at https://pzlast.riken.jp/meta without requiring registration. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Nanotube Active Water Pump Driven by Alternating Hydrophobicity.

Water transport must be efficiency controlled for the future sustainability of life. Various water transport systems using carbon nanotubes have been proposed in recent years. Although these systems are more permeable than aquaporins, their water transport is passive. In this study, we successfully demonstrate an active water pump driven by simple hydrophobic interaction through computer simulation. Even in the absence of a pressure- or density-gradient, the proposed pump can actively transport water molecules by alternately switching the hydrophobicity of the pump surface. The water transport rate can be easily controlled by varying the time interval of switching. The pump with optimized switching time exhibits prominent water permeance. The results obtained herein can be applied in various water transport technologies because of the simple mechanics. The proposed water pump has the potential to realize an effective device such as a low-energy artificial purification system.

Impulse measurement of laser induced ablation in a vacuum.

An impulse measurement system based on a simple pendulum is newly developed. The system has a resolution of 10-7 Ns for ablation events induced by a single laser at a pulse rate of 2 Hz or less. For ablation events at 10 Hz and above, the system can record the impulse as an average force. The impulse generated by a Nd:YAG pulse laser irradiating a 7075 aluminum alloy is investigated in vacuum. The impulse arises at 3 J/cm2 and the momentum coupling factor, Cm, plateaus at approximately 20 µNs/J over a range of 5 to 50 J/cm2 without producing a plasma shielding effect. Cm is characterized by only fluence independent of pulse width in the range of 10 to 20 ns. This result indicates that it should be feasible to deorbit a 150 kg abandoned satellite at an altitude of 1200 km using a chaser satellite equipped with a 100 W laser.

Kinetic analysis of homogeneous droplet nucleation using large-scale molecular dynamics simulations.

Studies on homogeneous nucleation have been conducted for decades, but a large gap between experiment and theory persists when evaluating the nucleation rate because the classical nucleation theory (CNT) with all its modifications still cannot fully incorporate the kinetics of homogeneous nucleation. Recent large-scale molecular dynamics (MD) simulations on homogeneous nucleation estimated a nucleation rate around the same order of magnitude as that obtained in experiments. This immensely improved agreement between experiment and theory is exciting because MD can provide detailed information on molecular trajectories. Therefore, a better understanding of the kinetics of homogeneous nucleation can now be obtained. In this study, large-scale MD simulations on homogeneous nucleation were performed. Through kinetic analysis of the simulation results, the nucleation rate, free energy barrier, and critical cluster size were found. Although the nucleation rates directly obtained from the simulations differed from those calculated from the CNT by 8-13 orders of magnitude, when the parameters calculated from the molecular trajectories were substituted into the classical theory, the discrepancy between the nucleation rates decreased to within an order of magnitude. This proves that the fundamental formulation of the theoretical equation is physically sound. We also calculated the cluster formation free energy and confirmed that the free energy barrier decreases with increasing supersaturation ratio. The estimated barrier height was twice that determined by theory, whereas the critical cluster size showed very good agreement between simulation and theory.

Theory of nanobubble formation and induced force in nanochannels.

This paper presents a fundamental theory of nanobubble formation and induced force in confined nanochannels. It is shown that nanobubble formation between hydrophobic plates can be predicted from their surface tension and geometry, with estimated values for the surface free energy and the force acting on the plates in good agreement with the results of molecular dynamics simulation and experimentation. When a bubble is formed between two plates, vertical attractive force and horizontal retract force due to the shifted plates are applied to the plates. The net force exerted on the plates is not dependent on the distance between them. The short-range force between hydrophobic surfaces due to hydrophobic interaction appears to correspond to the force estimated by our theory. We compared between experimental and theoretical values for the binding energy of a molecular motor system to validate our theory. The tendency that the binding energy increases as the size of the protein increases is consistent with the theory.

Self-assembly behaviours of primitive and modern lipid membrane solutions: a coarse-grained molecular simulation study.

Researchers have studied the origin of life and the process of evolution on early Earth for decades. However, we lack a comprehensive understanding of biogenesis, because there are many stages in the formation and growth of the first cell. We investigate the self-replication processes of coacervate protocells using computer simulations of single-chain lipid and phospholipid aqueous mixtures. Based on a morphological phase diagram, we develop a model of prebiotic self-replication driven by only environmental factors (i.e. temperature and lipid concentrations) without any external force. Moreover, we investigate high concentration structures during the process of self-replication. These structures have an advantage in fusion and repair of cell membranes. Therefore, lipid hot spots may have existed in primordial soup.

Understanding molecular motor walking along a microtubule: a themosensitive asymmetric Brownian motor driven by bubble formation.

The "asymmetric Brownian ratchet model", a variation of Feynman's ratchet and pawl system, is invoked to understand the kinesin walking behavior along a microtubule. The model system, consisting of a motor and a rail, can exhibit two distinct binding states, namely, the random Brownian state and the asymmetric potential state. When the system is transformed back and forth between the two states, the motor can be driven to "walk" in one direction. Previously, we suggested a fundamental mechanism, that is, bubble formation in a nanosized channel surrounded by hydrophobic atoms, to explain the transition between the two states. In this study, we propose a more realistic and viable switching method in our computer simulation of molecular motor walking. Specifically, we propose a thermosensitive polymer model with which the transition between the two states can be controlled by temperature pulses. Based on this new motor system, the stepping size and stepping time of the motor can be recorded. Remarkably, the "walking" behavior observed in the newly proposed model resembles that of the realistic motor protein. The bubble formation based motor not only can be highly efficient but also offers new insights into the physical mechanism of realistic biomolecule motors.

Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel.

The "asymmetric brownian ratchet model" is a variation of Feynman's ratchet and pawl system proposed. In this model, a system consisting of a motor and a rail has two binding states. One is the random brownian state, and the other is the asymmetric potential state. When the system is alternatively switched between these states, the motor can be driven in one direction. This model is believed to explain nanomotor behavior in biological systems. The feasibility of the model has been demonstrated using electrical and magnetic forces; however, switching of these forces is unlikely to be found in biological systems. In this paper, we propose an original mechanism of transition between states by bubble formation in a nanosized channel surrounded by hydrophobic atoms. This amounts to a nanoscale motor system using bubble propulsion. The motor system consists of a hydrophobic motor and a rail on which hydrophobic patterns are printed. Potential asymmetry can be produced by using a left-right asymmetric pattern shape. Hydrophobic interactions are believed to play an important role in the binding of biomolecules and molecular recognition. The bubble formation is controlled by changing the width of the channel by an atomic distance (∼0.1 nm). Therefore, the motor is potentially more efficient than systems controlled by other forces, in which a much larger change in the motor position is necessary. We have simulated the bubble-powered motor using dissipative particle dynamics and found behavior in good agreement with that of motor proteins. Energy efficiency is as high as 60%.

Formation of nuclear "pasta" in supernovae.

In supernova cores, nuclear "pasta" phases such as a triangular lattice of rodlike nuclei and layered structure of slablike nuclei are considered to exist. However, it is still unclear whether or not they are actually formed in collapsing supernova cores. Using ab initio simulations called quantum molecular dynamics, here we solve this problem by demonstrating that a lattice of rodlike nuclei is formed from a bcc lattice by compression. We also find that, in the transition process, the system undergoes a zigzag configuration of elongated nuclei, which are formed by a fusion of two original spherical nuclei.

Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface.

Water droplets on rugged hydrophobic surfaces typically exhibit one of the following two states: (i) the Wenzel state [Wenzel RN (1936) Ind Eng Chem 28:988-994] in which water droplets are in full contact with the rugged surface (referred as the wetted contact) or (ii) the Cassie state [Cassie, ABD, Baxter S (1944) Trans Faraday Soc 40:546-551] in which water droplets are in contact with peaks of the rugged surface as well as the "air pockets" trapped between surface grooves (the composite contact). Here, we show large-scale molecular dynamics simulation of transition between Wenzel state and Cassie state of water droplets on a periodic nanopillared hydrophobic surface. Physical conditions that can strongly affect the transition include the height of nanopillars, the spacing between pillars, the intrinsic contact angle, and the impinging velocity of water nanodroplet ("raining" simulation). There exists a critical pillar height beyond which water droplets on the pillared surface can be either in the Wenzel state or in the Cassie state, depending on their initial location. The free-energy barrier separating the Wenzel and Cassie state was computed on the basis of a statistical-mechanics method and kinetic raining simulation. The barrier ranges from a few tenths of k(B)T(0) (where k(B) is the Boltzmann constant, and T(0) is the ambient temperature) for a rugged surface at the critical pillar height to approximately 8 k(B)T(0) for the surface with pillar height greater than the length scale of water droplets. For a highly rugged surface, the barrier from the Wenzel-to-Cassie state is much higher than from Cassie-to-Wenzel state. Hence, once a droplet is trapped deeply inside the grooves, it would be much harder to relocate on top of high pillars.

Microscopic insights into nucleation in a sulfuric acid-water vapor mixture based on molecular dynamics simulation.

We conducted a molecular dynamics simulation of the binary nucleation in the vapor mixture consisting of water and a small amount of sulfuric acid and investigated the microscopic process in relation to the structure of the hydrate (binary cluster composed of sulfuric acid and water). It was observed that the nucleation rate increased with the concentration of sulfuric acid. It was found that the formation of the hydrate is stable as long as its size is small enough, and the hydrate growth by coagulation played a major part in the enhanced nucleation. The rate of coagulation became larger by the uptake of more sulfuric acid in the hydrate, while it was suppressed with increasing the hydration number. We found that such features came from the structure of the small hydrate which was a multishell structure composed of an inner shell of sulfuric acid and diffused outer shell of water.

Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data.

Accurate structural refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data was carried out using charge densities determined by the maximum-entropy method (MEM). The MEM charge density clearly revealed detailed features of the solvent region of the putative acylphosphatase crystalline structure, some of which had never been observed in conventional Fourier maps. The structural model in the solvent region was constructed as distributions of anisotropic water atoms. The omit-difference MEM maps and the difference MEM maps were effective in revealing details of the protein structure, such as multiple conformations of the side chains of amino-acid residues, anisotropy of atoms and H atoms. By model building using the MEM charge densities, the reliability factors R1 and R free in the SHELX refinement were dramatically improved from 17.9% and 18.3% to 9.6% and 10.0%, respectively. The present results prove the usefulness of MEM in improving the accuracy of refinement of protein crystal structures.

Epigenetics: application of virtual image restriction landmark genomic scanning (Vi-RLGS).

Restriction landmark genomic scanning (RLGS) is a powerful method for the systematic detection of genetic mutations in DNA length and epigenetic alteration due to DNA methylation. However, the identification of polymorphic spots is difficult because the resulting RLGS spots contain very little target DNA and many non-labeled DNA fragments. To overcome this, we developed a virtual image restriction landmark genomic scanning (Vi-RLGS) system to compare actual RLGS patterns with computer-simulated RLGS patterns (virtual RLGS patterns). Here, we demonstrate in detail the contents of the simulation program (rlgssim), based on the linear relationship between the reciprocal of mobility plotted against DNA fragment length and Vi-RLGS profiling of Arabidopsis thaliana.

Extended study of molecular dynamics simulation of homogeneous vapor-liquid nucleation of water.

Using the simple point charge/extended water model, we performed molecular dynamics simulations of homogeneous vapor-liquid nucleation at various values of temperature T and supersaturation S, from which the nucleation rate J, critical nucleus size n(*), and the cluster formation free energy DeltaG were derived. As well as providing lots of simulation data, the results were compared with theories on homogeneous nucleation, including the classical, semi-phenomenological, and scaled models, but none of these gave a satisfactory explanation for our results. It was found that two main factors made the theories fail: (1) The average cluster structure including the nonspherical shape and the core structure that is not like the bulk liquid and (2) the forward rate which is larger than assumed by the theories by about one order of magnitude. The quantitative evaluation of these factors is left for future investigations.

Structure and dynamics of RNA polymerase II elongation complex.

RNA polymerase (Pol) II is a fundamental and important enzyme in the transcription process. However, two mysterious questions have remained unsolved: how an unwound bubble of DNA is established and maintained, and how the enzyme moves along the DNA. To answer these questions, we constructed a model structure of the Pol II elongation complex with the 50 base pairs of DNA-24 bases of RNA including the unwound bubble of DNA and performed a molecular dynamics simulation. We obtained a reliable model structure of the Pol II elongation complex in the pre-translocation state which has not yet been determined by the X-ray crystallographic study. The model structure revealed that multiple protein loops work concertedly to form and maintain the bubble structure. We also found that the conformational change of a loop in the Pol II, fork loop 1, couples with the unidirectional movement of the Pol II along the DNA.

Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation.

We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained equilibrium. Particular attention is placed on the tendency of formation and stability of nanobubbles in between model nanoassemblies which are composed of hydrophobic clusters (or patches) embedded in a hydrophilic substrate. On the basis of physical behavior of nanobubble formation, we observed a change from short-range molecular hydrophobic interaction to midrange nanoscopic interaction when the length scale of hydrophobe approaches to about 1 nm. We investigated the behavior of nanobubble formation with several different patterns of nonpolar-site distribution on the nanoassemblies but always keeping a constant ratio of nonpolar to polar monomer sites. Dynamical properties of confined water molecules in between nanoassemblies are also calculated.

Dynamics of two-sign point vortices in positive and negative temperature states.

Dynamics of two-sign point vortices in two-dimensional circular boundary is examined by numerical simulations with MDGRAPE-2. The vortex system is characterized by the inverse temperature beta as determined from the density of states of the microcanonical ensemble of numerically generated 10(7) states. The massive simulation shows that different configurations appear in the time-asymptotic state depending on the sign of beta. Condensation of the same-sign vortices is observed when beta<0, while the both-sign vortices tend to be uniformly neutralized when beta>0. During the condensation, a part of the vortices gains energy to form clumps (patches), and the other part of the vortices loses energy to keep the total energy constant and mixes with vortices of the other sign. This observation demonstrates a characteristic feature of negative beta states that the system energy concentrates into the clumps of the same-sign vortices.

Simulation of transitions between "pasta" phases in dense matter.

Calculations of equilibrium properties of dense matter predict that at subnuclear densities nuclei can be rodlike or slablike. To investigate whether transitions between phases with nonspherical nuclei can occur during the collapse of a star, we perform quantum molecular dynamic simulations of the compression of dense matter. We have succeeded in simulating the transitions between rodlike and slablike nuclei and between slablike nuclei and cylindrical bubbles. Our results strongly suggest that nonspherical nuclei can be formed in the inner cores of collapsing stars.