Physics of Self-Organization Systems

Preface

Organizing Committees

Contents

The Newtonian revolution taught us how to dissect phenomena into contingencies (e.g., initial conditions) and fundamental laws (e.g., equations of motion). Since then, ‘fundamental physics’ has been pursuing purer and leaner fundamental laws. Consequently, to explain real phenomena a lot of auxiliary conditions become required. Isn't it now the time to start studying ‘auxiliary conditions’ seriously?

The study of biological systems has a possibility of shedding light on this neglected side of phenomena in physics, because we organisms were constructed by our parents who supplied indispensable auxiliary conditions; we never self-organize. Thus, studying the systems lacking self-organizing capability (such as complex systems) may indicate new directions to physics and biology (biophysics).

There have been attempts to construct a ‘general theoretical framework’ of biology, but most of them never seriously looked at the actual biological world. Every serious natural science must start with establishing a phenomenological framework. Therefore, this must be the main part of bio-physics. However, this article is addressed mainly to theoretical physicists and discusses only certain theoretical aspects (with real illustrative examples).

The ribosome is a molecular machine that translates the genetic code described on the messenger RNA (mRNA) into an amino acid sequence through repetitive cycles of transfer RNA (tRNA) selection, peptide bond formation and translocation. Although the detailed interactions between the translation components have been revealed by extensive structural and biochemical studies, it is not known how the precise regulation of macromolecular movements required at each stage of translation is achieved. Here we demonstrate an optical tweezer assay to measure the rupture force between a single ribosome complex and mRNA. The rupture force was compared between ribosome complexes assembled on an mRNA with and without a strong Shine-Dalgarno (SD) sequence. The removal of the SD sequence significantly reduced the rupture force, indicating that the SD interactions contribute significantly to the stability of the ribosomal complex on the mRNA in a pre-peptidyl transfer state. In contrast, the post-peptidyl transfer state weakened the rupture force as compared to the complex in a pre-peptidyl transfer state and it was the same for both the SD-containing and SD-deficient mRNAs. The results suggest that formation of the first peptide bond destabilizes the SD interaction, resulting in the weakening of the force with which the ribosome grips an mRNA. This might be an important requirement to facilitate movement of the ribosome along mRNA during the first translocation step. In this article, we discuss about the above new results including the introduction of the ribosome translation mechanism and the optical tweezer method.

Myosin V is a linear molecular motor that moves cargos along actin filaments in a cell. It has two ‘feet’ (conventionally called ‘heads’ or ‘motor domains’), each attached to a long and relatively stiff ‘leg’ (traditionally called ‘neck’ or ‘lever arm’), and walks by alternately swinging forward its feet, apparently similar to a human. I describe the mechanisms of how the trailing foot, once lifted, accesses the next forward landing site on actin, which have been revealed by directly observing the leg motion of a walking myosin V through a micrometer-sized biological rod attached to its leg. Next, I discuss our previously proposed mechanism for the lifted foot attaching to the next forward binding site. Finally, I comment on the usefulness of a rod probe as an experimental tool.

Biological systems include a large number and various kinds of molecular machines. Individual molecular machines work stochastically, while the systems constructed of the ensembles of these machines exhibit dynamically-ordered phenomena, rather than a simple sum of individual parts. Here we focus on the spontaneous oscillatory contraction (SPOC) observed in the contractile system of muscle. From the mechanical measurements in the precursor state of SPOC, we discuss how the functions of individual molecular motors are autonomously regulated in the contractile system.

F_O is a membrane-embedded part of ATP synthase, transforming proton current running within this molecule into a rotational motion taking place between two subunits, c-subunit and a-subunit. How the proton current could be transformed into the rotational motion remains unclear. In this paper, by means of molecular dynamics simulation, we studied basic properties of the rotational motion. In equilibrium, the c-ring, which consists of 10-12 c-subunits and interacts with the a-subunit, showed stepwise rotational motion. The rotational motions resulted in a free rotational diffusion in a longer period. The diffusion constant calculated as a function of temperature showed a glass-transition-like behavior: at the lower temperatures, diffusional motion was significantly suppressed, deviating from the Einstein's relation. Under a non-equilibrium condition where different heat baths with different temperatures are applied, respectively, to the c-ring and the a-subunit, we found that directionality arises in the rotational diffusion. We finally point out how the structural flexibility (i.e., softness) of protein molecules pertains to our results.

A review of recent advances in nonequilibrium statistical mechanics is presented. These new results explain how the time reversal symmetry is broken in the statistical description of nonequilibrium processes and the thermodynamic entropy production finds its origin in the time asymmetry of nonequilibrium fluctuations. These advances are based on new relationships expressing the time asymmetry in terms of the temporal disorder and the probability distributions of nonequilibrium fluctuations. These relationships apply to driven Brownian motion and molecular motors.

A purification scheme, proposed several years ago and aimed at extracting a pure state from an arbitrary initial mixed state by repeated measurements, is reviewed and the effects of environment on this scheme are clarified.

We explore the fluctuation theorem for a diffusion in a tilted washboard potential where both the quantum tunneling and the thermal activation play a role. The diffusion process is treated as a biased random walk where the transition rates are enhanced due to the quantum tunneling. Within this framework, the dissipation is easy to handle, since we need not to measure the experimentally inaccessible quantity like total Hamiltonian which includes the bath degrees of freedom.

We study earthquake interval time statistics, paying special attention to inter-occurrence times in the two-dimensional (2D) stick-slip (block-slider) model. Interoccurrence times are the time interval between successive earthquakes on all faults in a region. We select stiffness and friction parameters as tunable parameters because these physical quantities are considered as essential factors in describing fault dynamics. It is found that interoccurrence time statistics depend on the parameters. Varying stiffness and friction parameters systematically, we optimize these parameters so as to reproduce the interoccurrence time statistics in natural seismicity. For an optimal case, earthquakes produced by the model obey the Gutenberg-Richter law, which states that the magnitude-frequency distribution exhibits the power law with an exponent approximately unity.

Polar state in a quantum relaxor K_(1−x)Li_xTaO₃ (KLT) is investigated using second harmonic generation (SHG) and polarization microscopes. Temperature dependences of SHG image and interference color image related to birefringence are observed on three different processes (zero field heating after zero field cooling, field heating after zero field cooling, and field heating after field cooling processes). A remarkable history dependence in the T-E space which is one of the characteristic behaviors of relaxor is observed in SHG and polarization microscope observations. Ferroelectric phase transition occurs below the transition temperature T_p with tiny domain structures which is beyond the optical microscope diffraction limit. Under an electric field, these micro domain structures change to macroscopic structures. Based on these experiments, we propose a polar state model of KLT below T_p.

We report resistivity and thermopower of polycrystalline samples of Ni-doped LaRhO₃ from room temperature down to 4.2 K. The resistivity decreases with increasing Ni-doping, while the thermopower reaches almost a constant value (∼85 μV/K) at room temperature.

Tilted monolayers composed of chiral liquid crystals (LCs) are known to exhibit the molecular collective precession under the transmembrane water flow. The phenomenon has been explained from the macroscopic point of view as a two-dimensional-type “Lehmann effect,” but the microscopic mechanism has not been understood at all. In order to reveal the molecular motion, which could be the origin of the macroscopic precession, we calculated the rotational torque of an isolated chiral molecule under the mass flow of several materials. The result shows that single chiral molecule can obtain a certain torque under the mass flow along the molecular long axis, the magnitude of which depends on the chemical structure of flow materials.

We present a systematic study of the interplay of excitons with free carriers in determination of carrier tunneling in GaAs/AlGaAs double quantum wells for various temperatures and carrier densities using time-resolved pump and probe measurements. The tunneling time abruptly decreases above a critical temperature (T_c) while it remains almost constant below T_c. As for the carrier density dependence, the tunneling time increases with increasing excitation power at low temperature. At high temperatures, no dependence of tunneling time on carrier density was observed. These behaviors are well explained in terms of the reduction of the electron tunneling probability of exciton states compared with that of free electron states, and the temperature and carrier density dependences of the populations of electrons in the two states. The thermodynamical equilibrium established between excitons and free carriers after photoexcitation determines the relative change of the population. Furthermore, the competition between exciton formation and carrier tunneling was discussed in a special case with 1 ps tunneling time.

It is generally agreed that the primary goal of quantum gravity is to find the microscopic structure of spacetime. However, for the last half a century the cardinal principle upheld by most general relativists has been to find ways to quantize Einstein's general theory of relativity, a theory which has proven to be highly successful in describing the macroscopic structure of spacetime we live in today. A tacit assumption in this existing paradigm is that doing so will yield the micro-structures of spacetime. We challenge this supposition and present a different view. If general relativity is an effective theory valid only at the long wavelength and low energy limits, and the metric and connection forms are collective variables, then quantizing a classical theory such as general relativity valid in the macroscopic domain is unlikely to yield a theory of the microscopic structures of spacetime. To uncover the microscopic structures one needs to find ways to unravel the underlying microscopic structures from observed macroscopic phenomena rather than naively quantizing the macroscopic variables, two very different paradigms. This task is similar to deducing the molecular constituents or even their quantum features from hydrodynamics or universalities of microscopic theories from critical phenomena. The macro to micro road poses a new and perhaps more difficult challenge to the next generation of theorists, phenomenologists and experimentalists in quantum gravity. Here we need to address issues at the quantum-classical and micro-macro interfaces familiar in mesoscopic physics, focusing on quantum fluctuations and correlations, coarse-graining and backreaction, and adopt ideas of nonequilibrium statistical mechanics and techniques from quantum field theory to explore theories built upon general relativity in a ‘bottom-up’ approach or a ‘grass-root’ road to quantum gravity. This view also provides us with a natural resolution towards the ‘Origin of the Universe’ issue, viz, the ‘origin’ is merely the commencement of a new phase where spacetime began to take shape and assume a manifold structure. This realization would push us to ask the more challenging question: How do we characterize the phase before? Was it a foam-like structure of multiply-connected spactime? How did the phase transition take place – first or second order, discrete to continuum, stochastic to deterministic? An even more difficult question: How and ‘when’ did our concept of time and an arrow of time emerge whence we can ask how the universe came into being and evolved as far back as we can trace it?

It is known from the modern accurate observations, surprising us greatly, that the current universe is mainly about 90 percents fulfilled with the unknown dark components: dark energy and dark matter. The most recent WMAP observations are consistent with the universe made up of 74% dark energy, 22% dark matter, and 4% ordinary matter such as baryon. The modern universe not only needs the dark components but also inflaton leading to early accelerating expansion. These unknown components of the universe may be not independent of the unified theory of all forces existing in nature. For the recent studies of the unified theory, one of most promising approaches is a superstring theory, or M-theory, considered as a quantization of fields including gravitational interaction. The cosmological implications of string theory are currently receiving considerable attention, the so-called string cosmology. This interest has been inspired in part by the recent advances that have been made towards a non– perturbative formulation of the theory. The goal of superstring cosmology is to examine the dynamical evolution in these theories and re-examine cosmological questions in the light of our new understanding of string theory such as dark energy and dark matter. String theory has a much richer set of fundamental degree of freedom, consisting of D-branes. This fundamental objects, D-branes denote non–perturbative effects of string theory as “soliton” of strings, while string theory has been only described in perturbative form. Inspired by such speculation, recently a new paradigm on the early universe has been proposed, the so-called brane-world. The existence of models with more than one brane suggests that branes may collide. Colliding branes would be a fundamental phenomena in the string cosmology. We have studied several applications of colliding branes to string cosmology.

Based on the stochastic gravity, we study the loop corrections to the scalar and tensor perturbations during inflation. Since the loop corrections to scalar perturbations suffer the infrared(IR) divergence, we consider the IR regularization to obtain the finite value. We find that the loop correction is amplified by the e-folding, in other words there appears the logarithmic corrections, just as discussed by M.Sloth et.al. On the other hand, we find that the tensor perturbations do not suffer from the infrared divergence.

An equation of state (EOS) for uniform nuclear matter is constructed at zero and finite temperatures with the variational method starting from the realistic nuclear Hamiltonian, and applied to the Thomas-Fermi (TF) calculations for atomic nuclei, toward a nuclear EOS for supernova simulations. For uniform nuclear matter at zero temperature, the two-body energy is evaluated in the two-body cluster approximation and the contribution of the three nucleon interaction (TNI) is taken into account phenomenologically. Parameters included in the TNI energy are determined so as to reproduce the empirical saturation conditions. At finite temperatures, a variational method by Schmidt and Pandharipande is employed to evaluate the free energy and related thermodynamic quantities. In the TF calculations for atomic nuclei, the parameters in the uniform EOS are tuned to reproduce empirical masses and RMS charge radii for β-stable nuclei.

We constructed eight 20m elements in Nasu, and are observing radio transients over a wide-field at 1400 MHz. We report on two radio transients detected on consecutive drift scanning observations at declination 32 degrees over about two months. One of the two transients “WJN J1039+3200” appeared at α=10^h39^m40^s ±10^s, δ = 32° ±0.4° on March 4, 2005 and the other one “WJN J0645+3200” appeared at α=06^h45^m25^s ± 10^s, δ = 32° ±0.4° on March 24, 2005DBoth exhibited flux densities in excess of 1 Jy. The burst duration was within two days. There are few examples of radio transients outside the Galactic plane. Therefore, these are very important observations. We have already reported on four radio transients with features that looks like the two transients detected this time. The duration of five transients is within two days, and one transient is within three days. Four transients of six transients were detected at a high galactic latitude of b>30°. Counterparts of six WJN Transients were included X-ray sources in four events, and had a consistency of 66%. The consistency of γ-ray, PGC Galaxy, NVSS and FIRST source was concentrated at about 50%. We were not able to find a special feature in the counterpart The distribution was verified by making a logN-logS plot using those data and the newly detected data. As a result, the distribution of the radio transients that we observed might have an isotropic distribution not dependent on Galactic longitude and Galactic latitude. We cannot yet clarify these two radio transients, because their features are different from any radio burst observed in the past.

We perform hydrodynamical collapse and bounce simulations of neutron stars induced by QCD phase transition. We study how the phase transition affects the elements of the envelopes and crusts of neutron stars near the epoch of core-bounce. We assume the first-order phase transition, a chirally symmetric quark-gluon plasma for quark phase. The initial elements are adopted from the realistic evolutional calculations of neutron stars containing the cooling effects and the nucleosynthesis of envelope such as type I X-ray burst. We find that the elements of envelope can eject directly (without nucleosynthesis) for such a collapse and bounce by the transition.

Presentation Titles

Author Index