Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences

The folding/unfolding kinetics of a three-dimensional lattice protein was studied using a simple statistical mechanical model for protein folding that we developed earlier. We calculated a characteristic relaxation rate for the free energy profile starting from a completely unfolded structure (or native structure) that is assumed to be associated with a folding rate (or an unfolding rate). The chevron plot of these rates as a function of the inverse temperature was obtained for four lattice proteins, namely, proteins a1, a2, b1, and b2, in order to investigate the dependency of the folding and unfolding rates on their native structures and amino acid sequences. Proteins a1 and a2 fold to the same native conformation, but their amino acid sequences differ. The same is the case for proteins b1 and b2, but their native conformation is different from that of proteins a1 and a2. However, the chevron plots of proteins a1 and a2 are very similar to each other, and those of proteins b1 and b2 differ considerably. Since the contact orders of proteins b1 and b2 are identical, the differences in their kinetics should be attributed to the amino acid sequences and consequently to the interactions between the amino acid residues. A detailed analysis revealed that long-range interactions play an important role in causing the difference in the folding rates. The chevron plots for the four proteins exhibit a chevron rollover under both strongly folding and strongly unfolding conditions. The slower relaxation time on the broad and flat free energy surfaces of the unfolding conformations is considered to be the main origin of the chevron rollover, although the free energy surfaces have features that are rather complicated to be described in detail here. Finally, in order to concretely examine the relationship between changes in the free energy profiles and the chevron plots, we illustrate some examples of single amino acid substitutions that increase the folding rate.     

核子与核力决定的核形状(英文)

讨论了最近提出的作为量子多体系统重要潜在机制之一的量子自组织,原子核无疑是最好的实例。由于原子核内核子的单粒子和集体运动共存,它们的相互制约决定了核结构。集体模式因其驱动力,如使椭球形变的四极力及其阻力达到平衡形成,而单粒子能量就是产生阻力的一种根源。当存在较大单粒子能隙时,相关的集体运动更易受到阻碍。因此,一般认为,单粒子运动和集体运动是相互对抗的"天敌"。然而,由于核力的多样和复杂性,单极相互作用使单粒子能量改变也能减小其对集体运动的阻碍而加强集体模式,该现象将通过Zr同位素实例加以说明。这就导致了量子自组织的产生:单粒子能量由两种量子液体（质子和中子）和控制阻力的单极相互作用自组织。于是,不同于朗道费米液体理论的结论,原子核不一定像填装了自由核子的刚性瓶。Ⅱ型壳演化即是包含跨准幻壳能隙激发的直观实例。在重核中,量子自组织因其轨道和核子数更多而更为重要。We discuss the quantum self-organization introduced recently as one of the major underlying mechanisms of the quantum many-body systems. Atomic nuclei are actually a good example, because two types of the motion of nucleons, single-particle states and collective modes, interplay in determining their structure. The collective mode appears as a consequence of the balance between the effect of the mode-driving force (e.g., quadrupole force for the ellipsoidal deformation) and the resistance power against it. The single-particle energies are one of the sources to bring about such resistance power:a coherent collective motion is more hindered by larger spacings between relevant single particle states. Thus, the single-particle state and the collective mode are "enemies" against each other in the usual understanding. However, the nuclear forces are rich and complicated enough so as to enhance relevant collective mode by reducing the resistance power by changing single-particle energies for each eigenstate through monopole interactions. This will be demonstrated with the concrete example taken from Zr isotopes. In this way, the quantum self-organization occurs:single-particle energies can be self-organized by (i) two quantum liquids, e.g., protons and neutrons, (ii) monopole interaction (to control resistance). Thus, atomic nuclei are not necessarily like simple rigid vases containing almost free nucleons, in contrast to the naïve Fermi liquid picture a la Landau. Type Ⅱ shell evolution is considered to be a simple visible case involving excitations across a (sub)magic gap. The quantum self-organization becomes more important in heavier nuclei where the number of active orbits and the number of active nucleons are larger.     

Observation of the D1(2420)-->Dpi + pi- decays

We report on the first observation of D0/1(2420)-->D0pi- pi+ and D+/1(2420-->D+ pi- pi+ decays (where the contribution from the dominant known D1-->D*pi decay mode is excluded) in the B- -->D0/1pi-) and (-)B0-->D+/1pi- decays, respectively. The observation is based on 15.2 x 10(7) B(-)B events collected with the Belle detector at the KEKB collider. We also set 90% confidence level upper limits for the branching fractions of the four following decays: B- -->D0/1pi-, D01-->D(*0)pi- pi+, (-)B0-->D+/1pi-, D+/1-->D(*+) pi- pi+, B- -->D(*0)2(2460)pi-, D(*0)2 -->D(*0) pi- pi+, (-)B0-->D(*+)2(2460)pi-, D(*+)2-->D(*+)pi- pi+.     

Observation of a near-threshold omegaJ/psi mass enhancement in exclusive B-->KomegaJ/psi decays

We report the observation of a near-threshold enhancement in the omegaJ/psi invariant mass distribution for exclusive B-->KomegaJ/psi decays. The results are obtained from a 253 fb(-1) data sample that contains 275 x 10(6) BB pairs that were collected near the Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric energy e(+)e(-) collider. The statistical significance of the omegaJ/psi mass enhancement is estimated to be greater than 8sigma.     

Search for D0-D0 mixing in D0 --> K+ pi(-) decays and measurement of the doubly-Cabibbo-suppressed decay rate

We have searched for mixing in the D(0)-D (0) system by measuring the decay-time distribution of D(0) --> K(+) pi(-) decays. The analysis uses 90 fb(-1) of data collected by the Belle detector at the KEKB e(+) e(-) collider. We fit the decay-time distribution for the mixing parameters x' and y' and also for the parameter R(D), which is the ratio of the rate for the doubly-Cabibbo-suppressed decay D(0)--> K+ pi(-) to that for the Cabibbo-favored decay D(0)--> K-pi(+). We do these fits both assuming CP conservation and allowing for CP violation. We use a frequentist method to obtain a 95% C.L. region in the x'(2) - y' plane. Assuming no mixing, we measure R(D) = (0.381 +/- 0.017(+0.008)(-0.016))%.     

Measurement of time-dependent CP-violating asymmetries in B0 --> K(s)0K(s)0K(s)0 decay

We present a measurement of CP-violation parameters in the B0 --> K(s)0K(s)0K(s)0 decay based on a sample of 275 x 10(6) BB pairs collected at the upsilon(4S) resonance with the Belle detector at the KEKB energy-asymmetric e+e- collider. One neutral B meson is fully reconstructed in the decay B0 --> K(s)0K(s)0K(s)0, and the flavor of the accompanying B meson is identified from its decay products. CP-violation parameters are obtained from the asymmetry in the distributions of the proper-time interval between the two B decays: S = +1.26 +/- 0.68(stat) +/- 0.20(syst) and [symbol: see text] = +0.54 +/- 0.34(stat) +/- 0.09(syst).     

Effects of fine fuel droplets on a laminar flame stabilized in a partially prevaporized spray stream

A partially prevaporized spray burner was developed to investigate the interaction between fuel droplets and a flame. Monodispersed partially prevaporized ethanol sprays with narrow diameter distribution were generated by the condensation method using rapid pressure reduction of a saturated ethanol vapor–air mixture. A tilted flat flame was stabilized at the nozzle exit using a hot wire. Particle tracking velocimetry (PTV) was applied to measurements of the droplet velocity; the laminar burning velocity was obtained from gas velocity derived from the droplet velocity. Observations were made of flames in partially prevaporized spray streams with mean droplet diameters of 7 μm and the liquid equivalence ratios of 0.2; the total equivalence ratio was varied. In all cases, a sharp vaporization plane was observed in front of the blue flame. Flame oscillation was observed on the fuel-rich side. At strain rates under 50 s⁻¹, the change in the burning velocity with the strain rate is small in fuel-lean spray streams. In spray streams of 0.7 and 0.8 in the total equivalence ratio, burning velocity increases with strain rates of greater than 50 s⁻¹. However, in spray streams with 0.9 and 1.0 in the total equivalence ratio, burning velocity decreases as the strain rate increases. At strain rates greater than 80 s⁻¹, burning velocity decreases with an increased gas equivalence ratio. The effect of mean droplet diameter, and the entry length of droplets into a flame on the laminar burning velocity, were also investigated to interpret the effect of the strain rate on the laminar burning velocity of partially prevaporized sprays.     

Ignition enhancement by addition of NO and NO2 from a N2/O2 plasma torch in a supersonic flow

The effects of NO and NO₂ produced by using a plasma jet (PJ) of a N₂/O₂ mixture on ignition of hydrogen, methane, and ethylene in a supersonic airflow were experimentally and numerically investigated. Numerical analysis of ignition delay time showed that the addition of a small amount of NO or NO₂ drastically reduced ignition delay times of hydrogen and hydrocarbon fuels at a relatively low initial temperature. In particular, NO and NO₂ were more effective than O radicals for ignition of a CH₄/air mixture at 1200 K or lower. These ignition enhancement effects were examined by including the low temperature chemistry. Ignition tests by a N₂/O₂ PJ in a supersonic flow (M = 1.7) for using hydrogen, methane, and ethylene injected downstream of the PJ were conducted. The results showed that the ignitability of the N₂/O₂ PJ is affected by the composition of the feedstock and that pure O₂ is not the optimum condition for downstream fuel injection. This result of ignition tests with downstream fuel injection demonstrated a significant difference in ignition characteristics of the PJ from the ignition tests with upstream fuel injection.