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Autophagy is an intracellular degradation process that is mediated by de novo formation of autophagosomes. Autophagosome formation involves dynamic morphological changes; a disk-shaped membrane cisterna grows, bends to become a cup-shaped structure, and finally develops into a spherical autophagosome. We have constructed a theoretical model that integrates the membrane morphological change and entropic partitioning of putative curvature generators, which we have used to investigate the autophagosome formation process quantitatively. We show that the membrane curvature and the distribution of the curvature generators stabilize disk- and cup-shaped intermediate structures during autophagosome formation, which is quantitatively consistent with in vivo observations. These results suggest that various autophagy proteins with membrane curvature-sensing properties control morphological change by stabilizing these intermediate structures. Our model provides a framework for understanding autophagosome formation., Comment: 33 pages, 8 figures

An extended ensemble Monte Carlo algorithm is proposed by introducing a violation of the detailed balance condition to the update scheme of the inverse temperature in simulated tempering. Our method, irreversible simulated tempering, is constructed based on the framework of the skew detailed balance condition. By applying this method to the ferromagnetic Ising model in two dimensions on a square lattice as a benchmark, the dynamical behavior of the inverse temperature and an autocorrelation function of the magnetization are studied numerically. It is found that the relaxation dynamics of the inverse temperature changes qualitatively from diffusive to ballistic by violating the detailed balance condition. Consequently, the autocorrelation time of magnetization is several times smaller than that for the conventional algorithm satisfying the detailed balance condition., Comment: 8 pages, 9 figures

An irreversible Markov-chain Monte Carlo (MCMC) algorithm with skew detailed balance conditions originally proposed by Turitsyn et al. is extended to general discrete systems on the basis of the Metropolis-Hastings scheme. To evaluate the efficiency of our proposed method, the relaxation dynamics of the slowest mode and the asymptotic variance are studied analytically in a random walk on one dimension. It is found that the performance in irreversible MCMC methods violating the detailed balance condition is improved by appropriately choosing parameters in the algorithm., Comment: 14 pages, 6 figures

We investigate the phase structure of two-color QCD at both real and imaginary chemical potentials mu, performing lattice simulations and analyzing the data with the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model. Lattice QCD simulations are done on an 8^3 times 4 lattice with the clover-improved two-flavor Wilson fermion action and the renormalization-group improved Iwasaki gauge action. We test the analytic continuation of physical quantities from imaginary mu to real mu by comparing lattice QCD results calculated at real mu with the result of analytic function the coefficients of which are determined from lattice QCD results at imaginary mu. We also test the validity of the PNJL model by comparing model results with lattice QCD ones. The PNJL model is good in the deconfinement region, but less accurate in the transition and confinement regions. This problem is improved by introducing the baryon degree of freedom to the model. It is also found that the vector-type four-quark interaction is necessary to explain lattice data on the quark number density., Comment: 15 pages, 31 figures

We study an irreversible Markov chain Monte Carlo method based on a skew detailed balance condition for an one-dimensional Ising model. Dynamical behavior of the magnetization density is analyzed in order to understand the properties of this method. As a result, it is found theoretically that the relaxation time of the magnetization density is reduced by using some transition probabilities satisfying the skew detailed balance condition, in comparison to that with the corresponding transition probability with the detailed balance condition, and that one of the transition probabilities changes the dynamical critical exponent even with a local spin update., Comment: 9 pages, 17 figures

We investigate the confinement mechanism in three-flavor QCD with imaginary isospin chemical potentials $(\mu_u,\mu_d,\mu_s)=(i\theta T,-i\theta T,0)$, using the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model, where $T$ is temperature. As for three degenerate flavors, the system has $\mathbb{Z}_{3}$ symmetry at $\theta=2\pi/3$ and hence the Polyakov loop $\Phi$ vanishes there for small $T$. As for 2+1 flavors, the symmetry is not preserved for any $\theta$, but $\Phi$ becomes zero at $\theta=\theta_{\rm conf} < 2\pi/3$ for small $T$. The confinement phase defined by $\Phi=0$ is realized, even if the system does not have $\mathbb{Z}_{3}$ symmetry exactly. In the $\theta$-$T$ plane, there is a critical endpoint of deconfinement transition. The deconfinement crossover at zero chemical potential is a remnant of the first-order deconfinement transition at $\theta=\theta_{\rm conf}$. The relation between the non-diagonal element $\chi_{us}$ of quark number susceptibilities and the deconfinement transition is studied. The present results can be checked by lattice QCD simulations directly, since the simulations are free from the sign problem for any $\theta$., Comment: 21 pages, 22 figures. Typos have been revised. Six references are added

We propose a simple model with the Z_N symmetry in order to answer whether the symmetry is a good concept in QCD with light quark mass. The model is constructed by imposing the flavor-dependent twisted boundary condition (TBC) on the three-flavor Polyakov-loop extended Nambu-Jona-Lasinio model. In the model, the Z_N symmetry is preserved below some temperature T_c, but spontaneously broken above T_c. Dynamics of the simple model is similar to that of the original PNJL model without the TBC, indicating that the Z_N symmetry is a good concept. We also investigate the interplay between the Z_N symmetry and the emergence of the quarkyonic phase., Comment: 7 pages, 7 figures, Presented at The XXXth International Symposium on Lattice Field Theory, Lattice2012

We propose a practical way of circumventing the sign problem in lattice QCD simulations with a theta-vacuum term. This method is the reweighting method for the QCD Lagrangian after the chiral transformation. In the Lagrangian, the P-odd mass term as a cause of the sign problem is minimized. Additionally, we investigate theta-vacuum effects on the QCD phase diagram for the realistic 2+1 flavor system, using the three-flavor Polyakov-extended Nambu-Jona-Lasinio (PNJL) model and the entanglement PNJL model as an extension of the PNJL model. The theta-vacuum effects make the chiral transition sharper. We finally investigate theta dependence of the transition temperature and compare with the result of the pure gauge lattice simulation with imaginary theta parameter., Comment: 7 pages, 5 figures, Presented at The XXXth International Symposium on Lattice Field Theory, Lattice2012

We investigate the interplay between the Z_{Nc} symmetry and the emergence of the quarkyonic phase, adding the flavor-dependent complex chemical potentials \mu_f=\mu+iT\theta_f with (\theta_f)=(0, \theta, -\theta) to the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model. When \theta=0, the PNJL model with the \mu_f agrees with the standard PNJL model with the real chemical potential \mu. When \theta=2\pi/3, meanwhile, the PNJL model with the \mu_f has the Z_{Nc} symmetry exactly for any real \mu, so that the quarkyonic phase exists at small T and large \mu. Once \theta varies from 2\pi/3, the quarkyonic phase exists only on a line of T=0 and \mu larger than the dynamical quark mass, and the region at small T and large \mu is dominated by the quarkyonic-like phase in which the Polyakov loop is small but finite., Comment: 5 pages, 6 figures

We propose a QCD-like theory with the ZNc symmetry. The flavor-dependent twisted boundary condition (TBC) is imposed on Nc degenerate flavor quarksin the SU(Nc) gauge theory. The QCD-like theory is useful to understand the mechanism of color confinement. Dynamics of the QCD-like theory is studied by imposing the TBC on the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model. The TBC model is applied to two- and three-color cases. The ZNc symmetry is preserved below some temperature Tc, but spontaneously broken above Tc. The color confinement below Tc preserves the flavor symmetry. Above Tc, the flavor symmetry is broken, but the breaking is suppressed by the entanglement between the Polyakov loop and the chiral condensate. Particularly at low temperature, dynamics of the TBC model is similar to that of the PNJL model with the standard fermion boundary condition, indicating that the ZNc symmetry is a good approximate concept in the latter model even if the current quark mass is small. The present prediction can be tested in future by lattice QCD, since the QCD-like theory has no sign problem., Comment: 11 pages, 21 figures. Figures 15 and 16 are newly added, while Figs. 6, 10, 14d and 15d in the previous version have been omitted. Some sentences and typos have been revised

We investigate theta-vacuum effects on the QCD phase diagram for the realistic 2+1 flavor system, using the three-flavor Polyakov-extended Nambu-Jona-Lasinio (PNJL) model and the entanglement PNJL model as an extension of the PNJL model. The theta-vacuum effects make the chiral transition sharper. For large theta-vacuum angle the chiral transition becomes first order even if the quark number chemical potential is zero, when the entanglement coupling between the chiral condensate and the Polyakov loop is taken into account. We finally propose a way of circumventing the sign problem on lattice QCD with finite theta., Comment: 9 pages, 14 figures, Published version

The phase structure of two-flavor QCD is investigated at real isospin and imaginary quark chemical potentials by using the Polyakov-loop extended Nambu--Jona-Lasinio model. In the region, parity symmetry is spontaneously broken by the pion superfluidity phase transition, whereas charge-conjugation symmetry is spontaneously violated by the Roberge-Weiss transition. The chiral (deconfinement) crossover at zero isospin and quark chemical potentials is a remnant of the parity (charge-conjugation) violation. The interplay between the parity and charge-conjugation violations are analyzed, and it is investigated how the interplay is related to the correlation between the chiral and deconfinement crossovers at zero isospin and quark chemical potentials., Comment: 12 pages, 18 figures. Typos were revised. Symbols /P and /C were added in Figures 8a and 8b. Colors of the figures were changed. Some sentences were added and revised

We draw the three-flavor phase diagram as a function of light- and strange-quark masses for both zero and imaginary quark-number chemical potential, using the Polyakov-loop extended Nambu-Jona-Lasinio model with an effective four-quark vertex depending on the Polyakov loop. The model prediction is qualitatively consistent with 2+1 flavor lattice QCD prediction at zero chemical potential and with degenerate three-flavor lattice QCD prediction at imaginary chemical potential., Comment: 5 pages, 9 figures, published version

Theta vacuum effects on the QCD phase structure in the \mu-T plane are studied by using the Polyakov-loop extended Nambu-Jona-Lasinio model and its extension, where \mu is the quark chemical potential and T is temperature, respectively. As the parameter \theta of the theta vacuum increases, the chiral transition becomes stronger. For large \theta, it eventually becomes first order even at zero \mu., Comment: 7 pages, 6 figures

The equation of state and the phase diagram in two-flavor QCD are investigated by the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model with an entanglement vertex between the chiral condensate and the Polyakov-loop. The entanglement-PNJL (EPNJL) model reproduces LQCD data at zero and finite chemical potential better than the PNJL model. Hadronic degrees of freedom are taken into account by the free-hadron-gas (FHG) model with the volume-exclusion effect due to the hadron generation. The EPNJL+FHG model improves agreement of the EPNJL model with LQCD data particularly at small temperature. The quarkyonic phase survives, even if the correlation between the chiral condensate and the Polyakov loop is strong and hadron degrees of freedom are taken into account. However, the location of the quarkyonic phase is sensitive to the strength of the volume exclusion., Comment: 9 pages, 7 figures

Charge conjugation (C) and Parity (P) are exact symmetries at theta =pi and Theta = mu/(iT)=pi, where theta is the parameter of the so-called theta-vacuum, mu is the imaginary quark-number chemical potential and T is the temperature. Spontaneous breakings of these discrete symmetries are investigated by the the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model. At zero T, P symmetry is spontaneously broken while C symmetry is conserved. As T increases, P symmetry is restored just after C symmetry is spontaneously broken, so that either P or C symmetry or both the symmetries are spontaneously broken for any T. The chiral-symmetry restoration and the deconfinement transition at theta =Theta =0 are remnants of the P restoration and the C breaking at theta =Theta =pi, respectively., Comment: Twelve pages, 26 figures. Figure 7, 11 and 12 have been added. Figure 13(a) has been revised. Some sentences and references have been added. Typos have been corrected

Lattice QCD has the sign problem at real quark chemical potential. There are some regions with no sign problem; one is the imaginary quark chemical potential region and the others are the real and imaginary isospin chemical potential regions. We show that the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model can reproduce LQCD data in the regions. We also determine the model parameters from the data and predict the QCD phase diagram in the real quark chemical potential region., Comment: Presented at 28th International Symposium on Lattice Field Theory (Lattice 2010), Villasimius, Sardinia, Italy, 14-19 June, 2010

Using the PNJL model, we investigate C and P violations when theta =pi and Theta =mu/(iT)=\pi/3, where T, theta and mu are the temperature, the parameter of theta-vacuum and the quark number chemical potential, respectively. It is shown that the C violation and the P restoration happen almost simultaneously at theta=pi and Theta =pi/3, if the deconfinement and the chiral symmetry restoration happen almost simultaneously at theta =Theta =0., Comment: 3 pages, 4 figures, to be published in the proceedings for the YITP workshop YITP-W-10-08 on "Thermal Quantum Field Theories and Their Applications", Kyoto, August 30-September 1, 2010

We extend the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model by introducing an effective four-quark vertex depending on Polyakov loop. The effective vertex generates entanglement interactions between Polyakov loop and chiral condensate. The new model is consistent with lattice QCD data at imaginary quark-number chemical potential and real and imaginary isospin chemical potentials, particularly on strong correlation between the chiral and deconfinement transitions and also on the quark-mass dependence of the order of the Roberge-Weiss endpoint predicted by lattice QCD very lately. We investigate an influence of the entanglement interactions on a location of the tricritical point at real isospin chemical potential and a location of the critical endpoint at real quark-number chemical potential., Comment: 10 pages, 16 figures, published version

The average phase factor of the QCD determinant is evaluated at finite quark chemical potential ({\mu}_q) with the two-flavor version of the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model with the scalar-type eight-quark interaction. For {\mu}_q larger than half the pion mass at vacuum m_{\pi}, the average phase factor is finite only when the Polyakov loop is larger than 0.5, indicating that lattice QCD is feasible only in the deconfinement phase. A critical endpoint (CEP) lies in the region of the zero average phase factor. The scalar-type eight-quark interaction makes it shorter a relative distance of the CEP to the boundary of the region. For {\mu}_q < m_{\pi}/2, the PNJL model with dynamical mesonic fluctuations can reproduce lattice QCD data below the critical temperature., Comment: 8 pages, 6 figures

The phase structure of two-flavor QCD is explored for thermal systems with finite baryon- and isospin-chemical potentials, mu_B and mu_{iso}, by using the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model. The PNJL model with the scalar-type eight-quark interaction can reproduce lattice QCD data at not only mu_{iso}=mu_B=0 but also mu_{iso}>0 and mu_B=0. In the mu_{iso}-mu_{B}-T space, where T is temperature, the critical endpoint of the chiral phase transition in the mu_B-T plane at mu_{iso}=0 moves to the tricritical point of the pion-superfluidity phase transition in the mu_{iso}-T plane at mu_B=0 as mu_{iso} increases. The thermodynamics at small T is controlled by sqrt{sigma^2+pi^2} defined by the chiral and pion condensates, sigma and pi., Comment: 13 pages, 24 figures, published version, references added

We explore the phase diagram of two-flavor QCD at imaginary values of baryon and isospin chemical potentials analyzing the thermodynamic potential of QCD analytically and that of the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model numerically. QCD has no pion condensation at imaginary baryon and isospin chemical potentials, and therefore has discrete symmetries that are not present at real baryon and isospin chemical potentials. The PNJL model possesses all the discrete symmetries. The PNJL model can reproduce qualitatively lattice QCD data presented very lately., Comment: 11 pages, 20 figures

The Roberge-Weiss (RW) phase transition in the imaginary chemical potential region is analyzed by the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model. In the RW phase transition, the charge-conjugation symmetry is spontaneously broken, while the extended Z3 symmetry (the RW periodicity) is preserved. The RW transition is of second order at the endpoint. At the zero chemical potential, a crossover deconfinement transition appears as a remnant of the second-order RW phase transition at the endpoint, while the charge-conjugation symmetry is always preserved., Comment: 24 pages, 19 figures. Journal version. Some sentences have been revised and added. Fig. 9 has been revised. (New panels have been added.)

We test the reliability of the the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model, comparing the model result with the lattice data at nonzero imaginary chemical potential. The PNJL model with the vector-type four-quark and scalar-type eight-quark interactions reproduces the lattice data on the pseudocritical temperatures of the deconfinement and chiral phase transitions. The QCD phase diagram in the real chemical potential region is predicted by the PNJL model. The critical endpoint survives, even if the vector-type four-quark interaction is taken into account., Comment: 8 pages, 12 figures

The chemical-potential dependence of pi and sigma meson masses is analyzed at both real and imaginary chemical potentials, $\mu_\mathrm{R}$ and $\mu_\mathrm{I}$, by using the Polyakov-loop extended Nambu--Jona-Lasinio (PNJL) model that possesses both the extended ${\mathbb Z}_3$ symmetry and the chiral symmetry. In the $\mu_\mathrm{I}$ region, the meson masses have the Roberge-Weiss periodicity. Assuming that the meson masses will be measured at finite $\mu_\mathrm{I}$ by lattice QCD in future, we simulate how meson masses at finite $\mu_\mathrm{R}$ are extracted from those at finite $\mu_\mathrm{I}$, and propose a reliable extraction method., Comment: 8 pages, 6 figures, typo corrected, some discussions clarified, version accepted for publication in Phys. Rev. D

Effects of the vector-type four-quark interaction on QCD phase structure are investigated in the imaginary chemical potential region, by using the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model with the extended Z3 symmetry. In the course to this end, we clarify analytically the Roberge-Weiss periodicity and symmetry properties of various quantities under the existence of a vector-type four-quark interaction. In the imaginary chemical potential region, the chiral condensate and the quark number density are sensitive to the strength of the interaction. Based on this result, we propose a possibility to determine the strength of the vector-type interaction, which largely affects QCD phase structure in the real chemical potential region, by comparing the results of lattice simulations and effective model calculations in the imaginary chemical potential region., Comment: 8 pages, 11 figures

We show, in general, that when a discontinuity of either zeroth-order or first-order takes place in an order parameter such as the chiral condensate, discontinuities of the same order emerge in other order parameters such as the Polyakov loop. A condition for the coexistence theorem to be valid is clarified. Consequently, only when the condition breaks down, zeroth-order and first-order discontinuities can coexist on a phase boundary. We show with the Polyakov-loop extended Nambu--Jona-Lasinio model that such a type of coexistence is realized in the imaginary chemical potential region of the QCD phase diagram. We also present examples of coexistence of the same-order discontinuities in the real chemical potential region., Comment: 17 pages, 7 figures, version accepted for publication in J. Phys. G

Phase transitions in the imaginary chemical potential region are studied by the Polyakov loop extended Nambu-Jona-Lasinio (PNJL) model that possesses the extended Z3 symmetry. The extended Z3 invariant quantities such as the partition function, the chiral condensate and the modifed Polyakov loop have the Roberge-Weiss (RW) periodicity. There appear four types of phase transitions; deconfinement, chiral, Polykov-loop RW and chiral RW transitions. The orders of the chiral and deconfinement transitions depend on the presence or absence of current quark mass, but those of the Polykov-loop RW and chiral RW transitions do not. The scalar-type eightquark interaction newly added in the model makes the chiral transition line shift to the vicinity of the deconfiment transition line., Comment: 22 pages,17 figures

The Polyakov loop extended Nambu--Jona-Lasinio (PNJL) model with imaginary chemical potential is studied. The model possesses the extended ${\mathbb Z}_{3}$ symmetry that QCD does. Quantities invariant under the extended ${\mathbb Z}_{3}$ symmetry, such as the partition function, the chiral condensate and the modified Polyakov loop, have the Roberge-Weiss (RW) periodicity. The phase diagram of confinement/deconfinement transition derived with the PNJL model is consistent with the RW prediction on it and the results of lattice QCD. The phase diagram of chiral transition is also presented by the PNJL model., Comment: 5 pages, 5 figures