Chimera States mediated by nonlocally attractive-repulsive coupling in FitzHugh–Nagumo neural networks

The spontaneous occurrence of heterogeneous behaviors in homogeneous systems is an intriguing phenomenon. Recently, a remarkable heterogeneous behavior, called “chimera states”, which consists of spatially coherent and incoherent domains, has been studied in a great variety of systems including physical, chemical, biological, or optical. In this paper, chimera states in FitzHugh–Nagumo (FHN) neural networks are investigated. The identical FHN neurons are assigned in a ring and nonlocally coupled by attractive and repulsive couplings. We show that, the chimera states can be induced by the cooperation of nonlocally attractive and repulsive interactions between these neurons. Moreover, depending on the strength and range of attractive or repulsive couplings, the neural networks display different spatiotemporal behaviors, including chimera states, multi-cluster (MC) chimera states, traveling waves, traveling coherent states, solitary states, bursting synchronizations, and synchronizations. These results suggest that attractive and repulsive couplings may play a crucial role in mediating dynamic behavior of neural networks, and these results could be useful in understanding and predicting the rich dynamics of neural networks.     

Networks and emotion-driven user communities at popular blogs

Online communications at web portals represents technology-mediated user interactions, leading to massive data and potentially new techno-social phenomena not seen in real social mixing. Apart from being dynamically driven, the user interactions via posts is indirect, suggesting the importance of the contents of the posted material. We present a systematic way to study Blog data by combined approaches of physics of complex networks and computer science methods of text analysis. We are mapping the Blog data onto a bipartite network where users and posts with comments are two natural partitions. With the machine learning methods we classify the texts of posts and comments for their emotional contents as positive or negative, or otherwise objective (neutral). Using the spectral methods of weighted bipartite graphs, we identify topological communities featuring the users clustered around certain popular posts, and underly the role of emotional contents in the emergence and evolution of these communities.     

Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins

In this paper, AdaBoost algorithm, a popular and effective prediction method, is applied to predict the subcellular locations of Prokaryotic and Eukaryotic Proteins-a dataset derived from SWISSPROT 33.0. Its prediction ability was evaluated by re-substitution test, Leave-One-Out Cross validation (LOOCV) and jackknife test. By comparing its results with some most popular predictors such as Discriminant Function, neural networks, and SVM, we demonstrated that the AdaBoost predictor outperformed these predictors. As a result, we arrive at the conclusion that AdaBoost algorithm could be employed as a robust method to predict subcellular location. An online web server for predicting subcellular location of prokaryotic and eukaryotic proteins is available at http://chemdata.shu.edu.cn/subcell/ .     

Phase structure of a 3D nonlocal U(1) gauge theory: deconfinement by gapless matter fields

In this paper, we study a 3D compact U(1) lattice gauge theory with a variety of nonlocal interactions that simulates the effects of gapless/gapful matter fields. We restrict the nonlocal interactions among gauge variables only to those along the temporal direction and adjust their coupling constants optimally to simulate the isotropic nonlocal couplings of the original model. This theory is quite important to investigate the phase structures of QED₃ and strongly-correlated electron systems like the 2D quantum spin models, the fractional quantum Hall effect, the $t\text{–}J$ model of high-temperature superconductivity. We perform numerical studies of this theory to find that, for a certain class of power-decaying couplings, there appears a second-order phase transition to the deconfinement phase as the gauge coupling constant is decreased. On the other hand, for the exponentially-decaying coupling, there are no signals for second-order phase transition. These results indicate the possibility that introduction of sufficient number of massless matter fields destabilizes the permanent confinement in the 3D compact U(1) pure gauge theory due to instantons.     

On higher derivative corrections of tachyon action

We have examined the momentum expansion of the disk level S-matrix element of two tachyons and two gauge fields to find, up to on-shell ambiguity, the couplings of these fields in the world volume theory of N coincident non-BPS D-branes to all order of α^′. Using the proposal that the action of D-brane–anti-D-brane is given by the projection of the action of two non-BPS D-branes with (−1)^F_L, we find the corresponding couplings in the world volume theory of the brane–anti-brane system. Using these infinite tower of couplings, we then calculate the massless pole of the scattering amplitude of one RR field, two tachyons and one gauge field in the brane–anti-brane theory. We find that the massless pole of the field theory amplitude is exactly equal to the massless pole of the disk level S-matrix element of one RR, two tachyons and one gauge field to all order of α^′. We have also found the couplings of four tachyons to all order of α^′ by examining the S-matrix element of four tachyons.     

Superheavy fermions and horizontal symmetries

The mechanism which was formerly used to obtain neutrino masses is generalized to all light fermions. Correspondingly, several sets of superheavy fermions are introduced. Assignments under a horizontal symmetry group are arranged such that the heaviest among the light fermions acquire their masses, not from the ordinary Higgs-Yukawa couplings, but from couplings to the heavy fermions. Masses of the other light fermions are then obtained through horizontal gauge interactions. Accordingly, the resulting light fermion masses exhibit a hierarchical generation structure. Because of the construction, light Higgs fields do not induce dangerous flavor-changing neutral-current interactions.     

Synchronization of coupled chaotic dynamics on networks

We review some recent work on the synchronization of coupled dynamical systems on a variety of networks. When nodes show synchronized behaviour, two interesting phenomena can be observed. First, there are some nodes of the floating type that show intermittent behaviour between getting attached to some clusters and evolving independently. Secondly, two different ways of cluster formation can be identified, namely self-organized clusters which have mostly intra-cluster couplings and driven clusters which have mostly inter-cluster couplings.     

Exact solution of an integrable quantum spin chain with competing interactions

We construct an integrable quantum spin chain that includes the nearest-neighbor, next-nearest-neighbor, chiral three-spin couplings, Dzyloshinsky-Moriya interactions and unparallel boundary magnetic fields. Although the interactions in bulk materials are isotropic, the spins nearby the boundary fields are polarized, which induce the anisotropic exchanging interactions of the first and last bonds. The U(1) symmetry of the system is broken because of the off-diagonal boundary reflections. Using the off-diagonal Bethe ansatz, we obtain an exact solution to the system. The inhomogeneous T-Q relation and Bethe ansatz equations are given explicitly. We also calculate the ground state energy. The method given in this paper provides a general way to construct new integrable models with certain interesting interactions.     

Vectorial versus axial Goldstone bosons

The Yukawa interactions of fermions with Goldstone bosons are given in closed form for an arbitrary renormalizable field theory to all orders of perturbation theory or for a general effective Lagrangian. Although the diagonal couplings are always pseudoscalar there is an important difference between spontaneously broken vector and axial-vector global symmetries. Compared to the axial case, the diagonal couplings of “vectorial” Goldstone bosons to charged fermions are suppressed by mixing angles or appear only via radiative corrections involving gauge fields. This general result may be relevant for the problem of flavour symmetry breaking in composite models.     

Controlling electronic spin relaxation of cold molecules with electric fields

We present a theoretical study of atom-molecule collisions in superimposed electric and magnetic fields and show that dynamics of electronic spin relaxation in molecules at temperatures below 0.5 K can be manipulated by varying the strength and the relative orientation of the applied fields. The mechanism of electric field control of Zeeman transitions is based on an intricate interplay between intramolecular spin-rotation couplings and molecule-field interactions. We suggest that electric fields may affect chemical reactions through inducing nonadiabatic spin transitions and facilitate evaporative cooling of molecules in a magnetic trap.     

Using the nonlinear dimensionality reduction method for the prediction of subcellular localization of Gram-negative bacterial proteins

One of the central problems in computational biology is protein function identification in an automated fashion. A key step to achieve this is predicting to which subcellular location the protein belongs, since protein localization correlates closely with its function. A wide variety of methods for protein subcellular localization prediction have been proposed over recent years. Linear dimensionality reduction (DR) methods have been introduced to address the high-dimensionality problem by transforming the representation of protein sequences. However, this approach is not suitable for some complex biological systems that have nonlinear characteristics. Herein, we use nonlinear DR methods such as the kernel DR method to capture the nonlinear characteristics of a high-dimensional space. Then, the K-nearest-neighbor (K-NN) classifier is employed to identify the subcellular localization of Gram-negative bacterial proteins based on their reduced low-dimensional features. Experimental results thus obtained are quite encouraging, indicating that the applied nonlinear DR method is effective to deal with this complicated problem of predicting subcellular localization of Gram-negative bacterial proteins. An online web server for predicting subcellular location of Gram-negative bacterial proteins is available at .     

细菌反应调节蛋白RR468磷酸化和去磷酸化关键位点的NMR研究

反应调节蛋白是细菌双组分信号转导系统的重要组分,用于传递来自组氨酸激酶的信号并产生适应性反应.在整个信号转导过程中,反应调节蛋白的磷酸化和去磷酸化最终决定了该系统的信号输出和信号转导终止,因此其磷酸化和去磷酸化作用位点是控制其功能的关键要素．我们以来源于Thermotoga maritima中的反应调节蛋白RR468作为研究对象,将其分别位于loop b3-a3和loop b4-a4上的两个关键位点M55和K85进行突变,通过功能实验验证了这两个残基突变会对蛋白磷酸化和去磷酸化产生影响,并且利用液体核磁共振（NMR）手段对两个突变体的结构和动力学性质进行了研究．     

Renormalized soft-higgs theorems

The Higgs couplings to matter fields are proportional to their masses. Thus Higgs amplitudes can be obtained by differentiating amplitudes without Higgs with respect to masses. We show how this well-known statement can be extended to higher order when renormalization effects are taken into account. We establish the connection with the Callan-Symanzik and renormalization group equations and consider also pseudoscalar Higgs couplings to fermions. Furthermore, we address the case where the Higgs couples to a heavy particle that is integrated out from the low-energy effective Lagrangian. We derive effective interactions where mass logarithms are resummed by renormalization-group methods, and give expansions of the results up to next-to-leading order.     

Quantum computation with untunable couplings

Most quantum computer realizations require the ability to apply local fields and tune the couplings between qubits, in order to realize single bit and two bit gates which are necessary for universal quantum computation. We present a scheme to remove the necessity of switching the couplings between qubits for two bit gates, which are more costly in many cases. Our strategy is to compute with encoded qubits in and out of carefully designed interaction free subspaces analogous to decoherence free subspaces. We give two examples to show how universal quantum computation is realized in our scheme with local manipulations to physical qubits only, for both diagonal and off diagonal interactions.     

Heteronuclear dipolar recoupling in liquid crystals and solids by PISEMA-type pulse sequences

A pulse sequence is described for the recoupling of heteronuclear dipolar interactions under MAS. The method is similar to the PISEMA experiment, but employs a well-defined amplitude modulation of one of the two radio-frequency fields. The technique is used for measurements of 1H-13C dipolar couplings in unoriented solid and liquid-crystalline samples.     

Synchronization in complex networks by time-varying couplings

Synchronization in networks of complex topologies using couplings of time-varying strength is numerically investigated. The time-dependencies of coupling strengths are coupled to the dynamics of the nodes in a way to enhance synchronization. By time-varying couplings, oscillators are found to take quite a short time to reach synchronization state when the couplings are relatively strong. Even when a nearly regular networks of large-size with few shortcuts is difficult to be synchronized by fixed couplings, the time-varying couplings can easily enhance the emergence of synchronization.     

Phase synchronization of bursting neural networks with electrical and delayed dynamic chemical couplings

Diffusive electrical connections in neuronal networks are instantaneous, while excitatoryor inhibitory couplings through chemical synapses contain a transmission time-delay.Moreover, chemical synapses are nonlinear dynamical systems whose behavior can bedescribed by nonlinear differential equations. In this work, neuronal networks withdiffusive electrical couplings and time-delayed dynamic chemical couplings are considered.We investigate the effects of distributed time delays on phase synchronization of burstingneurons. We observe that in both excitatory and Inhibitory chemical connections, the phasesynchronization might be enhanced when time-delay is taken into account. This distributedtime delay can induce a variety of phase-coherent dynamical behaviors. We also study thecollective dynamics of network of bursting neurons. The network model presents theso-called Small-World property, encompassing neurons whose dynamics have two time scales(fast and slow time scales). The neuron parameters in such Small-World network, aresupposed to be slightly different such that, there may be synchronization of the bursting(slow) activity if the coupling strengths are large enough. Bounds for the criticalcoupling strengths to obtain burst synchronization in terms of the network structure aregiven. Our studies show that the network synchronizability is improved, as itsheterogeneity is reduced. The roles of synaptic parameters, more precisely those of thecoupling strengths and the network size are also investigated.     

Programmable quantum processor implemented with superconducting circuit

A quantum processor might execute certain computational tasks exponentially faster than a classical processor. Here, using superconducting quantum circuits we design a powerful universal quantum processor with the structure of symmetric all-to-all capacitive connection. We present the Hamiltonian and use it to demonstrate a full set of qubit operations needed in the programmable universal quantum computations. With the device the unwanted crosstalk and ZZ-type couplings between qubits can be effectively suppressed by tuning gate voltages, and the design allows efficient and high-quality couplings of qubits. Within available technology,the scheme may enable a practical programmable universal quantum computer.     

Atomic refinement with correlated solid-state NMR restraints

The orientation data provided by solid-state NMR can provide a great deal of structural information about membrane proteins. The quality of the information provided is, however, somewhat degraded by sign degeneracies in measurements of the dipolar coupling tensor. This is reflected in the dipolar coupling penalty function used in atomic refinement, which is less capable of properly restraining atoms when dipolar sign degeneracies are present. In this report we generate simulated solid-state NMR data using a variety of procedures, including back-calculation from crystal structures of alpha-helical and beta-sheet membrane proteins. We demonstrate that a large fraction of the dipolar sign degeneracies are resolved if anisotropic dipolar coupling measurements are correlated with anisotropic chemical shift measurements, and that all sign degeneracies can be resolved if three data types are correlated. The advantages of correlating data are demonstrated with atomic refinement of two test membrane proteins. When refinement is performed using correlated dipolar couplings and chemical shifts, perturbed structures converge to conformations with a larger fraction of correct dipolar signs than when data are uncorrelated. In addition, the final structures are closer to the original unperturbed structures when correlated data are used in the refinement. Thus, refinement with correlated data leads to improved atomic structures. The software used to correlate dipolar coupling and chemical shift data and to set up energy functions and their derivatives for refinement, CNS-SS02, is available at our web site.     

Wave Equations for Classical Two-Component Proca Fields in Curved Spacetimes with Torsionless Affinities

The world formulation of the full theory of classical Proca fields in generally relativistic spacetimes is reviewed. Subsequently, the entire set of field equations is transcribed in a straightforward way into the framework of one of the Infeld-van der Waerden formalisms. Some well-known calculational techniques are then utilized for deriving the wave equations that control the propagation of the fields allowed for. It appears that no interaction couplings between such fields and electromagnetic curvatures are ultimately carried by the wave equations at issue. What results is, in effect, that the only interactions which occur in the theoretical context under consideration involve strictly Proca fields and wave functions for gravitons.