‘Phase transitions’ in bacteria – From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms

Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.     

Plasticity-induced characteristic changes of pattern dynamics and the related phase transitions in small-world neuronal networks

Phase transitions widely exist in nature and occur when some control parameters are changed. In neural systems, their macroscopic states are represented by the activity states of neuron populations, and phase transitions between different activity states are closely related to corresponding functions in the brain. In particular, phase transitions to some rhythmic synchronous firing states play significant roles on diverse brain functions and disfunctions, such as encoding rhythmical external stimuli, epileptic seizure, etc. However, in previous studies, phase transitions in neuronal networks are almost driven by network parameters （e.g., external stimuli）, and there has been no investigation about the transitions between typical activity states of neuronal networks in a self-organized way by applying plastic connection weights. In this paper, we discuss phase transitions in electrically coupled and lattice-based small-world neuronal networks （LBSW networks） under spike-timing-dependent plasticity （STDP）. By applying STDP on all electrical synapses, various known and novel phase transitions could emerge in LBSW networks, particularly, the phenomenon of self-organized phase transitions （SOPTs）： repeated transitions between synchronous and asynchronous firing states. We further explore the mechanics generating SOPTs on the basis of synaptic weight dynamics.     

Contactless electroreflectance spectroscopy of optical transitions in low dimensional semiconductor structures

The authors present the application of contactless electroreflectance (CER) spectroscopy to study optical transitions in low dimensional semiconductor structures including quantum wells (QWs), step-like QWs, quantum dots (QDs), quantum dashes (QDashes), QDs and QDashes embedded in a QW, and QDashes coupled with a QW. For QWs optical transitions between the ground and excited states as well as optical transitions in QW barriers and step-like barriers have been clearly observed in CER spectra. Energies of these transitions have been compared with theoretical calculations and in this way the band structure has been determined for the investigated QWs. For QD and QDash structures optical transitions in QDs and QDashes as well as optical transitions in the wetting layer have been identified. For QDs and QDashes surrounded by a QW, in addition to energies of QD and QDash transitions, energies of optical transitions in the surrounded QW have been measured and the band structure has been determined for the surrounded QW. Finally some differences, which can be observed in CER and photo-reflectance spectra, have been presented and discussed for selected QW and QD structures.     

Discrimination of rising and falling simulated single-formant frequency transitions: practice and transition duration effects

Two experiments evaluated discrimination of simulated single-format frequency transitions. In the first experiment, listeners received practice with trial-by-trial feedback in discriminating either rising or falling frequency transitions of three different durations (30, 60, and 120 ms). Transitions either occurred in isolation or were followed by a steady-state sound matched in frequency to the transition end point. Some improvement in discrimination over practice runs occurred for the shortest transitions. Whether performance was evaluated at the beginning or end of practice, there were no differences attributable to transition direction or to whether transitions were followed by steady-state sound. Discrimination, however, was significantly better for the longest transitions. Just noticeable differences (jnd's) for the longest transitions, measured in Hz at transition onsets, were of approximately the same magnitude as jnd's for steady-state sounds that were equal in frequency to the midpoints of the transitions. Subjects of the second experiment discriminated the longer rising and falling transitions, but did not receive extensive practice. Results of experiment 2 replicated results of experiment 1 in showing similar jnd's. Experiment 2 also showed no differences attributable to transition direction or to the presence of the steady-state sound following transitions.     

A framework for the study of vocal registers

Register transitions are divided into two classes, periodicity transitions and timbre transitions. Periodicity transitions refer to changes in vocal quality that occur whenever glottal pulses are perceived as individual events rather than as a continuous auditory stimulus. Timbre transitions refer to changes in vocal quality associated with changes in spectral balance. Physiologically, these can be quantified with an abduction quotient. The singing registers appear to be based on timbre transitions resulting from subglottal resonances that interfere with the vocal fold driving pressure. Four of the major singing register shifts are predicted (in frequency and relative importance) on the basis of the first subglottal formant. Strategies for register equalization are proposed on the basis of supraglottal formant tuning (vowel modification) and adjustments in glottal adduction.     

Complex transitions between spike,burst or chaos synchronization states in coupled neurons with coexisting bursting patterns

We investigated the synchronization dynamics of a coupled neuronal system composed of two identical Chay model neurons. The Chay model showed coexisting period-1 and period-2 bursting patterns as a parameter and initial values are varied. We simulated multiple periodic and chaotic bursting patterns with non-(NS), burst phase(BS), spike phase(SS),complete(CS), and lag synchronization states. When the coexisting behavior is near period-2 bursting, the transitions of synchronization states of the coupled system follows very complex transitions that begins with transitions between BS and SS, moves to transitions between CS and SS, and to CS. Most initial values lead to the CS state of period-2 bursting while only a few lead to the CS state of period-1 bursting. When the coexisting behavior is near period-1 bursting, the transitions begin with NS, move to transitions between SS and BS, to transitions between SS and CS, and then to CS. Most initial values lead to the CS state of period-1 bursting but a few lead to the CS state of period-2 bursting. The BS was identified as chaos synchronization. The patterns for NS and transitions between BS and SS are insensitive to initial values. The patterns for transitions between CS and SS and the CS state are sensitive to them. The number of spikes per burst of non-CS bursting increases with increasing coupling strength. These results not only reveal the initial value- and parameterdependent synchronization transitions of coupled systems with coexisting behaviors, but also facilitate interpretation of various bursting patterns and synchronization transitions generated in the nervous system with weak coupling strength.     

Excitation of phase transitions in dipole lattices

Phase transitions in hexagonal lattices with three and four rows of dipoles arising as a result of the reorientation of different sets of dipoles by the external field have been studied. The conditions of the implementation of two types of symmetric phase transitions and the asymmetric transitions, when the configurations of the system to the left and to the right of the excitation region are different, have been established. Merging of two regions of the phase transitions has been considered. Unidirectional phase transitions, in which either the left or the right phase transition front propagates from the excitation region along the lattice, have been obtained in a lattice with four rows of dipoles. The variations of the total dipole moment of the system and the energy of the dipole-dipole interaction during the phase transitions have been given.     

Unseen Coherences Can Be Felt

Forbidden transitions are not observed in the continuous-wave electron paramagnetic resonance (EPR) spectrum nor in the free induction decay because, unlike allowed transitions, their coherences have no observable magnetic moment and are spectroscopically silent. Yet, the paramagnetic relaxation described by Redfield theory can cause coherence transfer between any types of transitions. Coherence transfer between allowed transitions is now known to cause noticeable changes in EPR spectra, but coherence transfer involving forbidden transitions has long been considered to be negligible because those coherences are silent and unseen. However, our simulations of a simple model system indicate that coherence transfer with silent transitions can introduce new features into EPR spectra. The EPR-silent coherence of a forbidden transition can be transferred to an allowed transition by paramagnetic relaxation. A silent coherence can have consequences felt in the EPR spectrum.     

Transitions in superionic crystals

A theory of phase transitions in solid electrolytes is developed. Using mean field approximation the expression for the free energy and the equation of state are analysed and shown to be determined by two dimensionless parameters which depend on the properties of the crystal. The parameter plane has eight characteristic regions. In two regions phase transitions are absent. Single transitions occur in four regions. The specificity of unsymmetrical systems is revealed in the remaining two regions in both of which two phase transitions take place. Expressions for the temperatures of the corresponding transitions are presented. It is shown that with the increase of temperature the degree of cation disorder may either decrease or increase. In symmetrical systems double transitions are absent. Comparison of the theory with experimental data is presented.     

Comments on the use of the Landau theory in some order-order transitions

The application of the Landau theory of phase transitions to a two-sublattice magnet results in a broad range of magnetic transitions. The use of a two-component order parameter enables one to describe both order-disorder and order-order transitions. In particular, the metamagnetic transitions exhibit the thermal hysteresis. It is shown that the Kittel model is a special case of the Landau expansion. Finally, an alternative one-component order parameter expansion is discussed.     

Quantum phase transitions in electronic systems

Quantum phase transitions occur at zero temperature when some non‐thermal control‐parameter like pressure or chemical composition is changed. They are driven by quantum rather than thermal fluctuations. In this review we first give a pedagogical introduction to quantum phase transitions and quantum critical behavior emphasizing similarities with and differences to classical thermal phase transitions. We then illustrate the general concepts by discussing a few examples of quantum phase transitions occurring in electronic systems. The ferromagnetic transition of itinerant electrons shows a very rich behavior since the magnetization couples to additional electronic soft modes which generates an effective long‐range interaction between the spin fluctuations. We then consider the influence of rare regions on quantum phase transitions in systems with quenched disorder, taking the antiferromagnetic transitions of itinerant electrons as a primary example. Finally we discuss some aspects of the metal‐insulator transition in the presence of quenched disorder and interactions.     

Weak first-order superfluid-solid quantum phase transitions

We study superfluid-solid zero-temperature transitions in two-dimensional lattice boson-spin models using worm-algorithm Monte Carlo simulations. We observe that such transitions are typically first order with the exception of special high-symmetry points which require fine-tuning in the Hamiltonian parameter space. We present evidence that the superfluid-checkerboard solid and superfluid-valence-bond solid transitions at half-integer filling factor are extremely weak first-order transitions and in small systems can be confused with continuous or high-symmetry points.     

Phase Transition Induced by Small Molecules in Confined Copolymer Films

We investigate the phase transition induced by small molecules in confined copolymer films by using density functional theory. It is found that the addition of small molecules can effectively promote the phase separation of copolymers. In a symmetric diblock copolymer film, the affinity and concentration of small molecules play an important role in the structure transitions. The disordered-lamellar transitions, larnellar-lamellar transitions and the re-entrant transitions of the same structures are observed. Our results have potential applications in the fabrication of new functional materials.     

ELECTRONIC TRANSITIONS OF DI-HYDROXY NAPHTHALENE MOLECULES

The electronic transitions of di-hydroxy naphthalene molecules are found to be shifted towards higher wavelength side, when hydroxyl groups are substituted in the naphthalene molecule. The changes in the position and intensity of the electronic bands depend upon the charge transfer property of the substituent. The present paper correlates the electronic transitions observed in the photoacoustic spectra of naphthalene, 1,3-dihydroxy naphthalene (DHN), 1,4-DHN and 1,5-DHN in the region 250–400 nm. The electronic transitions of these molecules have been interpreted using the optimised geometries and CNDO/S-CI methods. Assignments of the observed electronic transitions are made on the basis of radiative and non-radiative transitions. A good agreement is found between the experimental and calculated results.     

Effect of a magnetic field on the phonon-assisted two-photon absorption in semiconductors

The theory of the phonon-assisted two-photon transitions in a magnetic field is developed by means of perturbation theory. Three different band models have been introduced. The electronic transitions are defined by (i) interband-interband indirect transitions in the four-band model, (ii) interband-intraband indirect transitions in the three-band model, and (iii) intraband-intraband indirect transitions in the two-band model. These models differ from each other by the number of bands, the type of the photon matrix elements and the Landau selection rules. The result shows that by increasing the value of the magnetic field, the absorption co-efficient adopting the two-band model is strongly increased, but for a fixed value of the field the four-band model gives the largest contribution.     

Spin-allowed and forbidden rotational intensities in doublet-doublet transitions in asymmetric top molecules

Spin-orbit coupling allows anomalous transitions in spectra involving states of the same degenerate multiplicity, due to the relaxation of the spin selection rule ΔΣ = 0. This effect is discussed for doublet-doublet transitions in asymmetric top molecules. All the nonvanishing and independent transition moments, including those responsible for the anomalous transitions, are determined by symmetry and time reversal arguments. Rotational intensities are given for transitions between case (b) near-symmetric top eigenstates.     

相变的激光光散射研究进展

本文简述地评述了相变的激光非弹性光散射研究取得的进展。其内容包括光散学研究相变的历史,铁电相变、非公度相变以及高温钇钡铜氧超导体结构相变等晶格动力学方面。     

Selectivity control of Stark-ladder transitions in asymmetric double-well GaAs/AlAs superlattices by barrier sequence modulation

We have investigated field-induced features of optical transitions in asymmetric double-well superlattices (ADW-SLs) with and without barrier sequence modulation by low-temperature photocurrent (PC) spectroscopy. The difference between the heavy-hole confinement energies in the wide and narrow wells results in two types of Stark-ladder transitions, so that four ±1st-order spatially indirect transitions are expected to exist in the ADW-SL. The oscillator strength of these indirect transitions is affected by the strength and the direction of coupling between the wide and narrow wells. The introduction of the barrier sequence modulation into the ADW-SL realizes the control of these coupling mechanisms. This technique is a new method to modulate the oscillator strength of the indirect Stark-ladder transitions.     

Electron states in metal clusters

Radiative transitions in metal clusters are analyzed in terms of quantum transitions of valence electrons that interact with surrounding valence electrons and ion cores. The analysis is based on the solution of the Thomas-Fermi equation for valence electrons in a spherical cluster. The quantum states of valence electrons and the energy and the dipole moments of transitions are determined in the quasiclassical approximation. It is shown that the frequencies of dipole oscillations and the dipole moments of the transitions strongly depend on the size of a cluster.     

Transitions in spatial networks

Networks embedded in space can display all sorts of transitions when their structure is modified. The nature of these transitions (and in some cases crossovers) can differ from the usual appearance of a giant component as observed for the Erdös–Rényi graph, and spatial networks display a large variety of behaviors. We will discuss here some (mostly recent) results about topological transitions, ‘localization’ transitions seen in the shortest paths pattern, and also about the effect of congestion and fluctuations on the structure of optimal networks. The importance of spatial networks in real-world applications makes these transitions very relevant, and this review is meant as a step towards a deeper understanding of the effect of space on network structures.