Unidirectional Transitions Research Articles

Nonlinear mechanisms of two-dimensional wave-wave transformations in the initially coupled acoustic structure

The present study concerns two-dimensional nonlinear mechanisms of bidirectional and unidirectional channeling of longitudinal and shear waves emerging in the locally resonant acoustic structure. The system under consideration comprises an oscillatory chain of the axially coupled masses. Each mass of the chain is subject to the local linear potential along the lateral direction and incorporates the lightweight internal rotator. In the present work, we demonstrate the emergence of special resonant regimes of complete bi- and unidirectional transitions between the longitudinal and the shear waves of the locally resonant chain. These regimes are manifested by the two-dimensional energy channeling between the longitudinal and the shear traveling waves in the recurrent as well as the irreversible fashion. We show that the spatial control of the two dimensional energy flow between the longitudinal and the shear waves is solely governed by the motion of the internal rotators. Nonlinear analysis of the regimes of a bidirectional wave channeling unveils their global bifurcation structure and predicts the zones of their spontaneous transitions from a complete bi-directional wave channeling to the one-directional entrapment. An additional regime of a complete irreversible resonant transformation of the longitudinal wave into a shear wave is analyzed in the study. The intrinsic mechanism governing the unidirectional wave reorientation is described analytically. The results of the analysis of both mechanisms are substantiated by the numerical simulations of the full model and are found to be in a good agreement.

Cell Cycle Control: A System of Interlinking Oscillators.

The cell cycle is the sequence of events through which a cell duplicates its genome, grows, and divides. Key cell cycle transitions are driven by oscillators comprising cyclin-dependent kinases and other kinases. Different cell cycle oscillators are inextricably linked to ensure orderly activation of oscillators. A recurring theme in their regulation is the abundance of auto-amplifying loops that ensure switch-like and unidirectional cell cycle transitions. The periodicity of many cell cycle oscillators is choreographed by inherent mechanisms that promote automatic inactivation, often involving dephosphorylation and ubiquitin-mediated protein degradation. These inhibitory signals are subsequently suppressed to enable the next cell cycle to occur. Although the activation and inactivation of cell cycle oscillators are in essence autonomous during the unperturbed cell cycle, a number of checkpoint mechanisms are able to halt the cell cycle until defects are addressed. Together, these mechanisms orchestrate orderly progression of the cell cycle to produce more cells and to safeguard genome integrity.

One-way optical modal transition based on causality in momentum space.

The concept of parity-time (PT) symmetry has been used to identify a route toward unidirectional dynamics in optical k-space: imposing asymmetry on the flow of light. Although PT-symmetric potentials have been implemented under the requirement of V(x) = V*(-x), this precondition has only been interpreted within the mathematical framework for the symmetry of Hamiltonians and has not been directly linked to unidirectionality induced by PT symmetry. In this paper, within the context of light-matter interactions, we develop an alternative route toward unidirectionality in k-space by employing the concept of causality. We demonstrate that potentials with real and causal momentum spectra produce unidirectional transitions of optical modes inside the k-continuum, which corresponds to an exceptional point on the degree of PT symmetry. Our analysis reveals a critical link between non-Hermitian problems and spectral theory and also enables multi-dimensional designer manipulation of optical modes, in contrast to the one-dimensional approach that used a Schrödinger-like equation in previous PT-symmetric optics.

Arrays of stochastic oscillators: Nonlocal coupling, clustering, and wave formation.

We consider an array of units each of which can be in one of three states. Unidirectional transitions between these states are governed by Markovian rate processes. The interactions between units occur through a dependence of the transition rates of a unit on the states of the units with which it interacts. This coupling is nonlocal, that is, it is neither an all-to-all interaction (referred to as global coupling), nor is it a nearest neighbor interaction (referred to as local coupling). The coupling is chosen so as to disfavor the crowding of interacting units in the same state. As a result, there is no global synchronization. Instead, the resultant spatiotemporal configuration is one of clusters that move at a constant speed and that can be interpreted as traveling waves. We develop a mean field theory to describe the cluster formation and analyze this model analytically. The predictions of the model are compared favorably with the results obtained by direct numerical simulations.

An integral fluctuation theorem for systems with unidirectional transitions

The fluctuations of a Markovian jump process with one or more unidirectional transitions, where Rij > 0 but Rji = 0, are studied. We find that such systems satisfy an integral fluctuation theorem. The fluctuating quantity satisfying the theorem is a sum of the entropy produced in the bidirectional transitions and a dynamical contribution, which depends on the residence times in the states connected by the unidirectional transitions. The convergence of the integral fluctuation theorem is studied numerically and found to show the same qualitative features as systems exhibiting microreversibility.

A redescription of data does not count as a general theory.

Piazza and Deroche-Gamonet (PDG) seek to formulate aframeworkforaddictionsufficientlybroadtoencompassmostdatainthefieldand,notably,thoseproducedbytheBordeauxSchool of Psychobiology to which I also belong. Briefly,according to the PDG framework, the development of addic-tion would involve two unidirectional transitions across threeconsecutive stages of drug use: a first transition from recrea-tional drug use to escalated drug use and a second transitionfrom escalated drug use to compulsive drug use. Importantly,the likelihood that a given individual drug user will make atransition would depend on two types of psychobiologicalvulnerability that are transition-specific and differently mal-leable to drug availability. Specifically, the vulnerability totransition from recreational to escalated drug use would bedifferent fromand more drug-malleablethanthe vulnerabilityto transition from escalated to compulsive drug use.Overall, this is an interesting proposal. However, I wouldnotcallitageneraltheory,butaredescriptionofexistingdata.First, PDG framework does not advance any overarchingtheoretical construct and relies on a shaky theoretical founda-tion. The authors claim to have derived it from a carefulconsideration of both DSM-based and RDoC-like behavioralsymptoms, but how is this derivation made? What are thetheoretical principles and rules involved? How can one de-duce a dynamical multistage framework for the transition toaddiction from a heterogeneous set of static, operational, anddescriptive behavioral criteria? Clearly, something is missinghere. Without further explanation, PDG framework appearsmore as an ad hoc and arbitrary redescription of existing datathan a general theory of addiction. It indeed abounds inunjustified claims. For instance, what does forbid the exis-tence of a direct transition from recreational to compulsivedrug use without transitioning to the stage of escalated druguse? What does prevent a transition to be bidirectional andreversible instead of being unidirectional? Whatdoes excludea stage of abstinence and associated specific transitions andvulnerabilities? Abstinence necessarily precedes recreationaldruguseandshouldeventuallyfollowanyotherstageofdruguse at least in the majority of illegal drug users (Heyman2013). Second, the explanatory power of this framework iscurrently uncertain. At a minimum, one expects from a novelframework to be as good as or preferably better than thepreviousonesinorganizing,encompassing,and/orexplainingexisting data. Whether PDG framework meets this minimumrequirement is currently unknown, however, mainly becausethe authors donot makethe effortto compare their work withthat of others (e.g., Kendler et al. 2012;Redishetal.2008).Third, the heuristic value of PDG framework is low as mea-sured by its inability to generate truly novel and uniquepredictionsand/ortohelpseeandunderstandthingsdifferent-ly. I was at pain to formulate or even identify truly novelpredictions from PDG framework. The heuristic impotenceofPDGframeworkisnotsurprisinganddirectlyfollowsfromits ad hoc descriptive nature.A mere redescription of data is not necessarily a fatal flawand can even sometimes prove to be instrumental in theformulation of a general theory, as illustrated, for instance, bytheearlyhistoryofgeneticsorquantummechanics.However,inthe case of PDG framework, the data themselves are still openfor debate and reinterpretation. First, PDG interprets the clas-sic LR-HR rat model as a model of the transition from recre-ational to escalated drug use. This is inaccurate. It is true thatthe LR-HR model was highly influential in the 1990s andspawned a productive line of research on individual factors

Phase transitions in lattices of magnetic dipoles

Hexagonal magnetic-dipole lattices containing three to six rows are investigated. Conditions of the excitation of phase transitions that change the orientation configuration of the system are revealed on the basis of a numerical analysis. The changes in the magnetic moment of the system and in the energy of dipole-dipole interaction upon the emergence of phase transitions are found. Both symmetric phase transitions propagating identically on the two sides of the lattice away from the excitation region and asymmetric phase transitions such in which the configurations of the system to the left and to the right of the excitation region are different are considered. Conditions under which there occur unidirectional phase transitions in which either the left-or the right-hand front of the phase transition propagates along the lattice are found.

Noise-Induced Transitions in a Population Growth Model Based on Size-Dependent Carrying Capacity

The stochastic dynamics of a population growth model with size-dependent carrying capacity is considered. The effect of a fluctuating environment on population growth is modeled as a multiplicative dichotomous noise. At intermediate values of population size the deterministic counterpart of the model behaves similarly to the Von Foerster model for human population, but at small and very large values of population size substantial differences occur. In the stochastic case, an exact analytical solution for the stationary probability distribution is found. It is established that variation of noise correlation time can cause noise-induced transitions between three different states of the system characterized by qualitatively different behaviors of the probability distributions of the population size. Also, it is shown that, in some regions of the system parameters, variation of the amplitude of environmental fluctuations can induce single unidirectional abrupt transitions of the mean population size.

Protein electron transfer: Dynamics and statistics

Electron transfer between redox proteins participating in energy chains of biology is required to proceed with high energetic efficiency, minimizing losses of redox energy to heat. Within the standard models of electron transfer, this requirement, combined with the need for unidirectional (preferably activationless) transitions, is translated into the need to minimize the reorganization energy of electron transfer. This design program is, however, unrealistic for proteins whose active sites are typically positioned close to the polar and flexible protein-water interface to allow inter-protein electron tunneling. The high flexibility of the interfacial region makes both the hydration water and the surface protein layer act as highly polar solvents. The reorganization energy, as measured by fluctuations, is not minimized, but rather maximized in this region. Natural systems in fact utilize the broad breadth of interfacial electrostatic fluctuations, but in the ways not anticipated by the standard models based on equilibrium thermodynamics. The combination of the broad spectrum of static fluctuations with their dispersive dynamics offers the mechanism of dynamical freezing (ergodicity breaking) of subsets of nuclear modes on the time of reaction/residence of the electron at a redox cofactor. The separation of time-scales of nuclear modes coupled to electron transfer allows dynamical freezing. In particular, the separation between the relaxation time of electro-elastic fluctuations of the interface and the time of conformational transitions of the protein caused by changing redox state results in dynamical freezing of the latter for sufficiently fast electron transfer. The observable consequence of this dynamical freezing is significantly different reorganization energies describing the curvature at the bottom of electron-transfer free energy surfaces (large) and the distance between their minima (Stokes shift, small). The ratio of the two reorganization energies establishes the parameter by which the energetic efficiency of protein electron transfer is increased relative to the standard expectations, thus minimizing losses of energy to heat. Energetically efficient electron transfer occurs in a chain of conformationally quenched cofactors and is characterized by flattened free energy surfaces, reminiscent of the flat and rugged landscape at the stability basin of a folded protein.

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.

Computational classification of mitochondrial shapes reflects stress and redox state

Dynamic variations in mitochondrial shape have been related to function. However, tools to automatically classify and enumerate mitochondrial shapes are lacking, as are systematic studies exploring the relationship of such shapes to mitochondrial stress. Here we show that during increased generation of mitochondrial reactive oxygen species (mtROS), mitochondria change their shape from tubular to donut or blob forms, which can be computationally quantified. Imaging of cells treated with rotenone or antimycin, showed time and dose-dependent conversion of tubular forms to donut-shaped mitochondria followed by appearance of blob forms. Time-lapse images showed reversible transitions from tubular to donut shapes and unidirectional transitions between donut and blob shapes. Blobs were the predominant sources of mtROS and appeared to be related to mitochondrial-calcium influx. Mitochondrial shape change could be prevented by either pretreatment with antioxidants like N-acetyl cysteine or inhibition of the mitochondrial calcium uniporter. This work represents a novel approach towards relating mitochondrial shape to function, through integration of cellular markers and a novel shape classification algorithm.

Unidirectional Evolutionary Transitions in Fungal Mating Systems and the Role of Transposable Elements

In the fungal kingdom, the evolution of mating systems is highly dynamic, varying even among closely related species. Rearrangements in the mating-type (mat) locus, which contains the major regulators of sexual development, are expected to underlie the transitions between self-sterility (heterothallism) and self-fertility (homothallism). However, both the genetic mechanisms and the direction of evolutionary transitions in fungal mating systems are under debate. Here, we present new sequences of the mat locus of four homothallic and one heterothallic species of the model genus Neurospora (Ascomycota). By examining the patterns of synteny among these sequences and previously published data, we show that the locus is conserved among heterothallic species belonging to distinct phylogenetic clades, while different gene arrangements characterize the four homothallic species. These results allowed us to ascertain a heterothallic ancestor for the genus, confirming the prediction of the dead-end theory on unidirectional transitions toward selfing. We show that at least four shifts from heterothallism to homothallism have occurred in Neurospora, three of which involve the acquisition of sequences of both mating types into the same haploid genome. We present evidence for two genetic mechanisms allowing these shifts: translocation and unequal crossover. Finally, we identified two novel retrotransposons and suggest that these have played a major role in mating-system transitions, by facilitating multiple rearrangements of the mat locus.

Complete All-Optical Silica Fiber Isolator via Stimulated Brillouin Scattering

This study demonstrates the theoretical operation of an all-optical silica fiber isolator using stimulated Brillouin scattering. Two pump sources that copropagate through a double-mode fiber generate acoustic waves through electrostriction. These acoustic waves then induce unidirectional interband optical transitions between a separate pair of signal sources. With 1 W of total input pump power, complete optical isolation is achieved with a silica rod waveguide of radius 0.67 μm over a length of approximately 12 m, with pumps operating at a wavelength of 1.55 μm and signals at 1.50 μm.

Machine vision based stochastic analysis of cancer cell mitochondrial dysfunction induced by a BH3 domain

We have developed a versatile and rapid method for the quantitative estimation of cell death kinetics, following direct single-shot activation of the mitochondrial death pathway by a cell permeable BH3 activator peptide (D-R(8)BH3(BID)). This approach employs timelapse epifluorescent imaging of live cells and a machine- vision based feature extraction algorithm, to measure unidirectional stochastic transitions associated with mitochondrial inner membrane potential depolarization and/or permeability transition, at single cell resolution. This data is transformed to enable construction of a right step-wise survival function using the product limit estimator, and estimation of a median latency parameter (lambda), defined for the entire imaged cell population. Estimates of lambda computed for cells exhibiting two-colour fluorescence can be compared statistically using the Mantel-Hansel test. This general method has been applied to measure the kinetics and temporal ordering of BH3 domain induced mitochondrial depolarization and inner membrane permeabilization in cancer cells, and demonstrates the robustness of this technique in resolving temporally distinct intracellular events within individual cells.

Addendum to “Colored-noise-induced discontinuous transitions in symbiotic ecosystems”

A symbiotic ecosystem with Gompertz self-regulation and with adaptive competition between populations is studied by means of a N-species Lotka-Volterra stochastic model. The influence of fluctuating environment on the carrying capacity of a population is modeled as a dichotomous noise. The study is a follow up of previous investigations of symbiotic ecosystems subjected to the generalized Verhulst self-regulation [Phys. Rev. E 69, 061106 (2004); 65, 051108 (2002)]. In the framework of mean-field approximation the behavior of the solutions of the self-consistency equation for a stationary system is examined analytically in the full phase space of system parameters. Depending on the mutual interplay of symbiosis and competition of species, variation of noise parameters (amplitude, correlation time) can induce doubly unidirectional discontinuous transitions as well as single unidirectional discontinuous transitions of the mean population size.

Holocene evolution of coastal wetlands in wet-tropical northeastern Australia

Pollen in sediments drilled from the Innisfail coastal plain, northeast Queensland, Australia, was examined to reconstruct the evolution of Holocene wetlands in a wet-tropical environment. In contrast to monsoonal Australia, stable environmental conditions created by year-round rainfall and low tidal range caused abrupt, unidirectional transitions in wetland zonation as marine influence changed. This has enabled a detailed reconstruction of the marine transgression and subsequent progradation. Mangroves colonized in response to marine transgression at c. 7400 BP, as riverine mangroves of low salt tolerance migrated up the Mulgrave River. These were replaced around 7000 BP by extensive Rhizophora-dominated mangroves, coinciding with the development of a Rhizophora-dominated community in Wyvuri embayment. Mangroves reached their greatest extent as sea-level rise slowed towards 6000 BP, with a stillstand indicated by a brief return to terrestrial conditions at one site. High freshwater input depressed salt intrusion in the upper reaches of the Mulgrave estuary and prevented the development of hypersalinity in the upper tidal zone. Drainage conditions then controlled whether mangroves were succeeded by freshwater swamp or swamp-forest.

Membrane electroporation and direct gene transfer

The direct transfer of genetic material into cells by electroporation can be described in physico-chemical terms as an electroporation-resealing hysteresis. The hysteresis concept includes unidirectional state transitions of the membrane, coupled to electrodiffusive migration of DNA through cell wall structures and electroporated plasma membranes. Deeper insight into electroporation phenomena such as electrotransfection, electrofusion and electro-insertion is gained by the inspection of the electrosensitivity and the recovery curves of cell populations as well as by the analysis of the pulse strength—duration relationship. A theoretical framework is developed for an adequate comparison of data obtained with different pulse shapes. The results of the physicochemical analysis of electroporation data not only indicate possible molecular mechanisms but are also instrumental in developing a goal-directed optimization strategy for the various practical applications of electroporation techniques such as electric gene delivery, production of hybridoma cells for antibody secretion or the insertion of immune proteins into the membranes of blood organelles.

Membrane electroporation and direct gene transfer

The direct transfer of genetic material into cells by electroporation can be described in physicochemical terms as an electroporation-resealing hysteresis. The hysteresis concept includes unidirectional state transitions of the membrane, coupled to electrodiffusive migration of DNA through cell wall structures and electroporated plasma membranes. Deeper insight into electroporation phenomena such as electrotransfection, electrofusion and electro-insertion is gained by the inspection of the electrosensitivity and the recovery curves of cell populations as well as by the analysis of the pulse strength-duration relationship. A theoretical framework is developed for an adequate comparison of data obtained with different pulse shapes. The results of the physicochemical analysis of electroporation data not only indicate possible molecular mechanisms but are also instrumental in developing a goal-directed optimization strategy for the various practical applications of electroporation techniques such as electric gene delivery, production of hybridoma cells for antibody secretion or the insertion of immune proteins into the membranes of blood organelles.

Speciation and Stasis in Marine Ostracoda: Climatic Modulation of Evolution

Morphologic and paleozoogeographic analysis of Cenozoic marine Ostracoda from the Atlantic, Caribbean, and Pacific indicates that climatic change modulates evolution by disrupting long-term stasis and catalyzing speciation during sustained, unidirectional climatic transitions and, conversely, by maintaining morphologic stasis during rapid, high-frequency climatic oscillations. In the middle Pliocene, 4 to 3 million years ago, at least six new species of Puriana suddenly appeared as the Isthmus of Panama closed, changing oceanographic circulation and global climate. Since then morphologic stasis has characterized ancestral and descendant species during many glacial-interglacial cycles. The frequency and duration of climatic events have more impact on ostracode evolution than the magnitude of climatic changes.