Modeling receptor-ligand binding kinetics in immunological synapse formation

The formation of an immunological synapse between two immune cells is a central process in immunity allowing the exchange of information thatis of direct relevance for the cells’ activation states.The macromolecules at the cell-cell interface form a characteristic spatial pattern whose functional impact is largely unknown today.We perform computer simulations of the immunological synapse formationusing an agent-based model approach that monitors the motion and interactionof individual molecules and takes the binding kinetics of receptors and ligands explicitly into account.The emerging molecular patterns are in agreement with those observed ingeometrically repatterned immunological synapses.Furthermore, our model predicts that the diversity of molecular patterns,including dynamic and multifocal structures, is directly related to the receptor-ligand binding affinity.     

Rovelli’s World

Carlo Rovelli’s inspiring “Relational Quantum Mechanics” serves several aims at once: it provides a new vision of what the world of quantum mechanics is like, and it offers a program to derive the theory’s formalism from a set of simple postulates pertaining to information processing. I propose here to concentrate entirely on the former, to explore the world of quantum mechanics as Rovelli depicts it. It is a fascinating world in part because of Rovelli’s reliance on the information-theory approach to the foundations of quantum mechanics, and in part because its presentation involves taking sides on a fundamental divide within philosophy itself.     

Editorial: Ecological complex systems

Main aim of this topical issue is to report recent advances in noisy nonequilibrium processes useful to describe the dynamics of ecological systems and to address the mechanisms of spatio-temporal pattern formation in ecology both from the experimental and theoretical points of view. This is in order to understand the dynamical behaviour of ecological complex systems through the interplay between nonlinearity, noise, random and periodic environmental interactions. Discovering the microscopic rules and the local interactions which lead to the emergence of specific global patterns or global dynamical behaviour and the noise’s role in the nonlinear dynamics is an important, key aspect to understand and then to model ecological complex systems.     

From Euclidean to Minkowski space with the Cauchy–Riemann equations

We present an elementary method to obtain Green’s functions in non-perturbative quantum field theory in Minkowski space from Green’s functions calculated in Euclidean space. Since in non-perturbative field theory the analytical structure of amplitudes often is unknown, especially in the presence of confined fields, dispersive representations suffer from systematic uncertainties. Therefore, we suggest to use the Cauchy–Riemann equations, which perform the analytical continuation without assuming global information on the function in the entire complex plane, but only in the region through which the equations are solved. We use as example the quark propagator in Landau gauge quantum chromodynamics, which is known from lattice and Dyson–Schwinger studies in Euclidean space. The drawback of the method is the instability of the Cauchy–Riemann equations against high-frequency noise,which makes it difficult to achieve good accuracy. We also point out a few curious details related to the Wick rotation.     

Nose-cone calorimeter: PHENIX forward upgrade

PHENIX is a high rate experiment efficient at measuring rare processes, but has limited acceptance in azimuth and pseudorapidity (η). The Nose Cone Calorimeter (NCC), a W–Si sampling calorimeter in the region of 0.9<η<3, is one of the upgrades which will significantly increase coverage in both azimuth and pseudorapidity. The NCC will expand PHENIX’s precision measurements of electromagnetic probes in η, reconstruct jets, perform a wide scope of correlation measurements, and enhance triggering capabilities. The detector will significantly contribute to measurements of γ-jet correlations, quarkonia production, and low-x nuclear structure functions. This report discusses details of the detector design and its performance concerning a sample of the physics topics which will benefit from the NCC. In view of recent funding difficulties, outlook of the activities is discussed.     

A Simple Example of “Quantum Darwinism”: Redundant Information Storage in Many-Spin Environments

As quantum information science approaches the goal of constructing quantum computers, understanding loss of information through decoherence becomes increasingly important. The information about a system that can be obtained from its environment can facilitate quantum control and error correction. Moreover, observers gain most of their information indirectly, by monitoring (primarily photon) environments of the “objects of interest.” Exactly how this information is inscribed in the environment is essential for the emergence of “the classical” from the quantum substrate. In this paper, we examine how many-qubit (or many-spin) environments can store information about a single system. The information lost to the environment can be stored redundantly, or it can be encoded in entangled modes of the environment. We go on to show that randomly chosen states of the environment almost always encode the information so that an observer must capture a majority of the environment to deduce the system’s state. Conversely, in the states produced by a typical decoherence process, information about a particular observable of the system is stored redundantly. This selective proliferation of “the fittest information” (known as Quantum Darwinism) plays a key role in choosing the preferred, effectively classical observables of macroscopic systems. The developing appreciation that the environment functions not just as a garbage dump, but as a communication channel, is extending our understanding of the environment’s role in the quantum-classical transition beyond the traditional paradigm of decoherence.     

Efficiency based strategy spreading in the prisoner’s dilemma game

In contrast to well-mixed populations, discrete interaction patterns have been shown to support cooperation in the prisoner’s dilemma game, and a scale-free network topology may even lead to a dominance of cooperation over defection. The majority of studies assumes a strategy adoption scheme based on accumulated payoffs. The use of accumulated payoffs, however, is incompatible with the integral property of the underlying replicator dynamics to be invariant under a positive affine transformation of the payoff function. We show that using instead the payoff per interaction to determine the strategy spread, which has been suggested recently and recovers the required invariance, results in fundamentally different dynamical behavior under a synchronized strategy adoption considered here. Most notably, in such an efficiency based scenario the advantage of a scale-free network topology vanishes almost completely. We present a detailed explanation of the fundamentally altered dynamical behavior.     

Domain wall delocalization,dynamics and fluctuations in an exclusion process with two internal states

We investigate the delocalization transition appearing in an exclusion process with two internal states, respectively on two parallel lanes. At the transition, delocalized domain walls form in the density profiles of both internal states, in agreement with a mean-field approach. Remarkably, the topology of the system’s phase diagram allows for the delocalization of a (localized) domain wall when approaching the transition. We quantify the domain wall’s delocalization close to the transition by analytic results obtained within the framework of the domain wall picture. Power law dependences of the domain wall width on the distance to the delocalization transition as well as on the system size are uncovered, they agree with numerical results.     

Quantum-mechanical tunneling in associative neural networks

We investigate the quantum-mechanical tunneling between the “patterns" of the, so-called, associative neural networks. Being the relatively stable minima of the “configuration-energy" space of the networks, the “patterns" represent the macroscopically distinguishable states of the neural nets. Therefore, the tunneling represents a macroscopic quantum effect, but with some special characteristics. Particularly, we investigate the tunneling between the minima of approximately equal depth, thus requiring no energy exchange. If there are at least a few such minima, the tunneling represents a sort of the “random walk" process, which implies the quantum fluctuations in the system, and therefore “malfunctioning" in the information processing of the nets. Due to the finite number of the minima, the “random walk" reduces to a dynamics modeled by the, so-called, Pauli master equation. With some plausible assumptions, the set(s) of the Pauli master equations can be analytically solved. This way comes the main result of this paper: the quantum fluctuations due to the quantum-mechanical tunneling can be “minimized" if the “pattern"-formation is such that there are mutually “distant" groups of the “patterns", thus providing the “zone" structure of the “pattern" formation. This qualitative result can be considered as a basis of the efficient deterministic functioning of the associative neural nets. Received 15 July 1999     

Nematic order-disorder state transition in a liquid crystal analogue formed by oriented and migrating amoeboid cells

In cell culture, liquid crystal analogues are formed by elongated, migrating, and interacting amoeboid cells. An apolar nematic liquid crystal analogue is formed by different cell types like human melanocytes (=pigment cells of the skin), human fibroblasts (=connective tissue cells), human osteoblasts (=bone cells), human adipocytes (=fat cells), etc. The nematic analogue is quite well described by i) a stochastic machine equation responsible for cell orientation and ii) a self-organized extracellular guiding signal, E₂, which is proportional to the orientational order parameter as well as to the cell density. The investigations were mainly made with melanocytes. The transition to an isotropic state analogue can be accomplished either by changing the strength of interaction (e.g. variation of the cell density) or by influencing the cellular machinery by an externally applied signal: i) An isotropic gaseous state analogue is observed at low cell density (melanocytes/mm^2) and a nematic liquid crystal state analogue at higher cell density. ii) The nematic state analogue disappears if the bipolar shaped melanocytes are forced to become a star-like shape (induced by colchicine or staurosporine). The analogy between nematic liquid crystal state analogue formed by elongated, migrating and interacting cells and the nematic liquid crystal phase formed by interacting elongated molecules is discussed. Received 2 August 1999 and Received in final form 5 January 2000     

Efficient Hopfield pattern recognition on a scale-free neural network

Neural networks are supposed to recognise blurred images (or patterns) of N pixels (bits) each. Application of the network to an initial blurred version of one of P pre-assigned patterns should converge to the correct pattern. In the “standard" Hopfield model, the N “neurons” are connected to each other via N² bonds which contain the information on the stored patterns. Thus computer time and memory in general grow with N². The Hebb rule assigns synaptic coupling strengths proportional to the overlap of the stored patterns at the two coupled neurons. Here we simulate the Hopfield model on the Barabási-Albert scale-free network, in which each newly added neuron is connected to only m other neurons, and at the end the number of neurons with q neighbours decays as 1/q ³. Although the quality of retrieval decreases for small m, we find good associative memory for 1 ≪ m ≪ N. Hence, these networks gain a factor N/m ≫ 1 in the computer memory and time. Received 12 January 2003 Published online 11 April 2003 RID="a" ID="a"e-mail: stauffer@thp.uni-koeln.de     

Synchronization of oscillators coupled through an environment

We study synchronization of oscillators that are indirectly coupled through their interaction with an environment. We give criteria for the stability or instability of a synchronized oscillation. Using these criteria we investigate synchronization of systems of oscillators which are weakly coupled, in the sense that the influence of the oscillators on the environment is weak. We prove that arbitrarily weak coupling will synchronize the oscillators, provided that this coupling is of the ‘right’ sign. We illustrate our general results by applications to a model of coupled GnRH neuron oscillators proposed by Khadra and Li [A. Khadra, Y.X. Li, A model for the pulsatile secretion of gonadotropin-releasing hormone from synchronized hypothalamic neurons, Biophys. J. 91 (2006) 74-83.], and to indirectly weakly-coupled λ-ω oscillators.     

Femtosecond properties of photorefractive polymers

Photorefractive polymers allow to reversibly record holograms over a broad spectral range. This capability offers the possibility to store the information contained in ultrafast optical pulses (i.e., time domain) in the frequency domain. We demonstrate a storage bandwidth of >80 nm around 800 nm (i.e., >36 THz), giving a temporal resolution for Gaussian pulses of 13 fs at room temperature. Time reversal of a pulse train of 130 fs pulses confirms these capabilities.     

SPDM: light microscopy with single-molecule resolution at?the?nanoscale

Far-field fluorescence techniques based on the precise determination of object positions have the potential to circumvent the optical resolution limit of direct imaging given by diffraction theory. In order to use localization to obtain structural information far below the diffraction limit, the ‘point-like’ components of the structure have to be detected independently, even if their distance is lower than the conventional optical resolution limit. This goal can be achieved by exploiting various photo-physical properties of the fluorescence labeling (‘spectral signatures’). In first experiments, spectral precision distance microscopy/spectral position determination microscopy (SPDM) was limited to a relatively small number of components to be resolved within the observation volume. Recently, the introduction of photoconvertable molecules has dramatically increased the number of components which can be independently localized. Here, we present an extension of the SPDM concept, exploiting the novel spectral signature offered by reversible photobleaching of fluorescent proteins. In combination with spatially modulated illumination (SMI) microscopy, at the present stage, we have achieved an estimated effective optical resolution of approximately 20 nm in the lateral and 50 nm in the axial direction, or about 1/25th–1/10th of the exciting wavelength.     

Laser rapid thermal annealing of quantum semiconductor wafers: a one step bandgap engineering technique

We report on a new Laser Rapid Thermal Annealing (Laser-RTA) technique for one-step bandgap engineering at selected areas of quantum semiconductor wafers. The technique is based on using a 150 W 980 nm fiber coupled laser diode and a 30 W TEM00 1064 nm Nd:YAG laser for background heating and ‘writing’, respectively, the regions of the quantum well intermixed (QWI) material. The implementation of a 3D Finite Element Method for modeling of laser induced temperature profiles allows for the design of processing schemes that are required for accurate bandgap engineering at the wafer level. We demonstrate that arbitrary shaped lines of the QWI material can be fabricated with the Laser-RTA technique in InGaAs/InGaAsP quantum well microstructures.     

Assortativeness and information in scale-free networks

We analyze Shannon information of scale-free networks in terms of their assortativeness, and identify classes of networks according to the dependency of the joint remaining degree distribution on the assortativeness. We conjecture that these classes comprise minimalistic and maximalistic networks in terms of Shannon information. For the studied classes, the information is shown to depend non-linearly on the absolute value of the assortativeness, with the dominant term of the relationship being a power-law. We exemplify this dependency using a range of real-world networks. Optimization of scale-free networks according to information they contain depends on the landscape of parameters’ search-space, and we identify two regions of interest: a slope region and a stability region. In the slope region, there is more freedom to generate and evaluate candidate networks since the information content can be changed easily by modifying only the assortativeness, while even a small change in the power-law’s scaling exponent brings a reward in a higher rate of information change. This feature may explain why the exponents of real-world scale-free networks are within a certain range, defined by the slope and stability regions.     

Magnetic hysteresis in a molecular Ising ferrimagnet: Glauber dynamics approach

We use agent-based modeling to investigate the effect of conservatism and partisanship on the efficiency with which large populations solve the density classification task – a paradigmatic problem for information aggregation and consensus building. We find that conservative agents enhance the populations’ ability to efficiently solve the density classification task despite large levels of noise in the system. In contrast, we find that the presence of even a small fraction of partisans holding the minority position will result in deadlock or a consensus on an incorrect answer. Our results provide a possible explanation for the emergence of conservatism and suggest that even low levels of partisanship can lead to significant social costs. Electronic supplementary material  Supplementary Online Material     

Quantum Pseudo-Telepathy

Quantum information processing is at the crossroads of physics, mathematics and computer science. It is concerned with what we can and cannot do with quantum information that goes beyond the abilities of classical information processing devices. Communication complexity is an area of classical computer science that aims at quantifying the amount of communication necessary to solve distributed computational problems. Quantum communication complexity uses quantum mechanics to reduce the amount of communication that would be classically required. Pseudo-telepathy is a surprising application of quantum information processing to communication complexity. Thanks to entanglement, perhaps the most nonclassical manifestation of quantum mechanics, two or more quantum players can accomplish a distributed task with no need for communication whatsoever, which would be an impossible feat for classical players. After a detailed overview of the principle and purpose of pseudo-telepathy, we present a survey of recent and not-so-recent work on the subject. In particular, we describe and analyse all the pseudo-telepathy games currently known to the authors. Supported in Part by Canada’s Natural Sciences and Engineering Research Council (NSERC), the Canada Research Chair programme and the Canadian Institute for Advanced Research (CIAR). Supported in part by a scholarship from Canada’s NSERC. Supported in part by Canada’s NSERC Québec’s Fonds de recherche sur la nature et les technologies (FQRNT), the CIAR and the Mathematics of Information Technology and Complex Systems Network (MITACS).