Theoretical results concerning the influence of non‐random‐field defects

We shall focus on extended defect systems and review their critical behavior. Primarily, with two aims, one of which is to understand phase transitions and how to derive effective dimension of extended defects with various structures, and the other is to propose a new research-method for defect systems, we let extended defects grow on a triangular lattice with frustration in a similar fashion to diffusion-limited aggregation, and discuss the situation. The existence of phase transitions, phase diagram, effective defect dimension, etc. will be shown. Furthermore, we shall summarize theoretical studies of extended defect systems on phase diagrams, critical behavior, tricritical behavior, and crossover behavior as static properties, and on nonconserved systems and conserved systems as dynamic properties.     

Modeling spatial patterns in Dictyostelium

The life cycle of Dictyostelium discoideum provides a striking example of the transition from single cell behavior to multicellular cooperativity. In this paper the status of the attempts at making semiquantitative models of the aggregation phase of this cycle is reviewed. Specifically, it is discussed how the propagation of cAMP waves is a typical example of excitable signaling, which is then rendered unstable by coupling to cell chemotaxis. To investigate the streaming pattern that emerges from this clumping instability, we next turn to a new simulation strategy, which couples dynamical cell-like entities ("bions") to continuum chemical concentration fields. Finally, we discuss two directions for further research: One is the study of the robustness with respect to the variation of system parameters (such as the cell density) exhibited by the biological system, but not by any simple model. The other concerns going beyond the aggregation phase to tackle the three-dimensional problem of slug formation and motion.     

Scale Invariance of the PNG Droplet and the Airy Process

We establish that the static height fluctuations of a particular growth model, the PNG droplet, converges upon proper rescaling to a limit process, which we call the Airy process A(y). The Airy process is stationary, it has continuous sample paths, its single time (fixed y) distribution is the Tracy–Widom distribution of the largest eigenvalue of a GUE random matrix, and the Airy process has a slow decay of correlations as y ^–2. Roughly the Airy process describes the last line of Dyson's Brownian motion model for random matrices. Our construction uses a multi-layer version of the PNG model, which can be analyzed through fermionic techniques. Specializing our result to a fixed value of y, one reobtains the celebrated result of Baik, Deift, and Johansson on the length of the longest increasing subsequence of a random permutation.     

The use of the isotropic orientation factor in fluorescence resonance energy transfer (FRET) studies of the actin filament

A Dale-Eisinger style analysis (R. E. Daleet al., Biophys. J. 26, 161, 1979) is used to produce three-dimensional plots that display the limits on the average orientation factor k ² that is required to calculate molecular distances in F-actin from fluorescence resonance energy transfer measurements. Maxima and minima plots are generated for the transfer of energy from a donor to a single acceptor and for transfer to multiple acceptors that are related by F-actin helical symmetry. The analysis is performed in terms of dipole cone half-angles rather than depolarization factors, in order to facilitate the modeling of the multiple acceptor problem. Calculations are carried out under the restrictive condition of a single electric dipole moment per fluorophore. In addition, both surface and volume averaging of the donor and acceptor dipoles are considered. Comparisons between the plots show that for the multiple acceptor cases with F-actin symmetry, there is a great reduction in the range for maxima and minima limits on k ². The calculations also suggest guidelines for the choice of fluorescence label that will result in an average orientation factor occurring within acceptable limits, i.e., inside the limits for which k ²=2/3 may be employed. Thus, without having detailed knowledge of the mean donor or acceptor dipole relative orientations, the use of k ²=2/3 in radial coordinate studies of F-actin is more than reasonable and is fairly assured of being correct.     

Ethanol-induced conformational fluctuations of NMDA receptors

Alcohol addiction ranks among the leading global causes of preventable death and disabilities in human population. Understanding the sites of ethanol action that mediate its acute and chronic neural and behavioural effects is critical to develop appropriate treatment options for this disorder. The N-methyl-d-asparate (NMDA) receptors are ligand-gated heterotetrameric ion channels, which are known to directly interact with alcohol in a concentration-dependent manner. Yet, the exact molecular mechanisms and conformational dynamics of this interaction are not well understood. Here, we conducted a series of molecular dynamics simulations of the interaction of moderate ethanol concentrations with rat's wild-type GluN1–GluN2B NMDA Receptor under physiological conditions. The simulations suggest that glutamate or glycine alone induce an intermediate conformational state and point towards the transmembrane domain (TMD) as the site of action of ethanol molecules. Ethanol interacts by double hydrogen bonds with Trp635 and Phe638 at the transmembrane M3 helix of GluN2B. Alcohol not only reduces the pore radius of the ion channel within the TMD but also decreases accessibility of glutamate and glycine to the ligand-binding sites by altering the structure of the ligand-binding domain and significantly widening the receptor in that area.     

Evolution on a smooth landscape

We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population is governed by correlation functions that although being formally down by powers ofN (the population size), nonetheless control the evolution process after a very short transient. The long-time behavior can be found analytically since only one of these higher order correlators (the two-point function) is relevant. We compare and contrast the exact findings derived herein with a previously proposed phenomenological treatment employing mean-field theory supplemented with a cutoff at small population density. Finally, we relate our results to the recently studied case of mutation on a totally flat landscape.     

Homo- and heteronuclear 2D NMR approaches to analyse a mixture of deuterated unlike/like stereoisomers using weakly ordering chiral liquid crystals

We describe several homo- and heteronuclear 2D NMR strategies dedicated to the analysis of anisotropic (2)H spectra of a mixture of dideuterated unlike/like stereoisomers with two remote stereogenic centers, using weakly orienting chiral liquid crystals. To this end, we propose various 2D correlation experiments, denoted "D(H)(n)D" or "D(H)(n)C" (with n=1, 2), that involve two heteronuclear polarization transfers of INEPT-type with one or two proton relays. The analytical expressions of correlation signals for four pulse sequences reported here were calculated using the product-operators formalism for spin I=1 and S=1/2. The features and advantages of each scheme are presented and discussed. The efficiency of these 2D sequences is illustrated using various deuterated model molecules, dissolved in organic solutions of polypeptides made of poly-gamma-benzyl-L-glutamate (PBLG) or poly-epsilon-carbobenzyloxy-L-lysine (PCBLL) and NMR numerical simulations.     

Acoustic features of objects matched by an echolocating bottlenose dolphin

The focus of this study was to investigate how dolphins use acoustic features in returning echolocation signals to discriminate among objects. An echolocating dolphin performed a match-to-sample task with objects that varied in size, shape, material, and texture. After the task was completed, the features of the object echoes were measured (e.g., target strength, peak frequency). The dolphin's error patterns were examined in conjunction with the between-object variation in acoustic features to identify the acoustic features that the dolphin used to discriminate among the objects. The present study explored two hypotheses regarding the way dolphins use acoustic information in echoes: (1) use of a single feature, or (2) use of a linear combination of multiple features. The results suggested that dolphins do not use a single feature across all object sets or a linear combination of six echo features. Five features appeared to be important to the dolphin on four or more sets: the echo spectrum shape, the pattern of changes in target strength and number of highlights as a function of object orientation, and peak and center frequency. These data suggest that dolphins use multiple features and integrate information across echoes from a range of object orientations.