Collective Reorganization Research Articles

Toward a Unified Description of the Electrostatic Assembly of Microgels and Nanoparticles.

The interplay of soft responsive particles, such as microgels, with nanoparticles (NPs) yields highly versatile complexes that show great potential for applications, ranging from plasmonic sensing to catalysis and drug delivery. However, the microgel-NP assembly process has not been investigated so far at the microscopic level, thus hindering the possibility of designing such hybrid systems a priori. In this work, we combine state-of-the-art numerical simulations with experiments to elucidate the fundamental mechanisms taking place when microgel-NP assembly is controlled by electrostatic interactions and the associated effects on the structure of the resulting complexes. We find a general behavior where, by increasing the number of interacting NPs, the microgel deswells up to a minimum size after which a plateau behavior occurs. This occurs either when NPs are mainly adsorbed to the microgel corona via the folding of the more external chains or when NPs penetrate inside the microgel, thereby inducing a collective reorganization of the polymer network. By varying microgel properties, such as fraction of cross-linkers or charge, as well as NP size and charge, we further show that the microgel deswelling curves can be rescaled onto a single master curve, for both experiments and simulations, demonstrating that the process is entirely controlled by the charge of the whole microgel-NP complex. Our results thus have a direct relevance in fundamental materials science and offer novel tools to tailor the nanofabrication of hybrid devices of technological interest.

Collective dipole reorganization in magnetostructures

Neodymium spherical magnets are inexpensive objects that demonstrate how dipolar particles self-assemble into various structures ranging from 1D chains to 3D crystals. Assemblies of these magnets are nicknamed magnetostructures and this paper focuses on a variety called magnetotubes, which are some curved square lattices forming cylinders. We experimentally and numerically observe that such magnetotubes can self-buckle, above a critical aspect ratio. In fact, the underlying dipolar ordering of such structures is found to exhibit a collective reorganization, altering the mechanical stability of the entire system. We identify the conditions in which these phenomena occur, and we emphasize that metastable states coexist. This suggests that a wide variety of magnetostructures, including chains and magnetocrystals, may collapse due to the coexistence of multiple ground states and global reorientation of dipoles.

Surfing across industrial revolutions: A resilient sensemaking perspective on innovation

AbstractEmploying the sensemaking perspective, this paper aims to study the relationship between social innovation and resilience. The study highlights how sensemaking of social innovation is a process that takes place within existing social and economic representations. This study has a qualitative nature and is based on multiple case studies, which is the methodology best suited to highlight the drivers of social phenomena in specific socioeconomic contexts and which characteristics they manifest. The paper contributes to the literature along three different lines. First, it describes social innovation as the resilient outcome of sensemaking or the result of a capacity for collective reorganization following environmental, political, economic, and social disruptions. Second, it provides policymakers with a model to use to establish the intensity of social pressure and the openness of baseline social representations to change. Third, it allows policymakers to jointly observe and analyze the relationship between social representation and economic representation, highlighting the central role of firms in achieving social innovation. Although this paper presents the findings of a wide theoretical analysis, the developed model needs to be empirically tested by firms and policymakers.

Generic catastrophic poverty when selfish investors exploit a degradable common resource.

The productivity of a common pool of resources may degrade when overly exploited by a number of selfish investors, a situation known as the tragedy of the commons. Without regulations, agents optimize the size of their individual investments into the commons by balancing incurring costs with the returns received. The resulting Nash equilibrium involves a self-consistency loop between individual investment decisions and the state of the commons. As a consequence, several non-trivial properties emerge. For N investing actors we prove rigorously that typical payoffs do not scale as 1/N, the expected result for cooperating agents, but as (1/N)2. Payoffs are hence reduced with regard to the functional dependence on N, a situation denoted catastrophic poverty. We show that catastrophic poverty results from a fine-tuned balance between returns and costs. Additionally, a finite number of oligarchs may be present. Oligarchs are characterized by payoffs that are finite and not decreasing when N increases. Our results hold for generic classes of models, including convex and moderately concave cost functions. For strongly concave cost functions the Nash equilibrium undergoes a collective reorganization, being characterized instead by entry barriers and sudden death forced market exits.

Soft, malleable double diamond twin

A twin boundary (TB) is a common low energy planar defect in crystals including those with the atomic diamond structure (C, Si, Ge, etc.). We study twins in a self-assembled soft matter block copolymer (BCP) supramolecular crystal having the double diamond (DD) structure, consisting of two translationally shifted, interpenetrating diamond networks of the minority polydimethyl siloxane block embedded in a polystyrene block matrix. The coherent, low energy, mirror-symmetric double tubular network twin has one minority block network with its nodes offset from the (222) TB plane, while nodes of the second network lie in the plane of the boundary. The offset network, although at a scale about a factor of 103 larger, has precisely the same geometry and symmetry as a (111) twin in atomic single diamond where the tetrahedral units spanning the TB retain nearly the same strut (bond) lengths and strut (bond) angles as in the normal unit cell. In DD, the second network undergoes a dramatic restructuring-the tetrahedral nodes transform into two new types of mirror-symmetric nodes (pentahedral and trihedral) which alternate and link to form a hexagonal mesh in the plane of the TB. The collective reorganization of the supramolecular packing highlights the hierarchical structure of ordered BCP phases and emphasizes the remarkable malleability of soft matter.

Dynamical phase transitions and their relation to structural and thermodynamic aspects of glass physics.

We review recent developments in structural-dynamical phase transitions in trajectory space based on dynamic facilitation theory. An open question is how the dynamic facilitation perspective on the glass transition may be reconciled with thermodynamic theories that posit collective reorganization accompanied by a growing static length scale and, eventually, a vanishing configurational entropy. In contrast, dynamic facilitation theory invokes a dynamical phase transition between an active phase (close to the normal liquid) and an inactive phase, which is glassy and whose order parameter is either a time-averaged dynamic or structural quantity. In particular, the dynamical phase transition in systems with non-trivial thermodynamics manifests signatures of a lower critical point that lies between the mode-coupling crossover and the putative Kauzmann temperature, at which a thermodynamic phase transition to an ideal glass state would occur. We review these findings and discuss such criticality in the context of the low-temperature decrease in configurational entropy predicted by thermodynamic theories of the glass transition.

Restoration, archiving, and digitalization of the Museum collections (The case of Zoological Collections, Georgian National Museum)

The paper presents a pilot case of scientific revision and inventory process in the zoological collection of the Georgian National Museum (Tbilisi). By the special decree of the President of Georgia, the Georgian National Museum was established in 2004. Unifying fifteen museums, the National Gallery and two scientific centers it is the largest museum complex in the country. Its zoological collection is one of the oldest in Caucasia. Among them are endemic, relict, and other rare species protected by international conventions, and many are listed as endangered or deleted species in Georgia. Considering their importance, age and overall condition of the objects and documentation the reorganization of zoological collections was started as a pilot case in rehabilitation and cataloguing of GNM collections. Complete collections of Arachnidae (Opiliones) were studied and organized; Species of the family of Trogulidae, Nemastomatidae, Sclerosomatidae, Phalangiidae, order Harvestmen (Opiliones) from the class Arachnida, have been identified. There were in total 31 Harvestmen species from 4 families (Trogulidae, Nemastomatidae, Sclerosomatidae, and Phalangiidae) identified. One species of which - Odiellus zacariensis Mkheidze, 1952, is new for Azerbaijan fauna and four species: Trogulus rossicus Silhavy, 1968, Opilio sylvestris Snegovaya 2010, Opilio caucasicus Snegovaya 2010, Opilio nabozhenkoi Snegovaya 2010 are new for the fauna of Georgia. Also two new species: Rilaena kelbajarica Snegovaya et Pkhakadze, 2014 and Phalangium mcheidzeae, Snegovaya, 2014 [5-6] have been described. Museums today aim to become a platform for developing and spreading scientific knowledge. Based on different collections: art, anthropology, archaeology, natural history etc. � they become unique catalysers for interdisciplinary studies. Object-based scientific collections can open new areas of research across different disciplines. In this regard management of museum collections, information about them and making it accessible for scholars of different research fields and countries is a main task for a modern museum. Therefore, it is crucial to systematize the objects and collections, create new knowledge in collaboration with the academia and museum professionals internationally and promote the scientific knowledge for broader audience. The outcomes of the study will enhance the process of integration of GNM collections in international museum system and academia.

Thermal Transport across a Semiconductor/Semiconductor Interface: A First-Principles-Based Approach

Controlling heat flow across material heterojunctions is important for thermoelectrics and thermal management of electronic devices. A clear physical understanding of what transport mechanism dominates near an interface can help benefit technology. We present a theoretical investigation of phonon transport across a semiconductor/semiconductor interface, specifically Si/Ge, and demonstrate how inelastic scattering and non-equilibrium effects play a key role. We treat phonon transport with the McKelvey-Shockley flux method, which is efficient, captures ballistic and non-equilibrium effects, inelastic scattering, and has shown excellent agreement with the more computationally-demanding Boltzmann equation. The Si and Ge phonon dispersions and 3-phonon scattering rates, serving as input for the transport modeling, are calculated from first-principles. The results show that, while the maximum phonon frequency in Si is nearly double that of Ge, significant heat currents are carried by the high-frequency Si phonons above the Ge cutoff. When approaching the interface, inelastic scattering redistributes energy to the phonon frequencies that can transfer elastically across the Si/Ge junction. We explain how this collective reorganization of phonons is driven by non-equilibrium effects near the interface. We also include a model for the contact resistance of an ideal interface, that depends on both phonon dispersions, which provides a lower limit for a given material combination. These results help provide clear physical insights into what controls phonon transport at semiconductor/semiconductor interfaces.

Role of contact inhibition of locomotion and junctional mechanics in epithelial collective responses to injury

Epithelial tissues form physically integrated barriers against the external environment protecting organs from infection and invasion. Within each tissue, epithelial cells respond to different challenges that can potentially compromise tissue integrity. In particular, cells collectively respond to injuries by reorganizing their cell–cell junctions and migrating directionally towards the sites of damage. Notwithstanding, the mechanisms that drive collective responses in epithelial aggregates remain poorly understood. In this work, we develop a minimal mechanistic model that is able to capture the essential features of epithelial collective responses to injuries. We show that a model that integrates the mechanics of cells at the cell–cell and cell–substrate interfaces as well as contact inhibition of locomotion (CIL) correctly predicts two key properties of epithelial response to injury as: (1) local relaxation of the tissue and (2) collective reorganization involving the extension of cryptic lamellipodia that extend, on average, up to 3 cell diameters from the site of injury and morphometric changes in the basal regions. Our model also suggests that active responses (like the actomyosin purse string and softening of cell–cell junctions) are needed to drive morphometric changes in the apical region. Therefore, our results highlight the importance of the crosstalk between junctional biomechanics, cell substrate adhesion, and CIL, as well as active responses, in guiding the collective rearrangements that are required to preserve the epithelial barrier in response to injury.

Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β30-35 Chain in Water: A Molecular Dynamics Study.

We have studied the conformational landscape of the C-terminal fragment of the amyloid protein Aβ30-35 in water using well-tempered metadynamics simulations and found that it resembles an intrinsically disordered protein. The conformational fluctuations of the protein are facilitated by a collective reorganization of both protein and water hydrogen bond networks, combined with electrostatic interactions between termini as well as hydrophobic interactions of the side chains. The stabilization of hydrophobic interactions in one of the conformers involves a collective collapse of the side chains along with a squeeze-out of water sandwiched between them. The charged N- and C-termini play a critical role in stabilizing different types of protein conformations, including those involving contact-ion salt bridges as well as solvent-mediated interactions of the termini and the amide backbone. We have examined this by probing the distribution of directed water wires forming the hydrogen bond network enveloping the polypeptide. Water wires and their fluctuations form an integral part of structural signature of the protein conformation.

Water-anion hydrogen bonding dynamics: Ultrafast IR experiments and simulations.

Many of water's remarkable properties arise from its tendency to form an intricate and robust hydrogen bond network. Understanding the dynamics that govern this network is fundamental to elucidating the behavior of pure water and water in biological and physical systems. In ultrafast nonlinear infrared experiments, the accessible time scales are limited by water's rapid vibrational relaxation (1.8 ps for dilute HOD in H2O), precluding interrogation of slow hydrogen bond evolution in non-bulk systems. Here, hydrogen bonding dynamics in bulk D2O were studied from the perspective of the much longer lived (36.2 ps) CN stretch mode of selenocyanate (SeCN-) using polarization selective pump-probe (PSPP) experiments, two-dimensional infrared (2D IR) vibrational echo spectroscopy, and molecular dynamics simulations. The simulations make use of the empirical frequency mapping approach, applied to SeCN- for the first time. The PSPP experiments and simulations show that the orientational correlation function decays via fast (2.0 ps) restricted angular diffusion (wobbling-in-a-cone) and complete orientational diffusive randomization (4.5 ps). Spectral diffusion, quantified in terms of the frequency-frequency correlation function, occurs on two time scales. The initial 0.6 ps time scale is attributed to small length and angle fluctuations of the hydrogen bonds between water and SeCN-. The second 1.4 ps measured time scale, identical to that for HOD in bulk D2O, reports on the collective reorganization of the water hydrogen bond network around the anion. The experiments and simulations provide details of the anion-water hydrogen bonding and demonstrate that SeCN- is a reliable vibrational probe of the ultrafast spectroscopy of water.

Alternative Forms of Energy Production and Political Reconfigurations: Exploring Alternative Energies as Potentialities of Collective Reorganization

To a large extent and one that is highly structuring, energy choices that are made in a society are political choices. This article aims at studying how these choices can be redirected by technological developments associated with renewable energy, thus contributing to a redistribution of opportunities and correspondingly to social reorganizations. In order to show that the development of alternative energies not only depends on technological advances but can also, in the process, reveal political potentialities, three steps are proposed. The first step will clarify the theoretical arguments in favor of an approach in terms of “technological potentialism.” Second, we will extend this approach by identifying a set of potentialities linked with renewable energies and the model that could arise from these alternative forms or approaches. Finally, we will examine how these potentialities could find paths to become effective.

Spatiotemporal Patterns in Ultraslow Domain Wall Creep Dynamics.

In the presence of impurities, ferromagnetic and ferroelectric domain walls slide only above a finite external field. Close to this depinning threshold, they proceed by large and abrupt jumps called avalanches, while, at much smaller fields, these interfaces creep by thermal activation. In this Letter, we develop a novel numerical technique that captures the ultraslow creep regime over huge time scales. We point out the existence of activated events that involve collective reorganizations similar to avalanches, but, at variance with them, display correlated spatiotemporal patterns that resemble the complex sequence of aftershocks observed after a large earthquake. Remarkably, we show that events assemble in independent clusters that display at large scales the same statistics as critical depinning avalanches. We foresee these correlated dynamics being experimentally accessible by magnetooptical imaging of ferromagnetic films.

Dimensional Effects on the Charge Density Waves in Ultrathin Films of TiSe2.

Charge density wave (CDW) formation in solids is a critical phenomenon involving the collective reorganization of the electrons and atoms in the system into a wave structure, and it is expected to be sensitive to the geometric constraint of the system at the nanoscale. Here, we study the CDW transition in TiSe2, a quasi-two-dimensional layered material, to determine the effects of quantum confinement and changing dimensions in films ranging from a single layer to multilayers. Of key interest is the characteristic length scale for the transformation from a two-dimensional case to the three-dimensional limit. Angle-resolved photoemission spectroscopy (ARPES) measurements of films with thicknesses up to six layers reveal substantial variations in the energy structure of discrete quantum well states; however, the temperature-dependent band gap renormalization converges at just three layers. The results indicate a layer-dependent mixture of two transition temperatures and a very-short-range CDW interaction within a three-dimensional framework.

AVALANCHE DYNAMICS IN DISORDERED SYSTEMS

We describe the complex dynamics of an interface (like a magnetic domain wall) on a disordered landscape. In presence of a small external drive (i.e. an external magnetic filed) the motion of the interface is slow and jerky. Two different regimes can be distinguished: the thermally activated regime where the interface spend most of the time in deep metastable states separated by large barriers (creep regime) and the avalanche regime where motion persists also at zero temperature, but it involves collective re-organizations (depinning). Our results shed light on the interplay between these two regimes and on the avalanche statistics.

The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water.

In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

Femtosecond mid-infrared study of the reorientation of weakly hydrogen-bonded water molecules.

We study the hydrogen-bond and reorientation dynamics of weakly hydrogen-bonded water molecules by studying their spectral diffusion and anisotropy dynamics with polarization-resolved two-color femtosecond mid-infrared spectroscopy. We selectively excite weakly hydrogen-bonded water molecules by tuning a relatively narrow band excitation pulse far into the high-frequency wing of the O-D stretch vibration of HDO molecules in H2O water. We observe that the spectral diffusion and the anisotropy both show pronounced biexponential dynamics. On the basis of previous work, the fast component of the spectral dynamics with a time constant of ∼100 fs is assigned to rapid hydrogen-bond switching events. We observed that these switching events lead to a pronounced effect on the anisotropy of the excited O-D groups, which shows that the spectral relaxation is accompanied by a large change of the orientation of the O-D groups. The slow component of the spectral relaxation can be assigned to the collective structural reorganization of the hydrogen-bond network of liquid water. With increasing temperature, the spectral relaxation shows a similar acceleration as the average molecular reorientation, showing that these processes are intimately connected.

Utilizing a phylogenetic plant classification for systematic arrangements in botanic gardens and herbaria

The use of different and often outmoded systems for the arrangement of collections in botanic gardens and herbaria hampers international research because it makes finding the location of a specific genus and family unpredictable. Following a series of international workshops, intended to develop a set of widely accepted circumscriptions of vascular plant families, a European and Australian consortium, the Vascular Plant Classification Committee (VPCC), was formed in 2008 to address the challenge of harmonizing collections (of living and preserved material and associated literary archives) across Europe and Australia; this was envisaged as an ambitious first step towards a globally accepted alignment of family circumscriptions and the use of an accepted unified linear sequence. In 2009, agreement on this was reached among six of the largest European botanical organizations, a pioneering scientific and political accomplishment. Global acceptance of this arrangement is now beginning to gather pace. A network of organizations adopting this new classification and sequence (or intending to, when resources allow) is developing and now reaches across five continents. In this article, we outline the aims of and progress made by the VPCC, and acknowledge the resources required for the reorganization of large collections, with a particular focus on those at the Royal Botanic Gardens, Kew. The importance of a dynamic sequence, reflective of taxonomic changes, and the ways in which such changes can be incorporated into collections are discussed. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 127–141.

Nonadiabatic anharmonic electron transfer

The effect of an inner sphere, local mode vibration on an electron transfer is modeled using the nonadiabatic transition probability (rate) expression together with both the anharmonic Morse and the harmonic oscillator potential. For an anharmonic inner sphere mode, a variational analysis uses harmonic oscillator basis functions to overcome the difficulties evaluating Morse-model Franck-Condon overlap factors. Individual matrix elements are computed with the use of new, fast, robust, and flexible recurrence relations. The analysis therefore readily addresses changes in frequency and/or displacement of oscillator minimums in the different electron transfer states. Direct summation of the individual Boltzmann weighted Franck-Condon contributions avoids the limitations inherent in the use of the familiar high-temperature, gaussian form of the rate constant. The effect of harmonic versus anharmonic inner sphere modes on the electron transfer is readily seen, especially in the exoergic, inverted region. The behavior of the transition probability can also be displayed as a surface for all temperatures and values of the driving force/exoergicity Δ = -ΔG. The temperature insensitivity of the transfer rate is clearly seen when the exoergicity equals the collective reorganization energy (Δ = Λ(s)) along a maximum ln (w) vs. Δ ridge of the surface. The surface also reveals additional regions for Δ where ln (w) appears to be insensitive to temperature, or effectively activationless, for some kinds of inner sphere contributions.

Kinetics of the Terminal Electron Transfer Step in Cytochrome c Oxidase

Cytochrome c oxidase (cco) catalyzes the oxygen reduction reaction in most aerobically respiring organisms. Decades of research have uncovered many aspects relating to structure and function of this enzyme. However, the origin of the unusually fast terminal electron transfer step from heme a to heme a(3) in cco has been the subject of intense discussions over recent years. Yet, no satisfactory consensus has been achieved. Carrying out large-scale molecular dynamics simulation of the protein embedded in a solvated membrane, we obtain a reorganization free energy λ = 0.57 eV. Evaluation of the quantized single-mode rate equation using the experimental rate and the computed reorganization free energy gives a value of 1.5 meV for the average electronic coupling (H(ab)) between heme a and heme a(3). Thus, according to our calculations, the nanosecond electron transfer (ET) is due to a small but significant activation barrier (ΔG(‡) = 0.12 eV) in combination with effective electronic coupling between the two cofactors. The activation free energy is caused predominantly by collective reorganization of protein residues. We show that our results are consistent with the weak temperature dependence observed in experiment if one allows for very minor variations in the donor-acceptor distance as the temperature changes.