Modelling and analyzing adaptive self-assembling strategies with Maude

Building adaptive systems with predictable emergent behavior is a challenging task and it is becoming a critical need. The research community has accepted the challenge by introducing approaches of various nature: from software architectures, to programming paradigms, to analysis techniques. We recently proposed a conceptual framework for adaptation centered around the role of control data. In this paper we show that it can be naturally realized in a reflective logical language like Maude by using the Reflective Russian Dolls model. Moreover, we exploit this model to specify, validate and analyse a prominent example of adaptive system: robot swarms equipped with self-assembly strategies. The analysis exploits the statistical model checker PVeStA

Crossover from quasi-static to dense flow regime in compressed frictional granular media

We investigate the evolution of multi-scale mechanical properties towards the macroscopic mechanical instability in frictional granular media under multiaxial compressive loading. Spatial correlations of shear stress redistribution following nucleating contact sliding events and shear strain localization are investigated. We report growing correlation lengths associated to both shear stress and shear strain fields that diverge simultaneously as approaching the transition to a dense flow regime. This shows that the transition from quasi static to dense flow regime can be interpreted as a critical phase transition. Our results suggest that no shear band with a characteristic thickness has formed at the onset of instability

Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure

Patterns and Collective Behavior in Granular Media: Theoretical Concepts

Granular materials are ubiquitous in our daily lives. While they have been a subject of intensive engineering research for centuries, in the last decade granular matter attracted significant attention of physicists. Yet despite a major efforts by many groups, the theoretical description of granular systems remains largely a plethora of different, often contradicting concepts and approaches. Authors give an overview of various theoretical models emerged in the physics of granular matter, with the focus on the onset of collective behavior and pattern formation. Their aim is two-fold: to identify general principles common for granular systems and other complex non-equilibrium systems, and to elucidate important distinctions between collective behavior in granular and continuum pattern-forming systems.Comment: Submitted to Reviews of Modern Physics. Full text with figures (2Mb pdf) avaliable at http://mti.msd.anl.gov/AransonTsimringReview/aranson_tsimring.pdf Community responce is appreciated. Comments/suggestions send to [email protected]

Controlled formation of metallic nanowires via Au nanoparticle ac trapping

Applying ac voltages, we trapped gold nanoparticles between microfabricated electrodes under well-defined conditions. We demonstrate that the nanoparticles can be controllably fused together to form homogeneous gold nanowires with pre-defined diameters and conductance values. Whereas electromigration is known to form a gap when a dc voltage is applied, this ac technique achieves the opposite, thereby completing the toolkit for the fabrication of nanoscale junctions.Comment: Nanotechnology 18, 235202 (2007

TAO Conceptual Design Report: A Precision Measurement of the Reactor Antineutrino Spectrum with Sub-percent Energy Resolution

The Taishan Antineutrino Observatory (TAO, also known as JUNO-TAO) is a satellite experiment of the Jiangmen Underground Neutrino Observatory (JUNO). A ton-level liquid scintillator detector will be placed at about 30 m from a core of the Taishan Nuclear Power Plant. The reactor antineutrino spectrum will be measured with sub-percent energy resolution, to provide a reference spectrum for future reactor neutrino experiments, and to provide a benchmark measurement to test nuclear databases. A spherical acrylic vessel containing 2.8 ton gadolinium-doped liquid scintillator will be viewed by 10 m^2 Silicon Photomultipliers (SiPMs) of >50% photon detection efficiency with almost full coverage. The photoelectron yield is about 4500 per MeV, an order higher than any existing large-scale liquid scintillator detectors. The detector operates at -50 degree C to lower the dark noise of SiPMs to an acceptable level. The detector will measure about 2000 reactor antineutrinos per day, and is designed to be well shielded from cosmogenic backgrounds and ambient radioactivities to have about 10% background-to-signal ratio. The experiment is expected to start operation in 2022

Online Robot Introspection via Wrench-based Action Grammars

Robotic failure is all too common in unstructured robot tasks. Despite well-designed controllers, robots often fail due to unexpected events. How do robots measure unexpected events? Many do not. Most robots are driven by the sense-plan act paradigm, however more recently robots are undergoing a sense-plan-act-verify paradigm. In this work, we present a principled methodology to bootstrap online robot introspection for contact tasks. In effect, we are trying to enable the robot to answer the question: what did I do? Is my behavior as expected or not? To this end, we analyze noisy wrench data and postulate that the latter inherently contains patterns that can be effectively represented by a vocabulary. The vocabulary is generated by segmenting and encoding the data. When the wrench information represents a sequence of sub-tasks, we can think of the vocabulary forming a sentence (set of words with grammar rules) for a given sub-task; allowing the latter to be uniquely represented. The grammar, which can also include unexpected events, was classified in offline and online scenarios as well as for simulated and real robot experiments. Multiclass Support Vector Machines (SVMs) were used offline, while online probabilistic SVMs were are used to give temporal confidence to the introspection result. The contribution of our work is the presentation of a generalizable online semantic scheme that enables a robot to understand its high-level state whether nominal or abnormal. It is shown to work in offline and online scenarios for a particularly challenging contact task: snap assemblies. We perform the snap assembly in one-arm simulated and real one-arm experiments and a simulated two-arm experiment. This verification mechanism can be used by high-level planners or reasoning systems to enable intelligent failure recovery or determine the next most optima manipulation skill to be used.Comment: arXiv admin note: substantial text overlap with arXiv:1609.0494

Membrane penetration and trapping of an active particle

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrates through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing to accurately predict most of our results analytically. This analytical theory helps identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict mechanical properties of synthetic minimal membranes.Comment: 16 pages, 6 figures. Revised manuscript resubmitted to J. Chem. Phy

Stiffness pathologies in discrete granular systems: bifurcation, neutral equilibrium, and instability in the presence of kinematic constraints

The paper develops the stiffness relationship between the movements and forces among a system of discrete interacting grains. The approach is similar to that used in structural analysis, but the stiffness matrix of granular material is inherently non-symmetric because of the geometrics of particle interactions and of the frictional behavior of the contacts. Internal geometric constraints are imposed by the particles' shapes, in particular, by the surface curvatures of the particles at their points of contact. Moreover, the stiffness relationship is incrementally non-linear, and even small assemblies require the analysis of multiple stiffness branches, with each branch region being a pointed convex cone in displacement-space. These aspects of the particle-level stiffness relationship gives rise to three types of micro-scale failure: neutral equilibrium, bifurcation and path instability, and instability of equilibrium. These three pathologies are defined in the context of four types of displacement constraints, which can be readily analyzed with certain generalized inverses. That is, instability and non-uniqueness are investigated in the presence of kinematic constraints. Bifurcation paths can be either stable or unstable, as determined with the Hill-Bazant-Petryk criterion. Examples of simple granular systems of three, sixteen, and sixty four disks are analyzed. With each system, multiple contacts were assumed to be at the friction limit. Even with these small systems, micro-scale failure is expressed in many different forms, with some systems having hundreds of micro-scale failure modes. The examples suggest that micro-scale failure is pervasive within granular materials, with particle arrangements being in a nearly continual state of instability