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Self-Assembling Systems are Distributed Systems  [PDF]
Aaron Sterling
Computer Science , 2009,
Abstract: In 2004, Klavins et al. introduced the use of graph grammars to describe -- and to program -- systems of self-assembly. We show that these graph grammars can be embedded in a graph rewriting characterization of distributed systems that was proposed by Degano and Montanari over twenty years ago. We apply this embedding to generalize Soloveichik and Winfree's local determinism criterion (for achieving a unique terminal assembly), from assembly systems of 4-sided tiles that embed in the plane, to arbitrary graph assembly systems. We present a partial converse of the embedding result, by providing sufficient conditions under which systems of distributed processors can be simulated by graph assembly systems topologically, in the plane, and in 3-space. We conclude by defining a new complexity measure: "surface cost" (essentially the convex hull of the space inhabited by agents at the conclusion of a self-assembled computation). We show that, for growth-bounded graphs, executing a subroutine to find a Maximum Independent Set only increases the surface cost of a self-assembling computation by a constant factor. We obtain this complexity bound by using the simulation results to import the distributed computing notions of "local synchronizer" and "deterministic coin flipping" into self-assembly.
Self-assembling cyclic systems as drug carriers
A. Banerjee,A. Yadav
Applied Nanoscience , 2013, DOI: 10.1007/s13204-012-0154-0
Abstract: Self-assembling cyclic systems have been of interest to researchers for over a decade now, and their wide variety applications have been explored from electronic devices to medicinal purposes. But still their discovery for newer innovative applications remains as valuable as before. In this study, ab initio Hartree–Fock molecular orbital calculations have been performed on peptidic and peptidomimetic cyclic compounds to identify characteristics required in compounds for efficient self-aggregation. The effect of these characteristics in determining the pore size and length of nanotube has been studied. Effect of backbone and substituents on environment of outer and inner surface and carriage properties has been studied in detail. Self-aggregating compounds (Ala)12 and (Ala)10 have been predicted to form a tubular structure with dimensions in nanoscale. They have been predicted to work as novel drug carriers having inert outer wall and inner pore. A peptidic self-aggregating compound (Ala)12 has been studied and suggested as carrier for antibiotic gentamicin to exemplify carriage properties of the designed compound. Such novel self-aggregatory systems are expected to help simplify the drug delivery process and increase bioavailability of various drugs.
Formal Verification of Self-Assembling Systems  [PDF]
Aaron Sterling
Computer Science , 2010,
Abstract: This paper introduces the theory and practice of formal verification of self-assembling systems. We interpret a well-studied abstraction of nanomolecular self assembly, the Abstract Tile Assembly Model (aTAM), into Computation Tree Logic (CTL), a temporal logic often used in model checking. We then consider the class of "rectilinear" tile assembly systems. This class includes most aTAM systems studied in the theoretical literature, and all (algorithmic) DNA tile self-assembling systems that have been realized in laboratories to date. We present a polynomial-time algorithm that, given a tile assembly system T as input, either provides a counterexample to T's rectilinearity or verifies whether T has a unique terminal assembly. Using partial order reductions, the verification search space for this algorithm is reduced from exponential size to O(n^2), where n x n is the size of the assembly surface. That reduction is asymptotically the best possible. We report on experimental results obtained by translating tile assembly simulator files into a Petri net format manipulable by the SMART model checking engines devised by Ciardo et al. The model checker runs in O(|T| x n^4) time, where |T| is the number of tile types in tile assembly system T, and n x n is the surface size. Atypical for a model checking problem -- in which the practical limit usually is insufficient memory to store the state space -- the limit in this case was the amount of memory required to represent the rules of the model. (Storage of the state space and of the reachability graph were small by comparison.) We discuss how to overcome this obstacle by means of a front end tailored to the characteristics of self-assembly.
Photonic band structure of highly deformable, self-assembling systems  [PDF]
Peter A. Bermel,Mark Warner
Physics , 2001, DOI: 10.1103/PhysRevE.65.010702
Abstract: We calculate the photonic band structure at normal incidence of highly deformable, self-assembling systems - cholesteric elastomers subjected to external stress. Cholesterics display brilliant reflection and lasing owing to gaps in their photonic band structure. The band structure of cholesteric elastomers varies sensitively with strain, showing new gaps opening up and shifting in frequency. A novel prediction of a total band gap is made, and is expected to occur in the vicinity of the previously observed de Vries bandgap, which is only for one polarisation.
Bicontinuous surfaces in self-assembling amphiphilic systems  [PDF]
U. S. Schwarz,G. Gompper
Physics , 2003,
Abstract: Amphiphiles are molecules which have both hydrophilic and hydrophobic parts. In water- and/or oil-like solvent, they self-assemble into extended sheet-like structures due to the hydrophobic effect. The free energy of an amphiphilic system can be written as a functional of its interfacial geometry, and phase diagrams can be calculated by comparing the free energies following from different geometries. Here we focus on bicontinuous structures, where one highly convoluted interface spans the whole sample and thereby divides it into two separate labyrinths. The main models for surfaces of this class are triply periodic minimal surfaces, their constant mean curvature and parallel surface companions, and random surfaces. We discuss the geometrical properties of each of these types of surfaces and how they translate into the experimentally observed phase behavior of amphiphilic systems.
Extracting bulk properties of self-assembling systems from small simulations  [PDF]
Thomas E. Ouldridge,Ard A. Louis,Jonathan P. K. Doye
Physics , 2009, DOI: 10.1088/0953-8984/22/10/104102
Abstract: For systems that self assemble into finite-sized objects, it is sometimes convenient to compute the thermodynamics for a small system where a single assembly can form. However, we show that in the canonical ensemble the use of small systems can lead to significant finite-size effects due to the suppression of concentration fluctuations. We introduce methods to estimate the bulk-yields from simulations of small systems and to follow the convergence of yields with system size, under the assumptions that the various species behave ideally. We also propose an extension to the umbrella sampling technique that allows the formation of multiple finite-sized objects.
Thermosensitive Self-Assembling Block Copolymers as Drug Delivery Systems  [PDF]
Giulia Bonacucina,Marco Cespi,Giovanna Mencarelli,Gianfabio Giorgioni,Giovanni Filippo Palmieri
Polymers , 2011, DOI: 10.3390/polym3020779
Abstract: Self-assembling block copolymers (poloxamers, PEG/PLA and PEG/PLGA diblock and triblock copolymers, PEG/polycaprolactone, polyether modified poly(Acrylic Acid)) with large solubility difference between hydrophilic and hydrophobic moieties have the property of forming temperature dependent micellar aggregates and, after a further temperature increase, of gellifying due to micelle aggregation or packing. This property enables drugs to be mixed in the sol state at room temperature then the solution can be injected into a target tissue, forming a gel depot in-situ at body temperature with the goal of providing drug release control. The presence of micellar structures that give rise to thermoreversible gels, characterized by low toxicity and mucomimetic properties, makes this delivery system capable of solubilizing water-insoluble or poorly soluble drugs and of protecting labile molecules such as proteins and peptide drugs.
Optical Properties of the Self-Assembling Polymeric Colloidal Systems  [PDF]
Alexandra Mocanu,Edina Rusen,Aurel Diacon
International Journal of Polymer Science , 2013, DOI: 10.1155/2013/238567
Abstract: In the last decade, optical materials have gained much interest due to the high number of possible applications involving path or intensity control and filtering of light. The continuous emerging technology in the field of electrooptical devices or medical applications allowed the development of new innovative cost effective processes to obtain optical materials suited for future applications such as hybrid/polymeric solar cells, lasers, polymeric optical fibers, and chemo- and biosensing devices. Considering the above, the aim of this review is to present recent studies in the field of photonic crystals involving the use of polymeric materials. 1. Photonic Crystals Nanomaterials with well-defined 3D repetitive arrays have found application in photonic devices, sensors, selective membranes, and even microchips. Compared to a classic crystalline array, colloidal spherical particles replace the molecules, atoms, or ions in hexagonal close packed (HCP) structure or cubic close packed (CCP) structures [1–3] (Figure 1). Figure 1: Three-dimensional arrays: (a) HCP, (b) CCP [ 3]. Colloidal particles are able, through self-assembly processes, to be arranged into 3D structures leading to colloidal crystals. The resulting materials revealed interesting properties, presenting similar optical characteristics with synthetic opal and photonic crystals (Figure 2). One of the most facile routes for obtaining photonic crystals is based on the employment of polymer colloids with self-assembling properties [3–5]. Figure 2: (a) Synthetic opal; (b) structure of a photonic crystal [ 4]. A photonic crystal is a periodic nanostructured material that influences the propagation of electromagnetic waves in a similar manner as a semiconductor does for electrons [3]. Although photonic crystals have been studied since 1887, with one of the pioneers being Rayleigh [6], the term has been introduced only in 1987, after the papers of two physicist working independently Yablonovitch and John [7, 8]. In order to understand the behavior of photons inside a photonic crystal it is possible to compare it with the motion of electrons and vacancies in a semiconductor material as mentioned above. A proper example of photonic crystals occurring in nature is opals, which contain a natural periodic microstructure of silica microspheres of 15–900?nm, responsible for their iridescent color [9]. This structure allows the propagation of the photons through the crystal, while the interaction between the silica spheres and light makes possible the formation of allowed and forbidden energy bands, also
Virtual Nervous Systems for Self-Assembling Robots - A preliminary report  [PDF]
Nithin Mathews,Anders Lyhne Christensen,Rehan O'Grady,Marco Dorigo
Computer Science , 2015,
Abstract: We define the nervous system of a robot as the processing unit responsible for controlling the robot body, together with the links between the processing unit and the sensorimotor hardware of the robot - i.e., the equivalent of the central nervous system in biological organisms. We present autonomous robots that can merge their nervous systems when they physically connect to each other, creating a "virtual nervous system" (VNS). We show that robots with a VNS have capabilities beyond those found in any existing robotic system or biological organism: they can merge into larger bodies with a single brain (i.e., processing unit), split into separate bodies with independent brains, and temporarily acquire sensing and actuating capabilities of specialized peer robots. VNS-based robots can also self-heal by removing or replacing malfunctioning body parts, including the brain.
Confinement effects on diffusiophoretic self-propellers  [PDF]
M. N. Popescu,S. Dietrich,G. Oshanin
Physics , 2009, DOI: 10.1063/1.3133239
Abstract: We study theoretically the effects of spatial confinement on the phoretic motion of a dissolved particle driven by composition gradients generated by chemical reactions of its solvent, which are active only on certain parts of the particle surface. We show that the presence of confining walls increases in a similar way both the composition gradients and the viscous friction, and the overall result of these competing effects is an increase in the phoretic velocity of the particle. For the case of steric repulsion only between the particle and the product molecules of the chemical reactions, the absolute value of the velocity remains nonetheless rather small.
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