Computing Integrated Information (Φ) in Discrete Dynamical Systems with Multi-Valued Elements

Integrated information theory (IIT) provides a mathematical framework to characterize the cause-effect structure of a physical system and its amount of integrated information (Φ). An accompanying Python software package (“PyPhi”) was recently introduced to implement this framework for the causal analysis of discrete dynamical systems of binary elements. Here, we present an update to PyPhi that extends its applicability to systems constituted of discrete, but multi-valued elements. This allows us to analyze and compare general causal properties of random networks made up of binary, ternary, quaternary, and mixed nodes. Moreover, we apply the developed tools for causal analysis to a simple non-binary regulatory network model (p53-Mdm2) and discuss commonly used binarization methods in light of their capacity to preserve the causal structure of the original system with multi-valued elements.     

Uniqueness of isometric immersions with the same mean curvature

Motivated by the quasi-local mass problem in general relativity, we study the rigidity of isometric immersions with the same mean curvature into a warped product space. As a corollary of our main result, two star-shaped hypersurfaces in a spatial Schwarzschild or AdS-Schwarzschild manifold with nonzero mass differ only by a rotation if they are isometric and have the same mean curvature. We also prove similar results if the mean curvature condition is replaced by an ${\sigma }_2$-curvature condition.     

Effect of additive length and chemistry on the morphology of blends of conjugated thiophenes and fullerene derivative acceptor molecules

Small molecule additives have been shown to increase the device efficiency of conjugated polymer (donor) and fullerene derivative (acceptor) based organic solar cells by modifying the morphology of the device active layer. In this paper we conduct a systematic study of how additives affect the donor‐acceptor morphology using molecular dynamics simulations of blends of thiophene‐based oligomers, mimicking poly(3‐dodecylthiophene) (P3DDT) or poly(2,2′:5′,2”‐3,3”‐didocyl‐terthiophene) (PTTT), and fullerene derivatives with additives of varying length and chemical functionalization, mimicking experimentally used additives like methyl ester additives, diiodooctane, and alkanedithiols. We find that functionalization of additives with end groups that are attracted to acceptor molecules are necessary to induce increased donor‐acceptor macrophase separation. In blends where acceptors intercalate between oligomer alkyl side chains, functionalized additives decrease acceptor intercalation. Functionalized additives with shorter alkyl segments increase acceptor macrophase separation more than additives with same chemical functionalization but longer alkyl segments. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1046–1057     

Homogeneous variable exponent Besov and Triebel–Lizorkin spaces

We introduce homogeneous Besov and Triebel–Lizorkin spaces with variable indexes. We show that their study reduces to the study of inhomogeneous variable exponent spaces and homogeneous constant exponent spaces. Corollaries include trace space characterizations and Sobolev embeddings.     

Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study

Oligonucleic acids (ONAs), such as DNA and RNA, are used in various biotechnology and nanotechnology applications due to their ability to form a double helix that is stable at low temperature and melts at high temperatures. The melting temperature (T_m) of ONA duplexes can be tuned by the ONA composition, sequence, length and concentration, solvent quality, and salt concentration and by conjugation to other macromolecules. In this article, we use coarse‐grained (CG) molecular simulations to study ONAs conjugated with linear homopolymers that are relatively more solvophobic than the ONA. We study charged and stiff 8‐mer ONAs (e.g., DNA) and neutral and flexible 8‐mer ONAs (e.g., peptide nucleic acids or PNA), and vary the composition (or G‐C content) and sequence of ONA, conjugated homopolymer lengths and solvent quality for the polymer. For neutral and flexible ONAs, as the solvent quality worsens for the polymer, the ONA melting temperature increases from that of unconjugated ONA. The melting curves broaden with polymer length and worsening solvent quality, especially for ONAs with higher G‐C content. For charged and stiff ONAs, as the solvent quality worsens, the ONA melting temperature decreases compared to unconjugated ONA while the width of the melting curve remains the same. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1196–1208     

Self-assembly mechanism of PEG-b-PCL and PEG-b-PBO-b-PCL amphiphilic copolymer micelles in aqueous solution from coarse grain modeling

We followed the self-assembly of high-molecular weight MePEG- b -PCL (poly(methyl ethylene glycol)-block-poly(ε-caprolactone)) diblock and MePEG- b -PBO- b -PCL (poly(methyl ethylene glycol)-block-poly(1,2-butylene oxide)-block-poly(ε-caprolactone)) into micelles using molecular dynamics simulation with a coarse grain (CG) force field based on quantum mechanics (CGq FF). The triblock polymer included a short poly(1,2-butylene oxide) (PBO) at the hydrophilic-hydrophobic interface of these systems. Keeping the hydrophilic length fixed (MePEG₄₅), we considered 250 chains in which the hydrophobic length changed from PCL₄₄ or PBO₆- b -PCL₄₃ to PCL₆₂ or PBO₉- b -PCL₆₁. The polymers were solvated in explicit water for 2 μs of simulations at 310.15 K. We found that the longer diblock system undergoes a morphological transition from an intermediate rod-like micelle to a prolate-sphere, while the micelle formed from the longer triblock system is a stable rod-like micelle. The two shorter diblock and triblock systems show similar self-assembly processes, both resulting in slightly prolate-spheres. The dynamics of the self-assembly is quantified in terms of chain radius of gyration, shape anisotropy, and hydration of the micelle cores. The final micelle structures are analyzed in terms of the local density components. We conclude that the CG model accurately describes the molecular mechanisms of self-assembly and the equilibrium micellar structures of hydrophilic and hydrophobic chains, including the quantity of solvent trapped inside the micellar core.     

A survey on book-embedding of planar graphs

The book-embedding problem arises in several area, such as very large scale integration (VLSI) design and routing multilayer printed circuit boards (PCBs). It can be used into various practical application fields. A book embedding of a graph G is an embedding of its vertices along the spine of a book, and an embedding of its edges to the pages such that edges embedded on the same page do not intersect. The minimum number of pages in which a graph G can be embedded is called the pagenumber or book-thickness of the graph G. It is an important measure of the quality for book-embedding. It is NP-hard to research the pagenumber of book-embedding for a graph G. This paper summarizes the studies on the book-embedding of planar graphs in recent years.     

Corrigendum to “New algebraic properties of an amalgamated algebra along an ideal”

At some point, after publication, we realized that Proposition 4.1(2) and Theorem 4.4 in [2 D’Anna, M., Finocchiaro, C. A., Fontana, M. (2016). New algebraic properties of an amalgamated algebra along an ideal. Commun. Algebra 44(5):1836–1851.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]] hold under the assumption (not explicitly declared) that B = f(A)+J. Furthermore, we provide here the exact value for the embedding dimension of A?^fJ, also when B≠f(A)+J, under the hypothesis that J is finitely generated as an ideal of the ring f(A)+J.