Robust and emergent Physarum logical-computing

There have been many attempts for realization of emergent computing, but the notion of emergent computing is still ambiguous. In an open system, emergence and an error cannot be specified distinctly, because they are dependent on the dis-equilibration process between local and global behaviors. To manifest such an aspect, we implement a Boolean gate as a biological device made of slime mold Physarum polycephalum. A Physarum (slime mold) Boolean gate could be an internally instable machine, while it has the potential for emergent computing. First, we examined whether Physarum Boolean gate works properly, and then examined its behaviors when the gate is collapsed in terms of hardware. The behavior of Physarum changes and self-repairing computing is achieved as a result. The self-repairing against internal failure is one of attributes of emergent and robust computing.     

Amoeba-based computing for traveling salesman problem: Long-term correlations between spatially separated individual cells of Physarum polycephalum

A single-celled, multi-nucleated amoeboid organism, a plasmodium of the true slime mold Physarum polycephalum, can perform sophisticated computing by exhibiting complex spatiotemporal oscillatory dynamics while deforming its amorphous body. We previously devised an “amoeba-based computer (ABC)” to quantitatively evaluate the optimization capability of the amoeboid organism in searching for a solution to the traveling salesman problem (TSP) under optical feedback control. In ABC, the organism changes its shape to find a high quality solution (a relatively shorter TSP route) by alternately expanding and contracting its pseudopod-like branches that exhibit local photoavoidance behavior. The quality of the solution serves as a measure of the optimality of which the organism maximizes its global body area (nutrient absorption) while minimizing the risk of being illuminated (exposure to aversive stimuli). ABC found a high quality solution for the 8-city TSP with a high probability. However, it remains unclear whether intracellular communication among the branches of the organism is essential for computing. In this study, we conducted a series of control experiments using two individual cells (two single-celled organisms) to perform parallel searches in the absence of intercellular communication. We found that ABC drastically lost its ability to find a solution when it used two independent individuals. However, interestingly, when two individuals were prepared by dividing one individual, they found a solution for a few tens of minutes. That is, the two divided individuals remained correlated even though they were spatially separated. These results suggest the presence of a long-term memory in the intrinsic dynamics of this organism and its significance in performing sophisticated computing.     

Cell size in Dictyostelium

Cellular slime mold amoebae have become a model system for the study of cell motility and the cytoskeleton. A basic problem which all cells face that involves the cytoskeleton is how to control their size. The varied ways in which cellular slime mold amoebae change their cell size--by changing the size at which division occurs, by cell fusion, and by control over cytokinesis--are reviewed. A model is presented which attempts to explain how the mechanisms affected in certain cytokinesis mutants in Dictyostelium discoideum known as phg mutants could be involved in control of cell size in the predatory slime mold Dictyostelium caveatum.     

Sounds Synthesis with Slime Mould of Physarum Polycephalum

This paper introduces a novel application of bionic engineering: a bionic musical instrument using Physarum polycephalum. Physarum polycephalum is a huge single cell with thousands of nuclei, which behaves like a giant amoeba. During its foraging behavior this plasmodium produces electrical activity corresponding to different physiological states. We developed a method to render sounds from such electrical activity and thus represent spatio-temporal behavior of slime mould in a form apprehended auditorily. The electrical activity is captured by various electrodes placed on a Petri dish containing the cultured slime mold. Sounds are synthesized by a bank of parallel sinusoidal oscillators connected to the electrodes. Each electrode is responsible for one partial of the spectrum of the resulting sound. The behavior of the slime mould can be controlled to produce different timbres.     

Minimal model of a cell connecting amoebic motion and adaptive transport networks

A cell is a minimal self-sustaining system that can move and compute. Previous work has shown that a unicellular slime mold, Physarum, can be utilized as a biological computer based on cytoplasmic flow encapsulated by a membrane. Although the interplay between the modification of the boundary of a cell and the cytoplasmic flow surrounded by the boundary plays a key role in Physarum computing, no model of a cell has been developed to describe this interplay. Here we propose a toy model of a cell that shows amoebic motion and can solve a maze, Steiner minimum tree problem and a spanning tree problem. Only by assuming that cytoplasm is hardened after passing external matter (or softened part) through a cell, the shape of the cell and the cytoplasmic flow can be changed. Without cytoplasm hardening, a cell is easily destroyed. This suggests that cytoplasmic hardening and/or sol-gel transformation caused by external perturbation can keep a cell in a critical state leading to a wide variety of shapes and motion.     

Chemotaxis toward carbohydrates and amino acids in Physarum polycephalum

A method is described for assaying chemotaxis in the acellular slime mold Physarum polycephalum. It consists of measuring the amount of plasmodium that moves on a strip of nitrocellulose membrane filter Millipore in response to a gradient of an attractant. Time course of chemotactic response of the slime mold is described. Different factors that affect chemotaxis in the slime mold such as: culture care and stage of growth of microplasmodia, substratum used for cell movement, nature of the gradient, effect of salts, pH and temperature are described. From concentration-response curves for different attractants several parameters of the chemotactic effect, such as threshold concentration, half maximal concentration, and maximal effective concentration can be determined. As a group, sugars are more effective chemotactic agents than amino acids. Glucose and galactose, which support the growth of the slime mold, are shown to have high positive chemotactic effect. 3-O-Methyl- -glucose and 2-deoxy- -glucose are two sugars that do not support growth but are very effective attractants. Conversely, fructose which supports slime mold growth is at best a weak attractant. The results support the view that the chemotactic effects of different sugars are not dependent on their growth-supporting value.     

Fast parallel molecular solutions for DNA-based supercomputing: the subset-product problem

In this paper our main purpose is to give molecular solutions for the subset-product problem. In order to achieve this, we propose three DNA-based algorithms--parallel adder, parallel multiplier and parallel comparator--that formally verify our designed molecular solutions for the subset-product problem. We also show that Boolean circuits are not needed to perform mathematical operations on a molecular computer. Furthermore, this work indicates that the subset-product problem is solved and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations.     

Slime mold inspired routing protocols for wireless sensor networks

Many biological systems are composed of unreliable components which self-organize effectively into systems that achieve a balance between efficiency and robustness. One such example is the true slime mold Physarum polycephalum which is an amoeba-like organism that seeks and connects food sources and efficiently distributes nutrients throughout its cell body. The distribution of nutrients is accomplished by a self-assembled resource distribution network of small tubes with varying diameter which can evolve with changing environmental conditions without any global control. In this paper, we exploit two different mechanisms of the slime mold??s tubular network formation process via laboratory experiments and mathematical behavior modeling to design two corresponding localized routing protocols for wireless sensor networks (WSNs) that take both efficiency and robustness into account. In the first mechanism of path growth, slime mold explores its immediate surroundings to discover and connect new food sources during its growth cycle. We adapt this mechanism for a path growth routing protocol by treating data sources and sinks as singular potentials to establish routes from the sinks to all the data sources. The second mechanism of path evolution is the temporal evolution of existing tubes through nonlinear feedback in order to distribute nutrients efficiently throughout the organism. Specifically, the diameters of tubes carrying large fluxes of nutrients grow to expand their capacities, and tubes that are not used decline and disappear entirely. We adapt the tube dynamics of the slime mold for a path evolution routing protocol. In our protocol, we identify one key adaptation parameter to adjust the tradeoff between efficiency and robustness of network routes. Through extensive realistic network simulations and ideal closed form or numerical computations, we validate the effectiveness of both protocols, as well as the efficiency and robustness of the resulting network connectivity.     

Fluorographic detection of tritiated glycopeptides and oligosaccharides separated on polyacrylamide gels: analysis of glycans from Dictyostelium discoideum glycoproteins

Previous workers have shown that oligosaccharides and glycopeptides can be separated by electrophoresis in buffers containing borate ions. However, normal fluorography of tritium-labeled structures cannot be performed because the glycans are soluble and can diffuse during equilibration with scintillants. This problem has been circumvented by equilibration of the gel with 2,5-diphenyloxazole (PPO) prior to electrophoresis. The presence of PPO in the gel during electrophoresis does not alter mobility of the glycopeptides and oligosaccharides. After electrophoresis, the gel is simply dried and fluorography performed. This allows sensitive and precise comparisons of labeled samples in parallel lanes of a slab gel and, since mobilities are highly reproducible, between different gels. The procedure is preparative in that after fluorography the gel bands can be quantitatively eluted for further study, without any apparent modification by the procedure. In this report, the procedure is illustrated by fractionation of both neutral and anionic glycopeptides produced by the cellular slime mold Dictyostelium discoideum.     

Phosphofructokinase from Dictyostelium discoideum is a potent inhibitor of tubulin polymerization

We identified the nonallosteric phosphofructokinase from the slime mold Dictyostelium discoideum as a potent protein factor that inhibits the rate of polymerization of tubulin at a molar ratio of 1 molecule to about 300 tubulin dimers for half-maximal action (IC50 = 32 nM). This effect was (i) assessed by turbidity measurements, pelleting of microtubules, and electron microscopy, (ii) observed when tubulin assembly was induced by taxol as well as by GTP in the presence of microtubule-associated proteins or glutamate, and (iii) specific as it was not produced by the phosphofructokinase from rabbit muscle. Also in contrast to the latter, neither tubulin nor microtubules modified the catalytic activity of the slime mold isozyme. Immunoelectron microscopy provided further evidence that D. discoideumphosphofructokinase physically interacts with tubulin, leading to the formation of aggregates. The process seems to be reversible since microtubules eventually formed in the presence of the inhibitor with concomitant reduction of tubulin aggregates. Limited proteolysis by subtilisin showed that the hypervariable C-termini of tubulin is not involved in the interaction with the enzyme. The possible physiological relevance of this novel function of D. discoideum phosphofructokinase different from its glycolytic action is discussed.     

Pallidin. Purification and characterization of a carbohydrate-binding protein from Polysphondylium pallidum implicated in intercellular adhesion.

A carbohydrate-binding protein from Polysphondylium pallidum, a species of cellular slime mold, was purified to homogeneity by adsorption to formalinized erythrocytes and elution with D-galactose. The protein, for which we propose the name PALLIDIN, is assayed by its activity as an agglutinin of erythrocytes. It was previously shown to have different carbohydrate-binding specificities than discoidin, a carbohydrate-binding protein from Dictyostelium discoideum, another species of slime mold. Evidence has been presented previously that each of these proteins is detectable on the cell surface. In the present report we show that the physico-chemical properties of pallidin are different from discoidin. Pallidin has a subunit molecular weight of 24 800 +/- 1100 determined by polyacrylamide electrophoresis in the presence of dodecyl sulfate and 2-mercaptoethanol, compared to 26 100 +/- 1000 for discoidin. The weight-average molecular weight of pallidin is 250 000 +/- 50 000 determined by equilibrium sedimentation in the presence of D-galactose compared to 100 000 +/- 2000 for discoidin. In equilibrium sedimentation studies, pallidin exhibited some heterogeneity at equilibrium while discoidin was homogeneous. The amino acid composition of pallidin is generally similar but clearly different from the composition of discoidin. The isoelectric point of pallidin is 7.0 compared to 6.1 for discoidin. Like discoidin, pallidin contains no detectable hexosamine or neutral sugar. These results establish that agglutinins from two species of cellular slime molds are distinct. The different properties of the cell-surface agglutinins, pallidin and discoidin, are consistent with their suggested role in species-specific cellular recognition and adhesion in the species of slime mold from which they are derived.     

Identification of substrates for transglutaminase in Physarum polycephalum, an acellular slime mold, upon cellular mechanical damage

Transglutaminases are Ca(2+)-dependent enzymes that post-translationally modify proteins by crosslinking or polyamination at specific polypeptide-bound glutamine residues. Physarum polycephalum, an acellular slime mold, is the evolutionarily lowest organism expressing a transglutimase whose primary structure is similar to that of mammalian transglutimases. We observed transglutimase reaction products at injured sites in Physarum macroplasmodia upon mechanical damage. With use of a biotin-labeled primary amine, three major proteins constituting possible transglutimase substrates were affinity-purified from the damaged slime mold. The purified proteins were Physarum actin, a 40 kDa Ca(2+)-binding protein with four EF-hand motifs (CBP40), and a novel 33 kDa protein highly homologous to the eukaryotic adenine nucleotide translocator, which is expressed in mitochondria. Immunochemical analysis of extracts from the damaged macroplasmodia indicated that CBP40 is partly dimerized, whereas the other proteins migrated as monomers on SDS/PAGE. Of the three proteins, CBP40 accumulated most significantly around injured areas, as observed by immunofluoresence. These results suggested that transglutimase reactions function in the response to mechanical injury.     

DNA芯片在0-1规划问题中的应用

生物芯片技术和DNA计算分别是近年来生命科学与信息科学的新兴研究领域,对信息高度并行的获取与处理是二者的本质特性.而0-1规划问题作为运筹学中一个重要的问题,到目前为止还没有好的算法.在DNA计算和DNA芯片基础上,提出了基于DNA芯片解决0-1规划问题的DNA计算新模型,与以往DNA计算模型相比,该模型具有高信息量和操作易自动化的优点.同时指出DNA芯片技术有望作为新型生物计算的芯片.     

A parallel programming interface for out-of-core cluster applications

Clusters of workstations are a practical approach to parallel computing that provide high performance at a low cost for many scientific and engineering applications. In order to handle problems with increasing data sets, methods supporting parallel out-of-core computations must be investigated. Since writing an out-of-core version of a program is a difficult task and virtual memory systems do not perform well in some cases, we have developed a parallel programming interface and the support library to provide efficient and convenient access to the out-of-core data. This paper focuses on how these components extend the range of problem sizes that can be solved on the cluster of workstations. Execution time of Jacobi iteration when using our interface, virtual memory and PVFS are compared to characterize the performance for various problem sizes, and it is concluded that our new interface significantly increases the sizes of problems that can be efficiently solved. Jianqi Tang received B.Sc. and M.Sc. from Harbin Institute of Technology in 1997 and 1999 respectively, both in computer application. Currently, she is a Ph.D. candidate at the Department of Computer Science and engineering, Harbin Institute of Technology. She has participated in several National research projects. Her research interests include parallel computing, parallel I/O and grid computing. Binxing Fang received M.Sc. in 1984 from Tsinghua University and Ph.D. from Harbin Institute of Technology in 1989, both in computer science. From 1990 to 1993 he was with National University of Defense Technology as a postdoctor. Since 1984, he is a faculty member at the Department of Computer Science and engineering of Harbin Institute of Technology, where he is presently a Professor. He is a Member of the National Information Expert Consultant Group and a Standing Member of the Council of Chinese Society of Communications. His research efforts focus on parallel computing, computer network and information security. Professor Fang has implemented over 30 projects from the state and ministry/province. Mingzeng Hu was born in 1935. He has been with the Department of Computer Science and engineering in Harbin Institute of Technology since 1958, where he is currently a Professor. He was a visiting scholar in the Siemens Company, Germany from 1978 to 1979, a visiting associate professor in Chiba University, Japan from 1984 to 1985, and a visiting professor in York University, Canada from 1989 to 1995. He is the Director of the National Key Laboratory of Computer Information Content Security. He is also a Member of 3rd Academic Degree Committee under the State Council of China. Professor Hu’s research interests include high performance computer architecture and parallel processing technology, fault tolerant computing, network system, VL design, and computer system security technology. He has implemented many projects from the state and ministry/province and has won several Ministry Science and Technology Progress Awards. He published over 100 papers in core journals home and abroad and one book. Professor Hu has supervised over 20 doctoral students. Hongli Zhang received M.Sc in computer system software in 1996 and Ph.D. in computer architecture in 1999 from Harbin Institute of Technology. Currently, she is an Associate Professor at the Department of Computer Science and engineering, Harbin Institute of Technology. Her research interests include computer network security and parallel computing.     

Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens

We have performed computer searches in the database of known protein sequences for proteins similar in sequence to bacteriophage regulatory proteins of known 3-D structure. The searches are more selective than other methods due to the use of a length-dependent threshold in sequence similarity, above which structural homology is implied with high certainty. Two probable DNA binding proteins were identified which are predicted to have a three-dimensional structure very similar to bacteriophage cro and repressor proteins. Approximate three-dimensional model coordinates are available from the authors. Both proteins contain the helix-turn-helix sequence motif typical of a wide class of DNA binding proteins and their function is deduced by analogy to sequence-similar proteins of known function. We predict that the Y.Smal protein in the restriction-modification enzyme gene locus of the enterobacterium serratia marcescens is a regulator of endonuclease expression; and, that the vegetative specific gene VSH7 of the slime mold dictyostelium discoideum codes for a regulator of gene expression specific for the slime mold growth phase before the onset of the developmental program. Point mutations that would have a strong effect on growth regulation phenotype are suggested. The VSH7 protein would be the first eukaryotic representative of the cro/phage repressor class.     

Anti-leukemic activities of Dictyostelium secondary metabolites: a novel aromatic metabolite, 4-methyl-5-n-pentylbenzene-1,3-diol, isolated from Dictyostelium mucoroides suppresses cell growth in human leukemia K562 and HL-60 cells

It has previously been shown that DIF-1, a differentiation-inducing factor of the cellular slime mold Dictyostelium discoideum, possesses antitumor activities in mammalian tumor cells and that neuronal differentiation of PC12 cells can be induced with furanodictines (FDs), aminosugar analogs found in D. discoideum, or dictyoglucosamines (DGs), N-acetyl glucosamine derivatives (DG-A from D. purpureum and DG-B from D. discoideum). Thus, cellular slime molds are attractive natural resources that may provide valuable lead compounds to be utilized in the field of pharmacology and medicine. In this study, we have isolated a novel aromatic compound, 4-methyl-5-n-pentylbenzene-1,3-diol (MPBD), from fruiting bodies of the cellular slime mold D. mucoroides and assessed the in vitro antiproliferative activities of MPBD, FDs, and DGs in human leukemia K562 and HL-60 cells. MPBD at 20-80 microM dose-dependently suppressed cell growth in both K562 and HL-60 cells. While FDs at 10-80 microM did not affect cell growth, DGs at 10-40 microM dose-dependently suppressed cell growth in the cells. Although we failed to find the roles of FDs and DGs in the original organisms, MPBD at 5-20 microM was found to promote stalk cell formation in D. discoideum. The present results indicate that MPBD, DGs or their derivatives may have therapeutic potential in the treatment of cancer and confirm our expectations regarding cellular slime molds as drug resources.     

分子信标芯片计算在0-1整数规划问题中的应用

生物芯片技术和DNA计算分别是近年来生命科学与信息科学的新兴研究领域,对信息高度并行的获取与处理是二者的本质特性．而0-1整数规划问题作为运筹学中一个重要的问题,到目前为止还没有好的算法．在DNA计算和DNA芯片基础上,提出了基于分子信标芯片解决0-1整数规划问题的DNA计算新模型．与以往DNA计算模型相比,该模型具有高信息量和操作易自动化的优点,同时指出分子信标芯片技术有望作为新型生物计算的芯片．     

Bacterial glycoconjugates are natural ligands for the carbohydrate binding site of discoidin I and influence its cellular compartmentalization

Klebsiella pneumoniae, Escherichia coli, and Bacillus subtilis, bacteria commonly eaten by Dictyostelium discoideum, contain glycoconjugates that bind discoidin I, a lectin synthesized by the slime mold as it differentiates. In cells fed bacteria that contain abundant discoidin I-binding glycoconjugates, these ligands and endogenous discoidin I accumulated in specialized structures called multilamellar bodies. In contrast, in cells fed bacteria that had been treated to thoroughly deplete them of discoidin I-binding glycoconjugates, neither endogenous discoidin I nor complementary glycoconjugates were found in the multilamellar bodies. In such cells discoidin I was located in the cytoplasm, as indicated by both immunohistochemistry with the electron microscope and immunoassay of subcellular fractions. The results indicate that a function of the carbohydrate-binding site of discoidin I is to interact with bacterial glycoconjugates, which the slime mold does not degrade. This interaction directs compartmentalization of the lectin in multilamellar bodies and its externalization from the cell in these structures.     

A computer simulation of chemical signaling during the aggregation phase of Dictyostelium discoideum

A model for chemical signaling among cells during the aggregation phase of the cellular slime mold Dictyostelium discoideum is simulated using a computer. The resulting chemical concentration profiles are considered in terms of experimental observations. Considerable emphasis is placed on examination of the chemical environment at the center of an aggregation. Its unique nature suggests a mechanism for initially establishing the location of center. Effects of the dimensionality of the simulation universe are also discussed.     

Comparative study of histones from slime mold Physarum polycephalum and calf thymus

The histones from slime mold Physarum polycephalum and calf thymus were characterized in terms of some physico-chemical properties. The molecular weights of six principal histone fractions of Ph. polycephalum were found to be the following: P1--22 700, P3--15 700, P4a--15 000, P4b--14 300, P5--12 800 and P6--10 500. Electrophoretically homogenous histone fractions H1, H2b and H4 of calf thymus and histones P1, P3, P4b and P6 of slime mold were obtained by gel-filtration on Acrylex P-60. These findings suggest that fractions P1, P4a, P4b, P5 and P6 of slime mold Ph. polycephalum are homologus with respect to the histone fractions H1, H3, H2b, H2a and H4 of calf thymus. Only fraction P3 has no corresponding fraction in the calf thymus histones; a fraction corresponding to histone P3 of slime mold was absent.