Masami Hagiya

Theoretical Computer Science: Exploring New Frontiers of Theoretical Informatics

Breaking and fixing the Needham-Schroeder public-key protocol using FDR.- Reconciling Two Views of Cryptography.- Theory and Construction of Molecular Computers.- Theory and Construction of Molecular Computers.- On the hardness of the permanent.- List Decoding: Algorithms and Applications.- Approximation Algorithms for String Folding Problems.- Approximation Algorithms for String Folding Problems.- Fast multi-dimensional approximate string matching.- An Index for Two Dimensional String Matching Allowing Rotations.- Parallel Edge Coloring of a Tree on a Mesh Connected Computer.- Parallel Edge Coloring of a Tree on a Mesh Connected Computer.- Linear Time 1/2-Approximation Algorithm for Maximum Weighted Matching in General Graphs.- Parallel Approximation Algorithms for Maximum Weighted Matching in General Graphs.- It Is on the Boundary: Complexity Considerations for Polynomial Ideals.- It Is on the Boundary: Complexity Considerations for Polynomial Ideals.- An Efficient Parallel Algorithm for Scheduling Interval Ordered Tasks.- An Efficient Parallel Algorithm for Scheduling Interval Ordered Tasks.- Reducibility among combinatorial problems.- Task Distributions on Multiprocessor Systems.- Fast Interpolation Using Kohonen Self-Organizing Neural Networks.- Fast Interpolation Using Kohonen Self-Organizing Neural Networks.- Steganography Using Modern Arts.- Steganography Using Modern Arts.- Gossiping in Vertex-Disjoint Paths Mode in d-dimensional Grids and Planar Graphs.- Trade-Offs between Density and Robustness in Random Interconnection Graphs.- An effcient way for edge-connectivity augmentation.- The (? + 1)-Edge-Connectivity Augmentation Problem without Creating Multiple Edges of a Graph.- On the Approximability of NP-complete Optimization Problems.- On the Hardness of Approximating Some NP-Optimization Problems Related to Minimum Linear Ordering Problem.- How Many People Can Hide in a Terrain ?.- Maximum Clique and Minimum Clique Partition in Visibility Graphs.- Language recognition and the synchronization of cellular automata.- Real-Time Language Recognition by Alternating Cellular Automata.- Inducing an order on cellular automata by a grouping operation.- Damage Spreading and ?-Sensitivity on Cellular Automata.- Financial Applications of Monte Carlo and Quasi-Monte Carlo Methods.- Discrepancy Theory and Its Application to Finance.- Fully consistent extensions of partially defined Boolean functions with missing bits.- Fully Consistent Extensions of Partially Defined Boolean Functions with Missing Bitsv.- Dealing necessary and sufficient numbers of cards for sharing a one-bit secret key.- Characterization of Optimal Key Set Protocols.- Algebraic Complexity Theory.- On the Complexity of Integer Programming in the Blum-Shub-Smale Computational Model.- On Logarithmic Simulated Annealing.- On Logarithmic Simulated Annealing.- Specification and verification of concurrent programs in CESAR.- Hierarchical State Machines.- Validating firewalls in mobile ambients.- Ambient Groups and Mobility Types.- Multiway synchronization verified with coupled simulation.- An Asynchronous, Distributed Implementation of Mobile Ambients.- Graph types for monadic mobile processes.- Type Systems for Concurrent Processes: From Deadlock-Freedom to Livelock-Freedom, Time-Boundedness.- Aliasing Models for Mobile Objects.- Local ?-Calculus at Work: Mobile Objects as Mobile Processes.- Typed concurrent objects.- An Interpretation of Typed Concurrent Objects in the Blue Calculus.- Inductive definitions in the system coq. rules and properties.- A Higher-Order Specification of the ?-Calculus.- Compositionality through an operational semantics of contexts.- Open Ended Systems, Dynamic Bisimulation and Tile Logic.- Observe behaviour categorically.- Fibred Models of Processes: Discrete, Continuous, and Hybrid Systems.- The Equivalence Problem for Deterministic Pushdown Automata is Decidable.- On the Complexity of Bisimulation Problems for Pushdown Automata.- Session 2.4.- A Type-Theoretic Study on Partial Continuations.- Partially Typed Terms between Church-Style and Curry-Style.- Alternating Automata and Logics over Infinite Words.- Hypothesis Support for Information Integration in Four-Valued Logics.- Invited Talk 2.2.- Masaccio: A Formal Model for Embedded Components.- Session 2.5.- A Single Complete Refinement Rule for Demonic Specifications.- Reasoning about Composition Using Property Transformers and Their Conjugates.- Invited Talk 2.3.- Some New Directions in the Syntax and Semantics of Formal Languages.- Panel Discussion on New Challanges for TCS.- New Challenges for Theoretical Computer Science.- Algorithm Design Challenges.- Quantumization of Theoretical Informatics.- Two Problems in Wide Area Network Programming.- New Challenges for Computational Models.- Towards a Computational Theory of Everything.- Open Lectures.- On the Power of Interactive Computing.- The Varieties of Programming Language Semantics.

Robust and photocontrollable DNA capsules using azobenzenes.

Various three-dimensional structures have been created on a nanometer scale using the self-assembly of DNA molecules. However, ordinary DNA structures breakdown readily because of their flexibility. In addition, it is difficult to control them by inputs from environments. Here, we construct robust and photocontrollable DNA capsules using azobenzenes. This provides a method to construct DNA structures that can survive higher temperatures and can be controlled with ultraviolet irradiation.

Molecular Robotics: A New Paradigm for Artifacts

The rapid progress of molecular nanotechnology has opened the door to molecular robotics, which uses molecules as robot components. In order to promote this new paradigm, the Molecular Robotics Research Group was established in the Systems and Information Division of the Society of Instrument and Control Engineers (SICE) in 2010. The group consists of researchers from various fields including chemistry, biophysics, DNA nanotechnology, systems science and robotics, challenging this emerging new field. Last year, the group proposed a research project focusing on molecular robotics, and it was recently awarded a Grant-in-Aid for Scientific Research on Innovative Areas (FY2012-16), one of the large-scale research projects in Japan, by MEXT (Ministry of Education, Culture, Sports, Science and Technology, JAPAN). Here, we wish to clarify the fundamental concept and research direction of molecular robotics. For this purpose, we present a comprehensive view of molecular robotics based on the discussions held in the Molecular Robotics Research Group.

On a New Method for Dataflow Analysis of Java Virtual Machine Subroutines

The bytecode verifier of the Java Virtual Machine, which statically checks the type safety of Java bytecode, is the basis of the security model of Java and guarantees the safety of mobile code sent from an untrusted remote host. However, the type system for Java bytecode has some technical problems, one of which is in the handling of sub-routines. Based on the work of Stata and Abadi and that of Qian, this paper presents yet another type system for Java Virtual Machine sub-routines. Our type system includes types of the form last(x). A value whose type is last(x) is the same as that of the x-th variable of the caller of the subroutine. In addition, we represent the type of a return address by the form return(n), which means returning to the n-th outer caller. By virtue of these types, we can analyze instructions purely in terms of type, and as a result the correctness proof of bytecode verification becomes extremely simple. Moreover, for some programs, our method is more powerful than existing ones. In particular, our method has no restrictions on the number of entries and exits of a subroutine.

A decision procedure for the alternation-free two-way modal µ-calculus

The satisfiability checking problem is known to be decidable for a variety of modal/temporal logics such as the modal μ-calculus, but effective implementation has not necessarily been developed for all such logics. In this paper, we propose a decision procedure using the tableau method for the alternation-free two-way modal μ-calculus. Although the size of the tableau set maintained in the method might be large for complex formulas, the set and the operations on it can be expressed using BDD and therefore we can implement the method in an effective way.

Joining and rotating data with molecules

DNA-based computing is an attempt to solve computational problems with a large number of DNA molecules. Many theoretical results have been reported so far, but their conclusions are seldom supported in experiments. We suggest a data encoding in the form of (tag data tag)+, and report our experimental results of performing concatenation and rotation of DNA. Our results also show the possibility of join and other operations in a relational database with molecules.

From Molecular Computing to Molecular Programming

The purpose of this article is to survey the research in molecular computing, including the achievements of the Japanese Molecular Computer Project, and foresee the future of the field. In addition to describing the major achievements of the project, Suyamas Dynamic Programming Molecular Computer and Sakamotos Hairpin Engines, we summarize the computational paradigms related to molecular computing in order to provide a perspective on the field. We finally explain the idea of molecular programming, that the author is currently advocating.

Foundation of Logic Programming Based on Inductive Definition

A logical system of inference rules intended to give the foundation of logic programs is presented. The distinguished point of the approach taken here is the application of the theory of inductive definitions, which allows us to uniformly treat various kinds of induction schema and also allows us to regardnegation as failure as a kind of induction schema. This approach corresponds to the so-called least fixpoint semantics. Moreover, in our formalism, logic programs are extended so that a condition of a clause may be any first-order formula. This makes it possible to write a quantified specification as a logic program. It also makes the class of induction schemata much larger to include the usual course-of-values inductions.

Tunable synthetic phenotypic diversification on Waddington’s landscape through autonomous signaling

Phenotypic diversification of cells is crucial for developmental and regenerative processes in multicellular organisms. The diversification concept is described as the motion of marbles rolling down Waddington’s landscape, in which the number of stable states changes as development proceeds. In contrast to this simple concept, the complexity of natural biomolecular processes prevents comprehension of their design principles. We have constructed, in Escherichia coli, a synthetic circuit with just four genes, which programs cells to autonomously diversify as the motion on the landscape through cell–cell communication. The circuit design was based on the combination of a bistable toggle switch with an intercellular signaling system. The cells with the circuit diversified into two distinct cell states, “high” and “low,” in vivo and in silico, when all of the cells started from the low state. The synthetic diversification was affected by not only the shape of the landscape determined by the circuit design, which includes the synthesis rate of the signaling molecule, but also the number of cells in the experiments. This cell-number dependency is reminiscent of the “community effect”: The fates of developing cells are determined by their number. Our synthetic circuit could be a model system for studying diversification and differentiation in higher organisms. Prospectively, further integrations of our circuit with different cellular functions will provide unique tools for directing cell fates on the population level in tissue engineering.

Cache-Based Model Checking of Networked Applications: From Linear to Branching Time

Many applications are concurrent and communicate over a network. The non-determinism in the thread and communication schedules makes it desirable to model check such systems. However, a simple state space exploration scheme is not applicable, as backtracking results in repeated communication operations. A cache-based approach solves this problem by hiding redundant communication operations from the environment. In this work, we propose a change from a linear-time to a branching-time cache, allowing us to relax restrictions in previous work regarding communication traces that differ between schedules. We successfully applied the new algorithm to real-life programs where a previous solution is not applicable.