PROCEDURES FOR LOGIC AND ARITHMETIC OPERATIONS WITH DNA MOLECULES

2004 ◽  
Vol 15 (03) ◽  
pp. 461-474 ◽  
Author(s):  
AKIHIRO FUJIWARA ◽  
KEN'ICHI MATSUMOTO ◽  
WEI CHEN
Keyword(s):  
Truth Table ◽  
Boolean Operation ◽  
Dna Molecules ◽  
Boolean Operations ◽  
Arithmetic Operations ◽  
Input And Output ◽  
Dna Strands ◽  
Logic Operations ◽  
N Additions

In this paper, we consider procedures for logic and arithmetic operations with DNA molecules. We first show a DNA representation of n binary numbers of m bits, and propose a procedure to assign the same values for the representation. The representation enables addressing feature, and the procedure is applicable to n binary numbers of m bits in O(1) steps in parallel. Next, we propose a procedure for logic operations. The procedure enables any boolean operation whose input and output are defined by a truth table, and executes different kinds of boolean operations simultaneously for any pair of n binary numbers of m bits in O(1) lab steps using O(mn) DNA strands. Finally, we propose a procedure for additions of pairs of two binary numbers. The procedure executes O(n) additions of two m-bit binary numbers in O(1) steps using O(mn) DNA strands.

Sleptsov Net Computing

2018 ◽  
pp. 7731-7743 ◽  
Author(s):  
Dmitry A. Zaitsev
Keyword(s):  
Fuzzy Logic ◽  
Partial Differential Equations ◽  
Differential Equations ◽  
Flow Patterns ◽  
Data Encryption ◽  
Parallel Execution ◽  
Control Flow ◽  
Arithmetic Operations ◽  
Input And Output ◽  
New Models

Motivation for new models of hyper-computations was presented. Sleptsov net was introduced compared to Petri and Salwicki nets. A concept of universal Sleptsov net, as a prototype of a processor in Sleptsov net computing, was discussed. Small universal Sleptsov net that runs in polynomial time was constructed; it consists of 15 places and 29 transitions. Principles of programming in Sleptsov nets, as composition of reverse control flow and data, have been developed. Standard control flow patterns include sequence, branching, loop, and parallel execution. Basic modules, which implement efficiently copying, logic, and arithmetic operations, have been developed. Special dashed arcs were introduced for brief specification of input and output data of modules (subnets). Ways of hierarchical composition of a program via substitution of a transition by a module were discussed. Examples of Sleptsov net programs for data encryption, fuzzy logic, and partial differential equations have been presented. Enterprise implementation of Sleptsov net programming promises ultra-performance.

scholarly journals Sequence-Specific Detection of DNA Strands Using a Solid-State Nanopore Assisted by Microbeads

Micromachines ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1097
Author(s):  
Yin Zhang ◽  
Zengdao Gu ◽  
Jiabin Zhao ◽  
Liying Shao ◽  
Yajing Kan
Keyword(s):  
Low Cost ◽  
Local Concentration ◽  
Dna Molecules ◽  
Dna Translocation ◽  
Specific Sequence ◽  
Free Dna ◽  
Target Dna ◽  
Dna Strands ◽  
Ionic Pulse ◽  
Biotinylated Probes

Simple, rapid, and low-cost detection of DNA with specific sequence is crucial for molecular diagnosis and therapy applications. In this research, the target DNA molecules are bonded to the streptavidin-coated microbeads, after hybridizing with biotinylated probes. A nanopore with a diameter significantly smaller than the microbeads is used to detect DNA molecules through the ionic pulse signals. Because the DNA molecules attached on the microbead should dissociate from the beads before completely passing through the pore, the signal duration time for the target DNA is two orders of magnitude longer than free DNA. Moreover, the high local concentration of target DNA molecules on the surface of microbeads leads to multiple DNA molecules translocating through the pore simultaneously, which generates pulse signals with amplitude much larger than single free DNA translocation events. Therefore, the DNA molecules with specific sequence can be easily identified by a nanopore sensor assisted by microbeads according to the ionic pulse signals.

MTL: Memristor Ternary Logic Design

2020 ◽  
Vol 30 (15) ◽  
pp. 2050222
Author(s):  
Li Luo ◽  
Zhekang Dong ◽  
Xiaofang Hu ◽  
Lidan Wang ◽  
Shukai Duan
Keyword(s):  
Logic Circuits ◽  
Logic Design ◽  
Ternary Logic ◽  
Nanoscale Device ◽  
State Variable ◽  
Operation Speed ◽  
Input And Output ◽  
Single Input ◽  
Logic Operations ◽  
High Information

The nanoscale implementations of ternary logic circuits are particularly attractive because of high information density and operation speed that can be achieved by using emerging memristor technologies. Memristor is a nanoscale device with nonvolatility and adjustable multilevel states, which creates an intriguing opportunity for the implementation of ternary logic operations. This paper proposes a novel memristor-based design for stateful ternary logic, including AND, OR, NOT, NAND, NOR, and COPY operations. In the proposed memristor ternary logic (MTL) design, the resistance of memristor is the only logic state variable for representing the input and output. By sensing the value of the input memristors, the resistance of the output memristor changes accordingly. Furthermore, the MTL gates are not only capable of performing logic operations, but also storing logic values. To illustrate the potential of the methodology, a single-input-three-output ternary decoder is designed by using the proposed ternary logic circuits. Simulation results verify the effectiveness of the presented design.

Boolean operations, Borel sets, and Hausdorff's question

1996 ◽  
Vol 61 (4) ◽  
pp. 1287-1304
Author(s):  
Abhijit Dasgupta
Keyword(s):  
Polish Space ◽  
Descriptive Set Theory ◽  
Boolean Operation ◽  
Boolean Operations ◽  
Borel Sets ◽  
Systematic Fashion ◽  
Borel Hierarchy ◽  
The Difference ◽  
Projective Hierarchy ◽  
Descriptive Set

The study of infinitary Boolean operations was undertaken by the early researchers of descriptive set theory soon after Suslin's discovery of the important operation. The first attempt to lay down their theory in a systematic fashion was the work of Kantorovich and Livenson [5], where they call these the analytical operations. Earlier, Hausdorff had introduced the δs operations — essentially same as the monotoneω-ary Boolean operations, and Kolmogorov, independently of Hausdorff, had discovered the same objects, which were used in his study of the R operator.The ω-ary Boolean operations turned out to be closely related to most of the classical hierarchies over a fixed Polish space X, including, e. g., the Borel hierarchy (), the difference hierarchies of Hausdorff (Dη()), the C-hierarchy (Cξ) of Selivanovski, and the projective hierarchy (): for each of these hierarchies, every level can be expressed as the range of an ω-ary Boolean operation applied to all possible sequences of open subsets of X. In the terminology of Dougherty [3], every level is “open-ω-Boolean” (if and are collections of subsets of X and I is any set, is said to be -I-Boolean if there exists an I-ary Boolean operation Φ such that = Φ, i. e. is the range of Φ restricted to all possible I-sequences of sets from ). If in addition, the space X has a basis consisting of clopen sets, then the levels of the above hierarchies are also “clopen-ω-Boolean.”

Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami

Nanoscale ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 4707-4711 ◽  
Author(s):  
Lin Li ◽  
Ping Zhang ◽  
Jiang Li ◽  
Ying Wang ◽  
Yuhui Wei ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Dna Origami ◽  
Dna Molecules ◽  
Force Microscopy ◽  
Nanomechanical Properties ◽  
Atomic Force ◽  
Dna Strands

Characterization of the stiffness of thin DNA strands remains difficult.

PROCEDURES FOR MULTIPLE INPUT FUNCTIONS WITH DNA MOLECULES

2005 ◽  
Vol 16 (01) ◽  
pp. 37-54
Author(s):  
AKIHIRO FUJIWARA ◽  
SATOSHI KAMIO
Keyword(s):  
High Performance ◽  
Simple Procedure ◽  
Dna Molecules ◽  
Threshold Functions ◽  
Multiple Input ◽  
Dna Strands ◽  
Simple Logic ◽  
And Function ◽  
Logic Functions ◽  
Silicon Based

In recent works for high performance computing, computation with DNA molecules, that is, DNA computing, has been receiving considerable attention as an alternative for silicon based computers. In this paper, we propose two procedures for computing multiple input functions. We first propose a simple procedure for computing AND function. The procedure runs in O(1) steps using O(mn) DNA strands for n binary numbers of m bits. The procedure is also applicable to other simple logic functions, such as OR, NAND and NOR. We next propose a procedure for EX-OR function. The procedure runs in O(1) steps using O(mn2) DNA strands, and is also applicable to other functions, such as majority and threshold functions.

Experimental Demonstration of Hopfield Neural Network using DNA molecules

2011 ◽  
Vol 1346 ◽  
Author(s):  
Hayri E. Akin ◽  
Dundar Karabay ◽  
Allen P. Mills ◽  
Cengiz S. Ozkan ◽  
Mihrimah Ozkan
Keyword(s):  
Neural Network ◽  
Data Storage ◽  
Large Scale ◽  
Fault Tolerant ◽  
Hamiltonian Path ◽  
Hopfield Neural Network ◽  
Dna Molecules ◽  
Processing Power ◽  
Dna Strands ◽  
Molecular Reactions

ABSTRACTDNA Computing is a rapidly-developing interdisciplinary area which could benefit from more experimental results to solve problems with the current biological tools. In this study, we have integrated microelectronics and molecular biology techniques for showing the feasibility of Hopfield Neural Network using DNA molecules. Adleman’s seminal paper in 1994 showed that DNA strands using specific molecular reactions can be used to solve the Hamiltonian Path Problem. This accomplishment opened the way for possibilities of massively parallel processing power, remarkable energy efficiency and compact data storage ability with DNA. However, in various studies, small departures from the ideal selectivity of DNA hybridization lead to significant undesired pairings of strands and that leads to difficulties in schemes for implementing large Boolean functions using DNA. Therefore, these error prone reactions in the Boolean architecture of the first DNA computers will benefit from fault tolerance or error correction methods and these methods would be essential for large scale applications. In this study, we demonstrate the operation of six dimensional Hopfield associative memory storing various memories as an archetype fault tolerant neural network implemented using DNA molecular reactions. The response of the network suggests that the protocols could be scaled to a network of significantly larger dimensions. In addition the results are read on a Silicon CMOS platform exploiting the semiconductor processing knowledge for fast and accurate hybridization rates.

scholarly journals On Models and Capacity Bounds for DNA-based Storage Channels

2021 ◽  
Author(s):  
Zihui Yan ◽  
Cong Liang
Keyword(s):  
Data Storage ◽  
Storage System ◽  
Synchronization Error ◽  
Dna Molecules ◽  
Capacity Limits ◽  
Dna Storage ◽  
Capacity Bounds ◽  
Dna Strands ◽  
Term Data

In recent years, DNA-based systems have become a promising medium for long-term data storage. There are two layers of errors in DNA-based storage systems. The first is the dropouts of the DNA strands, which has been characterized in the shuffling-sampling channel. The second is insertions, deletions, and substitutions of nucleotides in individual DNA molecules. In this paper, we describe a DNA noisy synchronization error channel to characterize the errors in individual DNA molecules. We derive non-trivial lower and upper capacity bounds of the DNA noisy synchronization error channel based on information theory. By cascading these two channels, we provide theoretical capacity limits of the DNA storage system. These results reaffirm that DNA is a reliable storage medium with high storage density potential.

Sleptsov Net Computing

2019 ◽  
pp. 1660-1674 ◽  
Author(s):  
Dmitry A. Zaitsev
Keyword(s):  
Fuzzy Logic ◽  
Partial Differential Equations ◽  
Differential Equations ◽  
Flow Patterns ◽  
Data Encryption ◽  
Parallel Execution ◽  
Control Flow ◽  
Arithmetic Operations ◽  
Input And Output ◽  
New Models

Motivation for new models of hyper-computations was presented. Sleptsov net was introduced compared to Petri and Salwicki nets. A concept of universal Sleptsov net, as a prototype of a processor in Sleptsov net computing, was discussed. Small universal Sleptsov net that runs in polynomial time was constructed; it consists of 15 places and 29 transitions. Principles of programming in Sleptsov nets, as composition of reverse control flow and data, have been developed. Standard control flow patterns include sequence, branching, loop, and parallel execution. Basic modules, which implement efficiently copying, logic, and arithmetic operations, have been developed. Special dashed arcs were introduced for brief specification of input and output data of modules (subnets). Ways of hierarchical composition of a program via substitution of a transition by a module were discussed. Examples of Sleptsov net programs for data encryption, fuzzy logic, and partial differential equations have been presented. Enterprise implementation of Sleptsov net programming promises ultra-performance.

Transforming Activity in Both Complementary Strands of Bacillus subtilis DNA

1974 ◽  
Vol 29 (1-2) ◽  
pp. 63-65 ◽  
Author(s):  
Wolfgang Köhnlein
Keyword(s):  
Bacillus Subtilis ◽  
Gradient Centrifugation ◽  
Dna Molecules ◽  
Complementary Dna ◽  
Selective Degradation ◽  
Cscl Density Gradient ◽  
Dna Strands ◽  
Thymine Adenine ◽  
Acti Vity ◽  
Hybrid Dna

Abstract A Bacillus subtilis mutant (strain 168 try- thy-) with a thymine-adenine bias in complementary DNA strands was found. After BrU-incorporation into the DNA it was possible to separate physically hybrid DNA-molecules BrU-labeled in different complementary strands using CsCl density gradient centrifugation. These hybrid DNA preparations were used to investigate whether both strands can be informative during transformation. Taking advantage of the selective degradation of BrU-labeled DNA strands by long wavelength UV it was found that the loss of transforming acti vity was the same for both hybrid DNA preparations. Thus indicating that both complementary DNA strands can be genetically active during transformation. These results are supported by trans­ formation experiments with denatured and reannealed DNA-molecules and heteroduplex DNA-molecules.

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