Darko Stefanovic
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  • Publications
    • Science Forum: Building a community to engineer synthetic cells and organelles from the bottom-up
    • Complexing Deoxyribozymes with RNA Aptamers for Detection of the Small Molecule Theophylline
    • Diverse applications of DNAzymes in computing and nanotechnology
    • Development and Application of Catalytic DNA in Nanoscale Robotics
    • Robust heterochiral strand displacement using leakless translators
    • Reservoir Computing with Random Chemical Systems
    • The effect of polyvalency on tethered molecular walkers on independent 1D tracks
    • Repeated Reuse of Deoxyribozyme-Based Logic Gates
    • An example preprint / working paper
    • Microcompartments for Protection and Isolation of Nanoscale DNA Computing Elements
    • A simplified account of cooperative effects in molecular walker teams
    • Verifiably Lazy: Verified Compilation of Call-by-Need
    • A Microsphere-Supported Lipid Bilayer Platform for DNA Reactions on a Fluid Surface
    • Feedforward Chemical Neural Network: A Cellular Chemical System That Learns XOR
    • Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes
    • Towards Temporal Logic Computation Using DNA Strand Displacement Reactions
    • Logic Circuits Based on Molecular Spider Systems
    • Modular Verification of Chemical Reaction Network Encodings via Serializability Analysis
    • Cactus Environment Machine: Shared Environment Call-by-Need
    • Supervised Learning in Adaptive DNA Strand Displacement Networks
    • Stella: a Python-Based Domain-Specific Language for Simulations
    • Computational Capacity and Energy Consumption of Complex Resistive Switch Networks
    • Scalable Design of Logic Circuits Using an Active Molecular Spider System
    • An example journal article
    • Supervised Learning in an Adaptive DNA Strand Displacement Circuit
    • Hierarchical Composition of Memristive Networks for Real-Time Computing
    • Product reservoir computing: Time-Series Computation With Multiplicative Neurons
    • A Principled Approach to HPC Event Monitoring
    • Exploring Transfer Function Nonlinearity in Echo State Networks
    • A Unified Sensor Architecture for Isothermal Detection of Double-Stranded DNA, Oligonucleotides, and Small Molecules
    • Towards a Calculus of Echo State Networks
    • Design of a Biochemical Circuit Motif for Learning Linear Functions
    • Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering
    • Natural Computing, Volume 13, Issue 4
    • Pattern Formation by Spatially Organized Approximate Majority Reactions
    • Reservoir Computing Approach to Robust Computation Using Unreliable Nanoscale Networks
    • Visual Displays That Directly Interface and Provide Read Outs of Molecular States via Molecular Graphics Processing Units
    • A Model for Variation- and Fault-Tolerant Digital Logic Using Self-Assembled Nanowire Architectures
    • Signal Propagation in Multi-Layer DNAzyme Cascades Using Structured Chimeric Substrates
    • Exercises in Molecular Computing
    • Catalytic Molecular Logic Devices by DNAzyme Displacement
    • Training an Asymmetric Signal Perceptron Through Reinforcement in an Artificial Chemistry
    • Lattice Gases With a Point Source
    • The Effects of Multivalency and Kinetics in Nanoscale Search by Molecular Spiders
    • Catalytic Molecular Walkers: Aspects of Product Release
    • DNA Reservoir Computing: A Novel Molecular Computing Approach
    • Iterative Self-Assembly With Dynamic Strength Transformation and Temperature Control
    • Modular Verification of DNA Strand Displacement Networks via Serializability Analysis
    • First-Passage Time Properties of Molecular Spiders
    • An example conference paper
    • Computing Game Strategies
    • Superdiffusive Transport by Multivalent Molecular Walkers Moving Under Load
    • Cooperative Linear Cargo Transport With Molecular Spiders
    • Maze Exploration With Molecular-Scale Walkers
    • Towards a Biomolecular Learning Machine
    • DNA18, 18th International Conference on DNA Computing and Molecular Programming
    • Representing Uniqueness Constraints in Object-Relational Mapping: The Natural Entity Framework
    • The Effects of Multivalency and Kinetics in Nanoscale Search by Molecular Spiders
    • Optimizing Cross-Reactivity With Evolutionary Search for Sensors
    • Some Experiments and Models in Molecular Computing and Robotics
    • Multiple Molecular Spiders With a Single Localized Source - the One-Dimensional Case
    • Multivalent Random Walkers - A Model for Deoxyribozyme Walkers
    • ISO: Numeric Representation of Nucleic Acid Form
    • Chemistry at a Higher Level of Abstraction
    • Mechanism of Diffusive Transport in Molecular Spider Models
    • Shape Analysis With Reference Set Relations
    • Training a Molecular Automaton to Play a Game
    • Molecules That Reason
    • Advancing the Deoxyribozyme-Based Logic Gate Design Process
    • High-Resolution Cross Reactive Array for Alkaloids
    • Molecular Automata
    • Sharing Analysis of Arrays, Collections, and Recursive Structures
    • DNA Computers for Work and Play
    • Wake Up and Smell the Coffee: Evaluation Methodology for the 21st Century
    • Identification of Heap-Carried Data Dependence via Explicit Store Heap Models
    • Efficient Context-Sensitive Shape Analysis With Graph Based Heap Models
    • Emerging Models of Computation Directions in Molecular Computing
    • Nanocomputing
    • Heap Analysis in the Presence of Collection Libraries
    • A Rational Approach to Minimal High-Resolution Cross-Reactive Arrays
    • A Static Heap Analysis for Shape and Connectivity: Unified Memory Analysis: The Base Framework
    • Medium Scale Integration of Molecular Logic Gates in an Automaton
    • The DaCapo Benchmarks: Java Benchmarking Development and Analysis
    • Behavior of Polycatalytic Assemblies in a Substrate Displaying Matrix
    • On the Prediction of Java Object Lifetimes
    • Generating Object Lifetime Traces With Merlin
    • Characterization of Transverse Channel Concentration Prouploads Obtainable With a Class of Microfluidic Networks
    • Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder
    • Solution Phase Molecular Scale Computation With Deoxyribozyme Based Logic Gates and Fluorescent Readouts
    • Designing Nucleotide Sequences for Computation a Survey of Constraints
    • Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks
    • Deoxyribozyme-Based Ligase Logic Gates and Their Initial Circuits
    • Comparison of Garbage Collectors Operating in a Large Address Space
    • A Study of Garbage Collection With a Large Address Space for Server Applications
    • Randomized Instruction Set Emulation
    • Computing With Nucleic Acids
    • The Triton Branch Predictor
    • Building the Components for a Biomolecular Computer
    • Randomized Instruction Set Emulation to Disrupt Binary Code Injection Attacks
    • Model Checking Reconfigurable Processor Configurations for Safety Properties
    • A Deoxyribozyme-Based Molecular Automaton
    • Deoxyribozyme-Based Half Adder
    • Implicit-OR tiling of Deoxyribozymes: Construction of Molecular Scale OR, NAND, and Four-Input Logic Gates
    • Older-First Garbage Collection in Practice: Evaluation in a Java Virtual Machine
    • Error-Free Garbage Collection Traces: How to Cheat and Not Get Caught
    • Deoxyribozyme-Based Logic Gates
    • SIND: A Framework for Binary Translation
    • On Models for Object Lifetime Distributions
    • Limits and Graph Structure of Available Instruction Level Parallelism
    • On Availability of Bit-Narrow Operations in General-Purpose Applications
    • Age-Based Garbage Collection
    • Properties of Age Based Automatic Memory Reclamation Algorithms
    • Oldest-First Garbage Collection
    • Learning to Schedule Straight-Line Code
    • The Character of the Instruction Scheduling Problem
    • Characterisation of Object Behaviour in Standard ML of New Jersey
    • Generational Copying Garbage Collection for Standard ML: A Quantitative Study
    • The Garbage Collection Toolkit as an Experimentation Tool
    • A Comparative Performance Evaluation of Write Barrier Implementations

Diverse applications of DNAzymes in computing and nanotechnology

Aug 6, 2021·
Matthew R. Lakin
,
Darko Stefanovic
,
Milan N. Stojanovic
· 0 min read
DOI
Type
6
Publication
S. Müller, B. Masquida, W. Winkler (eds.), Ribozymes, Chapter 25. Wiley-VCH
Last updated on Aug 6, 2021
← Complexing Deoxyribozymes with RNA Aptamers for Detection of the Small Molecule Theophylline Nov 5, 2021
Development and Application of Catalytic DNA in Nanoscale Robotics Jan 15, 2021 →

© 2024 Darko Stefanovic. This work is licensed under CC BY NC ND 4.0

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