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thermodynamically Driven Signal Amplification 29

Thermodynamically Driven Signal Amplification

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29th international conference on dna computing and molecular programming, dna 2023

作者： Petrack, Joshua Soloveichik, David Doty, David University of California DavisCA United States University of Texas AustinTX United States

ISBN: (纸本)9783959772976

the field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. By modeling this physical phenomenon at different levels of specificity, different operative computational behavior is observed. thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which molecules are bound to each other in a "thermodynamically stable" sense. Stability is measured based only on how many bonds are formed and how many total complexes are in a configuration, without focusing on how molecules are binding or how they became bound. By defocusing on kinetic processes, TBNs attempt to naturally model the long-term behavior of a mixture (i.e., its thermodynamic equilibrium). We study the problem of signal amplification: detecting a small quantity of some molecule and amplifying its signal to something more easily detectable. this problem has natural applications such as disease diagnosis. By focusing on thermodynamically favored outcomes, we seek to design chemical systems that perform the task of signal amplification robustly without relying on kinetic pathways that can be error prone and require highly controlled conditions (e.g., PCR amplification). It might appear that a small change in concentrations can result in only small changes to the thermodynamic equilibrium of a molecular system. However, we show that it is possible to design a TBN that can "exponentially amplify" a signal represented by a single copy of a monomer called the analyte: this TBN has exactly one stable state before adding the analyte and exactly one stable state afterward, and those two states "look very different" from each other. In particular, their difference is exponential in the number of types of molecules and their sizes. the system can be programmed to any desired level of resilience to false positives and false negatives. To prove these results, we introduce new concepts to the TBN model, particul

关键词： Integer programming

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Modelling and Optimisation of a dna Stack Nano-Device Using Probabilistic Model Checking 28

Modelling and Optimisation of a DNA Stack Nano-Device Using ...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Li, Bowen Mackenzie, Neil Shirt-Ediss, Ben Krasnogor, Natalio Zuliani, Paolo Research Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom

ISBN: (纸本)9783959772532

A dna stack nano-device is a bio-computing system that can read and write molecular signals based on dna-dna hybridisation and strand displacement. In vitro implementation of the dna stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the dna stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? the results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. © Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani.

关键词： dna

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Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded dna Computer 29

Minimum Free Energy, Partition Function and Kinetics Simulat...

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29th international conference on dna computing and molecular programming, dna 2023

作者： Shalaby, Ahmed thachuk, Chris Woods, Damien Hamilton Institute Department of Computer Science Maynooth University Ireland Paul G. Allen School of Computer Science & Engineering University of Washington SeattleWA United States

ISBN: (纸本)9783959772976

Polynomial time dynamic programming algorithms play a crucial role in the design, analysis and engineering of nucleic acid systems including dna computers and dna/RNA nanostructures. However, in complex multistranded or pseudoknotted systems, computing the minimum free energy (MFE), and partition function of nucleic acid systems is NP-hard. Despite this, multistranded and/or pseudoknotted systems represent some of the most utilised and successful systems in the field. this leaves open the tempting possibility that many of the kinds of multistranded and/or pseudoknotted systems we wish to engineer actually fall into restricted classes, that do in fact have polynomial time algorithms, but we've just not found them yet. Here, we give polynomial time algorithms for MFE and partition function calculation for a restricted kind of multistranded system called the 1D scaffolded dna computer. this model of computation thermodynamically favours correct outputs over erroneous states, simulates finite state machines in 1D and Boolean circuits in 2D, and is amenable to dna storage applications. In an effort to begin to ask the question of whether we can naturally compare the expressivity of nucleic acid systems based on the computational complexity of prediction of their preferred energetic states, we show our MFE problem is in logspace (the complexity class L), making it perhaps one of the simplest known, natural, nucleic acid MFE problems. Finally, we provide a stochastic kinetic simulator for the 1D scaffolded dna computer and evaluate strategies for efficiently speeding up this thermodynamically favourable system in a constant-temperature kinetic regime. © Ahmed Shalaby, Chris thachuk, and Damien Woods;licensed under Creative Commons License CC-BY 4.0.

关键词： dna

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Tetracycline Intelligent Target-Inducing Logic Gate Based on Triple-Stranded dna Nanoswitch 16th

Tetracycline Intelligent Target-Inducing Logic Gate Based on...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Xi, Sunfan Wang, Yue Hu, Mengyang Wang, Luhui Cheng, Meng Dong, Yafei College of Life Science Shaanxi Normal University Shaanxi Xi’an710119 China School of Computer Science Shaanxi Normal University Shaanxi Xi’an710119 China

ISBN: (纸本)9789811912559

A previously unreported three-strand dna (ts-dna) non-metal structure with hairpin structure was designed based on a strategy of logic switching and tetracycline (TC) signaling molecule switching. Will target and TC-binding aptamer (TBA) is the combination of body, and its relation with three functional chain dna conformation, with programmable dna sensor signal by FAM input molecule fluorescence emission monitoring. After the combination, the input signal is converted to a fluorescent signal to perform a logical operation. By introducing a novel nanomaterial, graphene oxide (GO), as a signal regulator, the fluorescence response changed by intermolecular interactions is the key to achieving logical calculation. the harm of tetracycline can generally cause kidney damage, ear damage, gastrointestinal adverse reactions, skin allergies, *** tetracycline as a molecular trigger to induce conformational changes in dna, a logical operation target detection method was constructed. In addition, nanoscale devices can be reconfigured and optimized to accommodate additional logical calculations and target detection. © 2022, Springer Nature Singapore Pte Ltd.

关键词： dna

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dna Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification 29

DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identi...

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29th international conference on dna computing and molecular programming, dna 2023

作者： Becker, Florent Heydarshahi, Shahrzad Univ. Orléans INSA Centre Val de Loire LIFO EA 4022 OrléansF-45067 France

ISBN: (纸本)9783959772976

We introduce a new dna tile self-assembly model: the Surface Flexible Tile Assembly Model (SFTAM), where 2D tiles are placed on host 3D surfaces made of axis-parallel unit cubes glued together by their faces, called polycubes. the bonds are flexible, so that the assembly can bind on the edges of the polycube. We are interested in the study of SFTAM self-assemblies on 3D surfaces which are not always embeddable in the Euclidean plane, in order to compare their different behaviors and to compute the topological properties of the host surfaces. We focus on a family of polycubes called order-1 cuboids. Order-0 cuboids are polycubes that have six rectangular faces, and order-1 cuboids are made from two order-0 cuboids by substracting one from the other. thus, order-1 cuboids can be of genus 0 or of genus 1 (then they contain a tunnel). We are interested in the genus of these structures, and we present a SFTAM tile assembly system that determines the genus of a given order-1 cuboid. the SFTAM tile assembly system which we design, contains a specific set Y of tile types with the following properties. If the assembly is made on a host order-1 cuboid C of genus 0, no tile of Y appears in any producible assembly, but if C has genus 1, every terminal assembly contains at least one tile of Y. thus, for order-1 cuboids our system is able to distinguish the host surfaces according to their genus, by the tiles used in the assembly. this system is specific to order-1 cuboids but we can expect the techniques we use to be generalizable to other families of shapes. © Florent Becker and Shahrzad Heydarshahi;licensed under Creative Commons License CC-BY 4.0.

关键词： Assembly

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A Coupled Reconfiguration Mechanism for Single-Stranded dna Strand Displacement Systems 28

A Coupled Reconfiguration Mechanism for Single-Stranded DNA ...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Johnson, Hope Amber Condon, Anne The University of British Columbia Vancouver Canada

ISBN: (纸本)9783959772532

dna Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound dna strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms – sequences of basic reaction rules – that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with dna. Here we introduce a new mechanism, which we call controlled reconfiguration. We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties;for example it is capable of implementing reversible CRNs and uses just two distinct toeho

关键词： dna

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Accelerating Self-Assembly of Crisscross Slat Systems 29

Accelerating Self-Assembly of Crisscross Slat Systems

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29th international conference on dna computing and molecular programming, dna 2023

作者： Doty, David Fleming, Hunter Hader, Daniel Patitz, Matthew J. Vaughan, Lukas A. University of California DavisCA United States University of Arkansas FayettevilleAR United States

ISBN: (纸本)9783959772976

We present an abstract model of self-assembly of systems composed of "crisscross slats", which have been experimentally implemented as a single-stranded piece of dna [21] or as a complete dna origami structure [28]. We then introduce a more physically realistic "kinetic" model and show how important constants in the model were derived and tuned, and compare simulation-based results to experimental results [21,28]. Using these models, we show how we can apply optimizations to designs of slat systems in order to lower the numbers of unique slat types required to build target structures. In general, we apply two types of techniques to achieve greatly reduced numbers of slat types. Similar to the experimental work implementing dna origami-based slats, in our designs the slats oriented in horizontal and vertical directions are each restricted to their own plane and sets of them overlap each other in square regions which we refer to as macrotiles. Our first technique extends their previous work of reusing slat types within macrotiles and requires analyses of binding domain patterns to determine the potential for errors consisting of incorrect slat types attaching at undesired translations and reflections. the second technique leverages the power of algorithmic self-assembly to efficiently reuse entire macrotiles which self-assemble in patterns following designed algorithms that dictate the dimensions and patterns of growth. Using these designs, we demonstrate that in kinetic simulations the systems with reduced numbers of slat types self-assemble more quickly than those with greater numbers. this provides evidence that such optimizations will also result in greater assembly speeds in experimental systems. Furthermore, the reduced numbers of slat types required have the potential to vastly reduce the cost and number of lab steps for crisscross assembly experiments. © David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, and Lukas A. Vaughan;licensed under Creative C

关键词： dna

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DROM: Read Only Memory Storage in dna computing

DROM: Read Only Memory Storage in DNA Computing

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Sustainable Technologies for Industry 4.0 (STI), international conference on

作者： Tamanna Tabassum Fatema Akter Mohammed Nasir Uddin Dept of Computer Science and Engineering Jagannath University Bangladesh Dept of Computer Science and Engineering Green University Bangladesh Bangladesh

Biomolecular programming performs computing utilizing many sorts of reactions and stores the information in biological macromolecules (proteins and nucleic acids). dna (Deoxyribose Nucleic Acid) exhibits highly predictable molecular behavior, which assists in the construction of logical versions of operating systems and molecular computers. Read Only Memory (ROM), is a form of electronic storage that is built into a device during the manufacturing process. It might be a programmable general-purpose logic device, and a client can customize the storage device as a basic logic gate operation to complex mechanisms on a chip. In this proposed work, a ROM is designed using dna-based gates. the attributes of dna-based computing enable dna-based ROM to execute billions of operations consecutively as well as provide immense storage in a compact space.

关键词： Proteins Sequential analysis Operating systems dna molecular biophysics Logic gates programming

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16th international conference on Parallel computing Technologies, PaCT 2021

16th International Conference on Parallel Computing Technolo...

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16th international conference on Parallel computing Technologies, PaCT 2021

ISBN: (纸本)9783030863586

the proceedings contain 36 papers. the special focus in this conference is on Parallel computing Technologies. the topics include: High-Efficiency Specialized Support for Dense Linear Algebra Arithmetic in LuNA System;efficient Cluster Parallelization Technology for Aerothermodynamics Problems;computational Aspects of Solving Grid Equations in Heterogeneous computing Systems;optimized Hybrid Execution of Dense Matrix-Matrix Multiplication on Clusters of Heterogeneous Multicore and Many-Core Platforms;Parallelization of Robust Multigrid Technique Using OpenMP Technology;Network Reliability Calculation with Use of GPUs;implicit Data Layout Optimization for Portable Parallel programming in C++;On Defragmentation Algorithms for GPU-Native Octree-Based AMR Grids;zipped Data Structure for Adaptive Mesh Refinement;A New Model-Based Approach to Performance Comparison of MPI Collective Algorithms;automatic Parallel Tiled Code Generation Based on Dependence Approximation;Scalability Issues in FFT Computation;High Performance Implementation of Boris Particle Pusher on DPC++. A First Look at oneAPI;Evaluating the Performance of Kunpeng 920 Processors on Modern HPC Applications;optimization of Resources Allocation in High Performance Distributed computing with Utilization Uncertainty;influence of Execution Time Forecast Accuracy on the Efficiency of Scheduling Jobs in a Distributed Network of Supercomputers;Performance Estimation of a BOINC-Based Desktop Grid for Large-Scale molecular Docking;consensus-Free Ledgers When Operations of Distinct Processes are Commutative;design and Implementation of Highly Scalable Quantifiable Data Structures;optimal Concurrency for List-Based Sets;Deterministic OpenMP and the LBP Parallelizing Manycore Processor;mobile Agents Operating on a Grid: Some Non-conventional Issues in Parallel computing;parallel Computations in Integrated Environment of Engineering Modeling and Global Optimization.

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24th international conference on dna computing and molecular programming, dna 2018

24th International Conference on DNA Computing and Molecular...

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24th international conference on dna computing and molecular programming, dna 2018

ISBN: (纸本)9783030000295

the proceedings contain 12 papers. the special focus in this conference is on dna computing and molecular programming. the topics include: Construction of geometric structure by oritatami system;A reaction network scheme which implements the EM algorithm;know when to fold ’Em: Self-assembly of shapes by folding in Oritatami;Optimizing tile set size while preserving proofreading with a dna self-assembly compiler;A content-addressable dna database with learned sequence encodings;Temporal dna barcodes: A time-based approach for single-molecule imaging;hierarchical growth is necessary and (sometimes) sufficient to self-assemble discrete self-similar fractals;self-assembly of 3-D structures using 2-D folding tiles;forming tile shapes with simple robots;transcript design problem of oritatami systems.

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