Search Results - "Lakin, Matthew R"

Operant conditioning of stochastic chemical reaction networks by Arredondo, David, Lakin, Matthew R

“…Adapting one's behavior to environmental conditions and past experience is a key trait of living systems. In the biological world, there is evidence for…”
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Supervised Learning in Adaptive DNA Strand Displacement Networks by Lakin, Matthew R, Stefanovic, Darko

“…The development of engineered biochemical circuits that exhibit adaptive behavior is a key goal of synthetic biology and molecular computing. Such circuits…”
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Structure sampling for computational estimation of localized DNA interaction rates by Kumar, Sarika, Weisburd, Julian M., Lakin, Matthew R.

“…Molecular circuits implemented using molecular components tethered to a DNA tile nanostructure have certain advantages over solution-phase circuits. Tethering…”
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A bumpy road ahead for genetic biocontainment by George, Dalton R., Danciu, Mark, Davenport, Peter W., Lakin, Matthew R., Chappell, James, Frow, Emma K.

“…While the research community continues to develop novel proposals for intrinsic biocontainment of genetically engineered organisms, translation to real-world…”
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Isolation of nucleic acids using liquid–liquid phase separation of pH-sensitive elastin-like polypeptides by Díez Pérez, Telmo, Tafoya, Ashley N., Peabody, David S., Lakin, Matthew R., Hurwitz, Ivy, Carroll, Nick J., López, Gabriel P.

“…Extraction of nucleic acids (NAs) is critical for many methods in molecular biology and bioanalytical chemistry. NA extraction has been extensively studied and…”
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Abstractions for DNA circuit design by Lakin, Matthew R., Youssef, Simon, Cardelli, Luca, Phillips, Andrew

“…DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction…”
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Design and analysis of DNA strand displacement devices using probabilistic model checking by Lakin, Matthew R., Parker, David, Cardelli, Luca, Kwiatkowska, Marta, Phillips, Andrew

“…Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand…”
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Robust finite automata in stochastic chemical reaction networks by Arredondo, David, Lakin, Matthew R

“…Finite-state automata (FSA) are simple computational devices that can nevertheless illustrate interesting behaviours. We propose that FSA can be employed as…”
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Building a community to engineer synthetic cells and organelles from the bottom-up by Staufer, Oskar, De Lora, Jacqueline A, Bailoni, Eleonora, Bazrafshan, Alisina, Benk, Amelie S, Jahnke, Kevin, Manzer, Zachary A, Otrin, Lado, Díez Pérez, Telmo, Sharon, Judee, Steinkühler, Jan, Adamala, Katarzyna P, Jacobson, Bruna, Dogterom, Marileen, Göpfrich, Kerstin, Stefanovic, Darko, Atlas, Susan R, Grunze, Michael, Lakin, Matthew R, Shreve, Andrew P, Spatz, Joachim P, López, Gabriel P

“…Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences,…”
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Signal Propagation in Multi-Layer DNAzyme Cascades Using Structured Chimeric Substrates by Brown III, Carl W., Lakin, Matthew R., Horwitz, Eli K., Fanning, M. Leigh, West, Hannah E., Stefanovic, Darko, Graves, Steven W.

“…Signal propagation through enzyme cascades is a critical component of information processing in cellular systems. Although such systems have potential as…”
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Sequential super-resolution imaging using DNA strand displacement by Pallikkuth, Sandeep, Martin, Cheyenne, Farzam, Farzin, Edwards, Jeremy S, Lakin, Matthew R, Lidke, Diane S, Lidke, Keith A

“…Sequential labeling and imaging in fluorescence microscopy allows the imaging of multiple structures in the same cell using a single fluorophore species. In…”
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Supervised Learning in a Multilayer, Nonlinear Chemical Neural Network by Arredondo, David, Lakin, Matthew R.

“…The development of programmable or trainable molecular circuits is an important goal in the field of molecular programming. Multilayer, nonlinear, artificial…”
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A geometric framework for reaction enumeration in computational nucleic acid devices by Kumar, Sarika, Lakin, Matthew R

“…Cascades of DNA strand displacement reactions enable the design of potentially large circuits with complex behaviour. Computational modelling of such systems…”
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Visual DSD: a design and analysis tool for DNA strand displacement systems by Lakin, Matthew R., Youssef, Simon, Polo, Filippo, Emmott, Stephen, Phillips, Andrew

“…The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a…”
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Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering by Lakin, Matthew R, Brown, 3rd, Carl W, Horwitz, Eli K, Fanning, M Leigh, West, Hannah E, Stefanovic, Darko, Graves, Steven W

“…The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to…”
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A Logic Programming Language for Computational Nucleic Acid Devices by Spaccasassi, Carlo, Lakin, Matthew R, Phillips, Andrew

“…Computational nucleic acid devices show great potential for enabling a broad range of biotechnology applications, including smart probes for molecular biology…”
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Heterochiral modifications enhance robustness and function of DNA in living human cells by Mallette, Tracy L., Lidke, Diane S., Lakin, Matthew R.

“…Oligonucleotide therapeutics are becoming increasingly important as more are approved by the FDA, both for treatment and vaccination. Similarly, dynamic DNA…”
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Modular verification of chemical reaction network encodings via serializability analysis by Lakin, Matthew R., Stefanovic, Darko, Phillips, Andrew

“…Chemical reaction networks are a powerful means of specifying the intended behavior of synthetic biochemical systems. A high-level formal specification,…”
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Domain-Specific Programming Languages for Computational Nucleic Acid Systems by Lakin, Matthew R, Phillips, Andrew

“…The construction of models of system behavior is of great importance throughout science and engineering. In bioengineering and bionanotechnology, these often…”
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Protecting Heterochiral DNA Nanostructures against Exonuclease-Mediated Degradation by Mallette, Tracy L., Lakin, Matthew R.

“…Heterochiral DNA nanotechnology employs nucleic acids of both chiralities to construct nanoscale devices for applications in the intracellular environment…”
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