A5014037992- Modular Robots and Swarm Intelligence
- Gene Regulatory Network Analysis
- Formal Methods in Verification
- Plant Molecular Biology Research
- Distributed systems and fault tolerance
- Distributed Control Multi-Agent Systems
- CRISPR and Genetic Engineering
- DNA and Biological Computing
- Petri Nets in System Modeling
- RNA and protein synthesis mechanisms
- Plant Reproductive Biology
- Micro and Nano Robotics
- Fungal and yeast genetics research
- Advanced biosensing and bioanalysis techniques
- Protein Structure and Dynamics
- Manufacturing Process and Optimization
- Photosynthetic Processes and Mechanisms
- Model-Driven Software Engineering Techniques
- Advanced Control Systems Optimization
- Viral Infectious Diseases and Gene Expression in Insects
- Logic, programming, and type systems
- Cell Image Analysis Techniques
- Robotic Path Planning Algorithms
- Enzyme Structure and Function
- Evolution and Genetic Dynamics
University of Washington
2015-2024
Seattle University
2007-2023
Riga Technical University
2017
University of Toronto
2017
California Institute of Technology
2002-2007
University of Pennsylvania
2002
University of Michigan–Ann Arbor
1999-2002
The field of modular self-reconfigurable robotic systems addresses the design, fabrication, motion planning, and control autonomous kinematic machines with variable morphology. Modular have promise making significant technological advances to robotics in general. Their high versatility, value, robustness may lead a radical change automation. Currently, number researchers been addressing many challenges. While some progress has made, it is clear that challenges still exist. By illustrating...
In this paper, different research trends that use symbolic techniques for robot motion planning and control are illustrated. As it often happens in new areas, contributions to topic started at about the same time by groups with emphasis, approaches, notation. This article tries describe a framework which many of current methods ideas can be placed provide coherent picture what authors want do, have they got so far, main missing pieces are. Generally speaking, aim as is envisioned enable...
Abstract Natural genetic circuits enable cells to make sophisticated digital decisions. Building equally complex synthetic in eukaryotes remains difficult, however, because commonly used components leak transcriptionally, do not arbitrarily interconnect or have responses. Here, we designed dCas9-Mxi1- based NOR gates Saccharomyces cerevisiae that allow arbitrary connectivity and large circuits. Because the chromatin remodeller Mxi1 , our showed minimal We built a combinatorial library of...
Linear I/O systems are a fundamental tool in theory, and have been used to design complex circuits control variety of settings. Here we present principled method for implementing arbitrary linear with biochemical reactions. This relies on two levels abstraction: first, an implementation using idealised chemical reactions, second, approximate the ideal reactions enzyme-free, entropy-driven DNA The dynamics shown be closely approximated by model implementation. We illustrate approach...
Self-assembly is the phenomenon in which a collection of particles spontaneously arrange themselves into coherent structure. ubiquitous nature. In this article we consider task programming active self-assembling and self-organizing systems at level interactions among system. To demonstrate approach, use it to control an experimental system called programmable parts testbed (PPT). We also several illustrative examples, including polymerization, model molecular ratchet, cooperative scenario....
Explaining how the small molecule auxin triggers diverse yet specific responses is a long-standing challenge in plant biology. An essential step response degradation of Auxin/Indole-3-Acetic Acid (Aux/IAA, referred to hereafter as IAA) repressor proteins through interaction with receptors. To systematically characterize diversity behaviors among IAA|receptor pairs, we engineered auxin-induced IAA yeast (Saccharomyces cerevisiae). We found that dynamics vary widely, depending on which...
The FastDesign protocol in the molecular modeling program Rosetta iterates between sequence optimization and structure refinement to stabilize de novo designed protein structures complexes. has been used previously design novel folds assemblies with important applications research medicine. To promote sampling of alternative conformations sequences, includes stages where energy landscape is smoothened by reducing repulsive forces. Here, we discover that this process disfavors larger amino...
Engineered biological circuits are often disturbed by a variety of environmental factors. In batch culture, where the majority synthetic circuit characterization occurs, conditions vary as culture matures. Turbidostats powerful tools that provide static environments; however, they expensive, especially when purchased in custom configurations, and difficult to design construct lab. Here, we present low cost, open source multiplexed turbidostat can be manufactured used with minimal experience...
Developmental programs sculpt plant morphology to meet environmental challenges, and these same have been manipulated increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate programs, creating chemical circuitry (Vanstraelen Benková, 2012) that has represented in mathematical models (Refahi 2016; Prusinkiewicz 2009); however, model-guided engineering of limited by a lack tools (Parry 2009; Voytas Gao, 2014). Here, we introduce novel set synthetic modular...
In this paper, we define a class of graph grammars that can be used to model and direct concurrent robotic self-assembly similar self-organizing processes. We give several detailed examples the formalism then focus on problem synthesizing grammar so it generates given, prespecified assembly. particular, generate an acyclic synthesize binary (rules involve at most two parts), for general ternary three parts). both cases, characterize number steps required achieve also show result implies no...
The parameters in a complex synthetic gene network must be extensively tuned before the functions as designed. Here, we introduce simple and general approach to rapidly tune networks Escherichia coli using hypermutable sequence repeats embedded spacer region of ribosome binding site. By varying repeat length, generated expression libraries that incrementally predictably sample levels over 1,000-fold range. We demonstrate utility by creating bistable switch library programmatically samples...
Significance Auxin is a simple small molecule, yet it elicits an enormous variety of responses. How single molecule can encode such diverse and context-specific information long-standing question. One hypothesis that variation in auxin response components generates diversity local To test this, we transplanted the forward nuclear signal transduction pathway from plants into yeast. We found circuit composition tune dynamic response, identified which properties had largest impact on...
Auxin elicits diverse cell behaviors through a simple nuclear signaling pathway initiated by degradation of Aux/IAA co-repressors. Our previous work revealed that members the large Arabidopsis family exhibit range rates in synthetic contexts. However, it remained an unresolved issue whether differences turnover played significant role plant responses to auxin. Here, we use well-established model lateral root development directly test hypothesis rate auxin-induced sets pace for...
Significance De novo design of protein binders often requires experimental screening to select functional variants from a library. We have achieved high-throughput, quantitative characterization protein–protein binding interactions without requiring purified recombinant proteins, by linking interaction strength with yeast mating. Using next-generation sequencing output, we characterized networks consisting thousands pairwise in single tube and demonstrated the effect changing environment....
Recent advances in the design and construction of synthetic multicelled systems E. coli S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing frameworks for biology do not account unique morphologies growing microcolonies, interaction gene circuits spatial diffusion molecular signals, or relationship between parallel algorithms. Here, we introduce a framework specification simulation behaviors...
We introduce the Caltech Multi-Vehicle Wireless Testbed (MVWT), a platform for testing decentralized control methodologies multiple vehicle coordination and formation stabilization. The testbed consists of eight mobile vehicles, an overhead vision system that provides GPS-like state information wireless Ethernet communications. Each rests on omni-directional casters is powered by two high-performance ducted fans. Thus, unique feature our vehicles have second order dynamics, requiring...
Abstract The phytohormone auxin regulates virtually every aspect of plant development. hormone directly mediates the interaction between two members coreceptor complex, a TRANSPORT INHIBITOR RESPONSE (TIR1)/AUXIN SIGNALING F-BOX protein and an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressor. To learn more about these proteins, mutant screen was performed using yeast (Saccharomyces cerevisiae) two-hybrid system in Arabidopsis (Arabidopsis thaliana). Two tir1 mutations were...
An engineering framework for synthetic multicellular systems requires a programmable means of cell-cell communication. Such communication system would enable complex behaviors, such as pattern formation, division labor in microbial communities, and improved modularity circuits. However, it remains challenging to build cellular eukaryotes due lack molecular modules that are orthogonal the host machinery, easy reconfigure, scalable. Here, we present novel cell-to-cell Saccharomyces cerevisiae...
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As consequence, many designs be tested computationally and experimentally find ones, which is expensive terms time resources. Here we use high-throughput, low-fidelity assay evaluate stability approximately 200,000 novel proteins. These include wide range sequence perturbations,...
In this paper, we introduce a robotic implementation of the theory graph grammars (Klavins et al., 2005), which use to model and direct self-organization in formal, predictable provably-correct fashion. The robots, call programmable parts, float passively on an air table bind each other upon random collisions. Once attached, they execute local rules that determine how their internal states change whether should remain bound. We demonstrate through experiments can self-organize into global...