15 papers · ranked by Valyu relevance
Oliver Attie, Brian Sulkow, Chong Di, Wei-Gang Qiu
Learning algorithms have been proposed as a non-selective mechanism capable of creating complex adaptive systems in life. Evolutionary learning however has not been demonstrated to be a plausible cause for the origin of a specific molecular system. Here we show that genetic codes as optimal as the Standard Genetic Code…
Parth Chansoria, Dominic Rütsche, Anny Wang, Hao Liu + 7 more
Accelerating the designing and manufacturing of complex shapes has been a driving factor of modern industrialization. This has led to numerous advances in computational design and modeling and novel additive manufacturing (AM) techniques that can create complex shapes for bespoke applications. By combining a new…
Amelie Erben, Thomas Kellerer, Josefine Lissner, Constanze Eulenkamp + 4 more
Bioinspired 3D microfluidic systems that combine vascularization with extracellular matrix architectures of organotypic geometry, composition and biophysical traits can help advance our understanding of microorgan physiology. Here, two-photon stereolithography is adopted to fabricate freestanding perfusable 3D cell…
Ian Holmes
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by interleaving watermark and periodic marker signals; conversion from binary to…
Yun-Fei Liu, Marina Bedny
Programming is a cornerstone of modern society, yet its cognitive and neural basis remains poorly understood. In this study, we test the hypothesis that programming “recycles” pre-existing neural mechanisms and representations in fronto-parietal reasoning networks. Using fMRI, we scanned programming-naïve…
Anjali Jaiman, Mukund Thattai
An algorithm converts inputs to corresponding unique outputs through a sequence of actions. Algorithms are used as metaphors for complex biological processes such as organismal development. Here we make this metaphor rigorous for glycan biosynthesis. Glycans are branched sugar oligomers that are attached to…
Aditi T. Merchant, Daniel Guo, Ben Viggiano, Lucas Brennan-Almaraz + 6 more
Programmable composition of complex systems is a longstanding goal of biological research. Generative modeling has improved the reliability of computational design, but existing methods are highly specialized and are difficult to extend or compose. Here, we introduce Proto, a high-level programming language for…
Patrícia Verdugo Pascoal, Deborah Bambil, Rayane N. Lima, Marco Antônio de Oliveira + 3 more
Quantum biology is an emergent field that investigates quantum-mechanical phenomena, such as superposition, tunneling, and entanglement, in the context of data manipulation from living systems. The exploration and engineering of nucleotide sequences rely on quantum mechanical principles, particularly the use of qubit…
Angelo Gaeta, Valentin Zulkower, Giovanni Stracquadanio
Rapid engineering of biological systems is currently hindered by limited integration of manufacturing constraints into the design process, ultimately limiting the yield of many synthetic biology workflows. Here we tackle DNA engineering as a multi-objective optimization problem aiming at finding the best tradeoff…
John-Antonio Argyriadis, Yang-Hui He, Vishnu Jejjala, Djordje Minic
We study the dynamics of genetic code evolution. The algorithm of Vetsigian et al. [1] provides a solution that is both optimal and universal. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on achieving universality. We show that by…
Zhi Ping, Haoling Zhang, Shihong Chen, Qianlong Zhuang + 2 more
Chamaeleo is currently the only collection library that focuses on adapting multiple well-established coding schemes for DNA storage. It provides a tool for researchers to study various coding schemes and apply them in practice. Chamaeleo adheres to the concept of high aggregation and low coupling for software design…
Tristan Stérin, Abeer Eshra, Janet Adio, Constantine Glen Evans + 1 more
Like life, computers are out-of-equilibrium.^1,2^ Thermodynamically favoured error states are thwarted by energetically-costly processes such as kinetic proofreading of biological polymers, error-correcting codes in computer data storage, and redundancy in molecular programming. Decades of theoretical work shows that…
M. Ali Al-Radhawi, Anh Phong Tran, Elizabeth A. Ernst, Tianchi Chen + 2 more
Starting in the early 2000s, a sophisticated technology has been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order to achieve greater computational power has been hampered by many…
Frederick Starkey, Filippo Menolascina
Synthetic Biology aims to rationally engineer biological systems. Current methods often employ an initial human designed circuit topology and utilise iterative approaches, e.g. directed evolution, to fine-tune part function. This approach can be extremely time consuming and resource intensive whilst often reaching…
Inbal Preuss, Michael Rosenberg, Zohar Yakhini, Leon Anavy
With the world generating digital data at an exponential rate, DNA has emerged as a promising archival medium. It offers a more efficient and long-lasting digital storage solution due to its durability, physical density, and high information capacity. Research in the field includes the development of encoding schemes…