Temporal Pattern Recognition through Analog Molecular Computation

O’Brien, Jackson; Murugan, Arvind

doi:10.1021/acssynbio.8b00503

Cited by 16 publications

(18 citation statements)

References 63 publications

(123 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The deconvolution of hysteretic properties of an out-of-equilibrium system will facilitate harnessing environmental variables in the development of next-generation "smart" molecules with applications as sensors, 55,56 molecular machines, 57 in pattern recognition, 58 and logic gates. 59 Future work in this direction includes the study of architecture, such as sequence-defined copolymers, combined environmental effects, and mechanisms of dynamic assembly.…”

Section: Discussionmentioning

confidence: 99%

Temperature sensitive copolymers as a model system for understanding the physical basis of nonequilibrium assembly

Chittari

Obermeyer

Knight

2022

Preprint

View full text Add to dashboard Cite

Both natural biomaterials and synthetic materials benefit from complex energy landscapes that provide the foundation for structure-function relationships and environmental sensitivity. Understanding these nonequilibrium dynamics is important for the development of design principles to harness this behavior. Using a model system of poly(ethylene glycol) methacrylate-based lower critical solution temperature (LCST) copolymers, we explored the impact of composition, path, and macromolecular crowding effects on nonequilibrium thermal hysteretic behavior. Through turbidimetry analysis of non-superimposable heat-cool cycles, we observe that LCST copolymers show clear hysteresis that varies as a function of pendent side chain length and hydrophobicity. Hysteresis is further impacted by the temperature ramp rate, as insoluble states can be kinetically trapped under optimized temperature protocols. Finally, the use of common crowding agents shows that excluded volume effects diminish the hysteresis behavior. This systematic study brings to light practical design principles towards understanding and harnessing out-of-equilibrium effects in synthetic soft materials.

show abstract

Section: Discussionmentioning

confidence: 99%

Temperature sensitive copolymers as a model system for understanding the physical basis of nonequilibrium assembly

Chittari

Obermeyer

Knight

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Its underlying reason is the martingale property that the conditional expectation of probabilities for two hypotheses, given all prior history, is equal to their present value. The methodology developed here will be useful for the broad range of decision processes where SPRT is relevant, including neuroscience ( Gold and Shadlen, 2007 ; Bitzer et al, 2014 ) and synthetic biology ( O'Brien and Murugan, 2019 ; Pittayakanchit et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

Desponds

Vergassola

Walczak

2020

eLife

View full text Add to dashboard Cite

Cell fate decisions in the fly embryo are rapid: hunchback genes decide in minutes whether nuclei follow the anterior/posterior developmental blueprint by reading out positional information in the Bicoid morphogen. This developmental system is a prototype of regulatory decision processes that combine speed and accuracy. Traditional arguments based on fixed-time sampling of Bicoid concentration indicate that an accurate readout is impossible within the experimental times. This raises the general issue of how speed-accuracy tradeoffs are achieved. Here, we compare fixed-time to on-the-fly decisions, based on comparing the likelihoods of anterior/posterior locations. We found that these more efficient schemes complete reliable cell fate decisions within the short embryological timescales. We discuss the influence of promoter architectures on decision times and error rates, present concrete examples that rapidly readout the morphogen, and predictions for new experiments. Lastly, we suggest a simple mechanism for RNA production and degradation that approximates the log-likelihood function.

show abstract

“…Pattern recognition has been implemented in a variety of analog classical systems ranging from molecular self-assembly to elastic networks [55][56][57][58][59][60][61][62] . It is interesting to ask whether quantum systems possesses similar power.…”

Section: A Pattern Recognitionmentioning

confidence: 99%

Many-body localized hidden Born machine

Zhong¹,

Gao²,

Yelin³

et al. 2022

Preprint

View full text Add to dashboard Cite

Born Machines are quantum-inspired generative models that leverage the probabilistic nature of quantum states. Here, we present a new architecture called many-body localized (MBL) hidden Born machine that uses both MBL dynamics and hidden units as learning resources. We theoretically prove that MBL Born machines possess more expressive power than classical models, and the introduction of hidden units boosts its learning power. We numerically demonstrate that the MBL hidden Born machine is capable of learning a toy version of MNIST handwritten digits, quantum data obtained from quantum many-body states, and non-local parity data. In order to understand the mechanism behind learning, we track physical quantities such as von Neumann entanglement entropy and Hamming distance during learning, and compare the learning outcomes in the MBL, thermal, and Anderson localized phases. We show that the superior learning power of the MBL phase relies importantly on both localization and interaction. Our architecture and algorithm provide novel strategies of utilizing quantum many-body systems as learning resources, and reveal a powerful connection between disorder, interaction, and learning in quantum many-body systems.

show abstract

Temporal Pattern Recognition through Analog Molecular Computation

Cited by 16 publications

References 63 publications

Temperature sensitive copolymers as a model system for understanding the physical basis of nonequilibrium assembly

Temperature sensitive copolymers as a model system for understanding the physical basis of nonequilibrium assembly

A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

Many-body localized hidden Born machine

Contact Info

Product

Resources

About