12,379 research outputs found
Synthetic Gene Circuits: Design with Directed Evolution
Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical modeling with directed evolution offers one promising means for addressing this problem. Modeling identifies mutational targets and limits the evolutionary search space for directed evolution, which alters circuit performance without the need for detailed biophysical information. This review examines strategies for integrating modeling and directed evolution and discusses the utility and limitations of available methods
Synthetic Biology: A Bridge between Artificial and Natural Cells.
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications
Can biological quantum networks solve NP-hard problems?
There is a widespread view that the human brain is so complex that it cannot
be efficiently simulated by universal Turing machines. During the last decades
the question has therefore been raised whether we need to consider quantum
effects to explain the imagined cognitive power of a conscious mind.
This paper presents a personal view of several fields of philosophy and
computational neurobiology in an attempt to suggest a realistic picture of how
the brain might work as a basis for perception, consciousness and cognition.
The purpose is to be able to identify and evaluate instances where quantum
effects might play a significant role in cognitive processes.
Not surprisingly, the conclusion is that quantum-enhanced cognition and
intelligence are very unlikely to be found in biological brains. Quantum
effects may certainly influence the functionality of various components and
signalling pathways at the molecular level in the brain network, like ion
ports, synapses, sensors, and enzymes. This might evidently influence the
functionality of some nodes and perhaps even the overall intelligence of the
brain network, but hardly give it any dramatically enhanced functionality. So,
the conclusion is that biological quantum networks can only approximately solve
small instances of NP-hard problems.
On the other hand, artificial intelligence and machine learning implemented
in complex dynamical systems based on genuine quantum networks can certainly be
expected to show enhanced performance and quantum advantage compared with
classical networks. Nevertheless, even quantum networks can only be expected to
efficiently solve NP-hard problems approximately. In the end it is a question
of precision - Nature is approximate.Comment: 38 page
Recommended from our members
Direct observation of delithiation as the origin of analog memristance in LixNbO2
The discovery of analog LixNbO2 memristors revealed a promising new memristive mechanism wherein the diffusion of Li+ rather than O2- ions enables precise control of the resistive states. However, directly correlating lithium concentration with changes to the electronic structure in active layers remains a challenge and is required to truly understand the underlying physics. Chemically delithiated single crystals of LiNbO2 present a model system for correlating lithium variation with spectroscopic signatures from operando soft x-ray spectroscopy studies of device active layers. Using electronic structure modeling of the x-ray spectroscopy of LixNbO2 single crystals, we demonstrate that the intrinsic memristive behavior in LixNbO2 active layers results from field-induced degenerate p-type doping. We show that electrical operation of LixNbO2-based memristors is viable even at marginal Li deficiency and that the analog memristive switching occurs well before the system is fully metallic. This study serves as a benchmark for material synthesis and characterization of future LixNbO2-based memristor devices and suggests that valence change switching is a scalable alternative that circumvents the electroforming typically required for filamentary-based memristors
Spatio-temporal Learning with Arrays of Analog Nanosynapses
Emerging nanodevices such as resistive memories are being considered for
hardware realizations of a variety of artificial neural networks (ANNs),
including highly promising online variants of the learning approaches known as
reservoir computing (RC) and the extreme learning machine (ELM). We propose an
RC/ELM inspired learning system built with nanosynapses that performs both
on-chip projection and regression operations. To address time-dynamic tasks,
the hidden neurons of our system perform spatio-temporal integration and can be
further enhanced with variable sampling or multiple activation windows. We
detail the system and show its use in conjunction with a highly analog
nanosynapse device on a standard task with intrinsic timing dynamics- the TI-46
battery of spoken digits. The system achieves nearly perfect (99%) accuracy at
sufficient hidden layer size, which compares favorably with software results.
In addition, the model is extended to a larger dataset, the MNIST database of
handwritten digits. By translating the database into the time domain and using
variable integration windows, up to 95% classification accuracy is achieved. In
addition to an intrinsically low-power programming style, the proposed
architecture learns very quickly and can easily be converted into a spiking
system with negligible loss in performance- all features that confer
significant energy efficiency.Comment: 6 pages, 3 figures. Presented at 2017 IEEE/ACM Symposium on Nanoscale
architectures (NANOARCH
Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems.
Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues
Connecting the Brain to Itself through an Emulation.
Pilot clinical trials of human patients implanted with devices that can chronically record and stimulate ensembles of hundreds to thousands of individual neurons offer the possibility of expanding the substrate of cognition. Parallel trains of firing rate activity can be delivered in real-time to an array of intermediate external modules that in turn can trigger parallel trains of stimulation back into the brain. These modules may be built in software, VLSI firmware, or biological tissue as in vitro culture preparations or in vivo ectopic construct organoids. Arrays of modules can be constructed as early stage whole brain emulators, following canonical intra- and inter-regional circuits. By using machine learning algorithms and classic tasks known to activate quasi-orthogonal functional connectivity patterns, bedside testing can rapidly identify ensemble tuning properties and in turn cycle through a sequence of external module architectures to explore which can causatively alter perception and behavior. Whole brain emulation both (1) serves to augment human neural function, compensating for disease and injury as an auxiliary parallel system, and (2) has its independent operation bootstrapped by a human-in-the-loop to identify optimal micro- and macro-architectures, update synaptic weights, and entrain behaviors. In this manner, closed-loop brain-computer interface pilot clinical trials can advance strong artificial intelligence development and forge new therapies to restore independence in children and adults with neurological conditions
Hierarchical Composition of Memristive Networks for Real-Time Computing
Advances in materials science have led to physical instantiations of
self-assembled networks of memristive devices and demonstrations of their
computational capability through reservoir computing. Reservoir computing is an
approach that takes advantage of collective system dynamics for real-time
computing. A dynamical system, called a reservoir, is excited with a
time-varying signal and observations of its states are used to reconstruct a
desired output signal. However, such a monolithic assembly limits the
computational power due to signal interdependency and the resulting correlated
readouts. Here, we introduce an approach that hierarchically composes a set of
interconnected memristive networks into a larger reservoir. We use signal
amplification and restoration to reduce reservoir state correlation, which
improves the feature extraction from the input signals. Using the same number
of output signals, such a hierarchical composition of heterogeneous small
networks outperforms monolithic memristive networks by at least 20% on waveform
generation tasks. On the NARMA-10 task, we reduce the error by up to a factor
of 2 compared to homogeneous reservoirs with sigmoidal neurons, whereas single
memristive networks are unable to produce the correct result. Hierarchical
composition is key for solving more complex tasks with such novel nano-scale
hardware
"Going back to our roots": second generation biocomputing
Researchers in the field of biocomputing have, for many years, successfully
"harvested and exploited" the natural world for inspiration in developing
systems that are robust, adaptable and capable of generating novel and even
"creative" solutions to human-defined problems. However, in this position paper
we argue that the time has now come for a reassessment of how we exploit
biology to generate new computational systems. Previous solutions (the "first
generation" of biocomputing techniques), whilst reasonably effective, are crude
analogues of actual biological systems. We believe that a new, inherently
inter-disciplinary approach is needed for the development of the emerging
"second generation" of bio-inspired methods. This new modus operandi will
require much closer interaction between the engineering and life sciences
communities, as well as a bidirectional flow of concepts, applications and
expertise. We support our argument by examining, in this new light, three
existing areas of biocomputing (genetic programming, artificial immune systems
and evolvable hardware), as well as an emerging area (natural genetic
engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin
- β¦