137 research outputs found
DNA as a universal substrate for chemical kinetics
Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka–Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior
Delocalized single-photon Dicke states and the Leggett- Garg inequality in solid state systems
We show how to realize a single-photon Dicke state in a large one-dimensional
array of two- level systems, and discuss how to test its quantum properties.
Realization of single-photon Dicke states relies on the cooperative nature of
the interaction between a field reservoir and an array of two-level-emitters.
The resulting dynamics of the delocalized state can display Rabi-like
oscillations when the number of two-level emitters exceeds several hundred. In
this case the large array of emitters is essentially behaving like a
mirror-less cavity. We outline how this might be realized using a
multiple-quantum-well structure and discuss how the quantum nature of these
oscillations could be tested with the Leggett-Garg inequality and its
extensions.Comment: 29 pages, 5 figures, journal pape
Network Analysis of Biochemical Logic for Noise Reduction and Stability: A System of Three Coupled Enzymatic AND Gates
We develop an approach aimed at optimizing the parameters of a network of
biochemical logic gates for reduction of the "analog" noise buildup.
Experiments for three coupled enzymatic AND gates are reported, illustrating
our procedure. Specifically, starch - one of the controlled network inputs - is
converted to maltose by beta-amylase. With the use of phosphate (another
controlled input), maltose phosphorylase then produces glucose. Finally,
nicotinamide adenine dinucleotide (NAD+) - the third controlled input - is
reduced under the action of glucose dehydrogenase to yield the optically
detected signal. Network functioning is analyzed by varying selective inputs
and fitting standardized few-parameters "response-surface" functions assumed
for each gate. This allows a certain probe of the individual gate quality, but
primarily yields information on the relative contribution of the gates to noise
amplification. The derived information is then used to modify our experimental
system to put it in a regime of a less noisy operation.Comment: 31 pages, PD
Biomolecular Filters for Improved Separation of Output Signals in Enzyme Logic Systems Applied to Biomedical Analysis
Biomolecular logic systems processing biochemical input signals and producing
"digital" outputs in the form of YES/NO were developed for analysis of
physiological conditions characteristic of liver injury, soft tissue injury and
abdominal trauma. Injury biomarkers were used as input signals for activating
the logic systems. Their normal physiological concentrations were defined as
logic-0 level, while their pathologically elevated concentrations were defined
as logic-1 values. Since the input concentrations applied as logic 0 and 1
values were not sufficiently different, the output signals being at low and
high values (0, 1 outputs) were separated with a short gap making their
discrimination difficult. Coupled enzymatic reactions functioning as a
biomolecular signal processing system with a built-in filter property were
developed. The filter process involves a partial back-conversion of the
optical-output-signal-yielding product, but only at its low concentrations,
thus allowing the proper discrimination between 0 and 1 output values
Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit?
We report an experimental evaluation of the "input-output surface" for a
biochemical AND gate. The obtained data are modeled within the rate-equation
approach, with the aim to map out the gate function and cast it in the language
of logic variables appropriate for analysis of Boolean logic for scalability.
In order to minimize "analog" noise, we consider a theoretical approach for
determining an optimal set for the process parameters to minimize "analog"
noise amplification for gate concatenation. We establish that under optimized
conditions, presently studied biochemical gates can be concatenated for up to
order 10 processing steps. Beyond that, new paradigms for avoiding noise
build-up will have to be developed. We offer a general discussion of the ideas
and possible future challenges for both experimental and theoretical research
for advancing scalable biochemical computing
The Potential and Challenges of Nanopore Sequencing
A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced
in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing
a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of ‘third generation’ instruments that will sequence a diploid mammalian genome for ~$1,000 in ~24 h.Molecular and Cellular BiologyPhysic
Multiple Logic Functions Based on Small Molecular Fluorene Derivatives and Their Application in Cell Imaging
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