77 research outputs found
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
Employing the Metabolic âBranch Point Effectâ to Generate an All-or-None, Digital-like Response in Enzymatic Outputs and Enzyme-Based Sensors
Here, we demonstrate a strategy to convert the
graded MichaelisâMenten response typical of unregulated
enzymes into a sharp, effectively all-or-none response. We do
so using an approach analogous to the âbranch point effectâ, a
mechanism observed in naturally occurring metabolic networks
in which two or more enzymes compete for the same
substrate. As a model system, we used the enzymatic reaction
of glucose oxidase (GOx) and coupled it to a second,
nonsignaling reaction catalyzed by the higher affinity enzyme
hexokinase (HK) such that, at low substrate concentrations,
the second enzyme outcompetes the first, turning off the
latterâs response. Above an arbitrarily selected âthresholdâ substrate concentration, the nonsignaling HK enzyme saturates leading
to a âsuddenâ activation of the first signaling GOx enzyme and a far steeper doseâresponse curve than that observed for simple
MichaelisâMenten kinetics. Using the well-known GOx-based amperometric glucose sensor to validate our strategy, we have
steepen the normally graded response of this enzymatic sensor into a discrete yes/no output similar to that of a multimeric
cooperative enzyme with a Hill coefficient above 13. We have also shown that, by controlling the HK reaction we can precisely
tune the threshold target concentration at which we observe the enzyme output. Finally, we demonstrate the utility of this
strategy for achieving effective noise attenuation in enzyme logic gates. In addition to supporting the development of biosensors
with digital-like output, we envisage that the use of all-or-none enzymatic responses will also improve our ability to engineer
efficient enzyme-based catalysis reactions in synthetic biology applications
Towards Biochemical Filter with Sigmoidal Response to pH Changes: Buffered Biocatalytic Signal Transduction
We realize a biochemical filtering process by introducing a buffer in a
biocatalytic signal-transduction logic system based on the function of an
enzyme, esterase. The input, ethyl butyrate, is converted into butyric acid-the
output signal, which in turn is measured by the drop in the pH value. The
developed approach offers a versatile "network element" for increasing the
complexity of biochemical information processing systems. Evaluation of an
optimal regime for quality filtering is accomplished in the framework of a
kinetic rate-equation model.Comment: PDF, 23 page
All-Photonic Multifunctional Molecular Logic Device
Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously. Here, we report a molecule consisting of three linked photochromes that can be configured as AND, XOR, INH, half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate logic devices, all with a common initial state. The system demonstrates the advantages of light-responsive molecules as multifunctional, reconfigurable nanoscale logic devices that represent an approach to true molecular information processing units
Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate
We consider a realization of the XOR logic gate in a process biocatalyzed by
an enzyme (here horseradish peroxidase: HRP), the function of which can be
inhibited by a substrate (hydrogen peroxide for HRP), when the latter is
inputted at large enough concentrations. A model is developed for describing
such systems in an approach suitable for evaluation of the analog noise
amplification properties of the gate. The obtained data are fitted for gate
quality evaluation within the developed model, and we discuss aspects of
devising XOR gates for functioning in "biocomputing" systems utilizing
biomolecules for information processing
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
Label-Free, Dual-Analyte Electrochemical Biosensors: A New Class of Molecular-Electronic Logic Gates
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