Detection of Single Molecules Using Stochastic Resonance of Bistable Oligomers

Abstract

Ultra-sensitive elements for nanoscale devices capable of detecting single molecules are in demand for many important applications. It is generally accepted that the inevitable stochastic disturbance of a sensing element by its surroundings will limit detection at the molecular level. However, a phenomenon exists (stochastic resonance) in which the environmental noise acts abnormally: it amplifies, rather than distorts, a weak signal. Stochastic resonance is inherent in non-linear bistable systems with criticality at which the bistability emerges. Our computer simulations have shown that the large-scale conformational dynamics of a short oligomeric fragment of thermosrespective polymer, poly-N-isopropylmethacrylamid, resemble the mechanical movement of nonlinear bistable systems. The oligomers we have studied demonstrate spontaneous vibrations and stochastic resonance activated by conventional thermal noise. We have observed reasonable shifts of the spontaneous vibrations and stochastic resonance modes when attaching an analyte molecule to the oligomer. Our simulations have shown that spontaneous vibrations and stochastic resonance of the bistable thermoresponsive oligomers are sensitive to both the analyte molecular mass and the binding affinity. All these effects indicate that the oligomers with mechanic-like bistability may be utilized as ultrasensitive operational units capable of detecting single molecules.

Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

“…Following Kramer's rate approximation with the collision time for random perturbations ranging from 0.1-10 ps, one can roughly www.videleaf.com estimate the bistability barrier of the oligo-PF-5 spring as 10-15 kBT. Interestingly, the bistability barrier of the oligo-PF-5 spring turned out to be roughly equal to the same value as that for the oligomeric Euler arch described in [42,43]. Even though the reasons for the bistability of the oligo-PF-5 spring and the oligomeric Euler arch were different, the bistability barriers of both bistable oligomeric systems were about ten times larger than the characteristic scale of thermal fluctuations, kBT.…”

“…Based on these lifetimes and following Kramer's rate approximation with the collision time ranging from 0.1-10 ps, we estimated the bistability barriers of both springs as 10-15 𝑘 𝐵 𝑇. It is noteworthy that the time scales of spontaneous vibrations of the oligo-PF-5 and the oligo-PF-7 springs and their bistability barriers were approximately the same as those of the oligomeric Euler arch described in [42,43]. The bistability barriers of short PF springs appear to be high enough to separate the two states against the thermal noise; on the other hand, the same barriers allowed activation of the transitions between the two states by energetically enriched thermal fluctuations.…”

“…Some oligomeric molecules within a few nanometers could be assumed to represent such bistable systems. Indeed, bistable molecules demonstrating the dynamics of an Euler arch were re-cently found through intensive molecular dynamic simulations of short thermo-responsive oligomeric compounds that were subject to force loads [42,43]. The simulations showed mechanic-like bistability of specific oligomeric molecules with spontaneous vibrations and stochastic resonance that were activated by thermal fluctuations.…”

A Novel Piecewise Tri-Stable Stochastic Resonance System Driven by Dichotomous Noise

“…SR theory was proposed in 1981 to explain the glacier problem [ 1 ]. For many domains, SR can be used and has good performance [ 2 , 3 , 4 , 5 , 6 , 7 , 8 ]. In the aspect of feature extraction and signal enhancement of mechanical signals, SR is used more and more because it is different from other denoising methods [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 ].…”

Spontaneous Vibrations and Stochastic Resonance of Short Oligomeric Springs

“…This article focuses on nanoscale molecular structures whose dynamic prototypes are the textbook bistable mechanical systems known as Euler arches (a beautiful but simple example of a bistable machine which is composed of two rigid rods joined by a hinge with an elastic spring) [27][28][29] and Duffing oscillators [30,31]. In particular, using molecular dynamics simulations, it was found that the long-term conformational dynamics of short rod-shaped thermosensitive oligomers were similar to the bistable dynamics of a Euler arch [29,32,33], while particular oligomers of a helical form stabilized via weak intermolecular interactions could behave as bistable Duffing oscillators [29,34].…”