Spontaneous synchronization of two bistable pyridine-furan nanosprings connected by an oligomeric bridge

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose long-term conformational dynamics are similar to the dynamics of bistable mechanical systems such as Euler arches and Duffing oscillators. Collective synchrony in bistable dynamics of molecular-sized systems has attracted immense attention as a potential pathway to amplify the output signals of molecular nanodevices. Recently, pyridin-furan oligomers of helical shape that are a few nanometers in size and exhibit bistable dynamics similar to a Duffing oscillator have been identified through molecular dynamics simulations. In this article, we present the case of dynamical synchronization of these bistable systems. We show that two pyridine-furan springs connected by a rigid oligomeric bridge spontaneously synchronize vibrations and stochastic resonance enhances the synchronization effect

Spontaneous Vibrations and Stochastic Resonance of Short Oligomeric Springs

There is growing interest in molecular structures that exhibit dynamics similar to bistable mechanical systems. These structures have the potential to be used as nanodevices with two distinct states. Particularly intriguing are structures that display spontaneous vibrations and stochastic resonance. Previously, through molecular dynamics simulations, it was discovered that short pyridine-furan springs, when subjected to force loading, exhibit the bistable dynamics of a Duffing oscillator. In this study, we extend these simulations to include short pyridine-pyrrole and pyridine-furan springs in a hydrophobic solvent. Our findings demonstrate that these systems also display the bistable dynamics of a Duffing oscillator, accompanied by spontaneous vibrations and stochastic resonance activated by thermal noise.Comment: arXiv admin note: substantial text overlap with arXiv:2110.0409

ULTRAMETRIČNOST PROTEINA I PROJEKTOVANJE SINTETIČKIH MOLEKULARNIH MAŠINA

The idea of protein ultrametricity proposed nearly 35 years ago pertaining to CO binding by myoglobin is still questionable. In this overview, the contradicting attempts to describe the CO-rebinding kinetics in the framework of familiar approaches are discussed together with the ultrametric description. The overview is extended by new angle devoted to designing synthetic molecular machines using hierarchy and self-similarity as the design principles.Ideja o ultrametričnosti proteina predložena pre skoro 35 godina, koja se odnosi na vezivanje CO mioglobinom, je još uvek pod znakom pitanja. U ovom preglednom radu su diskutovani kontradiktorni pokušaji za opisivanje kinetike CO u okviru poznatih pristupa i ultrametričkog opisa. Pregled je proširen novim uglom gledanja na dizajniranje sintetičkih molekularnih mašina koristeći hijerarhiju i samosličnost kao principe dizajniranja

Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrate the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance

Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrate the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance