Three-state molecular potentiometer based on a non-symmetrically positioned in-backbone linker

2021 ◽  
Author(s):  
Lucia Palomino-Ruiz ◽  
Pablo Reiné ◽  
Irene R. Marquez ◽  
Luis Alvarez de Cienfuegos ◽  
Nicolas Agrait ◽  
...  
Keyword(s):  
Single Molecule ◽  
Theoretical Models ◽  
Phenylene Ethynylene ◽  
Conductance States

We report on the synthesis and single-molecule conductance of a para-oligo(phenylene)ethynylene (p-OPE) derivative with three well-defined conductance states. Employing theoretical models and comparing to reference compounds we show that this...

Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics

1999 ◽  
Vol 103 (49) ◽  
pp. 10477-10488 ◽  
Author(s):  
Gregory K. Schenter ◽  
H. Peter Lu ◽  
X. Sunney Xie
Keyword(s):  
Single Molecule ◽  
Theoretical Models ◽  
Statistical Analyses

scholarly journals Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments

2020 ◽  
Vol 117 (35) ◽  
pp. 21328-21335
Author(s):  
Zhijie Chen ◽  
Alan Shaw ◽  
Hugh Wilson ◽  
Maxime Woringer ◽  
Xavier Darzacq ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Single Molecule ◽  
Particle Tracking ◽  
Single Particle ◽  
Theoretical Models ◽  
Single Particle Tracking ◽  
Correlation Spectroscopy ◽  
Single Molecule Level ◽  
Diffusion Phenomena ◽  
Diffusion Enhancement

Theoretical and experimental observations that catalysis enhances the diffusion of enzymes have generated exciting implications about nanoscale energy flow, molecular chemotaxis, and self-powered nanomachines. However, contradictory claims on the origin, magnitude, and consequence of this phenomenon continue to arise. To date, experimental observations of catalysis-enhanced enzyme diffusion have relied almost exclusively on fluorescence correlation spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an anti-Brownian electrokinetic (ABEL) trap and in-solution single-particle tracking, we show that catalysis does not increase the diffusion of alkaline phosphatase (ALP) at the single-molecule level, in sharp contrast to the ∼20% enhancement seen in parallel FCS experiments usingp-nitrophenyl phosphate (pNPP) as substrate. Combining comprehensive FCS controls, ABEL trap, surface-based single-molecule fluorescence, and Monte Carlo simulations, we establish thatpNPP-induced dye blinking at the ∼10-ms timescale is responsible for the apparent diffusion enhancement seen in FCS. Our observations urge a crucial revisit of various experimental findings and theoretical models––including those of our own––in the field, and indicate that in-solution single-particle tracking and ABEL trap are more reliable means to investigate diffusion phenomena at the nanoscale.

scholarly journals Exploring the thermoelectric properties of oligo(phenylene-ethynylene) derivatives

Nanoscale ◽  
2020 ◽  
Vol 12 (28) ◽  
pp. 15150-15156
Author(s):  
Hang Chen ◽  
Sara Sangtarash ◽  
Guopeng Li ◽  
Markus Gantenbein ◽  
Wenqiang Cao ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Seebeck Coefficient ◽  
Thermoelectric Properties ◽  
Single Molecule ◽  
Phenylene Ethynylene ◽  
Single Molecule Junctions

Seebeck coefficient measurements provide unique insights into the electronic structure of single-molecule junctions.

scholarly journals Insights into the origin of the high energy-conversion efficiency of F1-ATPase

2019 ◽  
Vol 116 (32) ◽  
pp. 15924-15929 ◽  
Author(s):  
Kwangho Nam ◽  
Martin Karplus
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Theoretical Models ◽  
Adenosine Diphosphate ◽  
Energy Conversion Efficiency ◽  
High Energy ◽  
Structural Deformation ◽  
Coupling Mechanism ◽  
Surprising Result ◽  
X Ray Crystallography

Our understanding of the rotary-coupling mechanism of F1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkán-Kacsó and Marcus [S. Volkán-Kacsó, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed γ-rotation angle dependence of the adenosine triphosphate (ATP)/adenosine diphosphate (ADP) exchange rates of F1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and Pi along a well-defined pathway.

scholarly journals Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

2015 ◽  
Vol 6 ◽  
pp. 1558-1567 ◽  
Author(s):  
Riccardo Frisenda ◽  
Simge Tarkuç ◽  
Elena Galán ◽  
Mickael L Perrin ◽  
Rienk Eelkema ◽  
...  
Keyword(s):  
Single Molecule ◽  
Density Functional ◽  
Mechanical Stability ◽  
Phenylene Ethynylene ◽  
Current Voltage ◽  
Single Molecule Electronics ◽  
Level Model ◽  
Anchoring Groups ◽  
Experimental Findings

We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ) technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene) (OPE3), while having different aurophilic anchoring groups: thiol (SAc), methyl sulfide (SMe), pyridyl (Py) and amine (NH2). The focus of this paper is on the combined characterization of the electrical and mechanical properties determined by the anchoring groups. From conductance histograms we find that thiol anchored molecules provide the highest conductance; a single-level model fit to current–voltage characteristics suggests that SAc groups exhibit a higher electronic coupling to the electrodes, together with better level alignment than the other three groups. An analysis of the mechanical stability, recording the lifetime in a self-breaking method, shows that Py and SAc yield the most stable junctions while SMe form short-lived junctions. Density functional theory combined with non-equlibrium Green’s function calculations help in elucidating the experimental findings.

scholarly journals Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping

2002 ◽  
Vol 3 (5) ◽  
pp. 569-584 ◽  
Author(s):  
Simona Cocco ◽  
John F. Marko ◽  
Rémi Monasson
Keyword(s):  
Single Molecule ◽  
Theoretical Models ◽  
Dna And Rna

A computational study on a multimode spin conductance switching by coordination isomerization in organometallic single-molecule junctions

2018 ◽  
Vol 20 (30) ◽  
pp. 20280-20286 ◽  
Author(s):  
Yingjie Jiang ◽  
Xiaodong Xu ◽  
Yangyang Hu ◽  
Guiling Zhang ◽  
Zhewen Liang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Design ◽  
Computational Study ◽  
Conductance Switching ◽  
Single Molecule Junctions ◽  
Conductance States ◽  
Spin Conductance

Single-molecule junctions provide the additional flexibility of tuning the on/off conductance states through molecular design.

scholarly journals Nanomechanical Characterization of Amyloid Fibrils Using Single-Molecule Experiments and Computational Simulations

2016 ◽  
Vol 2016 ◽  
pp. 1-16 ◽  
Author(s):  
Bumjoon Choi ◽  
Taehee Kim ◽  
Sang Woo Lee ◽  
Kilho Eom
Keyword(s):  
Mechanical Properties ◽  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Amyloid Fibrils ◽  
Theoretical Models ◽  
Beam Model ◽  
Computational Simulations ◽  
Force Microscopy ◽  
Nanomechanical Properties ◽  
Atomic Force

Amyloid fibrils have recently received much attention due to not only their important role in disease pathogenesis but also their excellent mechanical properties, which are comparable to those of mechanically strong protein materials such as spider silk. This indicates the necessity of understanding fundamental principles providing insight into how amyloid fibrils exhibit the excellent mechanical properties, which may allow for developing biomimetic materials whose material (e.g., mechanical) properties can be controlled. Here, we describe recent efforts to characterize the nanomechanical properties of amyloid fibrils using computational simulations (e.g., atomistic simulations) and single-molecule experiments (e.g., atomic force microscopy experiments). This paper summarizes theoretical models, which are useful in analyzing the mechanical properties of amyloid fibrils based on simulations and experiments, such as continuum elastic (beam) model, elastic network model, and polymer statistical model. In this paper, we suggest how the nanomechanical properties of amyloid fibrils can be characterized and determined using computational simulations and/or atomic force microscopy experiments coupled with the theoretical models.

scholarly journals Enhancing the photostability of poly(phenylene ethynylene) for single particle studies

2017 ◽  
Vol 16 (12) ◽  
pp. 1821-1831 ◽  
Author(s):  
C. F. Calver ◽  
B. A. Lago ◽  
K. S. Schanze ◽  
G. Cosa
Keyword(s):  
Fluorescence Imaging ◽  
Single Molecule ◽  
Single Particle ◽  
Phenylene Ethynylene ◽  
Conjugated Polyelectrolytes ◽  
Imaging Studies ◽  
Single Molecule Fluorescence ◽  
Enhanced Photostability ◽  
The Way

Enhanced photostability of conjugated polyelectrolytes achieved by using anti-fading agents opens the way for advanced single molecule fluorescence imaging studies.

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