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Register a new userOn the influence of device handle in single-molecule experiments
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We deduce a fully analytical model to predict the artifacts of the measuring device handles in Single Molecule Force Spectroscopy experiments. As we show, neglecting the effects of the handle stiffness can lead to crucial overestimation or underestimation of the stability properties and transition thresholds of macromolecules.
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I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular interactions greatly influence chain dynamics. In this work, we directly observe the dynamics of DNA rings in semidilute ring-linear polymer blends using single molecule techniques. We systematically investigate ring polymer relaxation dynamics from high extension and transient and steady-state stretching dynamics in planar extensional flow for a series of ring-linear blends with varying ring fraction. Our results show multiple molecular sub-populations for ring relaxation in ring-linear blends, as well as large conformational fluctuations for rings in steady extensional flow, even long after the initial transient stretching process has subsided. We further quantify the magnitude and characteristic timescales of ring conformational fluctuations as a function of blend composition. Interestingly, we find that the magnitude of ring conformational fluctuations follows a non-monotonic response with increasing ring fraction, first increasing at low ring fraction and then substantially decreasing at large ring fraction in ring-linear blends. A unique set of ring polymer conformations are observed during the transient stretching process, which highlights the prevalence of molecular individualism and supports the notion of complex intermolecular interactions in ring-linear polymer blends. Together with results from molecular simulations, our results suggest that ring conformational fluctuations arise due to ring-linear threading and intermolecular hydrodynamic interactions (HI). Taken together, our results provide a new molecular understanding of ring polymer dynamics in ring-linear blends in nonequilibrium flow.
Amorphous organic semiconductors based on small molecules and polymers are used in many applications, most prominently organic light emitting diodes (OLEDs) and organic solar cells. Impurities and charge traps are omnipresent in most currently available organic semiconductors and limit charge transport and thus device efficiency. The microscopic cause as well as the chemical nature of these traps are presently not well understood. Using a multiscale model we characterize the influence of impurities on the density of states and charge transport in small-molecule amorphous organic semiconductors. We use the model to quantitatively describe the influence of water molecules and water-oxygen complexes on the electron and hole mobilities. These species are seen to impact the shape of the density of states and to act as explicit charge traps within the energy gap. Our results show that trap states introduced by molecular oxygen can be deep enough to limit the electron mobility in widely used materials.
The nonequilibrium dynamics of molecular devices is studied in the framework of a generic model for single-molecule transistors: a resonant level coupled by displacement to a single vibrational mode. In the limit of a broad level and in the vicinity of the resonance, the model can be controllably reduced to a form quadratic in bosonic operators, which in turn is exactly solvable. The response of the system to a broad class of sudden quenches and ac drives is thus computed in a nonperturbative manner, providing an asymptotically exact solution in the limit of weak electron-phonon coupling. From the analytic solution we are able to (1) explicitly show that the system thermalizes following a local quantum quench, (2) analyze in detail the time scales involved, (3) show that the relaxation time in response to a quantum quench depends on the observable in question, and (4) reveal how the amplitude of long-time oscillations evolves as the frequency of an ac drive is tuned across the resonance frequency. Explicit analytical expressions are given for all physical quantities and all nonequilibrium scenarios under study.
We present magnetization measurements on the single molecule magnet Fe8 in the presence of pulsed microwave radiation. A pump-probe technique is used with two microwave pulses with frequencies of 107 GHz and 118 GHz and pulse lengths of several nanoseconds to study the spin dynamics via time-resolved magnetization measurements using a Hall probe magnetometer. We find evidence for short spin-phonon relaxation times of the order of one microsecond. The temperature dependence of the spin-phonon relaxation time in our experiments is in good agreement with previously published theoretical results. We also established the presence of very short energy diffusion times, that act on a timescale of about 70 ns.
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