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Effects of intermediate bound states in dynamic force spectroscopy  [PDF]
Imre Derenyi,Denis Bartolo,Armand Ajdari
Physics , 2003, DOI: 10.1016/S0006-3495(04)74200-9
Abstract: We revisit here some aspects of the interpretation of dynamic force spectroscopy experiments. The standard theory predicts a typical unbinding force $f^*$ linearly proportional to the logarithm of the loading rate $r$ when a single energetical barrier controls the unbinding process; for a more complex situation of $N$ barriers, it predicts at most $N$ linear segments for the $f^*$ vs. $\log(r)$ curve, each segment characterizing a different barrier. We here extend this existing picture using a refined approximation, we provide a more general analytical formula, and show that in principle up to $N(N+1)/2$ segments can show up experimentally. As a consequence the interpretation of data can be ambiguous, for the characteristics and even the number of barriers. A further possible outcome of a multiple-barrier landscape is a bimodal or multimodal distribution of the unbinding force at a given loading rate, a feature recently observed experimentally.
Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments  [PDF]
Christopher P. Calderon,Kerry S. Bloom
Quantitative Biology , 2015, DOI: 10.1371/journal.pone.0137633
Abstract: Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state changes, e.g., changes induced by dynamic micro-environments, photobleaching, and other heterogeneity inherent in biological processes. This study focuses on techniques for analyzing Single Particle Tracking (SPT) data experiencing abrupt state changes. We demonstrate the approach on GFP tagged chromatids experiencing metaphase in yeast cells and probe the effective forces resulting from dynamic interactions that reflect the sum of a number of physical phenomena. State changes are induced by factors such as microtubule dynamics exerting force through the centromere, thermal polymer fluctuations, etc. Simulations are used to demonstrate the relevance of the approach in more general SPT data analyses. Refined force estimates are obtained by adopting and modifying a nonparametric Bayesian modeling technique, the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT applications. The HDP-SLDS method shows promise in systematically identifying dynamical regime changes induced by unobserved state changes when the number of underlying states is unknown in advance (a common problem in SPT applications). We expand on the relevance of the HDP-SLDS approach, review the relevant background of Hierarchical Dirichlet Processes, show how to map discrete time HDP-SLDS models to classic SPT models, and discuss limitations of the approach. In addition, we demonstrate new computational techniques for tuning hyperparameters and for checking the statistical consistency of model assumptions directly against individual experimental trajectories; the techniques circumvent the need for "ground-truth" and subjective information.
CAD-based robot programming: The role of Fuzzy-PI force control in unstructured environments  [PDF]
Pedro Neto,Nuno Mendes,Norberto Pires,Paulo Moreira
Computer Science , 2013, DOI: 10.1109/COASE.2010.5584058
Abstract: More and more, new ways of interaction between humans and robots are desired, something that allow us to program a robot in an intuitive way, quickly and with a high-level of abstraction from the robot language. In this paper is presented a CAD-based system that allows users with basic skills in CAD and without skills in robot programming to generate robot programs from a CAD model of a robotic cell. When the CAD model reproduces exactly the real scenario, the system presents a satisfactory performance. On the contrary, when the CAD model does not reproduce exactly the real scenario or the calibration process is poorly done, we are dealing with uncertain (unstructured environment). In order to minimize or eliminate the previously mentioned problems, it was introduced sensory feedback (force and torque sensing) in the robotic framework. By controlling the end-effector pose and specifying its relationship to the interaction/contact forces, robot programmers can ensure that the robot maneuvers in an unstructured environment, damping possible impacts and also increasing the tolerance to positioning errors from the calibration process. Fuzzy-PI reasoning was used as a force control technique. The effectiveness of the proposed approach was evaluated in a series of experiments.
GFP's Mechanical Intermediate States  [PDF]
John Saeger, Vesa P. Hyt?nen, Enrico Klotzsch, Viola Vogel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0046962
Abstract: Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP's different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal α-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests a mechanism how N-terminal deletions can switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off.
Double polarization experiments at intermediate energy  [PDF]
H. Schmieden
Physics , 1999, DOI: 10.1016/S0375-9474(99)00568-0
Abstract: At modern electron accelerators with highly polarized, intense, high duty factor beams double polarization coincidence experiments became feasible with good statistical accuracy. The strong potential towards the precise determination of small nucleon structure quantities is illustrated by two recent examples from MAMI. The measurement of $G_E^n$ in the quasifree reaction $D(\vec e, e'\vec n)p$ lead to a new parametrization of $G_E^n$ which is significantly above the previously preferred one from elastic $e-D$ scattering. A $p(\vec e, e'\vec p)\pi^0$ experiment at the energy of the $\Delta$ resonance yields preliminary results for the longitudinal quadrupole mixing. Both experimental errors and model uncertainties are complementary to unpolarized measurements.
Modeling force-induced bio-polymer unfolding  [PDF]
Anthony J. Guttmann,Jesper L. Jacobsen,Iwan Jensen,Sanjay Kumar
Physics , 2007,
Abstract: We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N=55 using exact enumeration techniques. We analyze in details the differences between the constant force and constant distance ensembles for large but finite N. At low temperatures, and in the constant force ensemble, the force-extension curve shows multiple plateaus (intermediate states), in contrast with the abrupt transition to an extended state prevailing in the $N \to \infty$ limit. In the constant distance ensemble, the same curve provides a unified response to pulling and compressing forces, and agrees qualitatively with recent experimental results. We identify a cross-over length, proportional to $N$, below which the critical force of unfolding decreases with temperature, while above, it increases wiyh temperature. Finally, the force-extension curve for stiff chains exhibits "saw-tooth" like behavior, as observed in protein unfolding experiments.
From Lorentz Force on Electron to Magnus Force on Vortex, Role of Experiments  [PDF]
X. -M. Zhu,B. Sundqvist
Physics , 1997,
Abstract: The vortex motion in a superfluid or a type II superconductor is similar to the electron motion in a magnetic field, because they both feel a transverse force. The vortex dynamics in a superconductor is a basic property of the superconductivity which remains controversial. It is also responsible for a large class of observed physical phenomena. We will examine this issue from the experimental point of view. In particular, we will compare the experiments which have set the stage to the Lorentz force and the experiments influencing our understanding of the Magnus force on vortices in superconductors.
On the Analysis of Intermediate-Energy Coulomb Excitation Experiments  [PDF]
Heiko Scheit,Alexandra Gade,Thomas Glasmacher,Tohru Motobayashi
Physics , 2007, DOI: 10.1016/j.physletb.2007.12.004
Abstract: In a recent publication (Bertulani et al., PLB 650 (2007) 233 and arXiv:0704.0060v2) the validity of analysis methods used for intermediate-energy Coulomb excitation experiments was called into question. Applying a refined theory large corrections of results in the literature seemed needed. We show that this is not the case and that the large deviations observed are due to the use of the wrong experimental parameters. We furthermore show that an approximate expression derived by Bertulani et al. is in fact equivalent to the theory of Winther and Alder (NPA 319 (1979) 518), an analysis method often used in the literature.
New Challenges and Directions in Casimir Force Experiments  [PDF]
Davide Iannuzzi,Ian Gelfand,Mariangela Lisanti,Federico Capasso
Physics , 2003,
Abstract: This article is divided in three sections. In the first section we briefly review some high precision experiments on the Casimir force, underlying an important aspect of the analysis of the data. In the second section we discuss our recent results in the measurement of the Casimir force using non-trivial materials. In the third section we present some original ideas for experiments on new phenomena related to the Casimir effects.
Tightening the knot in phytochrome by single molecule atomic force microscopy  [PDF]
T. Bornschloegl,D. M. Anstrom,E. Mey,J. Dzubiella,M. Rief,K. T. Forest
Physics , 2008, DOI: 10.1016/j.bpj.2008.11.012
Abstract: A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We have used protein engineering and atomic force microscopy to explore single-molecule mechanics of the figure-of-eight knot in the chromophore-binding domain of the red/far red photoreceptor, phytochrome. Under load, apo phytochrome unfolds at forces of ~47 pN, while phytochrome carrying its covalently bound tetrapyrrole chromophore unfolds at ~73 pN. These forces are among the lowest measured in mechanical protein unfolding, hence the presence of the knot does not automatically indicate a super-stable protein. Our experiments reveal a stable intermediate along the mechanical unfolding pathway, reflecting sequential unfolding of two distinct subdomains in phytochrome, potentially the GAF and PAS domains. For the first time, our experiments allow direct determination of knot size under load. In the unfolded chain, the tightened knot is reduced to 17 amino acids, resulting in apparent shortening of the polypeptide chain by 6.2 nm. Steered molecular dynamics simulations corroborate this number. Finally, we found that covalent phytochrome dimers created for these experiments retain characteristic photoreversibility, unexpectedly arguing against dramatic rearrangement of the native GAF dimer interface upon photoconversion.
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