Enhanced feedback performance in off-resonance AFM modes through pulse train sampling
Ontology highlight
ABSTRACT:
SUBMITTER:
PROVIDER: S-EPMC10840551 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Because of the small size of nanomechanical systems, their vibrations become nonlinear already for small amplitudes. Many nontrivial aspects of the vibration dynamics arise from the coexistence of several nonlinearly coupled modes. We show that such coupling can lead to anomalous decay of the modes where they go through nonlinear resonance, so that their amplitude-dependent frequencies become commensurate. We demonstrate the possibility of a strongly nonmonotonic dependence of the decay rate on the amplitude if one of the modes serves as a thermal reservoir for another mode. Where the decay of both modes is slow compared to the rate of resonant energy exchange, the decay is accompanied by amplitude oscillations. Depending on the initial conditions, with increasing time it can display an extremely sharp or a comparatively smooth crossover between different regimes. The results provide insight into recent experimental results by several groups and suggest new ways of characterizing and controlling nanomechanical systems.
| S-EPMC5741793 | biostudies-literature
Project description:Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.
| S-EPMC5980761 | biostudies-literature
Project description:We demonstrate experimentally that in photonic crystal sensors with a side-coupled cavity-waveguide configuration, group velocity of the propagating mode in the coupled waveguide at the frequency of the resonant mode plays an important role in enhancing the sensitivity. In linear L13 photonic crystal microcavities, with nearly same resonance mode quality factors ∼7000 in silicon-on-insulator devices, sensitivity increased from 57 nm/RIU to 66 nm/RIU as group index in the coupled waveguide increased from 10.2 to 13.2. Engineering for highest sensitivity in such planar integrated sensors, thus, requires careful slow light design for optimized sensor sensitivity.
| S-EPMC3574073 | biostudies-other
Project description:APOBEC3G (A3G) protein has antiviral activity against HIV and other pathogenic retroviruses. A3G has two domains: a catalytic C-terminal domain (CTD) that deaminates cytidine, and a N-terminal domain (NTD) that binds to ssDNA. Although abundant information exists about the biological activities of A3G protein, the interplay between sequence specific deaminase activity and A3G binding to ssDNA remains controversial. We used the topographic imaging and force spectroscopy modalities of Atomic Force Spectroscopy (AFM) to characterize the interaction of A3G protein with deaminase specific and nonspecific ssDNA substrates. AFM imaging demonstrated that A3G has elevated affinity for deaminase specific ssDNA than for nonspecific ssDNA. AFM force spectroscopy revealed two distinct binding modes by which A3G interacts with ssDNA. One mode requires sequence specificity, as demonstrated by stronger and more stable complexes with deaminase specific ssDNA than with nonspecific ssDNA. Overall these observations enforce prior studies suggesting that both domains of A3G contribute to the sequence specific binding of ssDNA.
| S-EPMC4621513 | biostudies-literature
Project description:Managerial feedback discussions often fail to produce the desired performance improvements. Three studies shed light on why performance feedback fails and how it can be made more effective. In Study 1, managers described recent performance feedback experiences in their work settings. In Studies 2 and 3, pairs of managers role-played a performance review meeting. In all studies, recipients of mixed and negative feedback doubted the accuracy of the feedback and the providers' qualifications to give it. Disagreement regarding past performance was greater following the feedback discussion than before, due to feedback recipients' increased self-protective and self-enhancing attributions. Managers were motivated to improve to the extent they perceived the feedback conversation to be focused on future actions rather than on past performance. Our findings have implications for the theory and practice of performance management.
| S-EPMC7304587 | biostudies-literature
Project description:Electrical stimulation of specific small fibers (Aδ- and C-fibers) is used in basic studies on nociception and neuropathic pain and to diagnose neuropathies. For selective stimulation of small fibers, the optimal stimulation waveform parameters are an important aspect together with the study of electrode design. However, determining an optimal stimulation condition is challenging, as it requires the characterization of the response of the small fibers to electrical stimulation. The perception thresholds are generally characterized using single-pulse stimulation based on the strength-duration curve. However, this does not account for the temporal effects of the different waveforms used in practical applications. In this study, we designed an experiment to characterize the effects of multiple pulse stimulation and proposed a computational model that considers electrostimulation of fibers and synaptic effects in a multiscale model. The measurements of perception thresholds showed that the pulse dependency of the threshold was an exponential decay with a maximum reduction of 55%. In addition, the frequency dependence of the threshold showed a U-shaped response with a reduction of 25% at 30 Hz. Moreover, the computational model explained the synaptic effects, which were also confirmed by evoked potential recordings. This study further characterized the activation of small fibers and clarified the synaptic effects, demonstrating the importance of waveform selection.
| S-EPMC8107290 | biostudies-literature
Project description:With a view to improving the consistency of free energy perturbation calculations in Monte Carlo simulations of protein-ligand complexes, we have implemented the replica exchange with solute tempering (REST) method in the MCPRO software. By augmenting the standard REST approach with regular attempted jumps in selected dihedral angles, our combined method facilitates sampling of ligand binding modes that are separated by high free energy barriers and ensures that computed free energy changes are considerably less dependent on the starting conditions and the chosen mutation pathway than those calculated with standard Monte Carlo sampling. We have applied the enhanced sampling method to the calculation of the activities of seven non-nucleoside inhibitors of HIV-1 reverse transcriptase, and its Tyr181Cys variant, and have shown that a range of binding orientations is possible depending on the nature of the ligand and the presence of mutations at the binding site.
| S-EPMC3985685 | biostudies-other
Project description:There is a growing concern regarding the dose delivered during x-ray fluoroscopy guided procedures, particularly in interventional cardiology and neuroradiology, and in real-time tumor tracking radiotherapy and radiosurgery. Many of these procedures involve long treatment times, and as such, there is cause for concern regarding the dose delivered and the associated radiation related risks. An insufficient dose, however, may convey less geometric information, which may lead to inaccuracy and imprecision in intervention placement. The purpose of this study is to investigate a method for achieving the required tracking uncertainty for a given interventional procedure using minimal dose.A simple model is used to demonstrate that a relationship exists between imaging dose and tracking uncertainty. A feedback framework is introduced that exploits this relationship to modulate the tube current (and hence the dose) in order to maintain the required uncertainty for a given interventional procedure. This framework is evaluated in the context of a fiducial tracking problem associated with image-guided radiotherapy in the lung. A particle filter algorithm is used to robustly track the fiducial as it traverses through regions of high and low quantum noise. Published motion models are incorporated in a tracking test suite to evaluate the dose-localization performance trade-offs.It is shown that using this framework, the entrance surface exposure can be reduced by up to 28.6% when feedback is employed to operate at a geometric tracking uncertainty of 0.3 mm.The analysis reveals a potentially powerful technique for dynamic optimization of fluoroscopic imaging parameters to control the applied dose by exploiting the trade-off between tracking uncertainty and x-ray exposure per frame.
| S-EPMC3104719 | biostudies-other
Project description:When laser radiation is skilfully applied, atoms and molecules can be cooled1-3, allowing the precise measurements and control of quantum systems. This is essential for the fundamental studies of physics as well as practical applications such as precision spectroscopy4-7, ultracold gases with quantum statistical properties8-10 and quantum computing. In laser cooling, atoms are slowed to otherwise unattainable velocities through repeated cycles of laser photon absorption and spontaneous emission in random directions. Simple systems can serve as rigorous testing grounds for fundamental physics-one such case is the purely leptonic positronium11,12, an exotic atom comprising an electron and its antiparticle, the positron. Laser cooling of positronium, however, has hitherto remained unrealized. Here we demonstrate the one-dimensional laser cooling of positronium. An innovative laser system emitting a train of broadband pulses with successively increasing central frequencies was used to overcome major challenges posed by the short positronium lifetime and the effects of Doppler broadening and recoil. One-dimensional chirp cooling was used to cool a portion of the dilute positronium gas to a velocity distribution of approximately 1 K in 100 ns. A major advancement in the field of low-temperature fundamental physics of antimatter, this study on a purely leptonic system complements work on antihydrogen13, a hadron-containing exotic atom. The successful application of laser cooling to positronium affords unique opportunities to rigorously test bound-state quantum electrodynamics and to potentially realize Bose-Einstein condensation14-18 in this matter-antimatter system.
| S-EPMC11424484 | biostudies-literature
Project description:High synthesis temperatures and specific growth substrates are typically required to obtain crystalline or oriented inorganic functional thin films, posing a significant challenge for their utilization in large-scale, low-cost (opto-)electronic applications on conventional flexible substrates. Here, we explore a pulse irradiation synthesis (PIS) to prepare thermoelectric metal chalcogenide (e.g., Bi2Se3, SnSe2, and Bi2Te3) films on multiple polymeric substrates. The self-propagating combustion process enables PIS to achieve a synthesis temperature as low as 150 °C, with an ultrafast reaction completed within one second. Beyond the photothermoelectric (PTE) property, the thermal coupling between polymeric substrates and bismuth selenide films is also examined to enhance the PTE performance, resulting in a responsivity of 71.9 V/W and a response time of less than 50 ms at 1550 nm, surpassing most of its counterparts. This PIS platform offers a promising route for realizing flexible PTE or thermoelectric devices in an energy-, time-, and cost-efficient manner.
| S-EPMC10810900 | biostudies-literature