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A new haptic interaction and visualization approach for rigid molecular docking in virtual environments
No full textMany biological activities take place through the physicochemical interaction of two molecules. This interaction occurs when one of the molecules finds a suitable location on the surface of the other for binding. This process is known as molecular docking, and it has applications to drug design. If we can determine which drug molecule binds to a particular protein, and how the protein interacts with the bonded molecule, we can possibly enhance or inhibit its activities. This information, in turn, can be used to develop new drugs that are more effective against diseases. In this paper, we propose a new approach based on a human-computer interaction paradigm for the solution of the rigid body molecular docking problem. In our approach, a rigid ligand molecule (i.e., drug) manipulated by the user is inserted into the cavities of a rigid protein molecule to search for the binding cavity, while the molecular interaction forces are conveyed to the user via a haptic device for guidance. We developed a new visualization concept, Active Haptic Workspace (AHW), for the efficient exploration of the large protein surface in high resolution using a haptic device having a small workspace. After the discovery of the true binding site and the rough alignment of the ligand molecule inside the cavity by the user, its final configuration is calculated off-line through time stepping molecular dynamics (MD) simulations. At each time step, the optimum rigid body transformations of the ligand molecule are calculated using a new approach, which minimizes the distance error between the previous rigid body coordinates of its atoms and their new coordinates calculated by the MD simulations. The simulations are continued until the ligand molecule arrives at the lowest energy configuration. Our experimental studies conducted with six human subjects testing six different molecular complexes demonstrate that given a ligand molecule and five potential binding sites on a protein surface, the subjects can successfully identify the true binding site using visual and haptic cues. Moreover, they can roughly align the ligand molecule inside the binding cavity such that the final configuration of the ligand molecule can be determined via the proposed MD simulations
FR4-based electromagnetic energy harvester for wireless tyre sensor nodes
No full textAn electromagnetic (EM) power generator having 46 Hz resonance frequency is designed to scavenge mechanical vibrations occurring in tyres due to lyre-road contact. The major innovation is the use of FR4 as a structural spring material as well as utilizing a spacer and stopper mechanism increasing the shock resistance by limiting the maximum deflection. The novel magnet assembly and spacer design provide high power density. The tangential acceleration waveforms of typical tyre rotation is used as an input in the experiments and 0.4 mW power is obtained over a 100 Omega load resistance for 15g peak-to-peak amplitude at 22,83 Hz, corresponding to about 150 kph vehicle speed. Maximum acceleration is limited with the shaker, larger power values are expected in actual operation. The performance is obtained off-resonance and superior to resonant Silicon MEMS based scavengers
Phase diffusion of a q-deformed oscillator
No full textWe examine the problem of phase diffusion rate in a U(1) global phase symmetry broken system, from the perspective of q-deformed oscillators where the deformation parameter represents the anharmonicity. It is shown that broken phase symmetry states, described by deformed coherent states, suffer phase diffusion at a rate determined by the deformation parameter. Analytical discussions are given for the case of weak deformations, while detailed numerical results are presented when strong anharmonicity is present in the system
Multiple piezo-patch energy harvesters integrated to a thin plate with AC-DC conversion: analytical modeling and numerical validation
No full textPlate-like components are widely used in numerous automotive, marine, and aerospace applications where they can be employed as host structures for vibration based energy harvesting. Piezoelectric patch harvesters can be easily attached to these structures to convert the vibrational energy to the electrical energy. Power output investigations of these harvesters require accurate models for energy harvesting performance evaluation and optimization. Equivalent circuit modeling of the cantilever-based vibration energy harvesters for estimation of electrical response has been proposed in recent years. However, equivalent circuit formulation and analytical modeling of multiple piezo-patch energy harvesters integrated to thin plates including nonlinear circuits has not been studied. In this study, equivalent circuit model of multiple parallel piezoelectric patch harvesters together with a resistive load is built in electronic circuit simulation software SPICE and voltage frequency response functions (FRFs) are validated using the analytical distributed-parameter model. Analytical formulation of the piezoelectric patches in parallel configuration for the DC voltage output is derived while the patches are connected to a standard AC-DC circuit. The analytic model is based on the equivalent load impedance approach for piezoelectric capacitance and AC-DC circuit elements. The analytic results are validated numerically via SPICE simulations. Finally, DC power outputs of the harvesters are computed and compared with the peak power amplitudes in the AC output case
The effects of odor and body posture on perceived duration
No full textThis study reports an examination of the internal clock model, according to which subjective time duration is influenced by attention and arousal state. In a time production task, we examine the hypothesis that an arousing odor and an upright body posture affect perceived duration. The experimental task was performed while participants were exposed to an odor and either sitting upright (arousing condition) or lying down in a relaxing chair (relaxing condition). They were allocated to one of three experimental odor conditions: rosemary (arousing condition), peppermint (relaxing condition), and no odor (control condition). The predicted effects of the odors were not borne out by the results. Self-reported arousal (SRA) and pleasure (PL) states were measured before, during (after each body posture condition) and postexperimentally. Heart rate (HR) and skin conductance were measured before and during the experiment. As expected, odor had an effect on perceived duration. When participants were exposed to rosemary odor, they produced significantly shorter time intervals than in the no odor condition. This effect, however, could not be explained by increased arousal. There was no effect of body posture on perceived duration, even though body posture did induce arousal. The results do not support the proposed arousal mechanism of the internal clock model
Einstein-Cartan-Dirac theory in (1+2)-dimensions
No full textEinstein-Cartan theory is formulated in (1 + 2) dimensions using the algebra of exterior differential forms. A Dirac spinor is coupled to gravity and the field equations are obtained by a variational principle. The space-time torsion is found to be given algebraically in terms of a quadratic spinor condensate field. Circularly symmetric, exact solutions that collapse to AdS(3) geometry in the absence of the Dirac condensate are found
Successful focal ablation in a patient with electrical storm in the early postinfarction period: case report
No full textElectrical storm (ES) is associated with a poor prognosis if it occurs in the early postinfarction period (within 4 weeks). There are limited data on the efficacy and safety of catheter ablation in the early period. In the patients with postinfarction cardiomyopathy, ventricular tachycardia (VT) is usually caused by re-entry through slowly conducting tissue within areas of a myocardial scar, whereas for the early postinfarction period, the underlying mechanism of ES is not fully understood. We report a case of ES for which macroreentry was excluded as a mechanism of VT because of the clinical and electrophysiological properties of the tachycardia. The tachycardia was terminated by focal radiofrequency catheter ablation of the earliest site. The total procedure time was only 35 minutes. During a 12-month follow-up period, the patient has remained free of monomorphic VT episodes. On the basis of this case, we aimed to discuss the underlying mechanism of ES in the early postinfarction period and to evaluate the role of radiofrequency catheter ablation as a primary approach for treating ES
Evaluation of iron deposition in the adrenal glands of beta thalassemia major patients using 3-Tesla MRI
No full textBackground: Beta-thalassemia major (beta-TM) patients need blood transfusions, which result in iron deposition. To regulate chelation therapy, iron load has to be measured. With MRI, the amount of signal loss and T2* decay time shortening are used for iron quantification. Objectives: The aim was to measure adrenal iron load with T2* relaxometry using MRI, and to compare it with liver and cardiac iron and serum ferritin, and to find out whether adrenal iron could be predicted from those parameters. Patients and Methods: Between October 2014 and March 2015, MRI was performed in 21 patients with beta-TM, recieving blood transfusions and chelation therapy. The control group (n = 11) included healthy volunteers with no known history of adrenal, hematologic, chronic disease, and blood transfusion. Results: Among patients, there was no significant correlation between plasma ferritin and adrenal T2*. Significant difference was detected among T2* values of adrenals between the patient and control groups. There was no significant correlation between adrenal gland and liver T2* in beta-TM patients, moderate correlation was detected between adrenal T2* and cardiac T2*. Conclusion: Adrenal iron in beta-TM can be reliably measured in 3 Tesla MRI. The results highlight the absence of correlation between adrenal iron deposition both with serum ferritin and hepatic iron
An optofluidic FRET laser using aqueous quantum dots as donors
No full textThe integration of optofluidic laser and FRET mechanism provides novel research frontiers, including sensitive biochemical analysis and novel photonic devices, such as on-chip coherent light sources and bio-tunable lasers. Here we investigated an optofluidic FRET laser using quantum dots (QDs) as FRET donors. We achieved lasing from Cy5 as the acceptor in the QD-Cy5 pair with excitation at 450 nm where Cy5 has negligible absorption by itself. The threshold was approximately 14 mu J/mm(2). The demonstrated capability of QDs as the donor in a FRET laser greatly improves the versatility of optofluidic laser operation due to the broad and large absorption cross section of QDs in the blue and UV spectral region. The excitation efficiency of the acceptor molecules through FRET channel was also analyzed, showing that the energy transfer rate and the non-radiative Auger recombination rate of QDs plays a significant role in FRET laser performance
Latitudinal dependence of static mesospheric E fields above thunderstorms
No full textElectrostatic fields generated by thunderclouds can significantly heat and modify the lower ionospheric electrons at altitudes of 70-80km. These fields can map to higher altitudes along the geomagnetic field lines and have been proposed as the mechanism for generation of whistler ducts. Previous 2-D modeling of these fields have been limited to azimuthally symmetric cases which requires a vertical magnetic field. We have developed a 3-D model of the electrostatic thundercloud fields which allows the consideration of effects of the geomagnetic field dip angle on the mapping of the fields to high altitudes. The results show stronger electric fields at altitudes of 70-110km with an equatorward and eastward shift of tens of kilometers at lower geomagnetic latitudes. These stronger fields are mapped into the magnetosphere and may therefore be important for whistler duct generation. The fields also indicate a more significant contribution of the quiescent heating on VLF early/fast events