Stationary Trap Research Articles

Interaction of a Polaron with a Trap. Influence of Adiabaticity

A lattice model of the interaction of a polaron with a stationary trap is considered in this work. For estimation of an electron-phonon interaction we used the Su – Schrieffer – Heeger approximation, which is more typical for DNA. The trap is localized at a lattice site with energy U < 0. Depending on the depth of the trap, there are two mechanisms for the interaction of the polaron with the trap. For a shallow trap, the interaction is adiabatic, and the trap does not capture the wave function. For a deeper trap, the dynamics of the interaction of the charge with the trap is determined by the nonadiabaticity of the process with the participation of excited electronic states. In a narrow range of values of the trap depth –0.6 ≤ U ≤ –0.4, a polaron is completely captured by the trap, and a stationary polaron is formed on the trap. For deeper traps, for U < –0.6, the polaron is not captured by the trap, and the wave function either tunnels through the trap or is reflected from it. The phase of the wave function provides useful information about the mechanism of interaction between the polaron and the trap.

Using logbook‐based catch‐rate data to detect yellow eel population trends in the southern Baltic Sea

AbstractWithin recent years, a slight but significant increase of European eel Anguilla anguilla (L.) recruitment has been documented, but it remains questionable whether or not the increased recruitment levels resulted in higher eel numbers at the regional scale. To detect the changes in yellow eel numbers, logbook data covering a 15‐year time series of catch per unit effort (CPUE) data from the German Baltic Sea were analysed. Monthly mean catch rates were calculated for two different size classes for two passive gears: fyke and stationary trap nets. Change‐point analysis was applied to discover changes in the catch data. After a period of decreasing or constant catch rates, the fyke net data indicated that yellow eel numbers increased slightly in recent years in the Baltic Sea. Besides increasing numbers of immigrating juvenile eels, other population dynamics or conservation efforts might have added to the observed positive stock trend.

Polaron interaction with a trap. Continuum approximation

An interaction of a moving polaron with a stationary trap is considered in the continuum approximation. Different scenarios — wave function capture and transmission, are possible depending on the polaron velocity. Intermediate cases can also occur. Numerical modelling was carried out for the polaron velocity varying by 3 orders of magnitude. At low polaron velocities, the process is adiabatic and the trap does not capture a charge. At high velocities, the interaction of a polaron with a trap is a highly non-adiabatic and the polaron passes through the trap. At intermediate velocities, the probability of charge capture/transmission oscillates with velocity.

Hypoxia augments edge effects of water column stratification on fish distribution

Hypoxic conditions in both freshwater and marine habitats have a significant effect on the distribution of fish in the water column, resulting in some fishes aggregating near the edges of the hypoxic zone. These aggregations may increase fish susceptibility to fishing gears, with attendant effects on stock assessment inferences. We investigated how hypoxic conditions influenced catch rates of yellow perch (Perca flavescens) in both fishery-independent bottom trawls and stationary commercial trap nets. Specifically, we examined how the presence of hypoxia affected trap net catch rates and how hypoxia interacted with hypolimnion thickness to modify trawl catch rates. Bottom trawl catch rates were significantly higher in hypoxic conditions than in normoxic conditions, and in each of these scenarios catch rates declined as hypolimnion thickness increased. By comparison, trap net catch rates had a dome-shaped response to the duration of hypoxia with the highest catch rates occurring at intermediate levels. Increased catch rates in hypoxic conditions potentially causes yellow perch population models, which rely on both trap net and trawl indices, to overestimate abundance and could result in overfishing.

Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.

In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.

Manipulating rod-shaped bacteria with optical tweezers

Optical tweezers have great potential in microbiology for holding and manipulating single cells under a microscope. However, the methodology to use optical tweezers for live cell studies is still at its infancy. In this work, we determined suitable parameters for stable trapping of single Escherichia coli bacteria, and identified the upper limits of IR-exposure that can be applied without affecting viability. We found that the maximum tolerable IR-exposure is 2.5-fold higher when employing oscillating instead of stationary optical trapping (20 J and 8 J, respectively). We found that good stability of cells in an oscillating trap is achieved when the effective trap length is 20% larger than the cell length, the oscillation frequency higher than 100 Hz and the trap oriented perpendicular to the medium flow direction. Further, we show, using an IR power just sufficient for stable holding, that bacteria remain viable during at least 30 min of holding in an oscillating trap. In this work, we established a method for long-term stable handling of single E. coli cells using optical tweezers. This work will pave the way for future use of optical tweezers in microbiology.

Force-Dependent Unbinding Rate of Molecular Motors from Stationary Optical Trap Data.

Molecular motors walk along filaments until they detach stochastically with a force-dependent unbinding rate. Here, we show how this unbinding rate can be obtained from the analysis of experimental data of molecular motors moving in stationary optical traps. Two complementary methods are presented, based on the analysis of the distribution for the unbinding forces and of the motor's force traces. In the first method, analytically derived force distributions for slip bonds, slip-ideal bonds, and catch bonds are used to fit the cumulative distributions of the unbinding forces. The second method is based on the statistical analysis of the observed force traces. We validate both methods with stochastic simulations and apply them to experimental data for kinesin-1.

Borrelia parkeri in Ornithodoros parkeri (Ixodida: Argasidae) Collected Using Compact Dry Ice Traps in Madera County, California.

Tick-borne relapsing fever (TBRF) is a potentially serious vector-borne disease endemic to the western United States. Vector surveillance is compromised by the nidicolous life history of the three Ornithodoros species that transmit TBRF to people in this region. Large-scale stationary trapping methods were developed to survey a wide geographical range of Ornithodoros spp. which are known to vector relapsing fever Borrelia spp. in California. Ninety-six Ornithodoros parkeri were collected from four locations in the foothills of Fresno and Madera Counties. Two of these O. parkeri nymphs were PCR positive for Borrelia parkeri, and their collection at a popular recreation site increases the public health concern.

Homoclinic bifurcation and the Belyakov degeneracy in a variant of the Romer model of endogenous growth

This paper explores the possibility of complex dynamics in a variant of the [29] model of endogenous growth. In particular, we derive the exact parametric configuration that allows for the emergence of a double-pulse homoclinic orbit, and the rise of globally indeterminate solutions, in the same area where local determinacy was found. Our results confirm that irregular patterns and oscillating solutions can be obtained along a subsidiary homoclinic orbit at which the periodic loop starts to double, so that the system might perpetually oscillate around the long run equilibrium, being thus confined in a stationary trapping region outside the neighborhood of the steady state. The economic implications of these results are finally discussed.

Fast atom transport and launching in a nonrigid trap

We study the shuttling of an atom in a trap with controllable position and frequency. Using invariant-based inverse engineering, protocols in which the trap is simultaneously displaced and expanded are proposed to speed up transport between stationary trap locations as well as launching processes with narrow final-velocity distributions. Depending on the physical constraints imposed, either simultaneous or sequential approaches may be faster. We consider first a perfectly harmonic trap, and then extend the treatment to generic traps. Finally, we apply this general framework to a double-well potential to separate different motional states with different launching velocities.

Model‐based estimators of density and connectivity to inform conservation of spatially structured populations

AbstractConservation and management of spatially structured populations is challenging because solutions must consider where individuals are located, but also differential individual space use as a result of landscape heterogeneity. A recent extension of spatial capture–recapture (SCR) models, the ecological distance model, uses spatial encounter histories of individuals (e.g., a record of where individuals are detected across space, often sequenced over multiple sampling occasions), to estimate the relationship between space use and characteristics of a landscape, allowing simultaneous estimation of both local densities of individuals across space and connectivity at the scale of individual movement. We developed two model‐based estimators derived from the SCR ecological distance model to quantify connectivity over a continuous surface: (1) potential connectivity—a metric of the connectivity of areas based on resistance to individual movement; and (2) density‐weighted connectivity (DWC)—potential connectivity weighted by estimated density. Estimates of potential connectivity and DWC can provide spatial representations of areas that are most important for the conservation of threatened species, or management of abundant populations (i.e., areas with high density and landscape connectivity), and thus generate predictions that have great potential to inform conservation and management actions. We used a simulation study with a stationary trap design across a range of landscape resistance scenarios to evaluate how well our model estimates resistance, potential connectivity, and DWC. Correlation between true and estimated potential connectivity was high, and there was positive correlation and high spatial accuracy between estimated DWC and true DWC. We applied our approach to data collected from a population of black bears in New York, and found that forested areas represented low levels of resistance for black bears. We demonstrate that formal inference about measures of landscape connectivity can be achieved from standard methods of studying animal populations which yield individual encounter history data such as camera trapping. Resulting biological parameters including resistance, potential connectivity, and DWC estimate the spatial distribution and connectivity of the population within a statistical framework, and we outline applications to many possible conservation and management problems.

Combination of dynamic magnetophoretic separation and stationary magnetic trap for highly sensitive and selective detection of Salmonella typhimurium in complex matrix.

Foodborne illnesses have always been a serious problem that threats public health, so it is necessary to develop a method that can detect the pathogens rapidly and sensitively. In this study, we designed a magnetic controlled microfluidic device which integrated the dynamic magnetophoretic separation and stationary magnetic trap together for sensitive and selective detection of Salmonella typhimurium (S. typhimurium). Coupled with immunomagnetic nanospheres (IMNs), this device could separate and enrich the target pathogens and realize the sensitive detection of target pathogens on chip. Based on the principle of sandwich immunoassays, the trapped target pathogens identified by streptavidin modified QDs (SA-QDs) were detected under an inverted fluorescence microscopy. A linear range was exhibited at the concentration from 1.0×10(4) to 1.0×10(6) colony-forming units/mL (CFU/mL), the limit of detection (LOD) was as low as 5.4×10(3) CFU/mL in milk (considering the sample volume, the absolute detection limit corresponded to 540C FU). Compared with the device with stationary magnetic trap alone, the integrated device enhanced anti-interference ability and increased detection sensitivity through dynamic magnetophoretic separation, and made the detection in complex samples more accurate. In addition, it had excellent specificity and good reproducibility. The developed system provides a rapid, sensitive and accurate approach to detect pathogens in practice samples.

Motility of Kinetochore Kinesin CENP-E is Enhanced by Tubulin Detyrosination

Targeted transport by intracellular motors can be regulated by posttranslational modifications of polymerized tubulins in the microtubule tracks, but little is known about such effects for motors that drive chromosome motions during mitosis. Microtubules that form mitotic spindle are differentially modified at the C-terminal residue of α-tubulin: polymers that point to the spindle equator, but not the astral microtubules, are preferentially detyrosinated. Here we examine the influence of tubulin detyrosination on CENP-E, the kinetochore-localized kinesin-7 that transports pole-proximal chromosomes to the spindle equator. We polymerized purified human tubulins that were fully tyrosinated or detyrosinated, and examined the suitability of these tracks for motility of recombinant GFP-tagged CENP-E motor. Using fluorescence microscopy we show that single molecules of CENP-E walk faster and more processively on detyrosinated microtubules. Moreover, on these tracks the CENP-E motor can generate larger force than on the tyrosinated microtubules, as determined using stationary optical trap. On both types of microtubules CENP-E took 8-nm steps, exhibited similar dwell times and frequencies of backward stepping. However, motor's detachment increased with resisting force faster when CENP-E was walking on tyrosinated microtubules, leading to the detachment from these polymers at on average smaller load, 4.5 pN vs. 6.4 pN for detyrosinated microtubules. The enhanced motility of CENP-E motor on detyrosinated microtubules, most notably its ability to carry a larger load, could potentially explain the targeted transport of mitotic chromosomes toward the spindle equator.

First-passage times, mobile traps, and Hopf bifurcations.

For a random walk on a confined one-dimensional domain, we consider mean first-passage times (MFPT) in the presence of a mobile trap. The question we address is whether a mobile trap can improve capture times over a stationary trap. We consider two scenarios: a randomly moving trap and an oscillating trap. In both cases, we find that a stationary trap actually performs better (in terms of reducing expected capture time) than a very slowly moving trap; however, a trap moving sufficiently fast performs better than a stationary trap. We explicitly compute the thresholds that separate the two regimes. In addition, we find a surprising relation between the oscillating trap problem and a moving-sink problem that describes reduced dynamics of a single spike in a certain regime of the Gray-Scott model. Namely, the above-mentioned threshold corresponds precisely to a Hopf bifurcation that induces oscillatory motion in the location of the spike. We use this correspondence to prove the uniqueness of the Hopf bifurcation.

Capturing self-propelled particles in a moving microwedge

Catching fish with a fishing net is typically done either by dragging a fishing net through quiescent water or by placing a stationary basket trap into a stream. We transfer these general concepts to micron-sized self-motile particles moving in a solvent at low Reynolds number and study their collective trapping behavior by means of computer simulations of a two-dimensional system of self-propelled rods. A chevron-shaped obstacle is dragged through the active suspension with a constant speed v and acts as a trapping "net." Three trapping states can be identified corresponding to no trapping, partial trapping, and complete trapping and their relative stability is studied as a function of the apex angle of the wedge, the swimmer density, and the drag speed v. When the net is dragged along the inner wedge, complete trapping is facilitated and a partially trapped state changes into a complete trapping state if the drag speed exceeds a certain value. Reversing the drag direction leads to a reentrant transition from no trapping to complete trapping and then back to no trapping upon increasing the drag speed along the outer wedge contour. The transition to complete trapping is marked by a templated self-assembly of rods forming polar smectic structures anchored onto the inner contour of the wedge. Our predictions can be verified in experiments of artificial or microbial swimmers confined in microfluidic trapping devices.

Lambda Exonuclease Activity Measured Using Optical Tweezers with Active Force Clamp Control

Exonucleases are part of many genetic recombination and repair systems. We use high-resolution optical tweezers to study bacteriophage lambda exonuclease. We trap a dumbbell construct (bead-DNA-bead) in an inverted microscope by dividing a CW laser beam into a stationary trap and a steerable trap. The inter-trap distance is actively controlled with 200 kHz update rate by acousto-optical deflectors (AOD) and field programmable gate array -card. In addition, we control the sample temperature by flowing heating fluid through aluminum jacket around the trapping objective. We follow the exonuclease activity through the length change of a 48kb dsDNA template to ssDNA-form. The dsDNA tether is attached from one strand to two streptavidin coated beads, leaving one 5’ phosphorylated end free for exonuclease to start catalytic removal of mononucleotides. At low forces the length of the ssDNA is significantly shorter than the dsDNA. The template is held in a dumbbell construct at constant force with active feedback control. This allows us to follow the enzymatic activity of the lambda exonuclease over ten micrometers while simultaneously applying a constant load between 0 and 50 pN. We apply different loads on the DNA template to measure how the template tension affects the activity of the lambda exonuclease. We also measure the activity under different ambient temperatures.

Measuring colloidal forces from particle position deviations inside an optical trap

We measure interaction forces between pairs of charged PMMA colloidal particles suspended in a relatively low-polar medium (5 $\lesssim \epsilon \lesssim$ 8) directly from the deviations of particle positions inside two time-shared optical traps. The particles are confined to optical point traps; one is held in a stationary trap and the other particle is brought closer in small steps while tracking the particle positions using confocal microscopy. From the observed particle positions inside the traps we calculate the interparticle forces using an ensemble-averaged particle displacement-force relationship. The force measurements are confirmed by independent measurements of the different parameters using electrophoresis and a scaling law for the liquid-solid phase transition. When increasing the salt concentration by exposing the sample to UV light, the force measurements agree well with the classical DLVO theory assuming a constant surface potential. On the other hand, when adding tetrabutylammonium chloride (TBAC) to vary the salt concentration, surface charge regulation seems to play an important role.

Exact path-integral evaluation of the heat distribution function of a trapped Brownian oscillator

Using path integrals, we derive an exact expression--valid at all times t--for the distribution P(Q,t) of the heat fluctuations Q of a brownian particle trapped in a stationary harmonic well. We find that P(Q,t) can be expressed in terms of a modified Bessel function of zeroth order that in the limit t→∞ exactly recovers the heat distribution function obtained recently by Imparato [Phys. Rev. E 76, 050101(R) (2007)] from the approximate solution to a Fokker-Planck equation. This long-time result is in very good agreement with experimental measurements carried out by the same group on the heat effects produced by single micron-sized polystyrene beads in a stationary optical trap. An earlier exact calculation of the heat distribution function of a trapped particle moving at a constant speed v was carried out by van Zon and Cohen [Phys. Rev. E 69, 056121 (2004)]; however, this calculation does not provide an expression for P(Q,t) itself, but only its Fourier transform (which cannot be analytically inverted), nor can it be used to obtain P(Q,t) for the case v=0 .

TweezPal – Optical tweezers analysis and calibration software

Optical tweezers, a powerful tool for optical trapping, micromanipulation and force transduction, have in recent years become a standard technique commonly used in many research laboratories and university courses. Knowledge about the optical force acting on a trapped object can be gained only after a calibration procedure which has to be performed (by an expert) for each type of trapped objects. In this paper we present TweezPal, a user-friendly, standalone Windows software tool for optical tweezers analysis and calibration. Using TweezPal, the procedure can be performed in a matter of minutes even by non-expert users. The calibration is based on the Brownian motion of a particle trapped in a stationary optical trap, which is being monitored using video or photodiode detection. The particle trajectory is imported into the software which instantly calculates position histogram, trapping potential, stiffness and anisotropy. Program summary Program title: TweezPal Catalogue identifier: AEGR_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 44 891 No. of bytes in distributed program, including test data, etc.: 792 653 Distribution format: tar.gz Programming language: Borland Delphi Computer: Any PC running Microsoft Windows Operating system: Windows 95, 98, 2000, XP, Vista, 7 RAM: 12 Mbytes Classification: 3, 4.14, 18, 23 Nature of problem: Quick, robust and user-friendly calibration and analysis of optical tweezers. The optical trap is calibrated from the trajectory of a trapped particle undergoing Brownian motion in a stationary optical trap (input data) using two methods. Solution method: Elimination of the experimental drift in position data. Direct calculation of the trap stiffness from the positional variance. Calculation of 1D optical trapping potential from the positional distribution of data points. Trap stiffness calculation by fitting a parabola to the trapping potential. Presentation of X – Y positional density for close inspection of the 2D trapping potential. Calculation of the trap anisotropy. Running time: Seconds

Active Force Clamp Control of Optical Tweezers

In a typical high-resolution optical tweezers (OT) experiment a molecular motor changes the contour length of a trapped dumbbell-construct. Unless the inter-trap distance is actively controlled the OT increases the load on the molecular motor as it steps along the template. To counter this phenomenon we implement a real-time controller for the OT to be used in constant force measurements.We trap a dumbbell construct (bead-DNA-bead) in an inverted microscope by dividing a CW laser beam into a stationary trap and a steerable trap. Separate low power detection lasers and position sensitive detectors in the back-focal plane measure the position of both beads. The position of the bead in the stationary trap is used for constant-force feedback control. The feedback algorithm runs a Proportional-Integral-Derivative-controller on a field programmable gate array, and acousto-optical deflectors update the steerable trap position at a rate of 200 kHz.We test the force clamp control with a 10kb dsDNA molecule and present a theory explaining the power spectrum of the force clamped bead's position. We study the effect of controller bandwidth by digitally filtering the signal used for feedback control, and test the response time of our real-time controlled optical tweezers with a RNA hairpin opening/closing reaction.