Trap Length Research Articles

Using long columns to quantify over 9200 unique protein groups from brain tissue in a single injection on an Orbitrap Exploris 480 mass spectrometer

The most exciting advancement in LC-MS/MS-based bottom-up proteomics has centered around enhancing mass spectrometers. Among these, the latest and most advanced mass spectrometer for bottom-up proteomics is the Orbitrap Astral that has the highest scan rate to accelerate throughput and the highest sensitivity to handle a very small amount of peptide samples and to achieve deeper proteomics. However, its affordability remains a challenge for most laboratories. While significant strides have been made in improving mass spectrometry, advancing liquid chromatography (LC) to achieve deeper proteomics has not achieved significant successes since the innovation of Multidimensional Protein Identification Technology (MudPIT) in 2001. To achieve deeper proteomics in a less labor-intensive and more reproducible approach while using a more cost-effective mass spectrometer, such as the Orbitrap Exploris 480, we evaluated trap columns as long as 40 cm and analytical column as long as 600 cm besides sample loading amount, gradient time, and analytical column particle size to enable a fractionation-free method for a single injection to obtain deeper proteomics. The length of trap and analytic columns is the key factor. Using a 30 cm trap column and 250 cm analytical column with other optimized LC conditions, we quantified over 9200 unique protein groups from brain tissue in a single injection using a 24-h gradient on an Orbitrap Exploris 480 mass spectrometer.

Pulse-stretching out of the CANREB EBIS

The CANadian Rare isotope facility with Electron-Beam ion source (CANREB) at TRIUMF is set to deliver rare isotope beams in high charge states. In the Electron Beam Ion Source (EBIS) ions are charge-bred by collisions with an electron beam of up to 500 mA. A strong magnetic field (up to 6T) maximizes the overlap between ions and electron beam and increases the breeding efficiency. Ion confinement is maintained by a combination of an electrostatic field and the electron beam space-charge potential. Ions are released by lowering the trapping potential with a step function. The system is operated at a pulse repetition frequency up to 100 Hz. Due to the short trap length, this fast extraction scheme produces pulses shorter than 10 µs with high instantaneous rates that can saturate detectors in experiments. Stretching the pulse can be done using a slowly varying voltage function to modify trap electrode potentials instead of a step function. The ideal function produces a pulse with a flat top distribution and can be calculated by knowing the ion energy distribution inside the trap. The latest pulse-stretching results will be discussed including the latest pulse duration up to 1.4 ms that have been produced. The slow extraction scheme has also been used for a measurement of the effective energy distribution of the ions inside the trap.

Quasi-1D sedimentation of Brownian particles along optical line traps

We studied the Brownian motion of single 1 and 3 µm particles moving along optical line traps oriented in the gravity axis. The finite linear traps are formed using holographic optical tweezers which redistributes the incoming light beam into an elongated super Gaussian profile. Direct observation of the particle’s motion along the gravity axis allowed us to distinguish the non-equilibrium sedimentation of the particle, when the average velocity is 〈uz〉≠0, followed by equilibrium sedimentation when 〈uz〉=0 and the particle establishes the so-called gravitational length. We found that the bottom edge of the linear trap functions as a virtual “floor”, and subsequent Boltzmann distribution analysis of the equilibrium particle trajectories allows the estimation of the particle’s mass in the hundreds of femtograms range. In parallel, we also induced the physisorption of a macromolecule (hyaluronic acid) onto polystyrene microparticle in solution, detecting an increment of the particle’ mass of around 2 picograms. This suggests that the present technique can be used in surface chemistry, as it detects analyte absorption in solutions containing colloids by estimating the mass of both, the colloidal particle and the layer formed around it. On the other hand, we also found that when the longitudinal confinement established by the optical trap length is smaller than twice the particle gravitational length, particles remain suspended indefinitely even in the presence of a density mismatch with the medium, i.e., the notion of sedimentation disappears. Finally, we observed that the optical forces along the linear trap do not alter the Brownian motion of the particles significantly but can exert an extra pushing force on the smallest particles (1 µm) considered.

Solute Trapping and the Mechanisms of Non‐Fickian Transport in Partially Saturated Porous Media

AbstractWe study the upscaling of pore‐scale solute transport in partially saturated porous media at different saturation degrees. The interaction between structural heterogeneity, phases distribution and small‐scale flow dynamics induces complex flow patterns and broad probability distributions of flow, which control key aspects of transport, such as residence and arrival times, dispersion, and spatial solute distributions, as well as chemical reactions. A continuous‐time random walk (CTRW) framework that integrates the processes of advection, diffusion, and trapping in immobile zones is used to upscale and evaluate the transport of diluted solutes. Results of this model were compared to direct numerical simulations solving the advection‐diffusion equation in experimental saturation patterns. The comparison between simulations results, with different Péclet numbers (Pe), and the physics‐based upscaled CTRW approach allows for a quantitative analysis of the governing factors of transport in partially saturated porous media. This analysis shows that the fluid phase saturation decreases the advective tortuosity, the media's characteristic length, the fraction of the immobile region, and the mean trapping time. At the same time, for a given saturation degree, the normalized mean trapping time is proportional to the Pe. This suggests that the characteristic trapping length is proportional to the media's characteristic (correlation) length. Moreover, the trapping frequency decreases with increasing Pe.

Deep-Current Intraseasonal Variability Interpreted as Topographic Rossby Waves and Deep Eddies in the Xisha Islands of the South China Sea

Abstract Strong subinertial variability near a seamount at the Xisha Islands in the South China Sea was revealed by mooring observations from January 2017 to January 2018. The intraseasonal deep flows presented two significant frequency bands, with periods of 9–20 and 30–120 days, corresponding to topographic Rossby waves (TRWs) and deep eddies, respectively. The TRW and deep eddy signals explained approximately 60% of the kinetic energy of the deep subinertial currents. The TRWs at the Ma, Mb, and Mc moorings had 297, 262, and 274 m vertical trapping lengths, and ∼43, 38, and 55 km wavelengths, respectively. Deep eddies were independent from the upper layer, with the largest temperature anomaly being >0.4°C. The generation of the TRWs was induced by mesoscale perturbations in the upper layer. The interaction between the cyclonic–anticyclonic eddy pair and the seamount topography contributed to the generation of deep eddies. Owing to the potential vorticity conservation, the westward-propagating tilted interface across the eddy pair squeezed the deep-water column, thereby giving rise to negative vorticity west of the seamount. The strong front between the eddy pair induced a northward deep flow, thereby generating a strong horizontal velocity shear because of lateral friction and enhanced negative vorticity. Approximately 4 years of observations further confirmed the high occurrence of TRWs and deep eddies. TRWs and deep eddies might be crucial for deep mixing near rough topographies by transferring mesoscale energy to small scales.

Survival probability of random walks leaping over traps

We consider one-dimensional discrete-time random walks (RWs) in the presence of finite size traps of length ℓ over which the RWs can jump. We study the survival probability of such RWs when the traps are periodically distributed and separated by a distance L. We obtain exact results for the mean first-passage time and the survival probability in the special case of a double-sided exponential jump distribution. While such RWs typically survive longer than if they could not leap over traps, their survival probability still decreases exponentially with the number of steps. The decay rate of the survival probability depends in a non-trivial way on the trap length ℓ and exhibits an interesting regime when ℓ → 0 as it tends to the ratio ℓ/L, which is reminiscent of strongly chaotic deterministic systems. We generalize our model to continuous-time RWs, where we introduce a power-law distributed waiting time before each jump. In this case, we find that the survival probability decays algebraically with an exponent that is independent of the trap length. Finally, we derive the diffusive limit of our model and show that, depending on the chosen scaling, we obtain either diffusion with uniform absorption, or diffusion with periodically distributed point absorbers.

Visual Quantitation of Copper Ions Based on a Microfluidic Particle Dam Reflecting the Cu(II)-Catalyzed Oxidative Damage of DNA.

Due to the use of copper water pipes and the discharge of industrial wastewater, contamination of copper ions in drinking water has become a severe hazard globally. To routinely check water safety on a daily basis, easy-to-use platforms for quantitative analysis of trace amounts of copper ions (Cu2+) in drinking water is needed. Here, we report microfluidic particle accumulation integrated with a Cu(II)-catalyzed Fenton reaction for visual and quantitative copper ion detection. Microparticles (MMPs) and polystyrene microparticles (PMPs) are connected via a single strand DNA, MB155. However, when Cu2+ is present, MB155 is cleaved by hydroxyl free radicals (•OH) produced from Cu2+/hydrogen peroxide (H2O2) Fenton reactions, causing an increased amount of free PMPs. To visually count them, the particle solution is loaded onto a microfluidic chip where free MMPs and MMPs–MB155–PMPs can be collected by the magnetic separator, while the free PMPs continue flowing until being accumulated at the particle dam. The results showed a good linear relationship between the trapping length of PMP accumulation and the Cu2+ concentration from 0 to 300 nM. A limit of detection (LOD) of 70.1 nM was achieved, which is approximately 449 times lower than the 2 × 103 μg·L−1 (~31.5 μM) required by the World Health Organization (WHO). Moreover, the results showed high selectivity and good tolerance to pH and hardness, indicating compatibility for detection in tap water, suggesting a potential platform for the routine monitoring of copper contamination in drinking water.

The Effectiveness of Malaise Traps, H-Traps, and Sticky Traps for Collecting Horseflies (Diptera: Tabanidae)

The Effectiveness of Malaise Traps, H-Traps, and Sticky Traps for Collecting Horseflies (Diptera: Tabanidae)

Дослідження впливу конструкції шлаковловлювача на ефективність затримки шлаку в середовищі параметричного моделювання SolidWorks Flow Simulation

The most common technology for the manufacture of metal parts and work pieces is casting. High-tech branches of mechanical engineering require the production of high-quality castings of complex configuration from modern alloys with a given chemical composition and mechanical properties. The analysis of the causes of slag inclusions and ways to prevent them showed that in addition to technological means related to quality preparation of metal before pouring, a significant role is played by quiet continuous pouring of metal and properly designed foundry system, including slag trap. However, the use of the most common foundry systems (braking, throttle, with centrifugal slag traps, rain, siphon) to increase the efficiency of slag retention is associated with increased metal consumption, and as a consequence, leads to an increase in the cost of casting. Conducting experimental research by varying the design of the slag trap leads to an increase in the number of field experiments, given their complexity, limited by great difficulties. On the other hand, computer flow modeling allows to study the influence of slag trap design on the flow rate of the melt at the design stage and significantly reduce the cost of introduction of new castings. In order to reliably capture slag and reduce the speed of movement of the melt in the foundries, which provides a smooth filling of the form with an alloy, but without additional costs of metal, the original design of the ribbed slag catcher is proposed. The results of parametric modeling of the melt flow in the channel of the ribbed slag trap showed a decrease in the flow rate along the cross-sectional height of the slag trap compared to traditional by 0.028 m / s or 14.5%. This allowed to reduce the length of the slag trap to the first feeder. The expected metal savings are 0.26%. The form made using a 3D model of the slag trap showed satisfactory molding ability. But the obtained research results are of a recommendatory nature and require practical verification in the production environment. In addition, by varying parameters such as the height of the ribs, the distance between them, the angle of inclination, we can obtain similar results for different castings of different alloys. Given all this, there is a need for further study of the impact of the design of the slag trap on the efficiency of slag retention.

Trapping in self-avoiding walks with nearest-neighbor attraction.

The statistics of self-avoiding random walks have been used to model polymer physics for decades. A self-avoiding walk that grows one step at a time on a lattice will eventually trap itself, which occurs after an average of 71 steps on a square lattice. Here, we consider the effect of nearest-neighbor attractive interactions on isolated growing self-avoiding walks, and we examine the effect that self-attraction has both on the statistics of trapping as well as on chain statistics through the transition between expanded and collapsed walks at the theta point. We find that the trapping length increases exponentially with the nearest-neighbor contact energy, but that there is a local minimum in trapping length for weakly self-attractive walks. While it has been controversial whether growing self-avoiding walks have the same asymptotic behavior as traditional self-avoiding walks, we find that the theta point is not at the same location for growing self-avoiding walks, and that the persistence length converges much more rapidly to a smaller value.

Impact of charge trapping on the energy resolution of Ge detectors for rare-event physics searches

Charge trapping degrades the energy resolution of germanium (Ge) detectors, which require increased experimental sensitivity in searching for dark matter and neutrinoless double-beta decay. We investigate the charge trapping processes utilizing nine planar detectors fabricated from USD-grown crystals with well-known net impurity levels. The charge collection efficiency as a function of charge trapping length is derived from the Shockley–Ramo theorem. Furthermore, we develop a model that correlates the energy resolution with the charge collection efficiency. This model is then applied to the experimental data. As a result, charge collection efficiency and charge trapping length are determined accordingly. Utilizing the Lax model (further developed by CDMS collaborators), the absolute impurity levels are determined for nine detectors. The knowledge of these parameters when combined with other traits such as the Fano factor serve as a reliable indicator of the intrinsic nature of charge trapping within the crystals. We demonstrate that electron trapping is more severe than hole trapping in a p-type detector and the charge collection efficiency depends on the absolute impurity level of the Ge crystal when an adequate bias voltage is applied to the detector. Negligible charge trapping is found when the absolute impurity level is less than 1.0 × 1011 cm−3 for collecting electrons and 2.0 × 1011 cm−3 for collecting holes.

Optimal trapping stability of Escherichia coli in oscillating optical tweezers.

Single-beam oscillating optical tweezers can be used to trap rod-shaped bacterial cells and align them with their long axis lying within the focal plane. While such configuration is useful for imaging applications, the corresponding imaging resolution is limited by the fluctuations of the trapped cell. We study the fluctuations of four of the coordinates of the trapped cell, two for its center of mass position and two for its angular orientation, showing the way they depend on the trap length and the trapping beam power. We find that optimal trapping stability is obtained when the trap length is about the same as the cell length and that cell fluctuations in the focal plane decrease like the inverse of the trapping power.

Developing Bicycle Serviceability Index (BSI) at mid-blocks for the roads carrying mixed traffic - case study of Delhi

Bicycles mid block movement in mixed traffic scenario is a complex phenomenon to be measured as vehicles having range of size and weight co exist on the same road without any separator. This study focuses on developing a bicycle serviceability index (BSI) for the traffic where bicycles are moving along with motorized vehicles without any separate track/lane- For present study, data have been collected at two locations in National Capital Region (NCR) capturing trap length of 10-20 meters. At both locations, videography has been carried out for 4 hours covering peak time. For data extraction, a grid of 0.5m×0.5m has been created on videotape. Data have been extracted to gather information regarding the location of bicycle on road (grid number), location and type of adjacent vehicle, flow, speed and space occupied by motorized and non-motorized vehicles at given point of time.

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.

KAJIAN LAJU ANGKUTAN SEDIMEN TOTAL PADA KANTONG LUMPUR BENDUNG AIR MUSI KEJALO

Bendung Air MusiKejalo has decreased productivity,one of the contributing factors is sedimentation. The purpose of research is to know the massive rate of sediment transport from weir which enter in sand trap using method of Shen and Hungs and Meyer Petter Muller method. Then plot the dimensions of the sludge pouch from the resulting sediment rate.The stages of the research implementation are sediment sample test, flow velocity measurement and channel dimension then calculation and data analysis.The result of calculation using method of Shen and Hungs, got the value of sediment rate discharge at sand trap is 0,1295 ton / day, and by Meyer Petter Muller method equal to 22,4966 ton / day. So the result of sediment rate discharge Meyer Petter Muller method used for planning dimension sand trap of Air Musi Kejalo Weir.Volume of sand trap Air Musi Kejalo Weir is 120 m3. Dimensions of sand trap length 61 m, width 4 m and depth of 1,3 m. The conclusion of this study is that with thedimensions of planned sludge pockets based on the volume of sediment obtained, the sand trap should be rinsed for 14 days once so that the sediment does not accumulate in the sand trap and using a construction is pairs of round stone with type of sand trap is square and type of main drain is trapezoid.

Influence of the trap length on the performance of Cassinian ion traps: A simulation study

Mass analyzers based on ion traps are well known in mass spectrometry as devices with very high resolving power. A relatively young representative for such devices is the Cassinian Trap, a variant of the Kingdon trap, which similarly works only with electrostatic fields. Since ion traps typically truncate the electric field at some point due to their geometric restrictions, especially when the trapping field should theoretically extend to infinity, it is important to know if and how this truncation affects the analytical performance which is based on the ions' motion. In this contribution we have analyzed how the trap length, i.e. the length along the longest trap axis, and the related field truncation (truncation since the trap should theoretically extent to infinity along that axis) affect the ion cloud motion in a second order Cassinian Trap with help of finite elements method simulations.

Accurate method for estimating hole trap concentration in n-type GaN via minority carrier transient spectroscopy

We propose an analysis method for the accurate estimation of the hole trap (H1, EV + 0.85 eV) concentration in n-type GaN via minority carrier transient spectroscopy (MCTS). The proposed method considers both the hole occupation during a filling (current injection) period and the quick carrier recombination via the hole traps near the depletion layer edge immediately after a reverse bias is applied. The reverse bias voltage dependence of the MCTS spectrum indicates that an accurate trap concentration, as well as the hole diffusion length and electron capture cross section of the hole trap, can be determined.

Modelling and simulation of particle-particle interaction in a magnetophoretic bio-separation chip

A Lagrangian particle trajectory model is developed to predict the interaction between cell-bead particle complexes and to track their trajectories in a magnetophoretic bio-separation chip. Magnetic flux gradients are simulated in the OpenFOAM CFD software and imported into MATLAB to obtain the trapping lengths and trajectories of the particles. A connector vector is introduced to calculate the interaction force between cell-bead complexes as they flow through a microfluidic device. The interaction force calculations are performed for cases where the connector vector is parallel, perpendicular, and at an angle of 45° with the applied magnetic field. The trajectories of the particles are simulated by solving a system of eight ordinary differential equations using a fourth order Runge-Kutta method. The model is then used to study the effects of geometric positions and angles of the connector vector between the particles as well as the cell size, number of beads per cell, and flow rate on the interaction force and trajectories of the particles. The results show that the interaction forces may be attractive or repulsive, depending on the orientation of the connector vector distance between the particle complexes and the applied magnetic field. When the interaction force is attractive, the particles are observed to merge and trap sooner than a single particle, whereas a repulsive interaction force has little or no effect on the trapping length.

Comparative Study of Density over Time by Several Approaches Using Individual and Sample Data in the Mixed Traffic

At the macroscopic perspective, traffic analysis requires the knowledge of Fundamental Diagram, which involves the relationship between the variables of density, flow, and speed. As one of the macroscopic traffic flow variables, density can be derived by several approaches. At first, the density of traffic was measured over space, which difficult to be collected mainly in the long section of the road. Therefore, the density variable was simply derived from the fundamental relation of macroscopic traffic flow variable. By this method, the individual speed and flow variable are required in the local measurement. Both traffic density and flow will apply the concept of PCU, which refers to the Indonesian Highway Capacity Manual, 1997 to consider the different characteristic of the vehicle. In the mixed traffic of developing countries, providing traffic data was difficult due to the limitation of the traffic sensor infrastructures. Frequently, providing density variable relies on the sample data for speed analysis. In the present study, the estimation of density will focus on the local measurement over a time interval. By using individual data, density is proposed to be measured directly over time, in which the equation can be modified to utilize the sample data. The number of sample for speed analysis will be varied to know the accuracy and the performance of each approach in the density estimation of mixed traffic. Several approaches for density estimation will be summarized and compared each other. Theoretically, the estimated density which measured over time and space by using individual data can provide the most appropriate result. So, this estimated density will be established as an actual density throughout the study. Then, the performance of each approach either using individual or sample data will be evaluated upon the actual traffic density by mean absolute percentage error (MAPE). The result shows by using the same trap length to measure the speed, the existing and the proposed approaches provide a good estimation of density either by utilizing individual data or sample data of the vehicle speed. This result was indicated by the MAPE value, which obtained under ten percent. Based on the further evaluation of the MAPE value, the performance of each approach was changed by utilizing the different category of data. In addition, estimation of traffic density which utilizes the sample data of vehicle speed has good reliability.

Torque Induced on Lipid Microtubules with Optical Tweezers

Chiral Phospholipids are found self-assembled into cylindrical tubules of 500 nm in diameter by helical winding of bilayer stripes under cooling in ethanol and water solution. Theoretical prediction and experimental evidence reported so far confirmed the modulated tilt direction in a helical striped pattern of the tubules. This molecular orientation morphology results in optically birefringent tubules. We investigate an individual lipid microtubule under a single optical trap of 532 nm linearly polarized laser. Spontaneous rotation of a lipid tubule induced by radiation torque was observed with only one sense of rotation caused by chirality of a lipid tubule. Rotation discontinued once the high refractive index axis of a lipid tubule aligned with a polarization axis of the laser. We further explored a lipid tubule under circularly polarized optical trap. It was found that a lipid tubule was continuously rotated confirming the tubule birefringent property. We modified the shape of optical trap by cylindrical lens obtaining an elliptical profile optical trap. A lipid tubule can be aligned along the elongated length of optical trap. We reported an investigation of competition between polarized light torque on a birefringent lipid tubule versus torque from intensity gradient of an elongated optical trap.