Proportion Of Trajectories Research Articles

Manipulating nonsequential double ionization of atoms by parallel polarized three-color laser fields

Nonsequential double ionization (NSDI) of He atoms in a parallel polarized three-color field is investigated by using a three-dimensional classical ensemble model. The driving field is composed of 1600-nm and 800-nm laser pulses with equal intensity. A weak 400-nm laser pulse is used as a controlling field. The results indicate that in the correlated electron momentum distribution and ion momentum distribution, the electron pairs and ions of the first returning recollision (FRR) trajectory, the odd-returning recollision (ORR) trajectory (excluding FRR), and the even-returning recollision (ERR) trajectory are located in different regions separated well from each other. The electron pairs from FRR trajectories mainly distribute around the origin, and those electron pairs from ORR and ERR trajectories respectively cluster in the first quadrant and the third quadrant. With the increase of the phase of the controlling field, the proportion of FRR trajectories in NSDI first increases and then decreases, and the proportions of those trajectories with the returning number more than one first decrease and then increase, which leads to the fact that with the increase of the phase of the controlling field, the anticorrelated emissions first increase and then decrease and correspondingly the ion momentum distribution evolves from a double-hump to a triple-hump and then to a double-hump structure. Moreover, NSDI from multiple-returning recollision trajectories mainly occur through recollision-induced direct ionization (RDI) mechanism, while NSDI from the FRR trajectories mainly occurs through recollision-induced excitation with subsequent ionization (RESI) mechanism. Thus the dominant NSDI ionization mechanism can also be controlled by changing the phase of the controlling field.

Effects of different stagnant meteorological conditions on aerosol chemistry and regional transport changes in Beijing, China

To study the aerosol chemistry and regional transport changes in Beijing under different stagnant meteorological conditions, a simultaneous combined observation of the nonrefractory submicron aerosol (NR-PM1) chemical compositions and vertical wind profiles was conducted at an urban site (Beijing) and a regional background site (Xinglong) in the North China Plain (NCP) from November 2018 to January 2019. The backward trajectories of PM1 species in Beijing under different pollution stages were calculated. The results showed that the proportion of backward trajectories from southern regions increased from 0% in the clean stage (PM1 < 35 μg m−3) to 47% in the pollution stage (PM1 > 75 μg m−3), suggesting the aerosol pollution in winter Beijing was greatly affected by regional transport from southern regions. Although the proportion of trajectories from the northwestern regions of Beijing decreased from the clean stage to the pollution stage, the trajectories still comprised a large proportion (53%), which indicates that the northwestern air mass can also cause heavy pollution in winter. Therefore, two typical episodes with air masses from the southwest (episode 1) and northwest (episode 2) regions were selected for further study. The results showed that episode 1 in Beijing lasted for several days and was initiated by regional transport and dominated by heterogeneous reactions, while episode 2 was dominated by rapid regional transport in a short time. Both water vapor and pollutants were transported from southern regions in episode 1, while only pollutants were transported in episode 2. Because of the stronger heterogeneous reactions in episode 1, inorganic aerosols in Beijing accounted for 71% of PM1 in episode 1, which was higher than that in episode 2 (56%). In addition, the transport of water vapor from southern China enhanced the secondary aerosol formation in Xinglong and expanded the scope of regional pollution. In comparison, the systematic south wind did not reach the background area in episode 2. Correspondingly, the PM1 concentration in Beijing was 62% higher than that in Xinglong in episode 2, which was much higher than that in episode 1 (11%). Our results showed that in addition to the enhancement of heterogeneous reactions caused by the increase in humidity, the rapid transport of pollutants because of the sudden change of wind field from north to south can also dominant heavy haze episodes in winter Beijing.

Folding kinetics of proteins with multiple domains: inference of transition rates from extinction times

In this paper we are concerned with the folding kinetics of large proteins that may have multiple binding/unbinding domains. The theory underlying such systems have received much less attention compared to small, ‘two-state’ (folded/unfolded) proteins. To analyze this problem, we model the reaction coordinate using a birth-death chain, a well-known stochastic process. Specifically, we consider a protein with N domains where every domain that unfolds (folds) increases (decreases) the reaction coordinate by an integer so that the state-space of the reaction coordinate is the set of integers {0, 1, …, N}. As input data, our method uses (i) the extinction time of trajectories, starting from when the protein leaves the 0 state for the first time and finishing when the protein re-enters state 0 for the first time and (ii) the maximum number of unfolded domains in the said trajectory. Since the maximum value n reached by each trajectory is known, we use the proportion of trajectories that do not exceed n and corresponding mean extinction times (ET) to recover the birth-death rates sequentially from 1 to N. In general, the initial error will propagate with the site number exponentially. However, with sufficient amount of input data, we can recover the rates with relatively small error. For instance, given 50 million ETs of an 11-site BDP, we can recover the rates with a relative error of about 3%.

Spontaneous Dimerization of Titin Protein Z1Z2 Domains Induces Strong Nanomechanical Anchoring

Muscle elasticity strongly relies on the mechanical anchoring of the giant protein titin to both the sarcomere M-band and the Z-disk. Such strong attachment ensures the reversible dynamics of the stretching-relaxing cycles determining the muscle passive elasticity. Similarly, the design of biomaterials with enhanced elastic function requires experimental strategies able to secure the constituent molecules to avoid mechanical failure. Here we show that an engineered titin-mimicking protein is able to spontaneously dimerize in solution. Our observations reveal that the titin Z1Z2 domains are key to induce dimerization over a long-range distance in proteins that would otherwise remain in their monomeric form. Using single molecule force spectroscopy, we measure the threshold force that triggers the noncovalent transition from protein dimer to monomer, occurring at ∼700 piconewtons. Such extremely high mechanical stability is likely to be a natural protective mechanism that guarantees muscle integrity. We propose a simple molecular model to understand the force-induced dimer-to-monomer transition based on the geometric distribution of forces occurring within a dimeric protein under mechanical tension.

Trajectory Sampling With Unreliable Reporting

We define and evaluate methods to perform robust network monitoring using trajectory sampling in the presence of report loss. The first challenge is to reconstruct an unambiguous set of packet trajectories from the reports on sampled packets received at a collector. In this paper we extend the reporting paradigm of trajectory sampling to enable the elimination of ambiguous groups of reports, but without introducing bias into any characterization of traffic based on the surviving reports. Even after the elimination, a proportion of trajectories are incomplete due to report loss. A second challenge is to adapt measurement based applications (including network engineering, path tracing, and passive performance measurement) to incomplete trajectories. To achieve this, we propose a method to join multiple incomplete trajectories for inference, and analyze its performance. We also show how applications can distinguish between packet and report loss at the statistical level.

Protein refolding Versus aggregation: computer simulations on an intermediate-resolution protein model

Computer simulations are performed on a system of eight model peptide chains to study how the competition between protein refolding and aggregation affects the optimal conditions for refolding of four-helix bundles. The discontinuous molecular dynamics algorithm is utilized along with an intermediate-resolution protein model that we developed for this work. Physically, the model is much more detailed than any model used to date for simulations of protein aggregation. Each model residue consists of a detailed, three-bead backbone and a simplified, single-bead side-chain. Excluded volume, hydrogen bond, and hydrophobic interactions are modeled with discontinuous (i.e. hard-sphere and square-well) potentials. Simulations efficiently sample conformational space, and complete folding trajectories from random initial configurations to two four-helix bundles are possible within two days on a single processor workstation. Folding of the bundles follows two main pathways, one through a trimeric intermediate and the other through an intermediate with two dimers. The proportion of trajectories that follow each route is significantly different for the eight-peptide system in this work than in a previously studied four-peptide system, which yields one four-helix bundle, suggesting, as our previous simulations have, that protein folding properties are strongly influenced by the presence of other proteins. Folding of the bundles is optimal within a fixed temperature range, with the high-temperature boundary a function of the complexity of the protein (or oligomer) to be folded and the low-temperature boundary a function of the complexity of the protein’s environment. Above the optimal temperature range for folding, the model chains tend to unfold; below the optimal range, the model chains tend to aggregate. As has been seen previously, aggregates have substantial levels of native secondary structure, suggesting that aggregates are composed largely of partially folded intermediates, not denatured chains.