An increment of diversity method for cell state trajectory inference of time-series scRNA-seq data

The increasing emergence of the time-series single-cell RNA sequencing(scRNA-seq)data,inferring developmental trajectory by connecting transcriptome similar cell states(i.e.,cell types or clusters)has become a major challenge.Most existing computational methods are designed for individual cells and do not take into account the available time series information.We present IDTI based on the Increment of Diversity for Trajectory Inference,which combines time series information and the minimum increment of diversity method to infer cell state trajectory of time-series scRNA-seq data.We apply IDTI to simulated and three real diverse tissue development datasets,and compare it with six other commonly used trajectory inference methods in terms of topology similarity and branching accuracy.The results have shown that the IDTI method accurately constructs the cell state trajectory without the requirement of starting cells.In the performance test,we further demonstrate that IDTI has the advantages of high accuracy and strong robustness.

Theoretical prediction of the optimal conditions for observing the stereodynamical vector properties of the C(~3P) + OH(X^2Π) → CO(X^1 Σ^+) + H(~2S) reaction

The best optimal initial reactant state and collision energy for observing the stereodynamical vector properties of the title reaction in the ground electronic state X2A’ potential energy surface （PES）[Zanchet et al. 2006 J. Phys. Chem. A 110 12017] are theoretically predicted using the quasi-classical trajectory （QCT） method for the first time. The calculated results reveal that the smallest value of the rotational quantum number j, larger vibrational quantum number v, and the lower strength of collision energy should be selected for offering the most obvious picture about the stereodynamical vector properties. Polarization-dependent differential cross sections and the angular momentum alignment distribution, P（θr） and P（Φr） in the center-of-mass frame, are obtained to gain an insight into the alignment and orientation of the product molecules. The rotational angular momentum vector j’ of CO is aligned to be perpendicular to reagent relative velocity k. The product polarizations align along the y axis, pointing to the positive direction of the y axis. A new method is developed to investigate massive reactions with various initial states and to further study the vector properties of the fundamental reactions in detail.

STATE TRANSFER CONTROL OF QUANTUM SYSTEMS ON THE BLOCH SPHERE

The state transfer under control fields is analyzed based on the Bloch sphere representation of a single qubit. In order to achieve the target from an arbitrary initial state to a target state, the conditions that parameters should satisfy are deduced separately in two different requirements： One is in the case of the rotation angle around the x-axis being fixed and another is in the situation with a given evolution time. Several typical states trajectories are demonstrated by numerical simulations on the Bloch sphere. The relations between parameters and the trajectories are analyzed.

Isotopic Effects on Stereodynamics of the C^+ + H_2→CH^+ + H Reaction

The effects of isotope substitution on stereodynamic properties for the reactions C^+ + H_2/HD/HT →CH^+ + H/D/T have been studied applying a quasi classical trajectory method occurring on the new ground state CH_2^+ potential energy surface [J. Chem. Phys. 142(2015) 124302]. In the center of mass coordinates applying the quasi classical trajectory method to investigate the orientation and the alignment of the product molecule. Differential cross section and three angle distribution functions P(θ_r), P(ф_r), P(θ_r, ф_r) on the potential energy surface that fixed the collision energy with a value is 40 kcal/mol have been studied. The isotope effect becomes more and more important with the reagent molecules H_2 changing into HD and HT. P(θ_r, ф_r) as the joint probability density function of both polar angles θ_r and ф_r, which can illustrate more detailed dynamics information. The isotope effect is obvious influence on the properties of stereodynamics in the reactions of C^+ + H_2/HD/HT → CH^+ + H/D/T.