RMSD and Symmetry

A common approach for comparing the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the pointwise root-mean-square deviation (RMSD). We present a new, robust numerical algorithm that computes the RMSD between two molecules or all the mutual RMSDs of a list of molecules and, if desired, the corresponding rotation matrix in a minimal number of operations as compared to previous algorithms. The RMSD gradient can also be computed. We address the problem of symmetry, both in alignment (possible alternative alignments due to indistinguishable atoms) as well as geometry. In the latter case, it is possible to have degenerate superposition. A necessary condition is optimal superimposability to one's mirror image. Double (respectively, triple) degeneracy results in a one- (respectively, two)-parameter family of rotations leaving the superposition invariant. The software, frmsd , is freely available at http://www.ams.stonybrook.edu/~coutsias/codes/frmsd.tgz . © 2019 Wiley Periodicals, Inc.     

Finite-horizon piecewise deterministic Markov decision processes with unbounded transition rates

This paper is concerned with the problem of minimizing the expected finite-horizon cost for piecewise deterministic Markov decision processes. The transition rates may be unbounded, and the cost functions are allowed to be unbounded from above and from below. The optimality is over the general history-dependent policies, where the control is continuously acting in time. The infinitesimal approach is employed to establish the associated Hamilton-Jacobi-Bellman equation, via which the existence of optimal policies is proved. An example is provided to verify all the assumptions proposed.     

Darcy-Forchheimer flow with nonlinear mixed convection

An analysis of the mixed convective flow of viscous fluids induced by a nonlinear inclined stretching surface is addressed. Heat and mass transfer phenomena are analyzed with additional effects of heat generation/absorption and activation energy, respectively. The nonlinear Darcy-Forchheimer relation is deliberated. The dimensionless problem is obtained through appropriate transformations. Convergent series solutions are obtained by utilizing an optimal homotopic analysis method (OHAM). Graphs depicting the consequence of influential variables on physical quantities are presented. Enhancement in the velocity is observed through the local mixed convection parameter while an opposite trend of the concentration field is noted for the chemical reaction rate parameter.     

Application of Optimal Control Theory to Fourier Transform Ion Cyclotron Resonance

We study the application of Optimal Control Theory to Ion Cyclotron Resonance. We test the validity and the efficiency of this approach for the robust excitation of an ensemble of ions with a wide range of cyclotron frequencies. Optimal analytical solutions are derived in the case without any pulse constraint. A gradient-based numerical optimization algorithm is proposed to take into account limitation in the control intensity. The efficiency of optimal pulses is investigated as a function of control time, maximum amplitude and range of excited frequencies. A comparison with adiabatic and SWIFT pulses is done. On the basis of recent results in Nuclear Magnetic Resonance, this study highlights the potential usefulness of optimal control in Ion Cyclotron Resonance.     

Optimal decay rates and small global solutions to the dissipative Boussinesq equation

This work is devoted to the small amplitude solutions for the initial value problem of the multidimensional dissipative Boussinesq equation. We firstly derive the pointwise estimates of the fundamental solutions by the energy method in the Fourier space. We give the asymptotic profiles of solutions to the corresponding linear problem to get the optimal decay rate for the -norm of solutions in all space dimensions. Under smallness assumptions on the initial data, we study the global existence and uniqueness of solutions by the contractive mapping principle in the solution spaces with time weighted norm.     

激光供能无人机的一种优化跟踪算法

航天事业的发展以及新能源技术的开发，使得小型电动无人机在现代战争、科学研究等方面具有较高的应用价值。激光无线能量传输技术能有效解决小型电动无人机续航时间短的问题，极大提高了无人机的工作能效。以无人机激光供能系统结构原理为基础，针对小型电动无人机激光无线供能的特点，提出了一种最大功率点优化跟踪方法:即采用恒定电压法（CV法）和萤火虫算法（FA法）相结合的优化控制算法，在激光投射到无人机上的光伏电池板上后，通过对无人机激光无线充电过程中最大功率点的跟踪，提高激光利用率及充电稳定性。并且通过数值仿真，验证了所提算法的准确性和适用性。     

Nonadiabatic geometric quantum computation with optimal control on superconducting circuits

Quantum gates, which are the essential building blocks of quantum computers, are very fragile. Thus, to realize robust quantum gates with high fidelity is the ultimate goal of quantum manipulation. Here, we propose a nonadiabatic geometric quantum computation scheme on superconducting circuits to engineer arbitrary quantum gates, which share both the robust merit of geometric phases and the capacity to combine with optimal control technique to further enhance the gate robustness. Specifically, in our proposal, arbitrary geometric single-qubit gates can be realized on a transmon qubit, by a resonant microwave field driving, with both the amplitude and phase of the driving being timedependent. Meanwhile, nontrivial two-qubit geometric gates can be implemented by two capacitively coupled transmon qubits, with one of the transmon qubits’ frequency being modulated to obtain effective resonant coupling between them. Therefore, our scheme provides a promising step towards fault-tolerant solid-state quantum computation.     

Minimization of Entropy Generation Rate in Hydrogen Iodide Decomposition Reactor Heated by High-Temperature Helium

The thermochemical sulfur-iodine cycle is a potential method for hydrogen production, and the hydrogen iodide (HI) decomposition is the key step to determine the efficiency of hydrogen production in the cycle. To further reduce the irreversibility of various transmission processes in the HI decomposition reaction, a one-dimensional plug flow model of HI decomposition tubular reactor is established, and performance optimization with entropy generate rate minimization (EGRM) in the decomposition reaction system as an optimization goal based on finite-time thermodynamics is carried out. The reference reactor is heated counter-currently by high-temperature helium gas, the optimal reactor and the modified reactor are designed based on the reference reactor design parameters. With the EGRM as the optimization goal, the optimal control method is used to solve the optimal configuration of the reactor under the condition that both the reactant inlet state and hydrogen production rate are fixed, and the optimal value of total EGR in the reactor is reduced by 13.3% compared with the reference value. The reference reactor is improved on the basis of the total EGR in the optimal reactor, two modified reactors with increased length are designed under the condition of changing the helium inlet state. The total EGR of the two modified reactors are the same as that of the optimal reactor, which are realized by decreasing the helium inlet temperature and helium inlet flow rate, respectively. The results show that the EGR of heat transfer accounts for a large proportion, and the decrease of total EGR is mainly caused by reducing heat transfer irreversibility. The local total EGR of the optimal reactor distribution is more uniform, which approximately confirms the principle of equipartition of entropy production. The EGR distributions of the modified reactors are similar to that of the reference reactor, but the reactor length increases significantly, bringing a relatively large pressure drop. The research results have certain guiding significance to the optimum design of HI decomposition reactors.