带凹槽的微通道中液滴运动数值模拟

运用改进的耗散粒子动力学方法模拟了液滴在由凹槽所构成的粗糙表面微通道内的运动行为.改进的耗散粒子动力学方法采用新近提出的一种短程排斥、长程吸引相互作用势能函数,从而可以模拟带有自由面的流体,如液滴等.模拟了新势能函数下液滴与固体壁面的静态接触角,并用2次多项式拟合了"接触角-a_wf/a_f"变化曲线.研究了液滴在带凹槽的微通道中运动时,微通道壁面浸润性、外场力、液滴温度对液滴流动特性的影响.研究表明壁面浸润性和外场力对液滴流动特性的影响较大,液滴温度对液滴流动特性的影响较小.研究结果对运用耗散粒子动力学方法模拟并分析微流体在复杂微通道的流动有一定的参考价值.     

He-H2S复合物的六维从头算势能面和束缚态

采用[CCSD(T)]-F12a/aug-cc-pVTZ方法，同时在基组中引入中心键函数(3s3p2d1f1g)构建了He-H$_2$S复合物的高精度六维势能面. 除分子间振动坐标，同时考虑了H₂S分子内的v₁对称伸缩振动Q₁正则模、v₂弯曲振动Q₂正则模和v₃反对称伸缩振动Q₃正则模三种振动模式. 将计算得到的六维势能面在Q₁，Q₂和Q₃方向上分别做积分得到H₂S单体分别处于振动基态、v和v₃激发态下的He-H₂S的三个振动平均势能面. 计算结果表明，每个平均势能面都有一个T形全局极小值、一个平面局部极小值、两个平面内鞍点和一个平面外鞍点. 全局极小值的几何构型位于R=3.46 ?，θ=109.9°和φ=0.0°，势阱深度为35.301 ^-1. 在径向部分采用离散变量表象法和角度部分采用有限基组表象法并结合Lanczos循环算法计算了He-H₂S的振转能级和束缚态. 计算发现He-(para-H₂S)在H₂S的v₂和v₃区域的带心位移分别为0.025 cm^-1和0.031 cm^-1，而He-(ortho-H₂S)的带心位移分别为0.041 cm^-1和0.060 cm^-1，都表现为蓝移.     

用直接方法和希耳伯变换计算二维瞬态势及其梯度

本文用直接方法和希耳伯变换给出了计算二维瞬态势及其梯度的新方法.这种方法可以计算复杂度从传统的O(N_t²)降低到O(N_t).在计算势及其梯度时,该方法的直接计算中所用的权重因子不随时间变化,因此它们只需在第一个时间步长时计算一次.所以,当用于二维瞬态散射的时间推进算法中时,该方法可节省大量的CPU时间.数值结果表明该方法的精度非常高.     

CH4-Ne体系的三维从头算势能面与光谱的模拟

本文在从头算CCSD(T)/AVXZ(X=T,Q)水平上计算了CH₄-Ne体系的三维势能面,同时在基组中加入了键函数,并且将基组外推到完全基组极限水平. 通过最小二乘法拟合摩斯长程势能函数形式,获得了三维分析势能面,其中对664个从头算格点的拟合的标准偏差仅为0.042 cm^-1. 随后,采用径向离散变量表象和角度有限基组表象相结合的杂化基函数方法,并基于Lanzcos迭代的方法获得了CH₄-Ne体系的振转能级,所预测的红外光谱与实验值非常吻合. 本文首次给出了CH₄-Ne体系的微波光谱数据. CH₄-Ne体系三维摩斯长程势能面分析的表达式为今后CH₄在Ne团簇动力学性质以及其碰撞诱导吸收光谱的研究中奠定了基础.     

基于Gay-Berne势能模型的粗粒化动力学模拟研究正丁醇的玻璃态相变

通过基于Gay-Berne势能模型的粗粒化动力学模拟,研究液态正丁醇体系的冷却过程. 采用密度泛函计算,拟合出适合正丁醇体系的GB势能参数. 体系的密度、平均势能等性质随温度的降低(由290 K降至50 K,间隔为10 K)发生特殊变化,即体系发生玻璃态相变,相变温度为T_g=120±10 K,与实验值110±1 K符合很好.     

Ar2-Ne聚合物的三维势能面和束缚态

使用单双激发并对三重激发作微扰处理的耦合簇方法计算了Ar₂-Ne聚合物的三维势能面. 使用的基组是aug-cc-pVqz并包括3s3p2d2f1g中点键函数. 用二维模型势对7个Ar₂键长值的每一个对应的二维格点(R,θ)上的能量进行了拟合. 再将7个二维模型势通过对(r—re) 的六次多项式内插得到三维势能面,并用于随后的振转能级计算,所得到的跃迁频率、光谱常数等与相应的实验结果进行了比较.     

基于激发态运动方程耦合簇的神经网络透热势能矩阵：苯硫酚1πσ*态-介导的光解

本文用最近发展的神经网络拟合方法[Chin. J. Chem. Phys. 34,825 (2021)]构造了一个新的涉及苯硫酚¹πσ^*态-介导光解的¹ππ^*和¹πσ^*态耦合非绝热势能面. 势能面包含了解离过程中的三个关键振动模式,即S-H伸缩、弯曲和扭转振动. 由于单双激发态运动方程耦合簇方法具有简单、效率高、精度高的优点,采用激发态运动方程耦合簇方法计算了苯硫酚激发态¹ππ^*和¹πσ^*的绝热能量. 神经网络拟合绝热激发态S₁和S₂态的均方根误差分别为0.89和1.33 meV,表明神经网络方法具有很高的拟合精度. 在构建非绝热势能面的过程中,仅利用了体系绝热势能,避免了非常耗时的非绝热耦合计算,极大地提高了效率. 为了检测新的非绝热势能面的可靠性,本文进一步展开了苯硫酚光解非绝热动力学模拟. 动力学计算得到的S₁振电态0⁰和3¹的寿命与实验和之前的理论结果均吻合,验证了基于激发态运动方程耦合簇绝热能量构建的非绝热势能面的可靠精确性,并可进一步应用到实际大分子体系中.     

N+ND反应的量子力学速率常数

在两个耦合的势能面1²A′和2²A′上对N+ND反应进行了非绝热量子动力学研究. 计算了N+ND→N₂+D反应和N′+ND→N′D+N反应在5 meV～1.0 eV碰撞能的反应几率和积分截面. 结果发现N+ND→N₂+D反应是N+ND反应的主要反应通道.另外,计算了N+ND→N₂+D 反应的速率常数.     

苯基叠氮在光吸收激发态上的结构动力学-共振拉曼和量子力学计算研究

采用共振拉曼光谱学和完全活化空间自洽场方法研究了苯基叠氮被激发到S₂(A')、S₃(A')和S₆(A')光吸收态后的结构动力学. 基于傅立叶变换拉曼、傅立叶变换红外、紫外、密度泛函计算和简正模式分析,指认了紫外吸收光谱和振动光谱. 获得了环己烷、乙腈和甲醇溶剂中273.9、252.7、245.9、228.7、223.1和208.8 nm等不同激发波长下的A、B和C带共振拉曼光谱,以探测Franck-Condon区域的结构动力学. CASSCF计算获得了单重电子激发态能量最低点和势能面交叉点的电子激发能和优化几何结构. 结果表明,苯基叠氮在S₂(A')、S₃(A')和S₆(A')态上的激发态结构动力学各不相同. 与Kasha规则相符,S₂S₁(1)和S₂S₁(2)势能面交叉点在S₂(A')激发态衰变动力学和N7=N8键解离中扮演着重要角色. 提出了两条主要衰减通道：S_2,min→S₀辐射通道和S_2,FC(ππ^*)→S₂(ππ^*)/S₁(nπ^*)→S₁(nπ^*)非辐射通道.     

对典型多通道反应H+CH3OH的模式特异动力学研究

H+CH₃OH作为典型的多通道反应,在燃烧和星际中起着重要的作用. 本文基于在UCCSD(T)-F12a/AVTZ水平上计算的大量数据点,构建了该体系的全维精确势能面,并基于该势能面,研究了不同产物通道的模式特异动力学. 结果表明,O-H 伸缩、沿C-O轴的扭转以及C$-$H伸缩等模式的振动激发对H₂+CH₃O、H₂+CH₂OH、H₂O+CH₃和H+CH₃OH四个产物通道有着不同的影响. 该研究有助于理解具有多个产物通道的复杂反应的模式特异动力学,进而帮助控制其竞争反应.     

Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules

Shadow hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large molecules, particularly biological molecules. It improves sampling of hybrid Monte Carlo (HMC) by allowing larger time steps and system sizes in the molecular dynamics (MD) step. The acceptance rate of HMC decreases exponentially with increasing system size N or time step δt. This is due to discretization errors introduced by the numerical integrator. SHMC achieves an asymptotic O(N^1/4) speedup over HMC by sampling from all of phase space using high order approximations to a shadow or modified Hamiltonian exactly integrated by a symplectic MD integrator. SHMC satisfies microscopic reversibility and is a rigorous sampling method. SHMC requires extra storage, modest computational overhead, and a reweighting step to obtain averages from the canonical ensemble. This is validated by numerical experiments that compute observables for different molecules, ranging from a small n-alkane butane with four united atoms to a larger solvated protein with 14,281 atoms. In these experiments, SHMC achieves an order magnitude speedup in sampling efficiency for medium sized proteins. Sampling efficiency is measured by monitoring the rate at which different conformations of the molecules' dihedral angles are visited, and by computing ergodic measures of some observables.     

Numerical stability of 2<Superscript>nd</Superscript> order Runge-Kutta integration algorithms for use in particle-in-cell codes

An essential ingredient of particle-in-cell (PIC) codes is a numerically accurate and stable integration scheme for the particle equations of motion. Such a scheme is the well known time-centered leapfrog (LF) method [1] accurate to 2^nd order with respect to the timestep Δt. However, this scheme can only be used forces independent of velocity unless a simple enough implicit implementation is possible. The LF scheme is therefore inapplicable in Monte-Carlo treatments of particle collisions [2] and/or interactions with radio-frequency fields [3]. We examine here the suitability of the 2^nd order Runge-Kutta (RK) method. We find that the basic RK scheme is nummerically unstable, but that conditional stability can be attained by an implementation which preserves phase space area. Examples are presented to illustrate the performance of the RK schemes. We compare analytic and computed electron orbits in a traveling nonlinear wave and also show self-consistent PIC simulations describing plasma flow in the vicinity of a lower hybrid antenna.     

Acceleration of canonical molecular dynamics simulations using macroscopic expansion of the fast multipole method combined with the multiple timestep integrator algorithm

A canonical molecular dynamics (MD) simulation was accelerated by using an efficient implementation of the multiple timestep integrator algorithm combined with the periodic fast multiple method (MEFMM) for both Coulombic and van der Waals interactions. Although a significant reduction in computational cost has been obtained previously by using the integrated method, in which the MEFMM was used only to calculate Coulombic interactions (Kawata, M., and Mikami, M., 2000, 98, J. Comput. Chem., in press), the extension of this method to include van der Waals interactions yielded further acceleration of the overall MD calculation by a factor of about two. Compared with conventional methods, such as the velocity-Verlet algorithm combined with the Ewald method (timestep of 0.25 fs), the speedup by using the extended integrated method amounted to a factor of 500 for a 100 ps simulation. Therefore, the extended method reduces substantially the computational effort of large scale MD simulations.     

Photonic temporal integration of broadband intensity waveforms over long operation time windows

We propose and experimentally demonstrate a novel design for temporal integration of microwave and optical intensity waveforms with combined high processing speed and a long operation time window. It is based on concatenating in series a discrete-time (low-speed) photonic integrator and a high-speed analog time-limited intensity integrator. This scheme is demonstrated here using a cascaded fiber-based interferometers' system (as a passive eight-point discrete-time integrator) and an analog time-limited intensity integrator. The latter is based on temporal intensity modulation of the input waveform with a rectangular-like incoherent energy spectrum followed by linear dispersion. Using this setup, we experimentally achieve accurate time integration of intensity signals with ~36 GHz bandwidths over an operation time window of ~4 ns, corresponding to a processing time-bandwidth product of >144.     

Numerical integration of projective Hamiltonian dynamics

Projective Hamiltonian dynamics [S. Melchionna, J. Chem. Phys. 121, 4534 (2004)] is an approach to reduce mode spreading in complex systems, thus improving the performances of Molecular Dynamics simulations. A numerical integration of the dynamics requires proper treatment of the non-separable form of the Hamiltonian. Due to its symplectic nature, the generalized leapfrog scheme is shown to provide robust and reliable numerical trajectories even in the case of stiff projective forces.     

Dynamical replica analysis of disordered Ising spin systems on finitely connected random graphs

We study the dynamics of macroscopic observables such as the magnetization and the energy per degree of freedom in Ising spin models on random graphs of finite connectivity, with random bonds and/or heterogeneous degree distributions. To do so, we generalize existing versions of dynamical replica theory and cavity field techniques to systems with strongly disordered and locally treelike interactions. We illustrate our results via application to, e.g., +/-J spin glasses on random graphs and of the overlap in finite connectivity Sourlas codes. All results are tested against Monte Carlo simulations.     

Anomalous scattering in supercooled ST2 water

ABSTRACT

Large-scale molecular dynamics (MD) simulations of systems containing up to 256,000 molecules were performed to investigate the scattering behaviour of the ST2 water model at deeply supercooled conditions. The simulations reveal that ST2 exhibits anomalous scattering, reminiscent of that observed in experiment, which is characterised by an increase in the static structure factor at low wavenumbers. This unusual behaviour in ST2 is linked with coupled fluctuations in density and local tetrahedral order in the liquid. The Ornstein–Zernike correlation length estimated from the anomalous scattering component exhibits power-law growth upon cooling, consistent with the existence of a liquid–liquid critical point (LLCP) in the ST2 model at ca. 245 K. Further, spontaneous liquid–liquid phase separation is observed upon thermally quenching a large system with 256,000 water molecules below the predicted critical temperature into the two-phase region. The large-scale MD simulations therefore confirm the existence of a metastable liquid–liquid phase transition in ST2 and support findings from previous computational studies performed using smaller systems containing only a few hundred molecules. We anticipate that our analysis may prove useful in interpreting recent scattering experiments that have been performed to search for an LLCP in deeply supercooled water.     

Rapidly calculating the partition function of macroscopic systems

It has remained an open problem to accurately compute the partition function of macroscopic systems since the establishment of statistical physics. A rapid method approaching this problem was presented and was strictly tested by molecular dynamic(MD) simulations on Ar atoms in both dense gaseous and liquid states. The outcomes from the method on the internal energy and the work of isothermal expansion(and therefore the free energy) are in good agreement with the MD simulations, suggesting the method would be immediately applied in vast areas.