Multifractals from Hamiltonian many-body molecular dynamics

Nonequilibrium simulations with time-reversible thermostats provide multifractal phase-space structures. But alternative stochastic approaches to temperature control rule out such fine-grained structures. Thus, the validity of the fractals has been questioned. I detail here the construction of the fully-Hamiltonian many-body problems which produce fractal structures isomorphic to those of the nonequilibrium simulations.     

Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking,molecular dynamics simulation and binding free energy calculation

Molecular Diversity - The pandemic outbreak of the Corona viral infection has become a critical global health issue. Biophysical and structural evidence shows that spike protein possesses a high...     

Visualising many-body electron dynamics using one-body densities and orbitals

As experimental techniques begin to probe electronic motions in increasing detail, the need is arising for compact and informative visualisations of simulations of such processes. The inherent challenge is that a full many-electron wavefunction is a high-dimensional object, representing the complicated correlations of strongly repulsive bodies in a small molecular volume. A general procedure is needed to distill this to a smaller amount of information that does not rely on any specific level of approximation. The result should allow for easy and intuitive interpretation while drawing out nontrivial aspects of the underlying many-body dynamics, such as the complex phase information inherent of a nonstationary state. Current visualisation schemes based on physical observables or the qualitative information contained in simple wavefunctions, such as time-dependent configuration-interaction-singles (TD-CIS) and time-dependent self-consistent-field (TD-SCF), are discussed. This information is compared to an analysis based on the one-body reduced density operator (1-RDO), which is well-defined for general wavefunctions. It is seen that the distinction between two paradigms of many-body dynamics, electron transport and energy transport, is reflected in the coherences of a difference-1-RDO, or lack thereof.     

Coherent molecular optics using ultracold sodium dimers

Coherent molecular optics is performed using two-photon Bragg scattering. Molecules were produced by sweeping an atomic Bose-Einstein condensate through a Feshbach resonance. The spectral width of the molecular Bragg resonance corresponded to an instantaneous temperature of 20 nK, indicating that atomic coherence was transferred directly to the molecules. An autocorrelating interference technique was used to observe the quadratic spatial dependence of the phase of an expanding molecular cloud. Finally, atoms initially prepared in two momentum states were observed to cross pair with one another, forming molecules in a third momentum state. This process is analogous to sum-frequency generation in optics.     

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metadynamics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.     

微粗糙结构表面液滴浸润特性的多体耗散粒子动力学研究

超疏水表面因其优异的自洁作用一直是表面科学领域关注的重点.本文使用多体耗散粒子动力学(many-body dissipative particle dynamics, MDPD)方法模拟研究了不同粗糙结构下液滴的浸润特性, 并与Cassie-Baxter理论进行了对比. 研究使用了一种具有长吸短斥作用的流固作用函数来获得不同的液滴浸润性, 并利用一种简洁的数值方法来测量接触角. 模拟结果表明本研究方法能够稳定地捕捉到液滴在粗糙表面的静态和动态特性. 模拟了粗糙结构对三相接触线运动的黏滞作用, 与物理实验结果相符合, 表明Cassie-Baxter理论在实际应用中尚存在一定局限性. 研究分析了在动态铺展过程中的能量转化关系, 并指出在低值表面容易引起液滴反弹.     

Vibrational and thermodynamic properties of metals from a model embedded-atom potential

This work provides the first systematic test of validity of the embedded-atom potentials of Mei et al. [Phys. Rev. B 43 (1991) 4653], via a complete study of the vibrational and thermodynamic properties of isoelectronic transition (Ni, Pd, Pt) and noble (Cu, Ag, Au) metals. Phonon dispersion curves and thermal properties are studied within the quasiharmonic approximation. Results for the temperature-dependence of the lattice constants, coefficients of linear thermal expansion, isothermal and adiabatic bulk moduli, heat capacities at constant volume and constant pressure, Debye temperatures and Grüneisen parameters are presented. Electronic contribution to the specific heat is included explicitly via density-functional calculation. The calculated phonon frequencies for Ag and Cu agree well with the results from inelastic neutron scattering experiments. Despite less satisfactory agreement between calculated and measured phonon frequencies for the other four metals, isothermal and adiabatic bulk moduli and the specific heats of all metals are reproduced reasonably well by the model, while the Grüneisen parameter and Debye temperature are underestimated by about 10%. The coefficient of linear thermal expansion is underestimated with respect to measured values in most cases except for Pt and Au. The results are good for Pt up to 1000 K and for Au up to 500 K.     

Electroless formation of silver nanoaggregates: an experimental and molecular dynamics approach

The ability to manipulate matter to create non-conventional structures is one of the key issues of material science. The understanding of assembling mechanism at the nanoscale allows us to engineer new nanomaterials, with physical properties intimately depending on their structure.

This paper describes new strategies to obtain and characterise metal nanostructures via the combination of a top-down method, such as electron beam lithography, and a bottom-up technique, such as the chemical electroless deposition. We realised silver nanoparticle aggregates within well-defined patterned holes created by electron beam lithography on silicon substrates. The quality characteristics of the nanoaggregates were verified by using scanning electron microscopy and atomic force microscopy imaging. Moreover, we compared the experimental findings to molecular dynamics simulations of nanoparticles growth. We observed a very high dependence of the structure characteristics on the pattern nanowell aspect ratio. We found that high-quality metal nanostructures may be obtained in patterns with well aspect ratio close to one, corresponding to a maximum diameter of 50 nm, a limit above which the fabricated structures become less regular and discontinuous. When regular shapes and sizes are necessary, as in nanophotonics, these results suggest the pattern characteristics to obtain isolated, uniform and reproducible metal nanospheres.     

NQR application to the study of hydrogen dynamics in hydrogen-bonded molecular dimers

The temperature dependences of ¹H NMR as well as ³⁵Cl NQR spin-lattice relaxation times T ₁ were investigated in order to study the hydrogen transfer dynamics in carboxylic acid dimers in 3,5-dichloro- and 2,6-dichlorobenzoic acids. The asymmetry energy A/ k _B and the activation energy V/ k _B for the hydrogen transfer were estimated to be 240 K and 900 K, and 840 K and 2500 K, respectively, for these compounds. In spite of a large asymmetric potential the quantum nature of hydrogen transfer is recognized in the slope of the temperature dependence of T ₁ on the low-temperature side of the T ₁ minimum. The NQR T ₁ measurements was revealed to be a good probe for the hydrogen transfer dynamics.     

Spectroscopy of collective excitations in interacting low-dimensional many-body systems using quench dynamics

We study the problem of rapid change of the interaction parameter (quench) in a many-body low-dimensional system. It is shown that, measuring the correlation functions after the quench, the information about a spectrum of collective excitations in a system can be obtained. This observation is supported by analysis of several integrable models and we argue that it is valid for nonintegrable models as well. Our conclusions are supplemented by performing exact numerical simulations on finite systems. We propose that measuring the power spectrum in a dynamically split 1D Bose-Einsten condensate into two coupled condensates can be used as an experimental test of our predictions.     

A molecular dynamics study of the mechanical properties of h-BCN monolayer using a modified Tersoff interatomic potential

Using molecular dynamics (MD) simulations, we investigate the mechanical properties of hexagonal BCN monolayer, a newly synthesized two-dimensional material with an atom ratio of B/C/N = 1:1:1. The Tersoff potential is modified to get good agreement between predicted and measured fracture strengths of graphene. With this modified Tersoff potential, we perform extensive MD simulations to study the effect of temperature, strain rate and vacancy defect on the mechanical properties of h-BCN. It is found that h-BCN is a strong material with fracture strength of 81.4–93.5 GPa, albeit ∼35% lower than that of graphene. Similar to graphene, temperature has strong effect on the mechanical properties of h-BCN. As the temperature increases from 10 K to 1300 K, the fracture strength and strain of h-BCN drops by 55% and 62%, respectively. The strain rate is found to have a moderate effect. When the strain rate increases from 0.00002 to 0.0125 ps⁻¹, the fracture strength and strain of h-BCN increases 6.1% and 12%, respectively. As for the atomic defect, a very small concentration (0.028%) of vacancy in h-BCN is able to cause a 28% reduction in fracture strength and a 35.5% reduction in fracture strain. These findings have significance for its future applications in nanodevices.     

纳米多孔银力学性能表征分子动力学模拟

纳米多孔金属拥有优异的物理、化学性能,在众多领域中极具应用前景.相关力学性能的认知是实现其功能化应用的重要基础之一.基于分子动力学模拟,以三种拓扑结构(立方体结构、金刚石结构、螺旋体结构)的纳米多孔银为对象,研究了单轴拉伸下的力学响应,探讨了拓扑结构和相对密度与其力学性能的内在联系.仿真结果表明,纳米多孔银的极限强度和杨氏模量随相对密度增大而增大的同时,还紧密地依赖于拓扑结构.其中,金刚石结构与螺旋体结构的模量随相对密度的变化趋势较为相近,而螺旋体结构中螺旋形式的孔棱在受力拉直的过程中抵抗变形,表现出相对较好的塑性.立方体结构中,孔棱分布形式单一,抵抗变形的能力较弱,模量值较低.同一相对密度下,金刚石结构的强度最大,立方体结构次之,螺旋体结构最小.金刚石结构中,交错的孔棱间形成三角骨架结构,具有一定的稳定性,表现出相对较高的强度.     

fcc金属层错能的EAM法计算

采用嵌入原子法(EAM)计算了Cu，Ag，Au，Ni，Al，Rh，Ir，Pd，Pt和Pb等10种面心立方(fcc)金属的层错能，除Rh和Ir两种金属外，其他金属的计算结果和实验结果基本一致. 关键词： 面心立方金属 层错能 EAM     

Spectroscopy of La0.5Sr1.5MnO4 orbital ordering: a cluster many-body calculation

Orbital ordering (OO) in La_0.5Sr_1.5MnO₄ has been studied using soft X-ray resonant diffraction (SXRD) at the Mn L_2,3 edges in combination with many-body cluster calculations. The SXRD intensity is modelled in second quantization using a small planar cluster consisting of a central active Mn site with first-neighbour shells comprising O and Mn sites. The effective Hamiltonian includes Slater-Koster parameters and charge transfer and electron correlation energies obtained from previous measurements on manganites. The energy dependence of the SXRD OO peak is calculated using the Jahn-Teller distortions of the oxygen octahedra and in-plane spin correlations as adjustable parameters. These contributions are clearly distinguished above the Néel temperature with a good spectroscopic agreement. The results also suggest a significant charge separation between the Mn sites.     

Constant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virial

In the present work we introduce a simple, Nosé—Hoover style isothermal—isobaric molecular dynamics method for systems with holonomic molecular constraints and the molecular representation of the virial. We prove, using the non-Hamiltonian dynamics approach, recently developed by Tuckerman et al. [1999, Europhys. Lett., 45, 149], that the phase space distribution, generated by our equations, samples the desired ensemble under all circumstances. We also write down the explicit reversible integrator for our equations. This integrator has been implemented in the last version of the DLProtein program.     

Novel methodology for the calculation of the enthalpy of enclathration of methane hydrates using molecular dynamics simulations

Methane hydrates are encountered in a plethora of industrial and geological or environmental applications. In the current study, we present a novel methodology which is based on molecular dynamics simulations for the calculation of the enthalpy of enclathration of sI methane hydrates. Simulations are performed along the three-phase (Hydrate – Liquid water – Vapour; H–L_w–V) equilibrium line in the temperature range 274–310?K. The methodology takes into account the two different types of cages that are present in the sI methane hydrate and provides results for the enthalpy of enclathration for both types of cages, while it avoids performing calculations with the metastable, completely empty hydrate lattice. The formulation proposed is general and can be also applied to sII hydrates, while it can be modified/extended appropriately for use in the case of sH hydrates. Comparison is provided with available data from the literature and good agreement is observed.