Root Mean Square Displacement Research Articles

Theoretical research on the relationships between aromatic ligands and spectroscopic properties of Pt(II) complexes

A series of cyclometalated platinum (II) complexes with aromatic ligands, such as pyridyl, pyrimidinyl, and pyrazolate, were investigated with theoretical calculations. To investigate the relationship between ligands with molecular orbital, molecular rigidity, electroluminescent properties, and spectroscopic properties, the electrostatic potential (ESP), density-of-states (DOS), and root mean squared displacement (RMSD) were calculated. On the basis of calculated absorption and phosphorescence data, the analysis of ‘hole’ and ‘electron’ have also been performed. From the RMSD and spin–orbit coupling (SOC) matrix elements calculations, complex 3 shows significant structural distortions on S1 state and it may be applied in thermal activation delayed fluorescence (TADF) materials. The electroluminescent properties calculations show that complex 1 is suitable for hole transport material and complex 4 can be applied to electron transport material.

Semi-active control of jacket structure using MR damper and a deformation enhancement device under random ocean waves

The effect of a lever arm arrangement on the dynamic response of jacket structure installed with a Magneto-Rheological (MR) damper is investigated in this study. The structure is excited by random ocean waves for significant wave heights of 5 m, 8 m, and 10 m using the Pierson–Moskowitz (PM) spectrum. MR dampers of capacity 1000 kN, 500 kN, and 200 kN are used to study the effect of the lever arm on the control performances of the structure. The jacket structure is numerically modeled using the Finite Element Method (FEM), and the dynamics of MR damper is represented using the phenomenological Bouc-Wen model. The Fuzzy Logic Controller (FLC) that provides the command voltage to the MR damper is optimized using the Genetic Algorithm (GA) with a fitness function based on Root Mean Square (RMS) values of tip displacement and acceleration. The lever arm arrangement was found to enhance the control force, which further aids in reducing the damper capacity although maintaining the same percentage of control. For a 30% lever ratio, the percentage control in RMS displacement achieved for 200 kN, 500 kN, and 1000 kN dampers are 31.9%, 45.2%, and 47%, respectively. The percentage control on RMS displacement was nearly constant for different significant wave heights because of the lever arm arrangement. The numerical results show that the FLC successfully controls the response of the structure, and the lever arm configuration helps in improving damper efficiency

An experimental study of tuned liquid column damper controlled multi-degree of freedom structure subject to harmonic and seismic excitations.

A tuned liquid column damper (TLCD) is a passive vibration control device that not only mitigates unwanted structural vibrations but also acts as a water storage facility in a building. These aspects of TLCD make its application specifically suited for building structures. Previously, many experimental works on TLCDs have been conducted considering a single degree of freedom (SDOF) structure. However, the performance of TLCDs to control the response of multi-degree of freedom (MDOF) structure has rarely been studied experimentally. Therefore, this study has investigated the performance of a tuned liquid column damper (TLCD) on a multi-degree of freedom (MDOF) structure using shake table testing. A four-storey steel frame structure equipped with TLCD at the top of the fourth storey has been studied. Experimental normalized frequency response curves for MDOF structure equipped with TLCD have been determined. For this purpose, a series of harmonic loadings including frequencies 0.65 Hz, 1.17 Hz, 1.30 Hz, 1.43 Hz and 1.95 Hz have been applied in addition to historic earthquake loading. Peak and root-mean-square (RMS) accelerations have been discussed in detail for all the applied loadings at each storey level of the structure. For comparison purposes, the percentage reductions in peak and RMS accelerations have been calculated and compared. Also, RMS displacements and inter-storey drifts have been presented for resonant and seismic excitations. Both in time and frequency domains, responses of controlled MDOF structure have been analyzed and compared with uncontrolled structure. Results confirmed that TLCD has improved the MDOF structure responses at harmonic loadings frequencies near resonance and historic earthquake excitations. Furthermore, the improvement in the responses of MDOF structure with TLCD is more prominent at harmonic loadings compared to historic earthquake loading.

Beam width and arm position but not cognitive task affect walking balance in older adults

Detection of changes in dynamic balance could help identify older adults at fall risk. Walking on a narrow beam with its width, cognitive load, and arm position manipulated could be an alternative to current tests. Therefore, we examined additive and interactive effects of beam width, cognitive task (CT), and arm position on dynamic balance during beam walking in older adults. Twenty older adults (69 ± 4y) walked on 6, 8, and 10-cm wide beams (2-cm high, 4-m-long), with and without CT, with three arm positions (free, crossed, akimbo). We determined cognitive errors, distance walked, step speed, root mean square (RMS) of center of mass (COM) displacement and trunk acceleration in the frontal plane. Beam width decrease progressively reduced distance walked and increased trunk acceleration RMS. Step speed decreased on the narrowest beam and with CT. Arm crossing decreased distance walked and step speed. COM displacement RMS and cognitive errors were not affected by any manipulation. In conclusion, distance walked indicated that beam width and arm position, but less so CT, affected dynamic balance, implying that beam walking has the potential to become a test of fall risk. Stability measurements suggested effective trunk adjustments to control COM position and keep dynamic balance during the task.

Predictions for the perturbed root mean square displacement of a vibrating structure using modal parameters

A harmonically vibrating structure is considered for this study and divided into segments. The objective of the proposed research is to use knowledge from the nominal structure to make predictions as to how the root mean squared (RMS) displacement of the structure will change when either the mass or stiffness of a segment is scaled. Typically, to calculate the value for the modified RMS displacement, a linear solve is required to determine the new displacement vector. Additionally, the Neumann series may be used. However, this approach requires computations of matrix-vector products, which may become expensive for larger Degrees of Freedom (DOF) systems. Here, a method is proposed to predict the RMS displacement for the modified system from scalar values of the nominal system. Since only scalar values from the nominal system are required, predictions for the perturbed system can be made cheaply. The proposed method is based on the modal displacement equation and the assumption that the system is forced near a natural frequency. This assumption is used in Rayleigh’s quotient to approximate the new natural frequency as a function of the approximated modal stiffness and mass. The limitations and accuracy will be explored. [Work supported by ONR Grant N00014-19-1-2100.]

Effects of weights on vibration suppression via a nonlinear energy sink under vertical stochastic excitations

A primary structure attached by a nonlinear energy sink (NES) moving vertically under a Gaussian white noise excitation is investigated. This paper demonstrates the stochastic responses and vibration suppression with emphasis on the effects of the weights. Four-dimensional state space equations which consider or ignore the weights in the vertical direction are given. Numerical probability density functions computed via the path integration method based on the Gauss-Legendre scheme are confirmed by Monte Carlo simulations. Probability density functions of the structure’s responses are compared between two cases under various random excitation intensities. The root-mean-square (RMS) displacement of the primary structure or random vibration suppression is estimated through the path integration method. Results reveal that the NES is able to suppress broadband random vibration of the structure. As the stochastic excitation decreases, the NES weight has significant effects on both probability density functions of the structure’s responses and RMS displacements of the primary structure. The NES parameters are discussed to explore random vibration suppression. For purpose of more accurate predictions, the effects of weights should be taken into consideration when the primary structure is excited by small random excitations or coupled with a large and reasonable NES mass. Simulations and discussions in this work provide theorical meanings to predict vibration suppression via a NES in stochastic environment.

Molecular dynamics simulations of adsorption behavior of DDAH, NaOL and mixed DDAH/NaOL surfactants on muscovite (001) surface in aqueous solution

The adsorption mechanism of collectors on minerals is of fundamental importance in the research and development of flotation science and processing technology. To examine the effect of cationic dodecylamine hydrochloride (DDAH), anionic sodium oleate (NaOL) and mixed DDAH/NaOL surfactants with different molar ratios on the adsorption behavior on the muscovite (001) surface, the adsorption mechanism of DDAH, NaOL and their mixture on the muscovite (001) surface in neutral aqueous solution was investigated by molecular dynamics (MD) simulations. The results showed that the cationic DDAH molecules absorb on the muscovite (001) surface by electrostatic interactions and hydrogen bonding, whereas the anionic NaOL molecules cannot independently adsorb on the muscovite surface. Based on the analysis of the density distribution profile, radial distribution function (RDF) and interaction energy between surfactant molecules and muscovite surface, and the root mean square displacement (RMSD) of surfactants on water-muscovite interface, individual DDAH surfactant is a superior collector for the muscovite flotation. The molar ratio of DDAH/NaOL surfactants is found to be a key factor in the flotation response of muscovite. No significant adsorption of 1:2, 1:3 and 1:4 mixed DDAH/NaOL surfactants on the muscovite surface can be detected, while an effective adsorption was observed for the DDAH/NaOL mixture in molar ratios of 1:1, 2:1, 3:1 and 4:1. The cationic DDAH surfactant was determined to play a primary role in the adsorption of the mixed surfactants on the muscovite surface, while the anionic NaOL molecules co-adsorb with the DDAH molecules. The additional micro-flotation experiments under neutral aqueous conditions also showed that the flotation recovery of muscovite was the highest in the presence of DDAH surfactant, which was consistent with the findings derived from MD simulations.

Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials.

An efficient yet accurate method for producing a large amount of energy data for molecular mechanical force field (MMFF) parameterization is on demand, especially for torsional angle parameters which are typically derived to reproduce ab initio rotational profiles or torsional potential energy surfaces (PESs). Recently, an active learning potential (ANI-1x) for organic molecules which can produce smooth and physically meaningful PESs has been developed. The high efficiency and accuracy make ANI-1x especially attractive for geometry optimization at low cost. To apply the ANI-1x potential in MMFF parameterization, one needs to perform constrained geometry optimization. In this work, we first developed a computational protocol to constrain rotatable torsional angles and other geometric parameters for a molecule whose geometry is described by Cartesian coordinates. The constraint is successfully achieved by force projection for the two conjugated gradient (CG) algorithms. We then conducted large-scale assessments on ANI-1x along with four different optimization algorithms in reproducing DFT energies and geometries for two CG algorithms, CG backtracking line search (CG-BS) and CG Wolfe line search (CG-WS), and two quasi-Newton algorithms, Broyden-Fletcher-Goldfarb-Shanno (BFGS) and low-memory BFGS (L-BFGS). Note that CG-BS is a new algorithm we developed in this work. All four algorithms take the ANI energies and forces to optimize a molecule geometry. Last, we conducted a large-scale assessment of applying ANI-1x in MMFF development in three aspects. First, we performed full optimizations for 100 drug molecules, each consisting of five distinct conformations. The average root-mean-square error (RMSE) between ANI-1x and DFT is about 1.3 kcal/mol, and the root-mean-square displacement (RMSD) of heavy atoms is about 0.35 Å. Second, we generated torsional PESs for 160 organic molecules, and constrained optimizations were performed for up to 18 conformations for each PES. We found that the RMSE of all the conformers is 1.23 kcal/mol. Last, we carried out constrained optimizations for alanine dipeptide with both ϕ and φ angles being frozen. The Ramachandran plots indicate that the two CG algorithms in conjunction with the ANI-1x potential could well reproduce the DFT-optimized geometries and torsional PESs. We concluded that CG-BS and CG-WS are good choices for generating PESs, while CG-WS or BFGS is ideal for performing full geometry optimization. With the continuously increased quality of ANI, it is expected that the computational algorithms and protocols presented in this work will have great applications in improving the quality of an existing small-molecule MMFF.

Research on seismic ground motion parameters applicable to the safety of rectangular shallow tunnel

The objective of this paper is to optimize the selection of seismic ground motion intensity indexes in the seismic fortification of urban shallow-buried rectangular tunnels. This paper takes a shallow-buried rectangular tunnel in a city as the research object, uses ABAQUS to establish a finite-infinite element coupling model, and selects 70 typical seismic ground motions for dynamic calculation. Using dynamic time history analysis method to study the seismic response of tunnel lining structure in terms of internal force, minimum safety factor and strain energy, and analyze their correlation with 15 seismic ground motion parameters. Selecting the seismic ground motion parameters with strong correlation, good effectiveness, and high credibility for safety evaluation. The research results show that: Peak acceleration (PGA) has a weak correlation with the seismic response of tunnel lining structures, and PGA as an independent seismic ground motion intensity index has greater uncertainty in the seismic fortification of tunnels; Peak displacement (PGD), Root-mean-square velocity (RMSV), Root-mean-square displacement (RMSD), and Specific energy density (SED) can be used as independent seismic ground motion intensity index, The linear regression model is used to evaluate the safety of the lining structure, and finally the evaluation result is verified by the incremental dynamic analysis method (IDA), which shows that the evaluation result is accurate. The research results can provide reference for the preliminary design of seismic fortification of rectangular shallow tunnels.

Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

Molecular docking and dynamics simulations were conducted to investigate the antiviral activity of Propolis Sulabiroin-A to inhibit the SARS-CoV-2 virus with quercetin, hesperidin, and remdesivir as control ligands. The parameters calculated were docking score and binding energy/molecular mechanics-generalized born surface area (MMGBSA), root mean square displacement (RMSD), and root mean square fluctuation (RMSF). Docking and MMGBSA scores showed that all the ligands demonstrate an excellent candidate as an inhibitor, and the order of both scores is hesperidin, remdesivir, quercetin, and sulabiroin-A. The molecular dynamics simulation showed that all the ligands are good candidates as inhibitors. Although the fluctuation of Sulabiroin-A is relatively high, it has less protein–ligand interaction time than other ligands. Overall, there is still a good possibility that sulabiroin-A can be used as an alternative inhibitor if a new structure of receptor SARS-CoV-2 is used.

TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation

The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependent G values in pure liquid water for ·OH, e– aq, and H2 with published experimental data. For H2O2 and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by 137Cs γ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependent G values and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for ·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.

CROSS-FLOW VORTEX-INDUCED VIBRATION OF A FLEXIBLE RISER WITH INTERNAL FLOW IN SHEAR CURRENT

As an important component transporting resources such as oil and mineral ores mixture from the seabed to the surface in ocean engineering, vortex-induced vibration (VIV) of flexible risers can be encountered when the risers are subjected to the external environmental conditions. As VIV can lead to structural fatigue for the riser system, which threatens to the facility safety during deepsea resource exploitation, it is of great significance to investigate VIV mechanism and dynamics. Therefore, VIV dynamics of a flexible fluid-conveying riser undergoing external shear current is studied based on the combination of the Euler-Bernoulli beam theory and the semi-empirical hydrodynamic model. The finite element method and Newmark-β method are adopted to discretize and solve the governing equation. The model is firstly validated by comparing with the experimental data in order to examine the accuracy of the present model. Subsequently, cross-flow (CF) VIV response of the fluid-conveying riser is mainly examined and analyzed while various internal flow velocity and fluid density are considered and changed. The results show that when the flexible riser is subjected to both internal flow and shear current, there appears multi-frequency response for CF VIV. And the CF vibrating frequency and the CF root mean square (RMS) displacement are evidently influenced by the internal flow velocity and fluid density. With the increase of the internal flow velocity and fluid density, the CF vibrating frequency decreases while the RMS displacement shows an increasing trend in CF direction. Furthermore, in addition to the variation of the CF vibrating frequency and RMS displacement, the change of internal flow densities can cause notable mode and frequency transitions.

Robust multimodal control of a large‐scale tensegrity dome using multiple tuned mass dampers

Tensegrity domes are reticulated prestressed structures composed of bars in compression and cables in tension. These structures are flexible lightweight systems with low structural damping, and thus, they are sensitive to vibrations induced by strong wind and earthquakes. The present work deals with the robust multimodal control of a large-scale tensegrity dome of Geiger's type. Assuming random excitations and linear behavior of the structure around an equilibrium prestressed configuration, the control is achieved in the low-frequency range using multiple tuned mass dampers (MTMDs). The optimal MTMD parameters, ensuring optimal performances, are obtained using a root mean square displacement (RMSD)-based approach. The optimization strategy is firstly applied, in a deterministic context where the structural parameters uncertainties are not included, to control the fundamental resonant frequency of the dome structure and then extended to perform multimodal control using multiobjective optimization. In addition, in real-life situations, it's very hard to describe actual engineering structures in precise model yielding to unavoidable internal and external uncertainties. To deal with these uncertainties, it has been shown that the proposed multimodal control is also able to carry out robust control in presence of structural uncertainties. The proposed optimization strategy applied to the dome structure is compared to other optimization strategies, from the open literature. The obtained results showed the efficiency of the proposed methodology of the passive control in both contexts, that is, the deterministic and the non-deterministic where uncertainties are considered.

Effect of soil-structure interaction on wind-induced responses of supertall buildings with large pile groups

A simplified three-dimensional soil-structural interaction (SSI) model is established for large pile groups-supertall buildings (>300 m height) to simulate the dynamic response of the building to wind loading. The displacement and acceleration responses to wind loading at the top of the supertall building are calculated using the established model. The effects of SSI on the wind-induced mean displacement, root-mean-square (RMS) displacement and RMS acceleration are analyzed considering different values of soil shear wave velocity and material damping, and different total mass, first natural frequency and damping ratio of the superstructure as well as different terrain conditions. The results from the comprehensive parametric study are used to derive empirical equations of the mean displacement, RMS displacement and RMS acceleration SSI factors. The findings demonstrate that the mean displacement of the top of supertall building increases considering SSI. As the soil shear wave velocity decreases, the mean displacement SSI factor increases. It was also found that the mean displacement SSI factor increases with the increase in total mass and first natural frequency of the superstructure. In addition, the RMS displacement and acceleration SSI factors decrease with the increase of the soil shear wave velocity and material damping. Finally, the RMS displacement and acceleration SSI factors increase as the superstructure first damping ratio increases.

Manipulating thermal conductivity of silicon nanowires through surrounded fins and Ge dopant

Manipulating the phonon transport using nanotechnologies is one of the commonly adopted ways to reduce the thermal conductivity and enhance the thermoelectric performance of thermoelectric materials. In this work, we proposed a resonant structure, surrounded fins, for Si nanowires. The effects of both surrounded fins and Ge dopant on the thermal transport in Si NWs are studied using the molecular dynamics simulations. The root-mean-square (RMS) displacement, phonon dispersion, density of states and transmission function have been calculated to understand the thermal conductivity reduction in Si NWs. The calculated results show that both the surrounded fins and Ge dopants could significantly decrease the thermal conductivity of Si NWs. The thermal conductivity of finned Si NWs decreases with increasing the height of the surrounded fins. The more surrounded fins added, the more significant the thermal conductivity decreases. The thermal conductivity of SiGe NWs decreases initially and then increases with increasing Ge concentration. Through the analysis of RMS displacement and phonon dispersion, we found that surround fins could not only enhance anharmonicity by activating atoms near to the edge, but also increase the low frequency phonons and decrease the group velocities by modifying phonon dispersion relationship. The phonon transmission function suggests that the surrounded fins and Ge dopants would mainly suppress the transport of low-frequency and high-frequency phonons, respectively. Phonon transport in Si NWs could be suppressed over the whole frequency range by combining the surrounded fins and Ge dopants. Our results provide useful guidance in the design of efficient thermoelectric devices made of nanowires.

Information Extraction and Population Estimates of Settlements from Historic Corona Satellite Imagery in the 1960s.

The Corona satellite program was a historic reconnaissance mission which provided high spatial resolution panchromatic images during the Cold War era. Nevertheless, and despite the historic uniqueness and importance of the dataset, efforts to extract tangible information from this dataset have primarily focused on visual interpretation. More sophisticated approaches have been either hampered or unrealized, often justified by the primitive quality of this early satellite product. In the current study we attempt to showcase the usability of Corona imagery outside the context of visual interpretation. Using a 1968 Corona image acquired over the city municipality of Plovdiv, Bulgaria, we reconstruct a panchromatic 1.8 m spatial resolution georegistered image with a relative displacement Root Mean Square Error (RMSE) of 6.616 (for x dimension) and 1.886 (for y dimension) and employ segmentation and texture analysis to discern agricultural parcels and settlements’ footprints. Population statistics of this past era are retrieved from national census and related to settlements’ footprints. An exponential relationship between the two variables was identified by applying a semi-log regression. The high adjusted R2 value found (76.54%) indicates that Corona images offer a unique opportunity for population data analysis of the past. Overall, we showcase that the Corona images’ usability extends beyond the visual interpretation, and features of interest extracted through image analysis can be subsequently used for further geographical and historical research.

Characterization of the fretting wear damage under random excitation

Conventional sinusoidal excitation is commonly used for investigating oscillatory fretting wear. However, in real life applications, the excitation force is random. This work provides a methodology for analyzing random fretting wear damage accumulation.The proposed wear energy characterization is based on the identification of the root mean square (RMS) displacement response of the fretting tribo-system to a random Gaussian excitation. To identify each sine component of the random signal, the Fourier transform is applied on the displacement, showing the signal magnitude as a function of frequency components. Based on the Power Spectral Density (PSD) definition, each frequency component can be related to specific sine amplitudes composing the original random signal. From this decomposition into sine components, new simplified approximations of the work rate and accumulated dissipated energy are proposed to characterize the fretting wear damage under true random vibrations.Tests were performed using two crossed cylinders (proprietary Zr alloy/nickel-based alloy 718) in the fretting wear configuration at high temperature (315 °C). True random tests were then performed using a Gaussian acceleration-control strategy. Imposing the PSD defining the acceleration level, the ratio between partial and gross slip domains is controlled through the mean and variance of the Gaussian displacement response, which can be related to the RMS displacement excitation parameter. This set of tests consisted of 6 × 106 cycles in the gross slip regime. Additional random simulation cases were generated to validate the proposed energy-based characterization parameter.Exact and simplified approximations of both work rate and accumulated dissipated energy are compared for real test conditions and simulated cases. The proposed approximations are function of the predominant frequency within the random signal response, the gross slip regime signal portion, and the RMS of the Gaussian random displacement response. Very good correlations were obtained, validating both work rate and energy loss simplified approximations.

Improving Low Frequency Isolation Performance of Optical Platforms Using Electromagnetic Active-Negative-Stiffness Method

To improve the low-frequency isolation performance of optical platforms, an electromagnetic active-negative-stiffness generator (EANSG) was proposed, using nano-resolution laser interferometry sensors to monitor the micro-vibration of an optical platform, and precision electromagnetic actuators integrated with a relative displacement feedback strategy to counteract the positive stiffness of pneumatic springs within a micro-vibration stroke, thereby producing high-static-low-dynamic stiffness characteristics. The effectiveness of the method was verified by both theoretical and experimental analyses. The experimental results show that the vertical natural frequency of the optical platform was reduced from 2.00 to 1.37 Hz, the root mean square of displacement was reduced from 1.28 to 0.69 μm, and the root mean square of velocity was reduced from 14.60 to 9.33 μm/s, proving that the proposed method can effectively enhance the low frequency isolation performance of optical platforms.

Spyrmsd: symmetry-corrected RMSD calculations in Python

Root mean square displacement (RMSD) calculations play a fundamental role in the comparison of different conformers of the same ligand. This is particularly important in the evaluation of protein-ligand docking, where different ligand poses are generated by docking software and their quality is usually assessed by RMSD calculations. Unfortunately, many RMSD calculation tools do not take into account the symmetry of the molecule, remain difficult to integrate flawlessly in cheminformatics and machine learning pipelines—which are often written in Python—or are shipped within large code bases. Here we present a new open-source RMSD calculation tool written in Python, designed to be extremely lightweight and easy to integrate into existing software.

Molecular dynamics simulation of thermal welding process of Ag nanoparticles

The thermal welding process of Ag nanoparticles was studied by molecular dynamics using embedded atoms method (EAM), and the melting point of Ag nanoparticles was analyzed by radial distribution function (RDF) and root mean square displacement (RMSD). The results show that for Ag nanoparticles with diameter less than 10 nm, driven by surface energy, the welding temperature will be much lower than the melting point when the spacing between nanoparticles is smaller than the radius of particle, the mechanism at low temperature is different from that at high temperature. The spontaneous rotation of nanoparticles during welding at suitable temperature makes the lattice orientation parallel to each other in three-dimensional space, which may be caused by collision of nanoparticles or short-range interaction near the surface. From the thermodynamic point of view, this behavior is driven by the reduction of surface energy, with the increase of temperature, the interface between particles will become chaotic gradually.