Assessing the mechanical behavior of proteins and metal nanowires using long timescale atomistic simulations

Classical molecular dynamics (MD) simulations have been widely used to study the physical properties of nanomaterials. However, MD suffers from the well-known drawback where it cannot, in the absence of special high-performance computing environments, simulate processes that take longer than microseconds. Nevertheless, many important processes in various fields of science and engineering take place on time scales that cannot be reached by MD. For example, while MD simulations have been used extensively to study the plasticity of nanostructures such as proteins and nanowires, their time scale limitations have prevented the study of the deformation mechanisms at experimentally-relevant forces, time scales and strain rates. In this thesis, a generic history-penalized self-learning metabasin escape (SLME) algorithm, which efficiently explores the potential energy surface, is utilized to overcome this issue by studying three canonical problems of interest: the unfolding of biological proteins under experimentally-relevant mechanical forces; the strain-rate-dependent plastic deformation mechanisms of bicrystalline FCC metal nanowires, and finally the constant stress (creep-induced) plastic deformation of single crystalline metallic nanowires at experimental time scales. The SLME method is first utilized to study the force-induced unfolding of biological proteins. The long time scale simulations not only provide atomistic details of time-dependent structural evolution under experimentally-relevant forces, but also show novel intermediate states that cannot be observed in MD simulations, which sheds new insight into the understanding of protein unfolding dynamics. This method is then utilized to investigate the strain rate effect on the plastic mechanisms of bicrystalline metal nanowires. A strain-rate-dependent incipient plasticity and yielding transition for bicrystalline metal nanowires at experimentally-relevant strain rates is observed. This transition leads to a ductile-to-brittle transition in failure mode, which is driven by differences in dislocation activity and grain boundary mobility at low strain rate as compared to the high strain rate case. Finally, the SLME method is also utilized to study the creep behavior of single crystalline metal nanowires at experimental time scales. Both copper and silver nanowires show significantly increased ductility and superplasticity under experimentally-relevant creep stresses, where the superplasticity is driven by a thermally-activated transition in defect nucleation from twinning to trailing partial dislocations at the micro or millisecond timescale

The role of binding site on the mechanical unfolding mechanism of ubiquitin.

We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied force clamping level of 100 pN, we find a new unfolding mechanism starting with the detachment between β5 and β3 involving the binding site of ubiquitin, the Ile44 residue. This new unfolding pathway leads to the discovery of new intermediate configurations, which correspond to the end-to-end extensions previously seen experimentally. More importantly, it demonstrates the novel finding that the binding site of ubiquitin can be responsible not only for its biological functions, but also its unfolding dynamics. We also report in contrast to previous single molecule constant force experiments that when the clamping force becomes smaller than about 300 pN, the number of intermediate configurations increases dramatically, where almost all unfolding events at 100 pN involve an intermediate configuration. By directly calculating the life times of the intermediate configurations from the height of the barriers that were crossed on the potential energy surface, we demonstrate that these intermediate states were likely not observed experimentally due to their lifetimes typically being about two orders of magnitude smaller than the experimental temporal resolution

Laboratory photo-chemistry of covalently bonded fluorene clusters: observation of an interesting PAH bowl-forming mechanism

The fullerene C$_{60}$, one of the largest molecules identified in the interstellar medium (ISM), has been proposed to form top-down through the photo-chemical processing of large (more than 60 C-atoms) polycyclic aromatic hydrocarbon (PAH) molecules. In this article, we focus on the opposite process, investigating the possibility that fullerenes form from small PAHs, in which bowl-forming plays a central role. We combine laboratory experiments and quantum chemical calculations to study the formation of larger PAHs from charged fluorene clusters. The experiments show that with visible laser irradiation, the fluorene dimer cation - [C$_{13}$H$_{9}$$-$C$_{13}$H$_{9}$]$^+$ - and the fluorene trimer cation - [C$_{13}$H$_{9}$$-$C$_{13}$H$_{8}$$-$C$_{13}$H$_{9}$]$^+$ - undergo photo-dehydrogenation and photo-isomerization resulting in bowl structured aromatic cluster-ions, C$_{26}$H$_{12}$$^+$ and C$_{39}$H$_{20}$$^+$, respectively. To study the details of this chemical process, we employ quantum chemistry that allows us to determine the structures of the newly formed cluster-ions, to calculate the hydrogen loss dissociation energies, and to derive the underlying reaction pathways. These results demonstrate that smaller PAH clusters (with less than 60 C-atoms) can convert to larger bowled geometries that might act as building blocks for fullerenes, as the bowl-forming mechanism greatly facilitates the conversion from dehydrogenated PAHs to cages. Moreover, the bowl-forming induces a permanent dipole moment that - in principle - allows to search for such species using radio astronomy.Comment: 8 pages, 7 figures, accepte

A Two-part Transformer Network for Controllable Motion Synthesis

Although part-based motion synthesis networks have been investigated to reduce the complexity of modeling heterogeneous human motions, their computational cost remains prohibitive in interactive applications. To this end, we propose a novel two-part transformer network that aims to achieve high-quality, controllable motion synthesis results in real-time. Our network separates the skeleton into the upper and lower body parts, reducing the expensive cross-part fusion operations, and models the motions of each part separately through two streams of auto-regressive modules formed by multi-head attention layers. However, such a design might not sufficiently capture the correlations between the parts. We thus intentionally let the two parts share the features of the root joint and design a consistency loss to penalize the difference in the estimated root features and motions by these two auto-regressive modules, significantly improving the quality of synthesized motions. After training on our motion dataset, our network can synthesize a wide range of heterogeneous motions, like cartwheels and twists. Experimental and user study results demonstrate that our network is superior to state-of-the-art human motion synthesis networks in the quality of generated motions.Comment: 16 pages, 26 figure

Eudemonia and Freedom: A Bibliometric Research on Frontiers and Evolution of Labour and Employment in China

Eudemonia, the highest and ultimate aim of moral thought and behaviour, is a rational activity pursuing what is worthwhile in life, and its integral part, virtue, is honoured as the noblest self-actualisation. Freedom, a human right naturally belonging to each citizen, should be balanced and valued together with eudemonia as they conjointly allow citizens to determine action avoiding intervene. In the contemporary, it can be seen as a virtue and a human right for citizens to be devoted to valuable work freely and independently. It is essential to ensure citizens' eudemonia and freedom deserved and promised, and the key is to stabilise and sustain employment, improving citizens' livelihood and well-being with appropriate positions and quality work, incidentally developing the economy. The paper researches the situation and solutions for labour and employment, using the literature from 2015 to 2021, and conducts spatiotemporal and co-occurrence analysis by bibliometric methods with citespace and vosviewer, sorting out the frontiers and evolution, followed by deduction and inference. The paper makes a summary and review, putting forward the optimality of eudemonia and freedom, and recommends China to adopt and guarantee

Acoustic diagnostics of femtosecond laser filamentation

The promising application of femtosecond laser filamentation in atmospheric remote sensing brings imperative demand for diagnosing the spatiotemporal dynamics of filamentation. Acoustic emission (AE) during filamentation opens a door to give the insight into the dynamic evolution of filaments in air. In particular, the frequency features of the acoustic emission provide relevant information on the conversion of laser energy to acoustic energy. Here, the acoustic emission of femtosecond laser filament manipulated by energy and the focal lengths was measured quantitatively by a broadband microphone, and the acoustic parameters were compared and analyzed. Our results showed that the acoustic power presents a squared dependence on the laser energy and the bandwidth of the acoustic spectrum showed a significant positive correlation with laser energy deposition. It was found that the spectrum of the acoustic pulse emitted from the middle of the filament has a larger bandwidth compared to those emitted from the ends of the filament and the spectrum of the acoustic pulse is also an indicator of the filament intensity distribution. These findings are helpful for studying the plasma filament properties and complex dynamic processes through acoustic parameters and allow the optimization of remote applications.Comment: 8 pages,5 figure