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Laboratory automation is an expensive and complicated endeavor with limited inflexible options for small-scale labs. We develop a prototype system for tending to a bench-top centrifuge using computer vision methods for color detection and circular Hough Transforms to detect and localize centrifuge buckets. Initial results show that the prototype is capable of automating the usage of regular bench-top lab equipment.

To autonomously collect soil in uncultivated terrain, robotic arms must distinguish between different amorphous materials and submerge themselves into the correct material. We develop a prototype that collects soil in heterogeneous terrain. If mounted to a mobile robot, it can be used to perform soil collection and analysis without human intervention. Unique among soil sampling robots, we use a general-purpose robotic arm rather than a soil core sampler.

Learned object detection methods based on fusion of LiDAR and camera data require labeled training samples, but niche applications, such as warehouse robotics or automated infrastructure, require semantic classes not available in large existing datasets. Therefore, to facilitate the rapid creation of multimodal object detection datasets and alleviate the burden of human labeling, we propose a novel automated annotation pipeline. Our method uses an indoor positioning system (IPS) to produce accurate detection labels for both point clouds and images and eliminates manual annotation entirely. In an experiment, the system annotates objects of interest 261.8 times faster than a human baseline and speeds up end-to-end dataset creation by 61.5%., Comment: Contains eight pages and 10 figures. A version of this document was accepted to IEEE IRC 2023

The multi-component density functional theory is faced with the challenge of capturing various types of inter- and intra-particle exchange-correlation effects beyond those introduced by the conventional electronic exchange-correlation functionals. Herein, we focus on evaluating the electron-proton/muon correlation functionals appearing in molecular/condensed-phase systems where a proton/muon is treated as a quantum particle on equal footing with electrons, beyond the Born-Oppenheimer paradigm. Five recently developed local correlation functionals, i.e., the epc series and e$\mu$c-1, are selected and their performances are analyzed by employing a two-particle model that includes an electron and a positively charged particle (PCP) with a variable mass, interacting through Coulombic forces, within a double harmonic trap. Using the Kohn-Sham (KS) inversion procedure, the exact two-component KS characterization of the model is deduced and its properties are compared to those derived from the considered functionals. The analysis demonstrates that these local functionals achieve their original parameterization objectives to reproduce the one-PCP densities and the electron-PCP correlation energies, but all fall short of reproducing the underlying PCP correlation potentials correctly. Moreover, a comprehensive error analysis reveals that the density-driven errors have a non-negligible contribution to the success of the considered functionals. Overall, the study shows the strengths as well as shortcomings of the considered functionals hopefully paving the way for designing more robust functionals in the future., Comment: 22 pages, 8 figures, 4 tables

In [Phys. Rev. B 107, 094433 (2023)], Deng et al. have proposed an electron-muon correlation functional within the context of the two-component density functional theory (TC-DFT) for crystals/molecules containing positively charged muons. In order to verify its performance, we applied the functional in conjunction with the B3LYP, as a hybrid electronic exchange-correlation functional, to a benchmark set of molecules. The results demonstrate that the proposed functional is not capable of reproducing the correct one-muon densities as well as some other key properties like muon's kinetic energy, the total energies and the mean muonic bond lengths. Using the muonium atom in a double-harmonic trap as a model we also demonstrate that the successful reproduction of the electron-muon contact hyperfine coupling constants by Deng et al. is probably the result of error cancellations. We also discuss some theoretical intricacies with the very definition of the electron-muon correlation energy within the context of the TC-DFT that must be taken into account in future efforts to design electron-muon correlation functionals., Comment: Main text plus supplemental material

The nature of the newly proposed two-positron bond in (PsH)2, which is composed of two protons, four electrons and two positrons, is considered in this contribution. The study is done at the multi-component-Hartree-Fock (MC-HF) and the Diffusion Monte Carlo (DMC) levels of theory by comparing ab initio data, analyzing the spatial structure of the DMC wavefunction, and applying the multi-component quantum theory of atoms in molecules and the two-component interacting quantum atoms energy partitioning schemes to the MC-HF wavefunction. The analysis demonstrates that (PsH)2 to a good approximation may be conceived of two slightly perturbed PsH atoms, bonded through a two-positron bond. In contrast to the usual two-electron bonds, the positron exchange phenomenon is quite marginal in the considered two-positron bond. The dominant stabilizing mechanism of bonding is a novel type of classical electrostatic interaction between the positrons, which are mainly localized between nuclei, and the surrounding electrons. To emphasize its uniqueness, this mechanism of bonding is proposed to be called gluonic which has also been previously identified as the main deriving mechanism behind formation of the one-positron bond in [H-, e+, H-]. We conclude that the studied two-positron bond should not be classified as a covalent bond and it must be seen as a brand-new type of bond, foreign to the electronic bonding modes discovered so far in the purely electronic systems., Comment: main text plus supporting information (The polished version of v3)

The proton between the two oxygen atoms of the malonaldehyde molecule experiences an effective double-well potential in which the proton wavefunction is delocalized between the two wells. Herein we employed the state-of-the-art multi-component quantum theory of atoms in molecules partitioning scheme to obtain the molecular structure, i.e. atoms in molecules and bonding network, from the superposed ab initio wavefunctions of malonaldehyde. In contrast to the familiar clamped-proton portrayal of malonaldehyde, in which the proton forms a hydrogen basin, for the superposed states the hydrogen basin disappears and two novel hybrid oxygen-hydrogen basins appear instead, with an even distribution of the proton population between the two basins. The interaction between the hybrid basins is stabilizing thanks to an unprecedented mechanism. This involves the stabilizing classical Coulomb interaction of the one-proton density in one of the basins with the one-electron density in the other basin. This stabilizing mechanism yields a bond foreign to the known bonding modes in chemistry., Comment: File contains the main text plus the supporting information

It is well-known experimentally that the positively-charged muon and the muonium atom may bind to molecules and solids, and through muon$'$s magnetic interaction with unpaired electrons, valuable information on the local environment surrounding the muon is deduced. Theoretical understanding of the structure and properties of resulting muonic species requires accurate and efficient quantum mechanical computational methodologies. In this paper the two-component density functional theory, TC-DFT, as a first principles method, which treats electrons and the positive muon on an equal footing as quantum particles, is introduced and implemented computationally. The main ingredient of this theory, apart from the electronic exchange-correlation functional, is the electron-positive muon correlation functional which is foreign to the purely electronic DFT. A Wigner-type local electron-positive muon correlation functional, termed e$\mu$c-1, is proposed in this paper and its capability is demonstrated through its computational application to a benchmark set of muonic organic molecules. The TC-DFT equations containing e$\mu$c-1 are not only capable of predicting the muon$'$s binding site correctly but they also reproduce muon$'$s zero-point vibrational energies and the muonic densities much more accurately than the TC-DFT equations lacking e$\mu$c-1. Thus, this study set the stage for developing accurate electron-positive muon functionals, which can be used within the context of the TC-DFT to elucidate the intricate interaction of the positive muon with complex molecular systems., Comment: Supplementary material included

Recently it has been proposed that the positron, the anti-particle analog of the electron, is capable of forming an anti-matter bond in a composite system of two hydride anions and a positron [Angew. Chem. Int. Ed. 57, 8859 (2018)]. In order to dig into the nature of this novel bond the newly developed multi-component quantum theory of atoms in molecules is applied to this positronic system. The topological analysis reveals that this species is composed of two atoms in molecules, each containing a proton and half of the electronic and the positronic populations. Further analysis elucidates that the electron exchange phenomenon is virtually non-existent between the two atoms and no electronic covalent bond is conceivable in between. On the other hand, it is demonstrated that the positron density enclosed in each atom is capable of stabilizing interactions with the electron density of the neighboring atom. This electrostatic interaction suffices to make the whole system bonded against all dissociation channels. Thus, the positron indeed acts like an anti-matter glue between the two atoms.

Recently we have proposed an effective Hartree-Fock (EHF) theory for the electrons of the muonic molecules that is formally equivalent to the HF theory within the context of the Nuclear-Electronic Orbital theory [Phys. Chem. Chem. Phys. 20, 4466 (2018)]. In the present report we extend the muon-specific effective electronic structure theory beyond the EHF level by introducing the effective second order Muller-Plesset perturbation theory (EMP2) and the effective coupled-cluster theory at single and double excitation levels (ECCSD) as well as an improved version including perturbative triple excitations (ECCSD(T)). These theories incorporate electron-electron correlation into the effective paradigm and through their computational implementation, a diverse set of small muonic species is considered as a benchmark at these post-EHF levels. A comparative computational study on this set demonstrates that the muonic bond length is in general non-negligibly longer than corresponding hydrogenic analogs. Next, the developed post-EHF theories are applied for the muoniated N-Heterocyclic carbene/silylene/germylene and the muoniated triazolium cation revealing the relative stability of the sticking sites of the muon in each species. The computational results, in line with previously reported experimental data demonstrate that the muon generally prefers to attach to the divalent atom with carbeneic nature. A detailed comparison of these muonic adducts with the corresponding hydrogenic adducts reveals subtle differences that have already been overlooked.

A set of effective electronic-only Kohn-Sham (EKS) equations are derived for the muonic molecules (containing a positively charged muon), which are completely equivalent to the coupled electronic-muonic Kohn-Sham equations derived previously within the framework of the Nuclear-Electronic Orbital density functional theory (NEO-DFT). The EKS equations contain effective non-coulombic external potentials depending on parameters describing muon vibration, which are optimized during the solution of the EKS equations making muon KS orbital reproducible. It is demonstrated that the EKS equations are derivable from a certain class of effective electronic Hamiltonians through applying the usual Hohenberg-Kohn theorems revealing a duality between the NEO-DFT and the effective electronic-only DFT methodologies. The EKS equations are computationally applied to a small set of muoniated organic radicals and it is demonstrated that a mean effective potential maybe derived for this class of muonic species while an electronic basis set is also designed for the muon. These computational ingredients are then applied to muoniated ferrocenyl radicals, which had been previously detected experimentally through adding muonium atom to ferrocene. In line with previous computational studies, from the six possible species the staggered conformer, where the muon is attached to the exo position of the cyclopentadienyl ring, is deduced to be the most stable ferrocenyl radical.

An effective set of the Hartree-Fock (HF) equations are derived for electrons of the muonic systems, i.e., molecules containing a positively charged muon, conceiving the muon as a quantum oscillator, which are completely equivalent to the usual two-component HF equations used to derive stationary states of the muonic molecules. In these effective equations, a non-Coulombic potential is added to the orthodox coulomb and exchange potential energy terms, which describes the interaction of the muon and the electrons effectively and is optimized during the self-consistent field cycles. While in the two-component HF equations muon is treated as a quantum wave, in the effective HF equations it is absorbed into the effective potential and practically transformed into an effective potential field experienced by electrons. The explicit form of the effective potential depends on the nature of muon vibrations and is derivable from the basis set used to expand the muonic spatial orbital. The resulting effective Hartree-Fock equations are implemented computationally and used successfully, as a proof of concept, in a series of the muonic molecules containing all atoms from the second and third rows of the Periodic Table. To solve the algebraic version of the equations muon-specific gaussian basis sets are designed for both muon and surrounding electrons and it is demonstrated that the optimized exponents are quite distinct from those derived for the hydrogen isotopes. The developed effective HF theory is quite general and in principle can be used for any muonic system while it is the starting point for a general effective electronic structure theory that incorporates various types of quantum correlations into the muonic systems beyond the HF equations.

In a recent study it was suggested that the positively charged muon is capable of forming its own "atoms in molecule"s (AIM) in the muonic hydrogen-like molecules, composed of two electrons, a muon and one of the hydrogen isotopes, thus deserved to be placed in the Periodic Table [Phys. Chem. Chem. Phys. 16, 6602, 2014]. In present report, the capacity of the positively charged muon in forming its own AIM is considered in a large set of molecules replacing muons with all protons in the hydrides of the second and third rows of the Periodic Table. Accordingly, in a comparative study the wavefunctions of both sets of hydrides and their muonic congeners are first derived beyond the Born-Oppenheimer (BO) paradigm, assuming protons and muons as quantum waves instead of clamped particles. Then, the non-BO wavefunctions are used to derive the AIM structures of both hydrides and muonic congeners within context of the multi-component quantum theory of atoms in molecules. The results of the analysis demonstrate that muons are generally capable of forming their own atomic basins and the properties of these basins are not fundamentally different from those AIM containing protons. Particularly, the bonding modes in the muonic species seem to be qualitatively similar to their congener hydrides and no new bonding models is required to describe the bonding of muons to a diverse set of neighboring atoms. All in all, the positively charged muon is similar to proton from structural and bonding viewpoint and deserved to be placed in the same box of hydrogen in the Periodic Table. This conclusion is in line with a large body of studies on the chemical kinetics of the muonic molecules portraying the positively charged muon as a lighter isotope of hydrogen., Comment: 32 pages, 4 figures, supporting information

The Structural theory of chemistry introduces chemical/molecular structure as a combination of relative arrangement and bonding patterns of atoms in molecule. Nowadays, the structure of atoms in molecules is derived from the topological analysis of the quantum theory of atoms in molecules (QTAIM). In this context a molecular structure is varied by large geometrical variations and concomitant reorganization of electronic structure that are usually taking place in chemical reactions or under extreme hydrostatic pressure. In this report a new mode of structural variation is introduced within the context of the newly proposed multi-component QTAIM (MC-QTAIM) that originates from mass variation of nuclei. Accordingly, XCN and CNX series of species are introduced where X stands for a quantum particle with a unit of positive charge and a variable mass that is varied in discrete steps between the masses of proton and positron. Ab initio non-Born-Oppenheimer (non-BO) calculations are done on both series of species and the resulting non-BO wavefunctions are used for the MC-QTAIM analysis revealing a triatomic structure for the proton mass and a diatomic structure for the positron mass. In both series of species a critical mass between that of proton and positron mass is discovered where the transition from triatomic to diatomic structure takes place. This abrupt structural transformation has a topological nature resembling the usual phase transitions in thermodynamics. The discovered mass induced structural transformation is a hidden aspect of the Structural theory which is revealed only beyond the BO paradigm when nuclei are treated as quantum waves instead of clamped point charges., Comment: 24 pages, 3 figures

The multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis is done on methane, ethylene, acetylene and benzene as selected basic hydrocarbons. This is the first report on applying the MC-QTAIM analysis on polyatomic species. In order to perform the MC-QTAIM analysis, at first step the nuclear-electronic orbital method at Hartree-Fock level (NEO-HF) is used as a non-Born-Oppenheimer (nBO) ab initio computational procedure assuming both electrons and protons as quantum waves while carbon nuclei as point charges in these systems. The ab initio calculations proceed substituting all the protons of each species first with deuterons and then tritons. At the next step, the derived nBO wavefunctions are used for the "atoms in molecules" (AIM) analysis. The results of topological analysis and integration of atomic properties demonstrate that the MC-QTAIM is capable of deciphering the underlying AIM structure of all the considered species. Also, the results of the analysis for each isotopic composition are distinct and the fingerprint of the mass difference of hydrogen isotopes is clearly seen in both topological and AIM analyses. This isotopic distinction is quite unique in the MC-QTAIM and not recovered by the orthodox QTAIM that treats nuclei as clamped particles. The results of the analysis also demonstrate that each quantum nucleus that forms an atomic basin resides within its own basin. The confinement of quantum nuclei within a single basin is used to simplify the basic equations of the MC-QTAIM paving the way for future theoretical studies., Comment: 31 pages, 1 Figure

This report is a primarily survey on the chemical nature of some exotic species containing the positively charged muon and the muonic Helium, i.e., the negatively charged muon plus helium nucleus, as exotic isotopes of hydrogen, using the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis, employing ab initio non-Born-Oppenhiemer wavefunctions. Accordingly, the "atoms in molecules" analysis performed on various asymmetric exotic isotopomers of hydrogen molecule, recently detected experimentally [Science 331, 448 (2011)], demonstrates that both the exotic isotopes are capable of forming atoms in molecules and retaining the identity of hydrogen atom. Various derived properties of atomic basins containing muonic helium cast no doubt that apart from its short life time, it is a heavier isotope of hydrogen while the properties of basins containing the positively charged muon are more remote from those of the orthodox hydrogen basins, capable of appreciable donation of electrons as well as large charge polarization; however, with some tolerance, they may be categorized also as hydrogen basins though with a smaller electronegativity. All in all, present study also clearly demonstrates that the MC-QTAIM analysis is an efficient approach to decipher the chemical nature of species containing exotic constituents, hard to be elucidated by experimental and/or alternative theoretical schemes., Comment: 33 pages, 5 figures

In this contribution, pursuing our research program extending the atoms in molecules analysis into unorthodox domains, another key ingredient of the two-component quantum theory of atoms in molecules (TC-QTAIM) namely, the theory of localization/delocalization of quantum particles, is disclosed. The unified proposed scheme is able not only to deal with the localization/delocalization of electrons in/between atomic basins, but also to treat nuclei as well as exotic particles like positrons and muons equally. Based on the general reduced second order density matrices for indistinguishable quantum particles, the quantum fluctuations of atomic basins are introduced and then used as a gauge to quantify the localization/delocalization introducing proper indexes. The explicit mass-dependence of the proposed indexes is demonstrated and it is shown that a single localization/delocalization index is capable of being used for all kind of quantum particles regardless of their masses or charge content. For various non-Born-Oppenhiemer (non-BO) wavefunctions, including Hartree-product as well as singlet and triplet determinants, the indices are calculated and then employed to rationalize the localization/delocalization of particles in a series of four-body model systems consist of two electrons and two positively charged particles with variable mass. The ab initio FV-MC_MO derived non-BO wavefunctions for the four-body series are used for a comprehensive computational TC-QTAIM analysis, including topological analysis as well as basin integrations, in a wide mass region, m=10me-10^13me (me stands for electron mass), disclosing various traits in these series of species that are unique to the TC-QTAIM. Finally, it is concluded that the proposed localization/delocalization scheme is capable of quantifying quantum tunneling of nuclei for systems containing delocalized protons., Comment: 36 pages, 5 figures, supporting information