Measurement errors in visual servoing

Abstract — In recent years, a number of hybrid visual servoing control algorithms have been proposed and evaluated. For some time now, it has been clear that classical control approaches — image and position based —- have some inherent problems. Hybrid approaches try to combine them in order to overcome these problems. However, most of the proposed approaches concentrate mainly on the design of the control law, neglecting the issue of errors resulting from the sensory system. This work deals with the effect of measurement errors in visual servoing. The particular contribution of this paper is the analysis of the propagation of image error through pose estimation and visual servoing control law. We have chosen to investigate the properties of the vision system and their effect to the performance of the control system. Two approaches are evaluated: i) position, and ii) 2 1/2 D visual servoing. We believe that our evaluation offers a valid tool to build and analyze hybrid control systems based on, for example, switching [1] or partitioning [2]. I

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

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Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction

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Multiobjective optimization identifies cancer-selective combination therapies

Author summary Cancer is diagnosed in nearly 40% of people in the U.S at some point during their lifetimes. Despite decades of research to lower cancer incidence and mortality, cancer remains a leading cause of deaths worldwide. Therefore, new targeted therapies are required to further reduce the death rates and toxic effects of treatments. Here we developed a mathematical optimization framework for finding cancer-selective treatments that optimally use drugs and their combinations. The method uses multiobjective optimization to identify drug combinations that simultaneously show maximal therapeutic potential and minimal non-selectivity, to avoid severe side effects. Our systematic search approach is applicable to various cancer types and it enables optimization of combinations involving both targeted therapies as well as standard chemotherapies. Combinatorial therapies are required to treat patients with advanced cancers that have become resistant to monotherapies through rewiring of redundant pathways. Due to a massive number of potential drug combinations, there is a need for systematic approaches to identify safe and effective combinations for each patient, using cost-effective methods. Here, we developed an exact multiobjective optimization method for identifying pairwise or higher-order combinations that show maximal cancer-selectivity. The prioritization of patient-specific combinations is based on Pareto-optimization in the search space spanned by the therapeutic and nonselective effects of combinations. We demonstrate the performance of the method in the context of BRAF-V600E melanoma treatment, where the optimal solutions predicted a number of co-inhibition partners for vemurafenib, a selective BRAF-V600E inhibitor, approved for advanced melanoma. We experimentally validated many of the predictions in BRAF-V600E melanoma cell line, and the results suggest that one can improve selective inhibition of BRAF-V600E melanoma cells by combinatorial targeting of MAPK/ERK and other compensatory pathways using pairwise and third-order drug combinations. Our mechanism-agnostic optimization method is widely applicable to various cancer types, and it takes as input only measurements of a subset of pairwise drug combinations, without requiring target information or genomic profiles. Such data-driven approaches may become useful for functional precision oncology applications that go beyond the cancer genetic dependency paradigm to optimize cancer-selective combinatorial treatments.Peer reviewe

To catalyze or not to catalyze: elucidation of the subtle differences between the hexameric capsules of pyrogallolarene and resorcinarene

The closely related, self-assembled resorcinarene and pyrogallolarene capsules display contrasting and puzzling encapsulation behaviors. Herein, we elucidate the reasons for these differences by combining experimental studies and DFT calculations. Furthermore, we report that, in contrast to the resorcinarene capsule, the pyrogallolarene derivative is not capable of catalyzing reactions with cationic transition states. The molecular mechanisms responsible for these observations are probed in detail

Benchmarking the performance of time-dependent density functional theory methods on biochromophores

Quantum chemical calculations are important for elucidating light-capturing mechanisms in photobiological systems. The time-dependent density functional theory (TDDFT) has become a popular methodology because of its balance between accuracy and computational scaling, despite its problems in describing, for example, charge transfer states. As a step toward systematically understanding the performance of TDDFT calculations on biomolecular systems, we study here 17 commonly used density functionals, including seven long-range separated functionals, and compare the obtained results with excitation energies calculated at the approximate second order coupled-cluster theory level (CC2). The benchmarking set includes the first five singlet excited states of 11 chemical analogues of biochromophores from the green fluorescent protein, rhodopsin/bacteriorhodopsin (Rh/bR), and the photoactive yellow protein. We find that commonly used pure density functionals such as BP86, PBE, M11-L, and hybrid functionals with 20-25% of Hartree-Fock (HF) exchange (B3LYP, PBE0) have a tendency to consistently underestimate vertical excitation energies (VEEs) relative to the CC2 values, whereas hybrid density functionals with around 50% HF exchange such as BHLYP, PBE50, and M06-2X and long-range corrected functionals such as CAM-B3LYP, omega PBE, omega PBEh, omega B97X, omega B97XD, BNL, and M11 overestimate the VEEs. We observe that calculations using the CAM-B3LYP and omega PBEh functionals with 65% and 100% long-range HF exchange, respectively, lead to an overestimation of the VEEs by 0.2-0.3 eV for the benchmarking set. To reduce the systematic error, we introduce here two new empirical functionals, CAMh-B3LYP and omega hPBE0, for which we adjusted the long-range HF exchange to 50%. The introduced parameterization reduces the mean signed average (MSA) deviation to 0.07 eV and the root mean square (rms) deviation to 0.17 eV as compared to the CC2 values. In the present study, TDDFT calculations using the aug-def2-TZVP basis sets, the best performing functionals relative to CC2 are omega hPBE0 (rms = 0.17, MSA = 0.06 eV); CAMh-B3LYP (rms = 0.16, MSA = 0.07 eV); and PBE0 (rms = 0.23, MSA = 0.14 eV). For the popular range-separated CAM-B3LYP functional, we obtain an rms value of 0.31 eV and an MSA value of 0.25 eV, which can be compared with the rms and MSA values of 0.37 and -0.31 eV, respectively, as obtained at the B3LYP level.Peer reviewe

On the validity of perturbative studies of the electroweak phase transition in the Two Higgs Doublet model

Making use of a dimensionally-reduced effective theory at high temperature, we perform a nonperturbative study of the electroweak phase transition in the Two Higgs Doublet model. We focus on two phenomenologically allowed points in the parameter space, carrying out dynamical lattice simulations to determine the equilibrium properties of the transition. We discuss the shortcomings of conventional perturbative approaches based on the resummed effective potential — regarding the insufficient handling of infrared resummation but also the need to account for corrections beyond 1-loop order in the presence of large scalar couplings — and demonstrate that greater accuracy can be achieved with perturbative methods within the effective theory. We find that in the presence of very large scalar couplings, strong phase transitions cannot be reliably studied with any of the methods.Peer reviewe

Host--parasite models on graphs

The behavior of two interacting populations, ``hosts''and ``parasites'', is investigated on Cayley trees and scale-free networks. In the former case analytical and numerical arguments elucidate a phase diagram, whose most interesting feature is the absence of a tri-critical point as a function of the two independent spreading parameters. For scale-free graphs, the parasite population can be described effectively by Susceptible-Infected-Susceptible-type dynamics in a host background. This is shown both by considering the appropriate dynamical equations and by numerical simulations on Barab\'asi-Albert networks with the major implication that in the termodynamic limit the critical parasite spreading parameter vanishes.Comment: 10 pages, 6 figures, submitted to PRE; analytics redone, new calculations added, references added, appendix remove

Absorption shifts of diastereotopically ligated chlorophyll dimers of photosystem I

The light-harvesting chlorophyll (Chl) molecules of photosynthetic systems form the basis for light-driven energy conversion. In biological environments, the Chl chromophores occur in two distinct diastereotopic configurations, where the alpha and beta configurations have a magnesium-ligating histidine residue and a 17-propionic acid moiety on the opposite side or on the same side of the Chl ring, respectively. Although beta-ligated Chl dimers occupy conserved positions around the reaction center of photosystem I (PSI), the functional relevance of the alpha/beta configuration of the ligation is poorly understood. We employ here correlated ab initio calculations using the algebraic-diagrammatic construction through second order (ADC(2)) and the approximate second-order coupled cluster (CC2) methods in combination with the reduced virtual space (RVS) approach in studies of the intrinsic excited-state properties of alpha-ligated and beta-ligated Chl dimers of PSI. Our ab initio calculations suggest that the absorption of the alpha-ligated reaction-center Chl dimer of PSI is redshifted by 0.13-0.14 eV in comparison to the beta-ligated dimers due to combined excitonic coupling and strain effects. We also show that time-dependent density functional theory (TDDFT) calculations using range-separated density functionals underestimate the absorption shift between the alpha- and beta-ligated dimers. Our findings may provide a molecular starting point for understanding the energy flow in natural photosynthetic systems, as well as a blueprint for developing new molecules that convert sunlight into other forms of energy.Peer reviewe