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Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence.
The use of molecular string representations for deep learning in chemistry has been steadily increasing in recent years. The complexity of existing string representations, and the difficulty in creating meaningful tokens from them, lead to the development of new string representations for chemical structures. In this study, the translation of chemical structure depictions in the form of bitmap images to corresponding molecular string representations was examined. An analysis of the recently developed DeepSMILES and SELFIES representations in comparison with the most commonly used SMILES representation is presented where the ability to translate image features into string representations with transformer models was specifically tested. The SMILES representation exhibits the best overall performance whereas SELFIES guarantee valid chemical structures. DeepSMILES perform in between SMILES and SELFIES, InChIs are not appropriate for the learning task. All investigations were performed using publicly available datasets and the code used to train and evaluate the models has been made available to the public.
The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER — Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field.
The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others. Here we present RanDepict, a toolkit for the creation of diverse sets of chemical structure depictions. The diversity of the image features is generated by making use of all available depiction parameters in the depiction functionalities of the CDK, RDKit, and Indigo. Furthermore, there is the option to enhance and augment the image with features such as curved arrows, chemical labels around the structure, or other kinds of distortions. Using depiction feature fingerprints, RanDepict ensures diversely picked image features. Here, the depiction and augmentation features are summarised in binary vectors and the MaxMin algorithm is used to pick diverse samples out of all valid options. By making all resources described herein publicly available, we hope to contribute to the development of deep learning-based OCSR systems.
Robot arms are one of many assistive technologies used by people with motor impairments. Assistive robot arms can allow people to perform activities of daily living (ADL) involving grasping and manipulating objects in their environment without the assistance of caregivers. Suitable input devices (e.g., joysticks) mostly have two Degrees of Freedom (DoF), while most assistive robot arms have six or more. This results in time-consuming and cognitively demanding mode switches to change the mapping of DoFs to control the robot. One option to decrease the difficulty of controlling a high-DoF assistive robot arm using a low-DoF input device is to assign different combinations of movement-DoFs to the device’s input DoFs depending on the current situation (adaptive control). To explore this method of control, we designed two adaptive control methods for a realistic virtual 3D environment. We evaluated our methods against a commonly used non-adaptive control method that requires the user to switch controls manually. This was conducted in a simulated remote study that used Virtual Reality and involved 39 non-disabled participants. Our results show that the number of mode switches necessary to complete a simple pick-and-place task decreases significantl when using an adaptive control type. In contrast, the task completion time and workload stay the same. A thematic analysis of qualitative feedback of our participants suggests that a longer period of training could further improve the performance of adaptive control methods.
Nowadays, robots are found in a growing number of areas where they collaborate closely with humans. Enabled by lightweight materials and safety sensors, these cobots are gaining increasing popularity in domestic care, where they support people with physical impairments in their everyday lives. However, when cobots perform actions autonomously, it remains challenging for human collaborators to understand and predict their behavior, which is crucial for achieving trust and user acceptance. One significant aspect of predicting cobot behavior is understanding their perception and comprehending how they “see” the world. To tackle this challenge, we compared three different visualization techniques for Spatial Augmented Reality. All of these communicate cobot perception by visually indicating which objects in the cobot’s surrounding have been identified by their sensors. We compared the well-established visualizations Wedge and Halo against our proposed visualization Line in a remote user experiment with participants suffering from physical impairments. In a second remote experiment, we validated these findings with a broader non-specific user base. Our findings show that Line, a lower complexity visualization, results in significantly faster reaction times compared to Halo, and lower task load compared to both Wedge and Halo. Overall, users prefer Line as a more straightforward visualization. In Spatial Augmented Reality, with its known disadvantage of limited projection area size, established off-screen visualizations are not effective in communicating cobot perception and Line presents an easy-to-understand alternative.
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day.
We study the dynamics of a quantum two-state system driven through an avoided crossing under the influence of a super-Ohmic environment. We determine the Landau–Zener probability employing the numerical exact quasi-adiabatic path integral and a Markovian weak coupling approach. Increasing the driving time in the numerical protocol, we find converged results which shows that super-Ohmic environments only influence the Landau Zener probability within a finite crossing time window. This crossing time is qualitatively determined by the environmental cut-off energy. At weak coupling, we show that the Markovian weak coupling approach provides an accurate description. Since pure dephasing of a super-Ohmic bath is non-Markovian, this highlights that pure dephasing hardly influences the Landau–Zener probability. The finite crossing time window, thus, results from the suppression of relaxation once the energy splitting exceeds the environmental cut-off energy.