Soft Docking Research Articles

Progress in protein pre-training models integrating structural knowledge

The AI revolution, sparked by natural language and image processing, has brought new ideas and research paradigms to the field of protein computing. One significant advancement is the development of pre-training protein language models through self-supervised learning from massive protein sequences. These pre-trained models encode various information about protein sequences, evolution, structures, and even functions, which can be easily transferred to various downstream tasks and demonstrate robust generalization capabilities. Recently, researchers have further developed multimodal pre-trained models that integrate more diverse types of data. The recent studies in this direction are summarized and reviewed from the following aspects in this paper. Firstly, the protein pre-training models that integrate protein structures into language models are reviewed: this is particularly important, for protein structure is the primary determinant of its function. Secondly, the pre-trained models that integrate protein dynamic information are introduced. These models may benefit downstream tasks such as protein-protein interactions, soft docking of ligands, and interactions involving allosteric proteins and intrinsic disordered proteins. Thirdly, the pre-trained models that integrate knowledge such as gene ontology are described. Fourthly, we briefly introduce pre-trained models in RNA fields. Finally, we introduce the most recent developments in protein designs and discuss the relationship of these models with the aforementioned pre-trained models that integrate protein structure information.

Subduction Initiation at the Solomon Back‐Arc Basin: Contributions From Both Island Arc Rheological Strength and Oceanic Plateau Collision

AbstractIt is generally accepted that the subduction polarity reversal (SPR) results from the strong collision of two plates. Yet, the SPR of the Solomon Back‐arc Basin is started in the “soft docking” stage, and the mechanism by which the “soft docking” induced subduction initiation (SI) remains elusive. We find that the mass depletion of the plateau influences the evolution of the subduction patterns during SI. And the island arc rheological strength affects the development of the shear zone between an island arc and back‐arc basin which favors SI. What's more, with the increase of the rheological strength difference, the SI is more easily to occur, and the contribution of the plateau collision to SI weakens. Hence, by combining the available geological evidence, we suggest that the Solomon Island Arc rheological strength and the Ontong‐Java plateau collision jointly controlled the SI during the “soft docking” stage.

Intracavitary Electron FLASH Radiotherapy in a Canine Cancer Patient With Oral Malignant Melanoma

Studies of electron FLASH radiotherapy (FLASH-RT) in companion animals are being conducted at several institutions. High energy electron beams are generally suitable for treatment of superficial cancers, but of limited use for deep-seated tumors. In this case report, the feasibility of intracavitary electron FLASH-RT is demonstrated.A canine cancer patient with a large oral malignant melanoma in the caudal part of the hard palate was palliatively treated with FLASH-RT at a modified clinical linear accelerator, using a cylindrical PMMA applicator (length 200 mm, inside diameter 50 mm). The patient had a poor prognosis, with an estimated survival of two weeks and no other available treatment options. A dose of 35 Gy was delivered to the depth of dose maximum in 26 pulses with a pulse dose rate of 4.5•105 Gy/s. The average dose rate was 280 Gy/s, corresponding to a total beam-on time of 125 months. One month after the treatment, the tumor was re-irradiated, using the same treatment parameters. The treatment head of the LINAC was fitted with a short electron applicator holder with a Cerrobend collimator at 65 cm from the source. The cylindrical PMMA applicator was aligned perpendicularly to the Cerrobend collimator using soft docking with a 1 cm gap. Prior to the treatments, the 2D dose distribution of the FLASH beam exiting the PMMA applicator was measured with radiographic film. In addition, the dosimetric effect of misalignment between the collimator and the electron applicator was studied based on intentional misalignments of 2.5°, 5°, 2.5 mm, and 5 mm.A partial response of the tumor and clinical improvement of the patient was observed two weeks after the first treatment. A hypopigmented area in the hard palate was observed, consistent with a grade 1 adverse event, but there were no signs of mucositis or reports of patient discomfort. However, due to the thickness of the tumor (> 3 cm), the posterior part only received a limited dose, and the tumor was still obstructing the airflow at one month post treatment. At this time, a second treatment was administered with limited normal tissue receiving full dose from both treatments. At one month post the second treatment, a partial response was achieved, and no evidence of side effects other than hypopigmentation was observed. The patient was euthanized 2.5 months after the initial therapy due to progressive disease involving the oropharynx. The dosimetric evaluation showed that a conformal dose distribution could be obtained by delivering the electron beam using a cylindrical PMMA applicator. Misalignments between the applicator and the collimator were shown to result in reduced dose homogeneity.This case report of a canine cancer patient, with a large oral malignant melanoma in the caudal part of the hard palate, has demonstrated the feasibility of intracavitary electron FLASH-RT. Two treatments of 35 Gy each, resulted in prolonged survival and increased quality-of-life.

Disturbance Observer-Based Nonsingular Terminal Sliding Mode Control for Spacecraft Electromagnetic Docking

This paper presents a novel nonlinear sliding mode control scheme that combines on-line model modification, a nonlinear sliding mode controller, and a disturbance observer to solve the essential problems in spacecraft electromagnetic docking control, such as model uncertainties, unknown external disturbances, and inherent strong nonlinearity and coupling. An improved far-field model of electromagnetic force which is much more accurate than the widely used far-field model is proposed to enable the model parameters to be on-line self-adjusting. Then, the relationship between magnetic moment allocation and energy consumption is derived, and the optimal direction of the magnetic moment vector is obtained. Based on the proposed improved far-field model and the research results of magnetic moment allocation law, a fast-nonsingular terminal mode controller driven by a disturbance observer is designed in the presence of model uncertainties and external disturbances. The proposed control method is guaranteed to be chattering-free and to possess superior properties such as finite-time convergence, high-precision tracking, and strong robustness. Two simulation scenarios are conducted to illustrate the necessity of modifying the far-field model and the effectiveness of the proposed control scheme. The simulation results indicate the realization of electromagnetic soft docking and validate the merits of the proposed control scheme. In the end of this paper, some conclusions are drawn.

Trajectory optimization for Rendezvous and Docking using Nonlinear Model Predictive Control

In this paper, MPC based constrained trajectory optimization algorithms has been applied for rendezvous and docking of two small satellites to achieve precise terminal soft docking with path constraints. A receding horizon MPC has been applied in order to reduce the computational load. The constraints such as thrust magnitude limit, chaser spacecraft positioning with in Line-of-Sight (LOS) while approaching the target spacecraft, and terminal velocity limit for soft-docking are considered. In addition debris avoidance constraints are considered and obstacles are assumed as spheres for simplicity. Nonlinear MPC optimization problem with constraints is solved by Sequential Quadratic Program (SQP) technique. The robustness of this control has been verified using nonlinear dynamics with perturbation model.

Strategy for the realization of soft docking with space debris by using a tether system

This study focuses on the dynamics of a rendezvous of a tug and large space debris connected by a viscoelastic tether. It is assumed that control is realized by changing the length of the tether. The goal is to study the dynamic of the maneuver of the rendezvous and to find the ways, which allow one to reduce the oscillation of the tether. The obtained results can be applied as applications for the tasks of implement rendezvous of two bodies using the tether.

Control method of high-precision soft docking of moving objects using low-accurate values of relative speed and distance

An analytical expression is constructed for the main vector of control forces, providing the pursuit of an unpredictably moving object with the purpose of shockless high-precision docking with it or its shockless capture in a finite period of time using low-accurate values of the measured relative velocity and distance. The constructed control ensures the pursuit of the goal on the principle of proportional navigation, brings the pursuing point in a finite time to the “initial position”, which provides the possibility of reducing the distance to the target, and then ensures the subsequent sliding movement of a point from the “initial position” along the line of discontinuity to the origin of the phase coordinate system. To solve the problem with large relative measurement errors, it was proposed to construct a continuous part of the control force, which provides the process of sliding movement of the representative point along the line of discontinuity, as a function, depending on the current values of the relative velocity and distance. The article also analyzes the issue related to the expansion of the class of control forces by introducing some positive parameter in the expression for the continuous component of the control force. The choice of this parameter affects the duration of the rapprochement of the pursued and pursuing points.

Soft docking with damping of two spacecraft using a tether

The paper focuses on the dynamics of a rendezvous of a chaser and a large space debris connected by a viscoelastic tether. It is assumed that constant thrust acts on the chaser and a control is realized by changing the length of the tether. The goal is to find the control law that provides a soft docking of two bodies on an orbit. Also, we considered a three-body system with an additional damping device. The results are expected to be applied for controlling a rendezvous of two bodies using a tether.

Dynamics of Reusable Tether System with Sliding Bead Capsule for Deorbiting Small Payloads

This paper is devoted to the problem of a small payload delivery from an orbit to the Earth by a reusable space tether system consisting of a satellite in circular orbit, a tether, and a bottom module. The payload is placed in a dynamically symmetrical bead capsule, which can slide along the tether. Three scenarios for the payload delivery are proposed: an uncontrolled sliding of the capsule, a soft docking with the bottom module following separation, and a soft docking and the tether spin-up. The objectives of the paper are developing a mathematical model of the system, conducting a numerical analysis of its behavior, and comparison of the descent scenarios. The mathematical model that takes into account the friction between the bead capsule and the inextensible three-segment tether is developed using the Lagrange formalism. The results show that high-frequency oscillations of the bead capsule, its sharp stop, and the tether tangling can be observed. The scenario comparison allows concluding that the third scenario is more effective in terms of the capsule’s orbit perigee radius minimizing, but it requires considerable time. The first scenario, compared with the second one, yields a significant decrease in perigee altitude, but it is more dangerous.

Coupled orbital and attitude control in spacecraft rendezvous and soft docking

This paper discusses coupled orbital and attitude control in spacecraft rendezvous and soft docking. The target spacecraft orbit can be either circular or elliptic. The high-fidelity model for this problem is intrinsically a nonlinear system but can be viewed as a linear time-varying system. Therefore, a model predictive control-based design is proposed to deal with the time-varying feature of the problem. A robust pole assignment method is used in the model predictive control-based design because of the following merits and/or considerations: (a) no oscillation crossing the horizontal line for the relative position and relative attitude (between the target and the chaser spacecraft) to achieve soft docking by placing all closed-loop poles in the negative real axis of the complex plan, which will avoid collision between the target and the chaser in the docking stage, (b) fast online computation, (c) measurement and control error tolerance, and (d) disturbance rejection. This paper will discuss these considerations and merits and use some design examples to demonstrate that the desired performance is indeed achieved.

Analysis and design of parameters in soft docking of micro/small satellites

Although substantial research has been conducted on the soft docking problem, the design of the docking mechanism is always conducted using experience. The challenge for conducting factor analysis and design lies in an accurate theoretical model, and the evaluation criteria of a successful docking. In this paper, the soft docking model of micro/small satellites is proposed using an analytical method and validated using a commercial FE package. The evaluation criterion of a successful docking is defined by considering the operational principle of the capturing mechanism used in micro (or small) paired satellites. The effect of the parameters on the soft docking result is discussed and their value domains are designed based on our proposed criteria of a successful docking.

Towards a standardized grasping and refuelling on-orbit servicing for geo spacecraft

Exploitation of space must benefit from the latest advances in robotics. On-orbit servicing is a clear candidate for the application of autonomous rendezvous and docking mechanisms. However, during the last three decades most of the trials took place combining extravehicular activities (EVAs) with telemanipulated robotic arms. The European Space Agency (ESA) considers that grasping and refuelling are promising near-mid-term capabilities that could be performed by servicing spacecraft. Minimal add-ons on spacecraft to enhance their serviceability may protect them for a changing future in which satellite servicing may become mainstream.ESA aims to conceive and promote standard refuelling provisions that can be installed in present and future European commercial geostationary orbit (GEO) satellite platforms and scientific spacecraft. For this purpose ESA has started the ASSIST activity addressing the analysis, design and validation of internal provisions (such as modifications to fuel, gas, electrical and data architecture to allow servicing) and external provisions (such as integrated berthing fixtures with peripheral electrical, gas, liquid connectors, leak check systems and corresponding optical and radio markers for cooperative rendezvous and docking). This refuelling approach is being agreed with European industry (OHB, Thales Alenia Space) and expected to be consolidated with European commercial operators as a first step to become an international standard; this approach is also being considered for on-orbit servicing spacecraft, such as the SpaceTug, by Airbus DS.This paper describes in detail the operational means, structure, geometry and accommodation of the system. Internal and external provisions will be designed with the minimum possible impact on the current architecture of GEO satellites without introducing additional risks in the development and commissioning of the satellite. End-effector and berthing fixtures are being designed in the range of few kilos and linear dimensions around 15cm. A central mechanical part is expected to perform first a soft docking followed by a motorized retraction ending during a hard docking phase using aligning pins. Mating and de-mating will be exhaustively analysed to ensure robustness of operations. Leakage-free valves would allow for the transfer of fuel to the serviced spacecraft. The validation of the ASSIST system through dedicated environmental tests in a vacuum chamber together with dynamic testing using an air-bearing table will allow for the demonstration of concept feasibility and its suitability for becoming a standard of the on-orbit space industry.

DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP.If there are significant matches, the holoenzymeand the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already 'plastic' binding site. Thus, DOCLASP presents a method for 'soft docking' ligands to proteins with low computational requirements.

DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP. If there are significant matches, the holoenzyme and the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already ’plastic’ binding site. Thus, DOCLASP presents a method for ’soft docking’ ligands to proteins with low computational requirements.

IMPACT DYNAMICS STUDY OF SOFT CONE BASED ON SPACE PROBE-CONE DOCKING MECHANISM

In this paper, a soft cone composed of the thin-walled plates as a buffer system based on space probe-cone docking mechanism for the medium and small-sized spacecraft in the process of docking is presented. The theoretical model of docking impact dynamics is derived according to Lagrange Analytical Mechanics theory and Hertz contact theory. Runge-Kutta numerical method is used to solve this theoretical model. Results of the theoretical model show a good agreement with the experimental and ANSYS/LS-DYNA simulation results. In addition, the influence of soft cone parameters on impact process is discussed based on theoretical model systemically. It is shown that the soft cone can help to greatly reduce the maximal impact force and absorb lots of impact energy through deformation in the linear elastic range. Keywords   ,, ,

Guidance, Navigation, and Control for Docking of Two Cubic Blimps

This paper focuses on the development of guidance, navigation and control for the docking of two cubic blimps, named Tryphons. The chaser and target Tryphons are assumed to be brought sufficiently close together through a rendezvous stage, where the docking stage then begins and the target is kept stationary. An ARtag fiducial marker system is used for position based visual servoing control with a glideslope guidance algorithm for soft docking. The physical docking of the Tryphons is achieved through contact of the protruder and receiver ends of the two electromagnetic docking mechanisms. Simulations of the docking process are carried out in the open source simulation software Gazebo, using Robot Operating System (ROS) and virtual sensors.

Accurate and consistent FE modelling of soft docking of micro/nano paired-satellites using variational inequalities

Time-dependent variational inequality-based formulations describing the behavior of elastodynamic contact problems have been used to model the soft docking of micro/nano paired-satellites. The solution strategy is based upon the iterative use of two subproblems. In the first subproblem, the technique of Quadratic Programming was used to predict the contact surface and the stresses acting on it. In the second subproblem, the technique of Lagrange multipliers was used to impose the boundary conditions and contact constraint obtained in step I. The solution accounts for the effect of friction through the use of an appropriate regularization technique in the virtual work expressions. The accuracy of the proposed variational inequality (VI) model of the soft docking process is validated by comparing the VI results with commercially available software. Finally, the effects of the bending stiffness of the docking probe, the friction between the candidate contact surfaces are investigated and analyzed using the newly developed model.

SU‐E‐T‐324: Dosimetric Evaluation of Soft Docking Sensitivity On An INTRAOP Mobetron IORT Device

Purpose:To assess Mobetron soft docking sensitivity thresholds by measuring dosimetric changes resulting from incremental displacements of isolated docking parameters.Methods:The Mobetron device uses a sensitive optical system to establish alignment of the collimator with a treatment cone. To assess the limits of this sensitivity, we isolated each docking parameter (transverse, tilt, and vertical) and varied each incrementally within the docking display range. Transverse displacements ranged in 1mm increments from 0.0cm to 0.4cm. Profiles were taken at dmax for each energy (6MeV, 9MeV and 12MeV) along the direction of displacement. Angular displacements ranged in 0.1° increments from 0.0° to 0.4°. Baseline corrected profiles were assessed with a point‐by‐point symmetry analysis and a max‐min flatness metric (90%‐1cm). Vertical displacements ranged from 0.0cm to 0.4cm in 1mm increments. Output factors were compared by % difference from baseline and PDDs were measured at each vertical displacement to assess changes in dmax and R50 values.Results:For 1mm lateral displacements, symmetry/flatness deviations for the 10cm cone were +0.48%/+0.38% at 6MeV, +0.95%/+1.04% at 9MeV, and +1.77%/+1.96% at 12MeV. Profiles in the direction orthogonal to gantry motion measured +0.99%/+1.29% symmetry/flatness changes at 4mm displacement. For 0.10 angular displacements, symmetry/flatness deviations for the 10cm cone were +0.07%/+0.05% at 6MeV +0.23%/+0.33% at 9MeV, and +0.34%/+0.59% at 12MeV. The 3cm and 6cm cones were less sensitive to transverse and angular displacements. At 4mm vertical displacement, the 3cm cone differed from baseline by 3.02%, 2.30%, and 2.42% (6MeV, 9MeV, and 12MeV respectively). Maximum combined deviation from baseline in quadrature for one extra docking light (half sensitivity) in each displacement vector was >2%.Conclusion:For transverse and vertical displacements, the docking sensitivity range is adequate to ensure flatness and symmetry differences <1.0%. However, for angular displacements, all energies with the 10cm cone deviated at or beyond this threshold.

К задаче управления маломерным свободнолетающим космическим роботом

Рассматривается возможность использования принципа обратной связи в решении задачи управления свободнолетающим космическим роботом в режиме манипуляционного функционирования. В рамках данного подхода вводится математическая модель космического манипуляционного робота (КМР), содержащая в явном виде координаты отклонения схвата от цели в инерциальном пространстве. Предлагается алгоритм вычисления оценок указанных координат при наличии информации о направлении на цель и расстоянии до нее, получаемой с помощью размещенной на корпусе КМР видеокамеры со встроенным дальномером. Решается задача формирования алгоритма управления манипуляционным захватом цели в инерциальном пространстве. Приводится пример компьютерного моделирования динамики космического робота, подтверждающий работоспособность предложенного алгоритма.

Angular-Momentum Management of Spacecraft Electromagnetic Docking Considering the Earth’s Magnetic Field

The spacecraft electromagnetic docking technique has distinct advantages, which could enable soft docking for more-frequent on-orbit servicing missions. When electromagnets are used, two kinds of magnetic torque exist: one due to the electromagnet and the other due to the Earth’s magnetic field. These affect the attitude motion, which may results in angular-momentum saturation and attitude control-system failure. In this paper, based on the requirements of relative trajectory control, an effective and robust angular-momentum management approach is proposed to mediate the effects caused by these two kinds of magnetic torque. This approach, including two operating modes: a “normal mode” and an “angular-momentum-reduction mode”, uses the Earth’s magnetic field to counteract the effect of inter-satellite electromagnetic torque and applies the extended state observer to estimate the combined disturbance for feedback control. The angular-momentum management of three spacecraft docking scenarios (-bar, -bar, and -bar) are studied, and the resulting magnetic-moment solutions are also given. At last, some simulation results are presented to validate the feasibility of this proposed robust angular-momentum management approach, and several useful conclusions follow.