Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Variable gain haptic coupling for molecular simulation

Molecularinteractionstypicallyhaveahighdynamicrange(HDR), combining short-range stiff repulsive effects with long-range, soft attractive and repulsive terms. As a result, faithful haptic renderingofsuchmolecularinteractionsisbothimportantanddifficult,in particularinapplicationswherethepreciseperceptionofmolecular forces is necessary (e.g. in molecular docking simulations). Traditionally,teleoperationcouplingusingconstantgaincontrolschemes have limited applications since they are unable to transmit to users low attractive forces without truncating repulsive ones. Furthermore, constant scaling displacement induces either instability or time-consuming experiments (displacements are slow), which deteriorates the ease of manipulation. In this paper, we describe a variable gain haptic coupling method specifically designed to render high dynamic range (molecular) forces. The proposed method is evaluated by user tests on an experiment involving two water molecules. We observe that variable force amplification is widely appreciated, whereas variable displacement scaling is appropriated only for users familiar with haptic manipulation. A complex experiment on a HIV molecule is carried out using this variable gain system. Advantages and limitations of thisapproach arediscussed.

Haptic molecular simulation based on force control

International audienceIn this paper, force control is proposed to connect a molecular simulator to a haptic device. Most of the works dealing with this kind of simulators use position control to manipulate the molecules, with major stability concerns. These two control modes are compared in terms of adequacy with the molecular simulator. Stability with respect to the scaling coefficients introduced to connect the macro and the nanoworlds is also considered. The theoretical results and the experiments carried out confirm that position control is sensitive to the gain tuning. Force control enables to get stable force feedback for varying gains, and is thus a promising coupling to perform manipulations on complex molecular systems

Variable gain haptic coupling for molecular simulation

International audienceMolecular interactions typically have a high dynamic range (HDR), combining short-range stiff repulsive effects with long-range, soft attractive and repulsive terms. As a result, faithful haptic rendering of such molecular interactions is both important and difficult, in particular in applications where the precise perception of molecular forces is necessary (e.g. in molecular docking simulations). Traditionally, teleoperation coupling using constant gain control schemes have limited applications since they are unable to transmit to users low attractive forces without truncating repulsive ones. Furthermore, constant scaling displacement induces either instability or time-consuming experiments (displacements are slow), which deteriorates the ease of manipulation. In this paper, we describe a variable gain haptic coupling method specifically designed to render high dynamic range (molecular) forces. The proposed method is evaluated by user tests on an experiment involving two water molecules. We observe that variable force amplification is widely appreciated, whereas variable displacement scaling is appropriated only for users familiar with haptic manipulation. A complex experiment on a HIV molecule is carried out using this variable gain system. Advantages and limitations of this approach are discussed

Molecular Docking With Haptic Guidance and Path Planning

Molecular docking drives many important biological processes including immune system recognition and cellular signalling. Molecular docking occurs when molecules interact and form complexes. Predicting how specific molecules dock with each other using computational methods has several applications including understanding diseases and virtual drug design. The goal of molecular docking prediction is to find the lowest energy ligand states. The lower the energy state, the more probable the state is docked and biologically feasible. Existing automated computational methods can be time intensive, especially when using direct molecular dynamic simulation. One way to reduce this computational cost is to use more coarse-grained models that approximate molecular docking. Coarse-grained molecular docking prediction is generally performed first by sampling ligand states using a rigid body model or a partial flexibility model to reduce computation, then by screening the states. The ligand states are screened using a scoring function, usually a potential energy function for interactions between the atoms in each molecule. Ligand state search algorithms still have a significant computational cost if a large portion of the state space is to be explored. Instead of an automated ligand state search method, a human operator can explore the state space instead. Haptic force feedback devices providing guidance based off the energy function can aid the human operator. Haptic-guidance has been used for immersive semi-automatic and manual molecular docking on a single operator scale. A large amount of ligand state space can be explored with many human operators in a crowdsourced effort. Players in an interactive crowdsourced protein folding puzzle game have aided in finding protein folding prediction solutions, but without haptic feedback. Interactive crowdsourced methods for molecular docking prediction is not well-explored, although non-interactive crowdsourced systems such as Folding@home can be adapted for molecular docking. This thesis presents a molecular docking game that produces low potential energy ligand states and motion paths with crowdsource scale potential. In an exploratory user study, participants were assigned four different types of devices with varying levels of haptic guidance to search for a potentially docked ligand state. The results demonstrate some effect on the type of device and haptic guidance seen in the study. However, differences are minimal thus potentially enabling the use of commonly available input devices in a crowdsourced setting

Vision-Augmented molecular dynamics simulation of nanoindentation

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London.This thesis has contributed to the literature by providing a pathway to simplify the process of carrying out molecular dynamics simulation. As a part of the investigation, a user-friendly vision-augmented technique was developed to set up and carry out atomistic simulations using hand-gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of preparing and carrying out molecular dynamics simulations in a more intuitive way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by performing parallel molecular dynamics simulations to study (i) crystal anisotropy of a diamond cubic substrate (crystalline silicon) using nanoindentation with a long-range (Screened bond order) Tersoff potential and (ii) crystal anisotropy of a body centre cubic metal (tantalum) using nanoindentation with an Embedded Atomic Method (EAM) type potential. The MD data was post-processed to reveal size effects observed in anisotropy of both these materials, namely, silicon and tantalum. The value of hardness and elastic modulus obtained from the MD data was found in accordance with what has been discovered previously by experiments, thereby validating the simulations. Based on this, it is anticipated that the proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.King Abdullah bin Abdul-Aziz Al- Saud Ministry of Higher Education and Northern Borders University, Kingdom of Saudi Arabi

Haptic feedback for molecular simulation

International audienceIn this paper, a new tool dedicated to the analysis and the conception of molecules is presented. It is composed of an adaptive simulation software and a haptic device used to interact with molecules while feeling either the forces applied by the environment or the internal forces. The adaptive articulated body algorithm allows fast simulations of complex flexible molecules. To handle the coupling with the force feedback device, two different control schemes designed for nanoscale applications and providing high transparency rendering are proposed and compared. The system we propose is highly flexible since either a single rigid body or the entire molecule can be manipulated via the haptic device. The user can choose between setting a desired position/orientation of the molecule, or apply forces/torques to manipulate it. It allows the operator to control each stage of the design process of new molecular structures. The validity of this tool is demonstrated through examples of haptic interaction between the HIV protease and its inhibitors, and unfolding one of these drugs

Haptic feedback for molecular simulation

Abstract—In this paper, a new tool dedicated to the analysis and the conception of molecules is presented. It is composed of an adaptive simulation software and a haptic device used to interactwithmoleculeswhilefeelingeithertheforcesappliedby the environment or the internal forces. The adaptive articulated body algorithm allows fast simulations of complex flexible molecules. To handle the coupling with the force feedback device, two different control schemes designed for nanoscale applications and providing high transparency rendering are proposed and compared. The system we propose is highly flexible since either a single rigid body or the entire molecule can be manipulated via the haptic device. The user can choose between setting a desired position/orientation of the molecule, or apply forces/torques to manipulate it. It allows the operator to control each stage of the design process of new molecular structures. The validity of this tool is demonstrated through examples of haptic interaction between the HIV protease and its inhibitors, and unfolding one of these drugs. I