Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500 Hz to 1 kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2 ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates

Efficient And Scalable Evaluation Of Continuous, Spatio-temporal Queries In Mobile Computing Environments

A variety of research exists for the processing of continuous queries in large, mobile environments. Each method tries, in its own way, to address the computational bottleneck of constantly processing so many queries. For this research, we present a two-pronged approach at addressing this problem. Firstly, we introduce an efficient and scalable system for monitoring traditional, continuous queries by leveraging the parallel processing capability of the Graphics Processing Unit. We examine a naive CPU-based solution for continuous range-monitoring queries, and we then extend this system using the GPU. Additionally, with mobile communication devices becoming commodity, location-based services will become ubiquitous. To cope with the very high intensity of location-based queries, we propose a view oriented approach of the location database, thereby reducing computation costs by exploiting computation sharing amongst queries requiring the same view. Our studies show that by exploiting the parallel processing power of the GPU, we are able to significantly scale the number of mobile objects, while maintaining an acceptable level of performance. Our second approach was to view this research problem as one belonging to the domain of data streams. Several works have convincingly argued that the two research fields of spatiotemporal data streams and the management of moving objects can naturally come together. [IlMI10, ChFr03, MoXA04] For example, the output of a GPS receiver, monitoring the position of a mobile object, is viewed as a data stream of location updates. This data stream of location updates, along with those from the plausibly many other mobile objects, is received at a centralized server, which processes the streams upon arrival, effectively updating the answers to the currently active queries in real time. iv For this second approach, we present GEDS, a scalable, Graphics Processing Unit (GPU)-based framework for the evaluation of continuous spatio-temporal queries over spatiotemporal data streams. Specifically, GEDS employs the computation sharing and parallel processing paradigms to deliver scalability in the evaluation of continuous, spatio-temporal range queries and continuous, spatio-temporal kNN queries. The GEDS framework utilizes the parallel processing capability of the GPU, a stream processor by trade, to handle the computation required in this application. Experimental evaluation shows promising performance and shows the scalability and efficacy of GEDS in spatio-temporal data streaming environments. Additional performance studies demonstrate that, even in light of the costs associated with memory transfers, the parallel processing power provided by GEDS clearly counters and outweighs any associated costs. Finally, in an effort to move beyond the analysis of specific algorithms over the GEDS framework, we take a broader approach in our analysis of GPU computing. What algorithms are appropriate for the GPU? What types of applications can benefit from the parallel and stream processing power of the GPU? And can we identify a class of algorithms that are best suited for GPU computing? To answer these questions, we develop an abstract performance model, detailing the relationship between the CPU and the GPU. From this model, we are able to extrapolate a list of attributes common to successful GPU-based applications, thereby providing insight into which algorithms and applications are best suited for the GPU and also providing an estimated theoretical speedup for said GPU-based application

GPU-based proximity query processing on unstructured triangular mesh model

This paper presents a novel proximity query (PQ) approach capable to detect the collision and calculate the minimal Euclidean distance between two non-convex objects in 3D, namely the robot and the environment. Such approaches are often considered as computationally demanding problems, but are of importance to many applications such as online simulation of haptic feedback and robot collision-free trajectory. Our approach enables to preserve the representation of unstructured environment in the form of triangular meshes. The proposed PQ algorithm is computationally parallel so that it can be effectively implemented on graphics processing units (GPUs). A GPU-based computation scheme is also developed and customized, which shows >200 times faster than an optimized CPU with single core. Comprehensive validation is also conducted on two simulated scenarios in order to demonstrate the practical values of its potential application in image-guided surgical robotics and humanoid robotic control.published_or_final_versio

Assessing metric structures on GPGPU environments

Similarity search consists on retrieving objects within a database that are similar or relevant to a particular query. It is a topic of great interest to scientific community because of its many fields of application, such as searching for words and images on the World Wide Web, pattern recognition, detection of plagiarism, multimedia databases, among others. It is modeled through metric spaces, in which objects are represented in a black-box that contains only the distance between objects; calculating the distance function is costly and search systems operate at a high query rate. Metrical structures have been developed to optimize this process; such structures work as indexes and preprocess data to decrease the distance evaluations during the search. Processing large volumes of data makes unfeasible the use of such structures without using parallel processing environments. Technologies based on multi- CPU and GPU architectures are among the most force due to its costs and performance.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Assessing metric structures on GPGPU environments

Similarity search consists on retrieving objects within a database that are similar or relevant to a particular query. It is a topic of great interest to scientific community because of its many fields of application, such as searching for words and images on the World Wide Web, pattern recognition, detection of plagiarism, multimedia databases, among others. It is modeled through metric spaces, in which objects are represented in a black-box that contains only the distance between objects; calculating the distance function is costly and search systems operate at a high query rate. Metrical structures have been developed to optimize this process; such structures work as indexes and preprocess data to decrease the distance evaluations during the search. Processing large volumes of data makes unfeasible the use of such structures without using parallel processing environments. Technologies based on multi- CPU and GPU architectures are among the most force due to its costs and performance.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Deep Fluids: A Generative Network for Parameterized Fluid Simulations

This paper presents a novel generative model to synthesize fluid simulations from a set of reduced parameters. A convolutional neural network is trained on a collection of discrete, parameterizable fluid simulation velocity fields. Due to the capability of deep learning architectures to learn representative features of the data, our generative model is able to accurately approximate the training data set, while providing plausible interpolated in-betweens. The proposed generative model is optimized for fluids by a novel loss function that guarantees divergence-free velocity fields at all times. In addition, we demonstrate that we can handle complex parameterizations in reduced spaces, and advance simulations in time by integrating in the latent space with a second network. Our method models a wide variety of fluid behaviors, thus enabling applications such as fast construction of simulations, interpolation of fluids with different parameters, time re-sampling, latent space simulations, and compression of fluid simulation data. Reconstructed velocity fields are generated up to 700x faster than re-simulating the data with the underlying CPU solver, while achieving compression rates of up to 1300x.Comment: Computer Graphics Forum (Proceedings of EUROGRAPHICS 2019), additional materials: http://www.byungsoo.me/project/deep-fluids

A real-time proximity querying algorithm for haptic-based molecular docking

Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware