A visual computing environment for very large scale biomolecular modeling

Abstract

Knowledge of the complex molecular structures of living cells is being accumulated at a tremendous rate. Key technologies enabling this success have been, high performance computing and powerful molecular graphics applications, but the technology is beginning to seriously lag behind challenges posed by the size and number of new structures and by the emerging opportunities in drug design and genetic engineering. A visual computing environment is being developed which permits interactive modeling of biopolymers by linking a 3D molecular graphics program with an efficient molecular dynamics simulation program executed on remote high-performance parallel computers. The system will be ideally suited for distributed computing environments, by utilizing both local 3D graphics facilities and the peak capacity of high-performance computers for the purpose of interactive biomolecular modeling. To create an interactive 3D environment three input methods will be explored: (1) a six degree of freedom "mouse" for controlling the space shared by the model and the user; (2) voice commands monitored through a microphone and recognized by a speech recognition interface; (3) hand gestures, detected through cameras and interpreted using computer vision techniques. Controlling 3D graphics connected to real time simulations and the use of voice with suitable language semantics, as well as hand gestures, promise great benefits for many types of problem solving environments. Our focus on structural biology takes advantage of existing sophisticated software, provides concrete objectives, defines a well-posed domain of tasks and offers a well-developed vocabulary for spoken communication.