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The quest for deeper understanding of biological systems has driven the acquisition of increasingly larger multidimensional image datasets. Inspecting and manipulating data of this complexity is very challenging in traditional visualization…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
During VR demos we have performed over last few years, many participants (in the absence of any haptic feedback) have commented on their perceived ability to 'feel' differences between simulated molecular objects. The mechanisms for such…
Bionic vision is a rapidly advancing field aimed at developing visual neuroprostheses ('bionic eyes') to restore useful vision to people who are blind. However, a major outstanding challenge is predicting what people 'see' when they use…
Modeling is a key activity in conceptual design and system design. Through collaborative modeling, end-users, stakeholders, experts, and entrepreneurs are able to create a shared understanding of a system representation. While the Unified…
Agent-based models (ABMs) and video games, including those taking advantage of virtual reality (VR), have undergone a remarkable parallel evolution, achieving impressive levels of complexity and sophistication. This paper argues that while…
State-of-the-art models represent proteins and molecules in separate embedding manifolds, limiting the modeling of systemic biological processes. We introduce ReactEmbed, a lightweight, plug-and-play module that bridges this gap. ReactEmbed…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture…
Biomolecular electrostatics is key in protein function and the chemical processes affecting it. Implicit-solvent models via the Poisson-Boltzmann (PB) equation provide insights with less computational cost than atomistic models, making…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
Understanding and designing biomolecules, such as proteins and small molecules, is central to advancing drug discovery, synthetic biology and enzyme engineering. Recent breakthroughs in artificial intelligence have revolutionized…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
The intricate design of real complex injection molds poses significant challenges. Mold design vali-dation often falls to operators with tool-handling experience but limited CAD proficiency. Unlike other industries, the scale and costs of…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
We contribute MolecuSense, a virtual version of a physical molecule construction kit, based on visualization in Virtual Reality (VR) and interaction with force-feedback gloves. Targeting at chemistry education, our goal is to make virtual…
This paper presents a new technique for the virtual reality (VR) visu-alization of complex volume images obtained from computer tomography (CT) and Magnetic Resonance Imaging (MRI) by combining three-dimensional (3D) mesh processing and…