Related papers: Physical Biomodeling: a new field enabled by 3-D p…
Three-dimensional (3D) printed preoperative planning models serve a critical role in the success of many medical procedures. However, many of these models do not portray the patient's complete anatomy due to their monolithic and static…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Design - especially of physical objects - can be understood as creative acts solving practical problems. In this paper we describe a biologically-inspired developmental model as the basis of a generative form-finding system. Using local…
We report recent research on computing with biology-based neural network models by means of physics-based opto-electronic hardware. New technology provides opportunities for very-high-speed computation and uncovers problems obstructing the…
Modeling complex physical dynamics is a fundamental task in science and engineering. Traditional physics-based models are sample efficient, and interpretable but often rely on rigid assumptions. Furthermore, direct numerical approximation…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Differentiable physics provides a new approach for modeling and understanding the physical systems by pairing the new technology of differentiable programming with classical numerical methods for physical simulation. We survey the rapidly…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life sciences majors. These efforts are complicated by the many…
Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields including protein structural modeling. Protein structural modeling, such as predicting…
Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
Physical visualizations (i.e., data representations by means of physical objects) have been used for many centuries in medical and anatomical education. Recently, 3D printing techniques started also to emerge. Still, other medical…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
3D modeling is becoming a well-developed field of medicine, but its applicability can be limited due to the lack of software allowing for easy utilizations of generated 3D visualizations. By leveraging recent advances in virtual reality, we…
The rapid advances in 3D scanning and acquisition techniques have given rise to the explosive increase of volumetric digital models in recent years. This dissertation systematically trailblazes a novel volumetric modeling framework to…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…