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This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Science is rich in abstract concepts that capture complex processes in astonishingly simple ways. A prominent example is the reduction of molecules to simple graphs. This work introduces a design principle for parametrized quantum circuits…
Data is omnipresent in the modern, digital world and a significant number of people need to make sense of data as part of their everyday social and professional life. Therefore, together with the rise of data, the design of graphical…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
Computer graphics, often associated with films, games, and visual effects, has long been a powerful tool for addressing scientific challenges--from its origins in 3D visualization for medical imaging to its role in modern computational…
Developing new molecular compounds is crucial to address pressing challenges, from health to environmental sustainability. However, exploring the molecular space to discover new molecules is difficult due to the vastness of the space. Here…
Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however,…
Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes…
This article examines recent research in molecular communications from a telecommunications system design perspective. In particular, it focuses on channel models and state-of-the-art physical layer techniques. The goal is to provide a…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Effective visual communication is a core competency for pharmacometricians, statisticians, and more generally any quantitative scientist. It is essential in every step of a quantitative workflow, from scoping to execution and communicating…