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Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…
Advances in sequencing have revealed that each individual carries about 10,000 missense variants. For the vast majority, we do not know what the functional consequences - if any - will be. Further, mechanistic insight, such as structural…
While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we…
Biological systems exhibit a continuous stream of movements, consisting of sequential segments, that allow them to perform complex tasks in a creative and versatile fashion. This observation has led researchers towards identifying…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Nature has engineered complex designs to achieve advanced properties and functionalities through evolution, over millions of years. Many organisms have adapted to their living environment producing extremely efficient materials and…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
The brain is a complex organ characterized by heterogeneous patterns of structural connections supporting unparalleled feats of cognition and a wide range of behaviors. New noninvasive imaging techniques now allow these patterns to be…
In biological systems, sensing is not performed by the brain alone: the body deforms, vibrates, and filters external stimuli before they are transduced into neural signals. In engineered systems, this processing burden is placed largely on…
MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…
The potential benefits of autonomous systems have been driving intensive development of such systems, and of supporting tools and methodologies. However, there are still major issues to be dealt with before such development becomes…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Biological muscles have always attracted robotics researchers due to their efficient capabilities in compliance, force generation, and mechanical work. Many groups are working on the development of artificial muscles, however,…
In the present work, irregular complex joints of the human arm are modelled in the computer-aided design environment. Accurately the geometric models of the joints and surrounding bony regions are developed from computed tomography data set…
Tailoring the design of robot bodies for control purposes is implicitly performed by engineers, however, a methodology or set of tools is largely absent and optimization of morphology (shape, material properties of robot bodies, etc.) is…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…