Related papers: Design principles for the glycoprotein quality con…
Clinical guidance systems have been widely adopted to help medical staffs to avoid preventable medical errors such as delay in diagnosis, treatment or untended deviations from best practice guidelines. However, because patient condition…
An efficient computational approach for imaging binary-type physical properties suitable for various models in biomedical applications is developed and validated. The proposed methodology includes gradient-based multiscale optimization with…
Connecting multiple smaller qubit modules by generating high-fidelity entangled states is a promising path for scaling quantum computing hardware. The performance of such a modular quantum computer is highly dependent on the quality and…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across…
Multi-step pathways, constituted of a sequence of reconfigurations, are central to a wide variety of natural and man-made systems. Such pathways autonomously execute in self-guided processes such as protein folding and self-assembly, but…
Generative modeling techniques such as Diffusion and Flow Matching have achieved significant successes in generating designable and diverse protein backbones. However, many current models are computationally expensive, requiring hundreds or…
Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at…
Intracellular protein patterns regulate a variety of vital cellular processes such as cell division and motility, which often involve dynamic changes of cell shape. These changes in cell shape may in turn affect the dynamics of…
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand.…
Quantum optimal control methods are widely used to design experimental control pulses such as laser amplitudes, phases, or detunings, that implement a target unitary evolution. In practice, what makes a pulse "good" depends not only on its…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
This paper aims to improve the path quality and computational efficiency of kinodynamic planners used for vehicular systems. It proposes a learning framework for identifying promising controls during the expansion process of sampling-based…
Exceptional points (EPs) in non-Hermitian systems give rise to enhanced sensitivity and chiral state transfer, which are important for quantum technologies. Although parameter trajectories encircling EPs can control symmetric and chiral…
Learning-based control methods utilize run-time data from the underlying process to improve the controller performance under model mismatch and unmodeled disturbances. This is beneficial for optimizing industrial processes, where the…
Electronic Control Units (ECUs) have played a pivotal role in transforming motorcars of yore into the modern vehicles we see on our roads today. They actively regulate the actuation of individual components and thus determine the…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…