相关论文: Simultaneous Design of Microbe and Bioreactor
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…
Bilevel optimization has recently attracted growing interests due to its wide applications in modern machine learning problems. Although recent studies have characterized the convergence rate for several such popular algorithms, it is still…
The performance of industrial robotic work cells depends on optimizing various hyperparameters referring to the cell layout, such as robot base placement, tool placement, and kinematic design. Achieving this requires a bilevel optimization…
In this work the robustness of a feedback optimization scheme is discussed. Previously known results in literature, on the convergence to local optima of the optimization problem of interest, are extended to the case where the sensitivities…
This paper addresses several critical stages of designing a walking robot, including optimal structural synthesis, introducing a novel 'rational' mechanical structure aimed at enhancing efficiency and simplifying control system, while…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
In a quantum processor, the device design and external controls together contribute to the quality of the target quantum operations. As we continuously seek better alternative qubit platforms, we explore the increasingly large device and…
Bayesian optimization is a popular method for optimizing expensive black-box functions. Yet it oftentimes struggles in high dimensions where the computation could be prohibitively heavy. To alleviate this problem, we introduce Coordinate…
Microgels are cross-linked, colloidal polymer networks with great potential for stimuli-response release in drug-delivery applications, as their size in the nanometer range allows them to pass human cell boundaries. For applications with…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
We present a self-contained analytical model for biphoton generation in microring resonators. Encompassing both all-pass and add-drop geometries, identical and distinct pump and biphoton coupling coefficients, and continuous-wave and pulsed…
Always-on AI applications, from environmental sensors to biomedical implants, require ultra-low power consumption. Analog circuits offer a path to sub-microwatt inference, yet existing analog implementations are limited to feedforward…
In this paper, we study multi-block min-max bilevel optimization problems, where the upper level is non-convex strongly-concave minimax objective and the lower level is a strongly convex objective, and there are multiple blocks of dual…
We consider the problem of optimally designing a system for repeated use under uncertainty. We develop a modeling framework that integrates design and operational phases, which are represented by a mixed-integer program and discounted-cost…
Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
In clinical practice, there is significant interest in integrating novel biomarkers with existing clinical data to construct interpretable and robust decision rules. Motivated by the need to improve decision-making for early disease…