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The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…

Biomolecules · Quantitative Biology 2021-10-26 Lyman Monroe , Daisuke Kihara

We study the problem of policy synthesis for uncertain partially observable Markov decision processes (uPOMDPs). The transition probability function of uPOMDPs is only known to belong to a so-called uncertainty set, for instance in the form…

Optimization and Control · Mathematics 2020-01-24 Marnix Suilen , Nils Jansen , Murat Cubuktepe , Ufuk Topcu

In this chapter, we are concerned with inverse optimal control problems, i.e., optimization models which are used to identify parameters in optimal control problems from given measurements. Here, we focus on linear-quadratic optimal control…

Optimization and Control · Mathematics 2023-11-27 Stephan Dempe , Markus Friedemann , Felix Harder , Patrick Mehlitz , Gerd Wachsmuth

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…

Statistical Mechanics · Physics 2009-09-25 Nikolay V. Dokholyan , Sergey V. Buldyrev , H. Eugene Stanley , Eugene I. Shakhnovich

Nonlinear programming is explicitly analyzed via a novel perspective/method and from a bottom-up manner. The philosophy is based on the recent findings on convex quadratic equation (CQE), which help clarify a geometric interpretation that…

Optimization and Control · Mathematics 2022-10-20 Li-Gang Lin , Yew-Wen Liang

By enabling constraint-aware online model adaptation, model predictive control using Gaussian process (GP) regression has exhibited impressive performance in real-world applications and received considerable attention in the learning-based…

Optimization and Control · Mathematics 2024-09-17 Amon Lahr , Andrea Zanelli , Andrea Carron , Melanie N. Zeilinger

This paper proposes a novel Kernelized Data-Driven Predictive Control (KDPC) scheme for robust, offset-free tracking of nonlinear systems. Our computationally efficient hybrid approach separates the prediction: (1) kernel ridge regression…

Systems and Control · Electrical Eng. & Systems 2026-01-26 Mahmood Mazare , Hossein Ramezani

Modelling and predicting protein configurations is crucial for advancing drug discovery, enabling the design of treatments for life-threatening diseases. A critical aspect of this challenge is rotamer optimisation - the determination of…

Quantum Physics · Physics 2025-07-28 Anastasia Agathangelou , Dilhan Manawadu , Ivano Tavernelli

This paper presents a unified framework that connects sequential quadratic programming (SQP) and the iterative linear-parameter-varying model predictive control (LPV-MPC) technique. Using the differential formulation of the LPV-MPC, we…

Systems and Control · Electrical Eng. & Systems 2026-04-10 Kristóf Floch , Amon Lahr , Roland Tóth , Melanie N. Zeilinger

A model predictive control (MPC) framework is developed for station-keeping in spacecraft formation flight along libration point orbits. At each control period, the MPC policy solves a multi-vehicle optimal control problem (MVOCP) that…

Systems and Control · Electrical Eng. & Systems 2026-03-11 Yuri Shimane , Purnanand Elango , Avishai Weiss

This paper presents a constraint-aware control framework for underactuated aerial manipulators, enabling accurate end-effector trajectory tracking while explicitly accounting for safety and feasibility constraints. The control problem is…

Quantum optimal control theory (QOCT) aims at finding an external field that drives a quantum system in such a way that optimally achieves some predefined target. In practice this normally means optimizing the value of some observable, a so…

Quantum Physics · Physics 2011-09-19 Alberto Castro , I. V. Tokatly

A self-learning optimal control algorithm for episodic fixed-horizon manufacturing processes with time-discrete control actions is proposed and evaluated on a simulated deep drawing process. The control model is built during consecutive…

Systems and Control · Computer Science 2020-01-07 Johannes Dornheim , Norbert Link , Peter Gumbsch

Predicting the 3D structure of proteins is one of the most important problems in current biochemical research. In this article, we explain how to combine recent deep learning advances with the well known technique of quantum walks applied…

Quantum Physics · Physics 2022-03-10 P A M Casares , Roberto Campos , M A Martin-Delgado

By optimizing the predicted performance over a receding horizon, model predictive control (MPC) provides the ability to enforce state and control constraints. The present paper considers an extension of MPC for nonlinear systems that can be…

Systems and Control · Electrical Eng. & Systems 2023-09-29 Mohammadreza Kamaldar , Dennis S. Bernstein

As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…

Biomolecules · Quantitative Biology 2015-11-03 Jacques M. Bahi , Nathalie M. -L. Cote , Christophe Guyeux

Protein language models (PLMs) have enabled advances in structure prediction and de novo protein design, yet they frequently collapse into pathological repetition during generation. Unlike in text, where repetition merely reduces…

Biomolecules · Quantitative Biology 2026-02-03 Jiahao Zhang , Zeqing Zhang , Di Wang , Lijie Hu

Automated synthesis of correct-by-construction controllers for autonomous systems is crucial for their deployment in safety-critical scenarios. Such autonomous systems are naturally modeled as stochastic dynamical models. The general…

Systems and Control · Electrical Eng. & Systems 2023-11-17 Thom Badings , Nils Jansen , Licio Romao , Alessandro Abate

This paper presents a new deep learning-based framework for robust nonlinear estimation and control using the concept of a Neural Contraction Metric (NCM). The NCM uses a deep long short-term memory recurrent neural network for a global…

Systems and Control · Electrical Eng. & Systems 2020-11-20 Hiroyasu Tsukamoto , Soon-Jo Chung

The goal of quantum tracking control is to identify shaped fields to steer observable expectation values along designated time-dependent tracks. The fields are determined via an iteration-free procedure, which is based on inverting the…

Quantum Physics · Physics 2024-02-06 Alicia B. Magann , Tak-San Ho , Christian Arenz , Herschel A. Rabitz