Related papers: Optimal Strategy for Stabilizing Protein Folding I…
Control of continuous time dynamics with multiplicative noise is a classic topic in stochastic optimal control. This work addresses the problem of designing infinite horizon optimal controls with stability guarantees for \textit{a single…
Optimal control theory deals with finding protocols to steer a system between assigned initial and final states, such that a trajectory-dependent cost function is minimized. The application of optimal control to stochastic systems is an…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
In this work we are interested in effectively solving the quasi-static, linear Biot model for poromechanics. We consider the fixed-stress splitting scheme, which is a popular method for iteratively solving Biot's equations. It is well-known…
This paper deals with time-optimal control of nonlinear continuous-time systems based on direct collocation. The underlying discretization grid is variable in time, as the time intervals are subject to optimization. This technique differs…
Dense protein clusters are known to play an important role in nucleation of protein crystals from dilute solutions. While these have generally been thought to be formed from a metastable phase, the observation of similar, if not identical,…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
This paper is concerned with a constrained stochastic linear-quadratic optimal control problem, in which the terminal state is fixed and the initial state is constrained to lie in a stochastic linear manifold. The controllability of…
This paper studies the stabilization for a kind of linear and impulse control systems in finite-dimensional spaces, where impulse instants appear periodically. We present several characterizations on the stabilization; show how to design…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
The study is devoted to mathematical modeling and optimal control design of longitudinal motions of a rectilinear elastic rod. The control inputs are a force, which is normal to the cross section and distributed piecewise constantly along…
We present an optimisation-based approach to ensure robust asymptotic stability stability of a desired set in the state space of nonlinear dynamical systems, while optimising a general control objective. The approach relies on the decrease…
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have…
In this contribution, we introduce an efficient method for solving the optimal control problem for an unconstrained nonlinear switched system with an arbitrary cost function. We assume that the sequence of the switching modes are given but…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
We solve the problem of optimal stopping of a Brownian motion subject to the constraint that the stopping time's distribution is a given measure consisting of finitely-many atoms. In particular, we show that this problem can be converted to…
Braiding of Majorana zero modes provides a promising platform for quantum information processing, which is topologically protected against errors. Strictly speaking, however, the scheme relies on infinite braiding times as it utilizes the…
This paper deals with the development and analysis of novel time-optimal point-to-point model predictive control concepts for nonlinear systems. Recent approaches in the literature apply a time transformation, however, which do not maintain…
Run-and-tumble particles constitute one of the simplest models of self-propelled active matter, and provide an ideal playground to the understanding of out-of-equilibrium systems. We consider an idealized setup where one such particle is…
Linear augmentation has recently been shown to be effective in targeting desired stationary solutions, suppressing bistablity, in regulating the dynamics of drive response systems and in controlling the dynamics of hidden attractors. The…