Related papers: Optimal Strategy for Stabilizing Protein Folding I…
In this article, we design the distributed pinning controllers to globally stabilize a Boolean network (BN), specially a sparsely connected large-scale one, towards a preassigned subset of state space through the node-to-node message…
The generation and storage of spin squeezing is an attracting topic in quantum metrology and the foundations of quantum mechanics. The major models to realize the spin squeezing are the one- and two-axis twisting models. Here, we consider a…
Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug design and protein design. Based on large scale data sets, we show that protein…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
We consider a classical stochastic control problem in which a diffusion process is controlled by a withdrawal process up to a termination time. The objective is to maximize the expected discounted value of the withdrawals until the…
This paper explores continuous-time and state-space optimal stopping problems from a reinforcement learning perspective. We begin by formulating the stopping problem using randomized stopping times, where the decision maker's control is…
In this paper, we investigate the rapid stabilizability of linear infinite-dimensional control systems with constant delays. Under the assumptions that the state operator generates an immediately compact semigroup and that the delay…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We consider optimal control of the scalar wave equation where the control enters as a coefficient in the principal part. Adding a total variation penalty allows showing existence of optimal controls, which requires continuity results for…
Kiiking is an extreme sport in which athletes alternate between standing and squatting to pump a standing swing till it is inverted and completes a rotation. A minimal model of the sport may be cast in terms of the control of an actively…
We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the…
This paper applies the recently developed framework for integral control on nonlinear spaces to two non-standard cases. First, we show that the property of perfect target stabilization in presence of actuation bias holds also if this bias…
The application of systems and control theory to membrane physiology is presented here. Modeling efforts have focused on describing those physiologically realistic mechanisms which govern the regulation of membrane permeability in nerve.…
Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed, but,…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane…
This study proposes a method for designing stabilizing suboptimal controllers for nonlinear stochastic systems. These systems include time-invariant stochastic parameters that represent uncertainty of dynamics, posing two key difficulties…
Bang-bang control is often used to implement a minimal-time shortcut to adiabaticity for efficient transport of atoms in a moving harmonic trap. However, drastic changes of the on-off controller, leading to high transport-mode excitation…