Related papers: Optimization of Non-Equilibrium Self-Assembly Prot…
In this paper, we develop a rigorous optimal control-theoretic approach to Transformer training that respects key structural constraints such as (i) realized-input-independence during execution, (ii) the ensemble control nature of the…
Non-equilibrium Markov State Modeling (MSM) has recently been proposed [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach…
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior.…
Model Predictive Control (MPC) is a successful control methodology, which is applied to increasingly complex systems. However, real-time feasibility of MPC can be challenging for complex systems, certainly when an (extremely) large number…
Model predictive control allows solving complex control tasks with control and state constraints. However, an optimal control problem must be solved in real-time to predict the future system behavior, which is hardly possible on embedded…
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on…
This paper is devoted to solving a time-inconsistent risk-sensitive control problem with parameter $\e$ and its limit case ($\e\rightarrow0^+$) for countable-stated Markov decision processes (MDPs for short). Since the cost functional is…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
We investigate a local incremental stationary scheme for the numerical solution of rate-independent systems. Such systems are characterized by a (possibly) non-convex energy and a dissipation potential, which is positively homogeneous of…
In this article we propose a Weighted Stochastic Mesh (WSM) Algorithm for approximating the value of a discrete and continuous time optimal stopping problem. We prove that in the discrete case the WSM algorithm leads to semi-tractability of…
Modern experimental methods enable the creation of self-assembly building blocks with tunable interactions, but optimally exploiting this tunability for the self-assembly of desired structures remains an important challenge. Many studies of…
We consider parametric version of fixed-delay continuous-time Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is…
In cyber-physical systems such as automobiles, measurement data from sensor nodes should be delivered to other consumer nodes such as actuators in a regular fashion. But, in practical systems over unreliable media such as wireless, it is a…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
This paper proposes to decouple performance optimization and enforcement of asymptotic convergence in Model Predictive Control (MPC) so that convergence to a given terminal set is achieved independently of how much performance is optimized…
Achieving precise control of colloidal self-assembly into specific patterns remains a longstanding challenge due to the complex process dynamics. Recently, machine learning-based state representation and reinforcement learning-based control…
In this paper, we tackle the state transformation problem in non-strict full state-constrained systems by introducing an adaptive fixed-time control method, utilizing a one-to-one asymmetric nonlinear mapping auxiliary system. Additionally,…
In topology optimization of compliant mechanisms, the specific placement of boundary conditions strongly affects the resulting material distribution and performance of the design. At the same time, the most effective locations of the loads…
Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled…
Self-assembly is a fundamental concept in biology and of significant interest to nanotechnology. Significant progress has been made in characterizing and controlling the properties of the resulting structures, both experimentally and…