Related papers: Optimization of Non-Equilibrium Self-Assembly Prot…
Rational design strategies for self-assembly require a detailed understanding of both the equilibrium state and the assembly kinetics. While the former is starting to be well understood, the latter remains a major theoretical challenge,…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
We propose a method for approximating solutions to optimization problems involving the global stability properties of parameter-dependent continuous-time autonomous dynamical systems. The method relies on an approximation of the…
Most approaches for designing self-assembled materials focus on the thermodynamic stability of a target structure or crystal polymorph. Yet in practice, the outcome of a self-assembly process is often controlled by kinetic pathways. Here we…
Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to…
We demonstrate a simple method by which time-dependent interactions can be exploited to improve self-assembly in colloidal systems. We apply this method to two systems: a model colloid with short-ranged attractive potentials that undergoes…
This article reviews recent inverse statistical-mechanical methodologies that we have devised to optimize interaction potentials in soft matter systems that correspond to stable "target" structures. We are interested in finding the…
While optimal control theory offers effective strategies for minimizing energetic costs in noisy microscopic systems over finite durations, a significant opportunity lies in exploiting the temporal structure of non-equilibrium forces. We…
A method is proposed to identify target states that optimize a metastability index amongst a set of trial states and use these target states as milestones (or core sets) to build Markov State Models (MSMs). If the optimized metastability…
We use analytic theory and computer simulation to study patterns formed during the growth of two-component assemblies in 2D and 3D. We show that these patterns undergo a nonequilibrium phase transition, at a particular growth rate, between…
This paper develops a new approach to the estimation of the degree of boundedness or stability of multidimensional nonlinear systems with time-dependent nonperiodic coefficients-an essential task in various engineering and natural science…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully…
We consider continuous-time, finite-horizon, optimal quadratic control of semi-Markov jump linear systems (S-MJLS), and develop principled approximations through Markov-like representations for the holding-time distributions. We adopt a…
Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
We develop a model-free approach to optimally control stochastic, Markovian systems subject to a reach-avoid constraint. Specifically, the state trajectory must remain within a safe set while reaching a target set within a finite time…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…
This paper presents a topology optimization framework for structural problems subjected to transient loading. The mechanical model assumes a linear elastic isotropic material, infinitesimal strains, and a dynamic response. The optimization…
An optimal control strategy is developed to construct nanostructures of desired geometry along line segments by means of directed self-assembly of charged particles. Such a control strategy determines the electric potentials of a set of…