Related papers: Infinite Switch Simulated Tempering in Force (FISS…

A default assumption in many machine learning scenarios is that the training and test samples are drawn from the same probability distribution. However, such an assumption is often violated in the real world due to non-stationarity of the…

Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a…

We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…

Advances in manufacturing and characterization of complex molecular systems have created a need for new methods for design at molecular length scales. Emerging approaches are increasingly relying on the use of Artificial Intelligence (AI),…

According to recent results, convergence in a prespecified or prescribed finite time can be achieved under extreme model uncertainty if control is applied continuously over time. This paper shows that this extreme amount of uncertainty…

We introduce a new discretization of a mixed formulation of the incompressible Stokes equations that includes symmetric viscous stresses. The method is built upon a mass conserving mixed formulation that we recently studied. The improvement…

Friction experiments were conducted on hydrogel thin films sliding against a rigid sphere in a low velocity regime where molecular adsorption at the sliding interface sets the friction force, through a dissipative…

We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…

Density-functional theory forces, stresses and energies comprise a database from which the optimal parameters of a spline-based empirical potential combining Stillinger-Weber and modified embedded-atom forms are determined. Accuracy of the…

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…

Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…

Diversity in the exhibited behavior of a given system is a desirable characteristic in a variety of application contexts. Synthesis of conformant implementations often proceeds by discovering witnessing Skolem functions, which are…

This work presents a fault-tolerant control scheme for sensory faults in robotic manipulators based on active inference. In the majority of existing schemes, a binary decision of whether a sensor is healthy (functional) or faulty is made…

Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…

Identifying dependency in multivariate data is a common inference task that arises in numerous applications. However, existing nonparametric independence tests typically require computation that scales at least quadratically with the sample…

This paper presents a stochastic model predictive control approach for nonlinear systems subject to time-invariant probabilistic uncertainties in model parameters and initial conditions. The stochastic optimal control problem entails a cost…

The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…

Search-Based Software Testing (SBST) automates test input generation but is frequently hindered by challenging fitness landscapes characterized by numerous deceptive local optima that impede search progress, as well as extended plateaus…

We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time…

Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…