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The smoothed particle hydrodynamics (SPH) method has been increasingly used to study fluid problems in recent years; but its computational cost can be high if high resolution is required. In this study, an adaptive resolution method based…
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component…
Particle production in central Pb-Pb collisions at LHC is discussed in the context of the Statistical Model. Predictions of various particle ratios are presented with the corresponding choice of model parameters made according to the…
Accessing the ballistic regime of single particles in liquids remains an experimental challenge that shrouds our understanding of the particle-liquid interactions on exceedingly short time scales. We demonstrate the ballistic measurements…
Reaction Coordinates (RCs) are indicators of hidden, low-dimensional mechanisms that govern the long-term behavior of high-dimensional stochastic processes. We present a novel and general variational characterization of optimal RCs and…
We construct a high-order adaptive time stepping scheme for vesicle suspensions with viscosity contrast. The high-order accuracy is achieved using a spectral deferred correction (SDC) method, and adaptivity is achieved by estimating the…
We propose a benchmark for 6D pose estimation of a rigid object from a single RGB-D input image. The training data consists of a texture-mapped 3D object model or images of the object in known 6D poses. The benchmark comprises of: i) eight…
For the Lagrangian-DNN relaxation of quadratic optimization problems (QOPs), we propose a Newton-bracketing method to improve the performance of the bisection-projection method implemented in BBCPOP [to appear in ACM Tran. Softw., 2019].…
We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray…
We develop and analyze a stochastic genetic interacting particle method (SGIP) for reaction-diffusion-advection (RDA) equations. The SGIP method employs operator splitting to approximate the advection-diffusion and reaction processes,…
Many applications require a learner to make sequential decisions given uncertainty regarding both the system's payoff function and safety constraints. In safety-critical systems, it is paramount that the learner's actions do not violate the…
We consider a surface code suffering decoherence due to coupling to a bath of bosonic modes at finite temperature and study the time available before the unavoidable breakdown of error correction occurs as a function of coupling and bath…
Rare but critical events in complex systems, such as protein folding, chemical reactions, disease progression, and extreme weather or climate phenomena, are governed by complex, high-dimensional, stochastic dynamics. Identifying an optimal…
This work proposes a safety-critical local reactive controller that enables the robot to navigate in unknown and cluttered environments. In particular, the trajectory tracking task is formulated as a constrained polynomial optimization…
Optimal gait design is important for micro-organisms and micro-robots that propel themselves in a fluid environment in the absence of external force or torque. The simplest models of shape changes are those that comprise a series of…
It has been shown recently that predictions from Mode-Coupling Theory for the glass transition of hard-spheres become increasingly bad when dimensionality increases, whereas replica theory predicts a correct scaling. Nevertheless if one…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Water is an associated liquid in which the main intermolecular interaction is the hydrogen bond (HB) which is limited to four per atom, independently of the number of neighbours. We have considered a hydrogen bond net superposed on Bernal's…
We study a coarse-grained model for a water monolayer that cannot crystallize due to the presence of confining interfaces, such as protein powders or inorganic surfaces. Using both Monte Carlo simulations and mean field calculations, we…
Conformal prediction (CP) is an important tool for distribution-free predictive uncertainty quantification. Yet, a major challenge is to balance computational efficiency and prediction accuracy, particularly for multiple predictions. We…