Related papers: How wet should be the reaction coordinate for liga…
Background. The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. We demonstrate the accuracy and effectiveness of a Lagrangian particle-based…
We solve the output-feedback stabilization problem for a tank with a liquid modeled by the viscous Saint-Venant PDE system. The control input is the acceleration of the tank and a Control Lyapunov Functional methodology is used. The…
Single-chain nanoparticles (SCNP) are a new class of bio and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or inter-polymer bonds. Here we numerically show that a fully-entropic…
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments…
We present results of testing of the ability of eleven popular scoring functions to predict native docked positions using a recently developed method [1] for estimation the entropy contributions of relative motions to protein-ligand binding…
In this paper, we use and further develop upon a recently proposed multivariate, distribution-free Goodness-of-Fit (GoF) test based on the theory of Optimal Transport (OT) called the Rank Energy (RE) [1], for non-parametric and unsupervised…
We show that the failure of the real-space RG method in the 1D tight-binding model is not intrinsic to the method as considered so far but depends on the choice of boundary conditions. For fixed BC's the failure does happen. For free BC's…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Spatial filters have played a central role in large eddy simulation and, more recently, in reduced order model (ROM) stabilization for convection-dominated flows. Nevertheless, important open questions remain: in under-resolved regimes,…
We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of…
Deciding which sensing capabilities to deploy on an agent in uncertain domains is a fundamental engineering challenge, in which one balances task achievability against the high costs of hardware and processing. This problem has previously…
Stokesian Dynamics (SD) is a numerical framework used for simulating hydrodynamic interactions in particle suspensions at low Reynolds number. It combines far-field approximations with near-field lubrication corrections, offering a balance…
Ozawa et. al [1] presented numerical results for the configurational entropy density, $s_c$, of a model glass-forming liquid in the presence of random pinning. The location of a "phase boundary" in the pin density ($c$) - temperature ($T$)…
For the problem of task-agnostic reinforcement learning (RL), an agent first collects samples from an unknown environment without the supervision of reward signals, then is revealed with a reward and is asked to compute a corresponding…
We present the evaluation methodology, datasets and results of the BOP Challenge 2023, the fifth in a series of public competitions organized to capture the state of the art in model-based 6D object pose estimation from an RGB/RGB-D image…
We examine the momentum and energy dependence of the scattering rate of the high temperature cuprate superconductors using angle resolved photoemission spectroscopy. The scattering rate is of the form a + b*w. The inelastic coefficient b is…
Ab initio molecular dynamics simulations of liquid water under equilibrium ambient conditions, together with a novel energy decomposition analysis, have recently shown that a substantial fraction of water molecules exhibit a significant…
When a liquid is cooled below its melting temperature, if crystallization is avoided, it forms a glass. This phenomenon, called glass transition, is characterized by a marked increase of viscosity, about 14 orders of magnitude, in a narrow…
We advance a quantitative description of the critical shear rate $\dot{\gamma_c}$ needed to dislodge a spherical particle resting on a surface with a model asperity in laminar and turbulent fluid flows. We have built a cone-plane…
We analyze solutions to a superconducting gap equation based on the two-dimensional Hubbard model with nearest and next-to-nearest neighbor hopping. The Cooper pair potential can be calculated exactly and expressed in terms of elliptic…