相关论文: How wet should be the reaction coordinate for liga…

We consider a range of model potentials with metastable states undergoing molecular dynamics coupled to a thermal bath in the high friction regime, and consider how the optimal reaction coordinate depends on the diffusion anisotropy. For…

Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation…

Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these…

A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but…

Demanding a consistent quantum field theory description of spin 1/2 particles near a circular Fermi surface in 2d leads to a unique fermionic theory with relevant quartic interactions which has an emergent Lorentz symmetry and automatically…

Reaction coordinates (RCs) are low-dimensional representations of complex dynamical systems that capture their long-term dynamics. In this work, we focus on the criteria of lumpability and decomposability, previously established for…

Estimating rate coefficients from complex chemical reactions is essential for advancing detailed chemistry. However, the stiffness inherent in real-world atmospheric chemistry systems poses severe challenges, leading to training instability…

Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and this can be integral to proper cellular function. Broadly,…

The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…

The worst-case robust adaptive beamforming problem for general-rank signal model is considered. Its formulation is to maximize the worst-case signal-to-interference-plus-noise ratio (SINR), incorporating a positive semidefinite constraint…

Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…

We propose Co-op, a novel method for accurately and robustly estimating the 6DoF pose of objects unseen during training from a single RGB image. Our method requires only the CAD model of the target object and can precisely estimate its pose…

We investigate the stochastic gradient descent (SGD) method where the step size lies within a banded region instead of being given by a fixed formula. The optimal convergence rate under mild conditions and large initial step size is proved.…

Inexpensive numerical methods are key to enable simulations of systems of a large number of particles of different shapes in Stokes flow. Several approximate methods have been introduced for this purpose. We study the accuracy of the…

Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and…

This paper extends the second-order accurate BGK finite volume schemes for the ultra-relativistic flow simulations [5] to the 1D and 2D special relativistic hydrodynamics with the Synge equation of state. It is shown that such 2D schemes…

Recent work in data-driven control has revived behavioral theory to perform a variety of complex control tasks, by directly plugging libraries of past input-output trajectories into optimal control problems. Despite recent advances, a key…

Online Conformal Prediction (CP) struggles to balance temporal adaptability and structural stability. Feedback-driven methods (e.g., Adaptive Conformal Inference (ACI)) suffer from systemic marginal under-coverage and high interval variance…

We derive analytic expressions for the critical temperatures of the superconducting (SC) and pseudogap (PG) phases of the high-Tc cuprates, which are in excellent agreement with the experimental data for single-layered materials such as…

Patterned surfaces with large effective slip lengths, such as super-hydrophobic surfaces containing trapped gas bubbles, have the potential to reduce hydrodynamic drag. Based on lubrication theory, we analyze an approach of a hydrophilic…