相关论文: Quantifying Energetic and Entropic Pathways in Mol…

The complex dynamics of an increasing number of systems is attributed to the emergence of a rugged energy landscape with an exponential number of metastable states. To develop this picture into a predictive dynamical theory I discuss how to…

Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…

Characterizing the entropy of a system is a crucial, and often computationally costly, step in understanding its thermodynamics. It plays a key role in the study of phase transitions, pattern formation, protein folding and more. Current…

Machine Learning Inter-atomic Potentials (MLIPs) have become a common tool in use by computational chemists due to their combination of accuracy and speed. Yet, it is still not clear how well these tools behave at or near transitions states…

Entropy production (EP) is a key quantity in thermodynamics, and yet measuring EP has remained a challenging task. Here we introduce an EP estimator, called multidimensional entropic bound (MEB), utilizing an ensemble of trajectories…

The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…

Electrical submersible pumps (ESPs) are prevalently utilized as artificial lift systems in the oil and gas industry. These pumps frequently encounter multiphase flows comprising a complex mixture of hydrocarbons, water, and sediments. Such…

A Spectral Neighbor Analysis (SNAP) machine learning interatomic potential (MLIP) has been developed for simulations of carbon at extreme pressures (up to 5 TPa) and temperatures (up to 20,000 K). This was achieved using a large database of…

Information bottleneck (IB) is a technique for extracting information in one random variable $X$ that is relevant for predicting another random variable $Y$. IB works by encoding $X$ in a compressed "bottleneck" random variable $M$ from…

In this work, we developed a nonlinear System Identification (SID) method that we called Entropic Regression. Our method adopts an information-theoretic measure for the data-driven discovery of the underlying dynamics. Our method shows…

The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to…

The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but…

The extension of thermodynamic principles to active matter remains a challenge due to the non-equilibrium nature inherent to active systems. In this study, we introduce a framework to assess entropy in our minimal macroscopic experiment…

Configuration transitions of individual molecules and atoms on surfaces are traditionally described with energy barriers and attempt rates using an Arrhenius law. This approach yields consistent energy barrier values, but also attempt rates…

The Information Bottleneck (IB) method frequently suffers from unstable optimization, characterized by abrupt representation shifts near critical points of the IB trade-off parameter, beta. In this paper, I introduce a novel approach to…

The modeling of solid-state transformations, such as polymorphic transitions and chemical reactions in molecular crystals, is vital for many applications including drug design or the development of new synthesis methods. However, a…

We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…

Entropy is a central concept in physics, but can be challenging to calculate even for systems that are easily simulated. This is exacerbated out of equilibrium, where generally little is known about the distribution characterizing simulated…

A transition matrix can be constructed through the partial contraction of two given quantum states. We analyze and compare four different definitions of entropy for transition matrices, including (modified) pseudo entropy, SVD entropy, and…

Thermodynamics with internal variables is a common approach in continuum mechanics to model inelastic (i.e., non-equilibrium) material behavior. While this approach is computationally and theoretically attractive, it currently lacks a…