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

Machine learning interatomic potentials (MLIPs) have achieved remarkable accuracy on standard benchmarks, yet their ability to reproduce molecular kinetics -- critical for reaction rate calculations -- remains largely unexplored. We…

An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…

Boolean network models of strongly connected modules are capable of capturing the high regulatory complexity of many biological gene regulatory circuits. We study numerically the previously introduced basin entropy, a parameter for the…

In many complex systems, we observe that `interesting behaviour' is often the consequence of a system exploiting the existence of an Information Bottleneck (IB). These bottlenecks can occur at different scales, between individuals or…

Information Bottleneck (IB) is a generalization of rate-distortion theory that naturally incorporates compression and relevance trade-offs for learning. Though the original IB has been extensively studied, there has not been much…

Interacting particle system (IPS) models have proven to be highly successful for describing the spatial movement of organisms. However, it has proven challenging to infer the interaction rules directly from data. In the field of equation…

Information bottleneck is an information-theoretic principle of representation learning that aims to learn a maximally compressed representation that preserves as much information about labels as possible. Under this principle, two…

The rapid development of computational materials science powered by machine learning (ML) is gradually leading to solutions to several previously intractable scientific problems. One of the most prominent is machine learning interatomic…

Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…

Minimum energy path (MEP) search is a vital but often very time-consuming method to predict the transition states of versatile dynamic processes in chemistry, physics, and materials science. In this study, we reveal that the chemical bond…

The Replica Exchange Wang-Landau Method is used to estimate the energy landscape of a polymer composed of a simple hydrophobic and polar sequence using the HP protein model. Calculations of state transitions between the energy levels of the…

In principle, all of the dynamical complexities of many-body systems are encapsulated in the potential energy landscapes on which the atoms move - an observation that suggests that the essentials of the dynamics ought to be determined by…

In the Information Bottleneck (IB), when tuning the relative strength between compression and prediction terms, how do the two terms behave, and what's their relationship with the dataset and the learned representation? In this paper, we…

Efficient simulation of quantum mechanical problems can be performed in a quantum computer where the interactions of qubits lead to the realization of various problems possessing quantum nature. Spin-Boson Model (SBM) is one of the striking…

The information bottleneck (IB) principle has been adopted to explain deep learning in terms of information compression and prediction, which are balanced by a trade-off hyperparameter. How to optimize the IB principle for better robustness…

A numerical model is built, simulating the principles of kinetic gas theory, to predict pressures of molecules in a spherical pressure vessel; the model tracks a single particle and multiplies the force on the spherical walls by a mole of…

We show that active transport processes in biological systems can be understood through a local equilibrium description formulated at the mesoscale, the scale to describe stochastic processes. This new approach uses the method established…

We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…

Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…

Ultrafast non-equilibrium dynamics offer a route to study the microscopic interactions that govern macroscopic behavior. In particular, photo-induced phase transitions (PIPTs) in solids provide a test case for how forces, and the resulting…