相关论文: Reaction Coordinates for Conformational Transition…
Second-order phase transitions appear as a divergence in one of the linear response functions. For a system of correlated electrons, the relevant divergent response can and does involve many-particle observables, most famously the double…
A nonlinear response theory is developed and applied to electrostatic interactions between spherical macroions, screened by surrounding microions, in charge-stabilized colloidal suspensions. The theory describes leading-order nonlinear…
The paper considers a coupled system of linear Boltzmann transport equations (BTE), and its Continuous Slowing Down Approximation (CSDA). This system can be used to model the relevant transport of particles used e.g. in dose calculation in…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Originating from the pioneering study of Alan Turing, the bifurcation analysis predicting spatial pattern formation from a spatially uniform state for diffusing morphogens or chemical species that interact through nonlinear reactions is a…
Linear discriminant analysis (LDA) is a well-known method for multiclass classification and dimensionality reduction. However, in general, ordinary LDA does not achieve high prediction accuracy when observations in some classes are…
Many processes of scientific and technological interest are characterized by time scales that render their simulation impossible if one uses present day simulation capabilities. To overcome this challenge a variety of enhanced simulation…
Linear response theory has found many applications in statistical physics. One of these is to compute minimal-work protocols that drive nonequilibrium systems between different thermodynamic states, which are useful for designing engineered…
We propose new measures of localization and cooperativity for the analysis of atomic rearrangements. We show that for both clusters and bulk material cooperative rearrangements usually have significantly lower barriers than uncooperative…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
We present an extensive set of surface and chemisorption energies calculated using state of the art many-body perturbation theory. In the first part of the paper we consider ten surface reactions in the low coverage regime where…
The validity of two fundamental concepts of classical chemical kinetics - the notion of "Chemical Equilibrium" and the "Law of Mass Action" - are re-examined for reversible \textit{diffusion-limited} reactions (DLR), as exemplified here by…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
The random phase approximation (RPA) has received a considerable interest in the field of modeling systems where noncovalent interactions are important. Its advantages over widely used density functional theory (DFT) approximations are the…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
How much time does it take two molecules to react? If a reaction occurs upon contact, the answer to this question boils down to the classic first-passage time problem: find the time it takes the two molecules to meet. However, this is not…
A new formalism and computer code, ASTRA (AttoSecond TRAnsitions), has been developed to treat the interactions of short, intense radiation with molecules. The formalism makes extensive use of transition density matrices, computed using a…
Within a nonperturbative dynamical two-body approach - based on coupled equations of motion for the one-body density matrix and the two-body correlation function - we study the distribution of occupation numbers in a correlated system close…
One essential ingredient in many machine learning (ML) based methods for atomistic modeling of materials and molecules is the use of locality. While allowing better system-size scaling, this systematically neglects long-range (LR) effects,…
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…