Related papers: Enhanced Sampling for Free Energy Profiles with Po…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
Locating transition states is crucial for investigating transition mechanisms in wide-ranging phenomena, from atomistic to macroscale systems. Existing methods, however, can struggle in problems with a large number of degrees of freedom,…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
The framework of transition state theory (TST) provides a powerful way for analyzing the dynamics of physical and chemical reactions. While TST has already been successfully used to obtain reaction rates for systems with a single…
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
We determine the equation of state of 2+1-flavor QCD with physical quark masses, in the presence of a constant (electro)magnetic background field on the lattice. To determine the free energy at nonzero magnetic fields we develop a new…
A microscopically resolved picture of energy flow in atom-diatom collisions is essential for understanding the non-equilibrium chemistry in rarefied and hypersonic gas flow. Here, a comprehensive ensemble of quasi-classical trajectories on…
The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Conical intersections serve as critical gateways in photochemical reactions, enabling rapid nonradiative transitions between potential energy surfaces that underpin fundamental processes such as photosynthesis or vision. Their calculation…
An electric-field-induced phase transition and pattern formation in a binary dielectric fluid layer are studied using a coarse-grained free energy functional. The electrostatic part of the free energy is a nonlinear functional of the…
We present a new method to evaluate vibrational free energies of atomic systems without a priori specification of an interatomic potential. Our model-agnostic approach leverages descriptors, high-dimensional feature vectors of atomic…
We present a precise and general method to map the activity of electrocatalysts across multiple sites. Starting from a mean-field statistical mechanics model, we introduce an effective adsorption free energy descriptor that explicitly…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…