相关论文: Building intuition for binding free energy calcula…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
Symmetry-resolved entanglement, capturing the refined structure of quantum entanglement in systems with global symmetries, has attracted a lot of attention recently. In this manuscript, introducing the notion of symmetry-resolved…
Examination of symmetry energy is carried out on the basis of an elementary binding-energy formula. Constraints are obtained on the energy value at the normal nuclear density and on the density dependence of the energy at subnormal…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
Relationships between the coupling constant and the binding energy of threshold bound states are obtained in a simple manner from an iterative algorithm for solving the eigenvalue problem. The absence of threshold bound states in higher…
In quantum theory, bound states are described by eigenvalue equations, which usually cannot be solved exactly. However, some simple general theorems allow to derive rigorous statements about the corresponding solutions, that is, energy…
Symmetry is one of the most general and useful concepts in physics. A theory or a system that has a symmetry is fundamentally constrained by it. The same constraints do not apply when the symmetry is broken. The quantitative determination…
Real physical systems are only understood, experimentally or theoretically, to a finite resolution so in their analysis there is generally an ignorance of possible short-range phenomena. It is also well-known that the boundary conditions of…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
We seek to clarify the concept of active inference by disentangling it from the Free Energy Principle. We show how the optimizations that need to be carried out in order to implement active inference in discrete state spaces can be…
The excess entanglement resulting from exciting a finite number of quasiparticles above the ground state of a free integrable quantum field theory has been investigated quite extensively in the literature. It has been found that it takes a…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
The recent development of bootstrap methods based on semidefinite relaxations of positivity constraints has enabled rigorous two-sided bounds on local observables directly in the thermodynamic limit. However, these bounds inevitably become…
Symmetry is one of the most central concepts in physics, and it is no surprise that it has also been widely adopted as an inductive bias for machine-learning models applied to the physical sciences. This is especially true for models…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
Fast and accurate evaluation of free energy has broad applications from drug design to material engineering. Computing the absolute free energy is of particular interest since it allows the assessment of the relative stability between…
In this work, we revisit a problem we addressed in previous publications with various collaborators, that is, the computation of the symmetry resolved entanglement entropies of zero-density excited states in infinite volume. The universal…
The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from…
Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free…