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Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
The prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) of small molecules from their molecular structure is a central problem in medicinal chemistry with great practical importance in drug discovery.…
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential.…
Many models of interest in the natural and social sciences have no closed-form likelihood function, which means that they cannot be treated using the usual techniques of statistical inference. In the case where such models can be…
The hydration or binding free energy of a drug-like molecule is a key data for early stage drug discovery. Hundreds of thousands of evaluations are needed, which rules out the exhaustive use of atomistic simulations and free energy methods.…
The accurate but fast calculation of molecular excited states is still a very challenging topic. For many applications, detailed knowledge of the energy funnel in larger molecular aggregates is of key importance requiring highly accurate…
We discuss certain basic features of the equation-free (EF) approach to modeling and computation for complex/multiscale systems. We focus on links between the equation-free approach and tools from systems and control theory (design of…
The free energy principle (FEP) in the neurosciences stipulates that all viable agents induce and minimize informational free energy in the brain to fit their environmental niche. In this study, we continue our effort to make the FEP a more…
The free energy principle (FEP) from neuroscience provides a framework called active inference for the joint estimation and control of state space systems, subjected to colored noise. However, the active inference community has been…
Efficient sampling from the Boltzmann distribution given its energy function is a key challenge for modeling complex physical systems such as molecules. Boltzmann Generators address this problem by leveraging continuous normalizing flows to…
Boron phosphide (BP) is a (super)hard semiconductor constituted of light elements, which is promising for high demand applications at extreme conditions. The behavior of BP at high temperatures and pressures is of special interest but is…
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…
The 'free energy principle' (FEP) has been suggested to provide a unified theory of the brain, integrating data and theory relating to action, perception, and learning. The theory and implementation of the FEP combines insights from…
Understanding the applicability and limitations of electronic-structure methods needs careful and efficient comparison with accurate reference data. Knowledge of the quality and errors of electronic-structure calculations is crucial to…
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties.…
Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data. Recent experiment-guided generators attempt to address this by steering…
The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic…