Related papers: Binding Free Energies without Alchemy
This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from…
Flow Matching (FM) models have emerged as a leading paradigm for high-fidelity synthesis. However, their reliance on iterative Ordinary Differential Equation (ODE) solving creates a significant latency bottleneck. Existing solutions face a…
The scaled boundary finite element method (SBFEM) is a relatively recent boundary element method that allows the approximation of solutions to PDEs without the need of a fundamental solution. A theoretical framework for the convergence…
In this work we propose a chemically-informed data-driven approach to benchmark the approximate density-functional tight-binding (DFTB) excited state (ES) methods that are currently available within the DFTB+ suite. By taking advantage of…
For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built.…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…
Ensemble density functional theory (eDFT) is an exact time-independent alternative to time-dependent DFT (TD-DFT) for the calculation of excitation energies. Despite its formal simplicity and advantages in contrast to TD-DFT (multiple…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
This article fills a gap in the mathematical analysis of Adaptive Biasing algorithms, which are extensively used in molecular dynamics computations. Given a reaction coordinate, ideally, the bias in the overdamped Langevin dynamics would be…
This paper studies the distributed optimal bilinear equalizer (OBE) beamforming design for both the uplink and downlink cell-free massive multiple-input multiple-output networks. We consider arbitrary statistics-based channel estimators…
We consider the classical molecular beam epitaxy (MBE) model with logarithmic type potential known as no-slope-selection. We employ a third order backward differentiation (BDF3) in time with implicit treatment of the surface diffusion term.…
Existing works are dedicated to untangling atomized numerical components (features) from the hidden states of Large Language Models (LLMs). However, they typically rely on autoencoders constrained by some training-time regularization on…
We present a novel inference algorithm for arbitrary, binary, undirected graphs. Unlike loopy belief propagation, which iterates fixed point equations, we directly descend on the Bethe free energy. The algorithm consists of two phases,…
This work presents an unfitted boundary algebraic equation (BAE) method for solving three-dimensional elliptic partial differential equations on complex geometries using finite difference on structured meshes. We demonstrate that replacing…
Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
Several research groups have recently reported {\em ab initio} calculations of the melting properties of metals based on density functional theory, but there have been unexpectedly large disagreements between results obtained by different…
A thermodynamic integration (TI) protocol incorporating dummy atoms is introduced to calculate free energy differences for disulfide bond formation in proteins. This method successfully reproduces experimental redox potentials for multiple…