Related papers: A Bayesian approach for extracting free energy pro…
We apply the iterative Expectation-Maximization algorithm (EM) to estimate the power spectrum of the CMB from multifrequency microwave maps. In addition, we are also able to provide a reconstruction of the CMB map. By assuming that the…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
An efficient computational approach for optimal reconstruction of binary-type images suitable for models in various applications including biomedical imaging is developed and validated. The methodology includes derivative-free optimization…
In single particle reconstruction (SPR) from cryo-electron microscopy (cryo-EM), the 3D structure of a molecule needs to be determined from its 2D projection images taken at unknown viewing directions. Zvi Kam showed already in 1980 that…
Free energy biasing methods have proven to be powerful tools to accelerate the simulation of important conformational changes of molecules by modifying the sampling measure. However, most of these methods rely on the prior knowledge of…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include `phase flipping', which corrects only for the Fourier phases but…
Energy-based models (EBMs) provide a powerful and flexible way of learning a joint probability distribution over data by constructing an energy surface. This energy surface enables insight extraction and conditional sampling. We apply EBMs…
Half of wavefunction information is undetected by conventional transmission electron microscopy (CTEM) as only the intensity, and not the phase, of an image is recorded. Following successful applications of deep learning to optical hologram…
Classifying structural variability in noisy projections of biological macromolecules is a central problem in Cryo-EM. In this work, we build on a previous method for estimating the covariance matrix of the three-dimensional structure…
Cryo-electron microscopy can now routinely deliver atomic resolution structures for a variety of biological systems. The relevance and value of these structures is directly related to their ability to help rationalize experimental…
In this PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and…
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…
In diffusion MRI (dMRI), a good sampling scheme is important for efficient acquisition and robust reconstruction. Diffusion weighted signal is normally acquired on single or multiple shells in q-space. Signal samples are typically…
The challenge of optimal design of experiments (DOE) pervades materials science, physics, chemistry, and biology. Bayesian optimization has been used to address this challenge in vast sample spaces, although it requires framing experimental…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
Scanning transmission electron microscopy (STEM) is now the primary tool for exploring functional materials on the atomic level. Often, features of interest are highly localized in specific regions in the material, such as ferroelectric…
Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…
Conditional video diffusion models (CDM) have shown promising results for video synthesis, potentially enabling the generation of realistic echocardiograms to address the problem of data scarcity. However, current CDMs require a paired…