arXiv subjects

Igal Szleifer

Publications and source records attributed to Igal Szleifer.

4 recordsLinked to original sources

arXiv2025

RN-SDEs: Limited-Angle CT Reconstruction with Residual Null-Space Diffusion Stochastic Differential Equations

Computed tomography is a widely used imaging modality with applications ranging from medical imaging to material analysis. One major challenge arises from the lack of scanning information at certain angles, resulting in distortion or artifacts in the reconstructed images. This is referred to as the Limited Angle Computed Tomography (LACT) reconstruction problem. To address this problem, we propose the use of Residual Null-Space Diffusion Stochastic Differential Equations (RN-SDEs), which are a variant of diffusion models that characterize the diffusion process with mean-reverting (MR) stochastic differential equations. To demonstrate the generalizability of RN-SDEs, we conducted experiments with two different LACT datasets, ChromSTEM and C4KC-KiTS. Through extensive experiments, we demonstrate that by leveraging learned MR-SDEs as a prior and emphasizing data consistency using Range-Null Space Decomposition (RNSD) based rectification, we can recover high-quality images from severely degraded ones and achieve state-of-the-art performance in most LACT tasks. Additionally, we present a quantitative comparison of RN-SDE with other networks, in terms of computational complexity and runtime efficiency, highlighting the superior effectiveness of our proposed approach.

eess.IV↗

arXiv2024

Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as Rad21 degradation.

physics.bio-ph↗

arXiv2018

Association Free Energies of Metal Cations with Mesylate and Acetate in Brine Calculated via Molecular Dynamics Simulation

Here we report results from fully-atomistic molecular dynamics simulations and present the calculated binding free energies of the associations between metal cations and anionic functional groups under brine condition. Specifically the ion pair formations of Na+ and Ca2+ metal cations with sulfonate and carboxylate functional groups were considered. In our simulations, sulfonate and carboxylate functional groups in polyelectrolytes were modeled by mesylate and acetate anions, respectively. The simulations show that the binding strengths of Na+ and Ca2+ with sulfonate group are relatively weak with correlation times for the contact ion pairs being around 300-400 ps. In the case of acetate, the binding strength with Na+ was found to be comparable to the case of sulfonate group, while the binding of acetate with Ca2+ was found to be much stronger with a correlation time of the order of hundreds of nanoseconds. The binding free energies of Na+ and Ca2+ with sulfonate as well as that of Na+ with acetate have been calculated directly from the radial distribution functions. For the case of binding between Ca2+ and acetate constrained MD simulations with umbrella sampling were carried out to improve the sampling of the phase space and the potential of mean force was obtained by the weighted histogram analysis method. The binding free energy of a 2:1 binding event between one Ca2+ ion and two acetates was also calculated. Finally the binding free energies between Ca2+ and acetate were compared for different force field parameters and water models, and also with experimental and calculated values reported in the literature.

physics.chem-ph↗

arXiv2013

The water supercooled regime as described by four common water models

The temperature scale of simple water models in general does not coincide with the natural one. Therefore, in order to make a meaningful evaluation of different water models a temperature rescaling is necessary. In this paper we introduce a rescaling using the melting temperature and the temperature corresponding to the maximum of the heat capacity to evaluate four common water models (TIP4P-Ew, TIP4P-2005, TIP5P-Ew and Six-Sites) in the supercooled regime. Although all the models show the same general qualitative behavior, the TIP5P-Ew appears as the best representation of the supercooled regime when the rescaled temperature is used. We also analyze, using thermodynamic arguments, the critical nucleus size for ice growth. Finally, we speculate on the possible reasons why atomistic models do not usually crystalize while the coarse grained mW model do crystallize.

physics.chem-ph↗