arXiv subjects

Surahit Chewle

Publications and source records attributed to Surahit Chewle.

3 recordsLinked to original sources

arXiv2024

Topological analysis reveals multiple pathways in molecular dynamics

Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of generated data. In this work, we present Molecular Kinetics via Topology (MoKiTo), a novel approach that combines the ISOKANN algorithm to determine the reaction coordinate of a molecular system with a topological analysis inspired by the Mapper algorithm. Our strategy efficiently identifies and characterizes distinct molecular pathways, enabling the detection and visualization of critical conformational transitions and rare events. This method offers deeper insights into molecular mechanisms, facilitating the design of targeted interventions in drug discovery and protein engineering.

physics.chem-ph↗

arXiv2024

Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions

Markov processes serve as foundational models in many scientific disciplines, such as molecular dynamics, and their simulation forms a common basis for analysis. While simulations produce useful trajectories, obtaining macroscopic information directly from microstate data presents significant challenges. This paper addresses this gap by introducing the concept of membership functions being the macrostates themselves. We derive equations for the holding times of these macrostates and demonstrate their consistency with the classical definition. Furthermore, we discuss the application of the ISOKANN method for learning these quantities from simulation data. In addition, we present a novel method for extracting transition paths from simulations based on the ISOKANN results and demonstrate its efficacy by applying it to simulations of the μ-opioid receptor. With this approach we provide a new perspective on the analysis of macroscopic behaviour of Markov systems.

physics.chem-ph↗

arXiv2020

Analyzing Raman Spectral Data without Separability Assumption

Raman spectroscopy is a well established tool for the analysis of vibration spectra, which then allow for the determination of individual substances in a chemical sample, or for their phase transitions. In the Time-Resolved-Raman-Sprectroscopy the vibration spectra of a chemical sample are recorded sequentially over a time interval, such that conclusions for intermediate products (transients) can be drawn within a chemical process. The observed data-matrix $M$ from a Raman spectroscopy can be regarded as a matrix product of two unknown matrices $W$ and $H$, where the first is representing the contribution of the spectra and the latter represents the chemical spectra. One approach for obtaining $W$ and $H$ is the non-negative matrix factorization. We propose a novel approach, which does not need the commonly used separability assumption. The performance of this approach is shown on a real world chemical example.

math.NA↗