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The analysis of the mutational landscape of cancer, including mutual exclusivity and co-occurrence of mutations, has been instrumental in studying the disease. We hypothesized that exploring the interplay between co-occurrence, mutual…
We introduce a computational framework for generating realistic transition paths between distinct conformations of large bio-molecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
Joinable Column Discovery is a critical challenge in automating enterprise data analysis. While existing approaches focus on syntactic overlap and semantic similarity, there remains limited understanding of which methods perform best for…
We theoretically investigate the many-body dynamics of a tight-binding chain with dephasing noise on the infinite interval. We obtain the exact solution of an average particle-density profile for the domain wall and the alternating initial…
39 detailed mechanisms for combustion of hydrogen, carbon monoxide and methanol are investigated using ReactionKinetics, a Mathematica based package. The obtained results in most cases do not depend on the choice of reaction rate…
A variety of high-energy astrophysical phenomena are powered by the release -- via magnetic reconnection -- of the energy stored in oppositely directed fields. Single-fluid resistive magnetohydrodynamic (MHD) simulations with uniform…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
The Alchemical Transfer Method (ATM) is herein validated against the relative binding free energies of a diverse set of protein-ligand complexes. We employed a streamlined setup workflow, a bespoke force field, and the AToM-OpenMM software…
We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of…
Classification and identification of amino acids in aqueous solutions is important in the study of biomacromolecules. Laser Induced Breakdown Spectroscopy (LIBS) uses high energy laser-pulses for ablation of chemical compounds whose…
The discovery of dynamical models from data represents a crucial step in advancing our understanding of physical systems. Library-based sparse regression has emerged as a powerful method for inferring governing equations directly from…
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…
The manner in which transport properties vary over the entire parameter-space of coupling and magnetization strength is explored for the first time. Four regimes are identified based on the relative size of the gyroradius compared to other…
We review the standard lock and key (LK) model for binding small ligands to larger adsorbent molecule. We discuss three levels of the traditional LK model for binding. Within this model the binding constant or the Gibbs energy of the…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
Linear and non-linear transport properties through an atomic-size point contact based on oxides two-dimensional electron gas is examined using the tight-binding method and the $\mathbf{k\cdot p}$ approach. The ballistic transport is…