Related papers: Application of Information Spectrum Method on Smal…
At the international linear collider, measurement of the beam profile at the interaction point is a key issue to achieve high luminosity. We report a simulation study on a new beam profile monitor, called the pair monitor, which uses the…
Interactions between pieces of information (entities) play a substantial role in the way an individual acts on them: adoption of a product, the spread of news, strategy choice, etc. However, the underlying interaction mechanisms are often…
Molecular property prediction is a fundamental task in the drug and material industries. Physically, the properties of a molecule are determined by its own electronic structure, which is a quantum many-body system and can be exactly…
The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Total Internal Reflection Microscopy (TIRM) is a sensitive non-invasive technique to measure the interaction potentials between a colloidal particle and a wall with femtonewton resolution. The equilibrium distribution of the particle-wall…
A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
We present a source engineering concept for a binary quantum mixture suitable as input for differential, precision atom interferometry with drift times of several seconds. To solve the non-linear dynamics of the mixture, we develop a set of…
Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
A joint design of both sensing and communication can lead to substantial enhancement for both subsystems in terms of size, cost as well as spectrum and hardware efficiency. In the last decade, integrated sensing and communications (ISAC)…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
This paper explores the development of the Six Stages of Information Search Model and its enhancement through the application of the Large Language Model (LLM) powered Information Search Processes (ISP) in healthcare. The Six Stages Model,…
Computational simulation of chemical and biological systems using ab initio molecular dynamics has been a challenge over decades. Researchers have attempted to address the problem with machine learning and fragmentation-based methods.…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used…
The increasing volume of drug combinations in modern therapeutic regimens needs reliable methods for predicting drug-drug interactions (DDIs). While Large Language Models (LLMs) have revolutionized various domains, their potential in…