Academic Articles & Research Papers

Unraveling the formation mechanism of 3-methylindole from tryptophan in the glucose-mediated Maillard reaction: a combined ReaxFF MD, DFT, and experimental study

3-Methylindole is a concentration-dependent aroma compound, and its formation mechanism in the tryptophan-glucose Maillard reaction is crucial for flavor regulation but remains incompletely elucidated. Using gas chromatography-olfactometry-...

Gas Transport in Shale Nanopores with Miscible Zone

Based on the results of molecular dynamics simulation, in a gas-water miscible zone, the velocity profiles of the flowing water film do not increase monotonously but increase first and then decrease, which is due to the interaction between ...

Conserved lipid-facing basic residues promote the insertion of the porin OmpC into the E. coli outer membrane

ABSTRACT Almost all integral membrane proteins that reside in the outer membrane (OM) of gram-negative bacteria contain a closed amphipathic β sheet (“β barrel”) that serves as a membrane anchor. The membrane integration of β barrel structu...

Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties

Structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are potential drug targets due to their role in the virus life cycle. The envelope (E) protein is one of the structural proteins; plays a critical role in v...

Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern

Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosyl...

Kinetic Theory of a Confined Quasi-Two-Dimensional Gas of Hard Spheres

The dynamics of a system of hard spheres enclosed between two parallel plates separated a distance smaller than two particle diameters is described at the level of kinetic theory. The interest focuses on the behavior of the quasi-two-dimens...

Molecular Quantum Dynamics: A Quantum Computing Perspective

ConspectusSimulating molecular dynamics (MD) within a comprehensive quantum framework has been a long-standing challenge in computational chemistry. An exponential scaling of computational cost renders solving the time dependent Schrödinger...

A Computational Quantum-Based Perspective on the Molecular Origins of Life’s Building Blocks

The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the...

Cross-Linking Simulation at Metal Oxide-Thermoset Interfaces Using Quantum Chemical and Molecular Dynamics Methods.

Mechanism-oriented design of magnetic COF adsorbents for efficient extraction of phenoxy acid herbicides: Insights from DFT calculations and molecular dynamics simulations.

Atomic heat transfer in nanoscale contacts mediated by van der Waals interactions

Abstract Van der Waals-interfacial heat transfer is a key element in thermal problems in atomic-scale devices including quantum computing devices, solid-state batteries, and solar power generation devices. However, its characterization rema...

Transport Properties of Mie Fluids: Molecular Dynamics Simulations and Entropy Scaling.

Lipid-mediated gating of a miniature mechanosensitive MscS channel from Trypanosoma cruzi

Abstract The mechanosensitive channel of small conductance (MscS) from E. coli (EcMscS) has served as the prevailing model system for understanding mechanotransduction in ion channels. Trypanosoma cruzi, the protozoan parasite causing Chaga...

Bypassing the Kohn-Sham equations with machine learning

Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy fun...

Identification of novel serotonin transporter (SERT) inhibitors via large-scale machine learning-based virtual screening and molecular dynamics simulations.

Designing novel linagliptin analogs through combined generative artificial intelligence, molecular docking, molecular dynamics simulation, and binding energy estimation for targeting fibroblast activation protein

Fibroblast activation protein (FAP) is a highly specific biomarker overexpressed in cancer-associated fibroblasts, making it a promising diagnostic target. Developing novel high-affinity molecular probes for FAP-targeted diagnostics remains...