Academic Articles & Research Papers

Large-scale screening of high-entropy materials for superionic solid electrolytes

Abstract Solid electrolytes have emerged as a promising alternative to conventional liquid electrolytes that have posed safety concerns. However, the relatively low ionic conductivity of solid electrolytes is one of the challenges for their...

Immunoinformatics and Reverse Vaccinology Approach for the Identification of Potential Vaccine Candidates against <i>Vandammella animalimors</i>

Vandammella animalimorsus is a Gram-negative and non-motile bacterium typically transmitted to humans through direct contact with the saliva of infected animals, primarily through biting, scratches, or licks on fractured skin. The absence o...

Dynamic Assembly of Microgels and Polymers at Non‐Aqueous Liquid/Liquid Interfaces

Abstract Particle assembly at liquid–liquid interfaces presents a promising bottom‐up strategy for creating supramolecular materials with advanced functionalities. However, the significantly lower interfacial tension observed in immiscible ...

In silico design of a triple-negative breast cancer vaccine by targeting cancer testis antigens

Introduction: Triple-negative breast cancer (TNBC) is an important subtype of breast cancer, which occurs in the absence of estrogen, progesterone and HER-2 receptors. According to the recent studies, TNBC may be a cancer testis antigen (CT...

Evaluation of resistance modulation in MDR Pseudomonas aeruginosa and Klebsiella pneumoniae using peppermint oil nanoemulsion: integrating antibacterial assays and molecular modeling

IntroductionMultidrug-resistant urinary tract pathogens, primarily Klebsiella pneumoniae and Pseudomonas aeruginosa, represent a significant and growing public health challenge. The overuse of antibiotics has accelerated the development of ...

Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation app...

Evaluating the Effects of Molecular Dynamic And Docking of Abemaciclib, Hymenialdisine, and Indirubin on CDK-2 Inhibition by Simulation Study

Background & objectives: Cyclin-dependent kinase 2 (CDK-2) is a serine/threonine protein kinase with regulatory activity in the cell cycle. Inhibitors of this protein are the treatment of choice for a variety of cancers by stopping the cell...

Investigating the Design of ssPalmO-Derived Lipid Nanoparticles for mRNA Delivery Applications Using Molecular Dynamics Simulations

Polymer brush in articular cartilage lubrication: Nanoscale modelling and simulation

Human knee joints move smoothly under high load conditions due to articular cartilage and synovial fluid. Much attention is paid to the role of proteoglycans. It is suggested that a part of proteoglycan forms aggregate on the cartilage surf...

Multi-Cohort Transcriptomics Combined with Mendelian Randomization Identifies PPARGC1A, NAAA and GIPC2 as NLRP3 Inflammasome-Related Key Genes in Ulcerative Colitis

Jian Cheng, Yangfeng Huang Department of Traditional Chinese Medicine, Sichuan Provincial People’s Hospital, School of Medicine,University of Electronic Science and Technology of China, Chengdu, Sichuan, People’s Republic of ChinaCorrespond...

Dislocation-Grain Boundary Interaction Dataset for FCC Cu

Abstract Interactions between dislocations and grain boundaries play a major role in controlling the strength and ductility of structural materials. Experimentally, assessing and probing geometric and stress-based criteria at the local leve...

Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet

SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2...

Molecular Dynamics and In Vitro Studies Elucidating the Tunable Features of Reconfigurable Nanodiscs for Guiding the Optimal Design of Curcumin Formulation

In this study, we advance our exploration of Apolipoprotein A-I (apoA-I) peptide analogs (APAs) for their application in nanodisc (ND) assembly, focusing on the dynamic conformational characteristics and the potential for drug delivery. We ...

Developing a Framework for Using Molecular Dynamics in Additive Manufacturing Process Modelling

Additive Manufacturing (AM), or else Smart Manufacturing, has been an intrinsic concept in Industry 4.0, offering flexibility and material efficiency. Certain limitations prevent AM from being used in the industrial setting extensively, des...

Effective analysis of neurotoxicity and mechanisms of dioctyl terephthalate using network toxicology

ObjectiveDioctyl terephthalate (DOTP), a widely used plasticizer in food packaging and environmental materials, has raised concerns regarding its potential impact on human health. This study aims to investigate the neurotoxicity-related mec...

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...