molecular dynamics Articles
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Exploring dynamic pathways by action-derived molecular dynamics
Action-derived molecular dynamics for the simulation of rare event and slow mode systems is reviewed. Theoretical background, implementation details, and comparison with other methods are presented. Numerical examples demonstrated include the structural formation and transformation of carbon fullerenes, and molecular reconfiguration of alanine dipeptide and valine dipeptide. It is shown that the ...
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Ring-crack initiation in micrometer-scale Hertz indentation simulated by controlled molecular dynamics
Hertz indentation has been simulated using the controlled molecular dynamics proposed by the authors. The result of the simulation shows that a defect, which may develop into a ring crack, can be initiated during indentation even in monocrystalline silicon with no preexisting defect. The defect initiation occurs just outside the outer periphery of the contact surface between silicon and a diamond ...
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What Are Potentials in Molecular Dynamics Simulation?
Introduction The atoms in biomolecules are always in constant motion, and the functions of molecules and the interactions between them are closely related to the dynamics of the molecules involved. In other words, to understand the working mechanism of proteins or other biomolecules, molecular biologists must first be able to clearly know the movement patterns of these biomolecules, and can ...
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Molecular dynamics simulations of breaking metallic nanowires
In the present work, we have reviewed the importance of conductance histograms as an experimental tool able to address the statistical behaviour of the electronic transport through metallic nanowires. We have described how molecular dynamics techniques combined with embedded-atom method (EAM) are able to reproduce the general features noticed during metallic nanowire breaking experiments. We have ...
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Decoding the Language of Proteins: Insights from Molecular Dynamics Simulation
Molecular dynamics simulation is a powerful and widely employed computational method that investigates the motion and interactions of molecules under different conditions, revealing the structure, dynamics, and physical-chemical properties of molecules. This article aims to delve into the fundamental principles, applications, and key techniques of molecular dynamics simulation, providing you with ...
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Molecular dynamics simulation of the nano–ejection system with various interfacial wettabilities
Because of the significance of the interfacial phenomenon, this study examines the nanojet ejection systems with various interfacial wettabilities. A modified Lennard–Jones potential function was used to simulate the various solid–liquid interfacials from strongly hydrophilic to strongly hydrophobic. The properties distributions with various hydrophilic/hydrophobic interfaces are shown and ...
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Mesoscale modelling: recent developments and applications to nanocomposites, drug delivery and precipitation membranes
Mesoscale simulations have traditionally been used to investigate structural morphology of polymers in solution, melts and blends. Recently, such modelling methods are being pushed to important areas of Nanotechnology and Drug delivery that are well out of reach of classical molecular dynamics. This paper describes our current efforts in three important emerging areas: polymer-nanotube ...
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Molecular interactions of degradable and non-degradable polymers with hydroxyapatite influence mechanics of polymer-hydroxyapatite nanocomposite biomaterials
Implant materials composed of hard and soft phases (composite materials) have shown much promise for total bone replacement. Interfacial interactions between the components in these composite biomaterials affect the overall mechanical response. Here, the role of interfacial interactions on the load deformation behaviour of soft phase (polymer) have been analysed using constant velocity Steered ...
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Dendrimers at the air-water interface: surface dynamics and molecular ordering
In recent years considerable effort has been devoted to the fabrication of molecular devices by exploiting ultra thin organic films. Our attention has been focused on dendrimers, one of the most promising candidates for use in preparing highly functionalised devices due to their flexible architecture and unique properties. Thin films of dendrimers provide better control over the inter-distance ...
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Distinct mechanisms of endocrine disruption of DDT‐related pesticides toward ER α and ERR γ
Dichlorodiphenyl‐trichloroethane (DDT) is ubiquitous in the environment, and the exposure to DDT and its related pesticides has long been linked to endocrine disruption. The mechanism of endocrine disruption toward targeted receptors, however, remains unclear. Probing the molecular recognition of DDT analogs by targeted receptors at the atomic level is critical for deciphering this mechanism. ...
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Application of site-identification by ligand competitive saturation in computer-aided drug design
Abstract Site Identification by Ligand Competitive Saturation (SILCS) is a molecular simulation approach that uses diverse small solutes in aqueous solution to obtain functional group affinity patterns of a protein or other macromolecule. This involves employing a combined Grand Canonical Monte Carlo (GCMC)-molecular dynamics (MD) method to sample the full 3D space of the protein, including ...
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Useful Approaches for Labeling Peptides with Fluorescent Dyes
Due to the high sensitivity, flexibility, selectivity, and environmental stability, fluorescent techniques are broadly applied in biological research. Peptides provide unique possibilities for the development of efficient and selective fluorescent sensors because of their modular nature, synthetic accessibility, and biomolecular recognition potential. Accordingly, labeling peptides with ...
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The Key Factor of Excellent Drug Efficacy: Chemical Structure of Drug
How to keep the drug active and give full play to its therapeutic effect has always been the primary problem to be solved by researchers in the field of pharmacy. It is a very complex process from drug administration to the generation of drug efficacy. Scientists have divided this process into three phases: Pharmaceutical phase, pharmacokinetic phase and pharmacodynamic phase. Only by ensuring ...
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The Mode of Action of Basic Proteins Involved in Cancer and Alzheimer's Disease Found
These proteins belonging to the HAT family are essential for life because they transport amino acids to the cell membrane. Although members of the family are nearly identical, they selectively transport certain amino acids. This specificity determines their involvement in specific functions, such as cell growth or neuronal function, and consequently in related diseases, such as cancer or ...
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New Technology to Promote Drug Development-AI Technology
For a long time, the research and development of each new drug has faced the challenges of high cost and long cycle. In response to these challenges, major pharmaceutical companies have shifted from targeting common diseases to developing drugs for specific diseases. At the same time, these companies are constantly looking for new technologies for new drug development, such as high-throughput ...
By BOC Sciences
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Novel Mechanism of Glycosylation Regulating Pancreatic Cancer Reveled
Pancreatic cancer is a highly malignant digestive system tumor, and the five-year survival rate of patients after diagnosis is only about 10%. Changes in metabolism are one of the important features of tumor cells. Tumor cells undergo metabolic reprogramming to generate the substances, energy, and redox forces required for their rapid proliferation. The proliferation of pancreatic ductal ...
By CD BioGlyco.
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Bile Acid: A Comprehensive Exploration of Function and Metabolism
In the realm of biological sciences, bile acids stand as pivotal molecules, playing a multifaceted role in various physiological processes within organisms. Bile acids are specialized molecules synthesized from cholesterol within the liver. These amphipathic compounds possess a hydrophilic region (carboxylic acid moiety) and a hydrophobic region (steroid backbone). Their distinctive structure ...
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