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Extended Systems
Studying extended systems like gases, fluids, or solids is very important in science. 3D extended systems include crystals, amorphous materials, or...
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Implementation of Molecular Dynamics in Simulations
In this chapter, we will briefly describe the practical aspects of molecular dynamics simulations, such as designing the constraints, periodic...
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Particle-Based Methods for Mesoscopic Transport Processes
Biological phenomena at cellular and subcellular levels involve transport of reacting biochemical species, including proteins, enzymes, and...
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Drag force on a microrobot propelled through blood
Controlling microrobot locomotion in vessels and capillaries is crucial for precise drug delivery and minimally invasive surgeries. However, this is...
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Application of the Crystal Structure of the SARS-CoV-2 Spike Protein for the Development of a Peptide Vaccine against Virus
AbstractBased on the spike protein of the SARS-CoV-2 virus, a protein capable of causing an immune answer has been predicted. The protein stability...
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Application of Protein Crystallography and Machine Learning Data for the Development of a Peptide Vaccine against African Swine Fever
AbstractThe genome of African swine fever (ASF) has been analyzed, and a protein that can serve an immunogen has been identified. A water-soluble...
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Large-scale dark matter simulations
We review the field of collisionless numerical simulations for the large-scale structure of the Universe. We start by providing the main set of...
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The Atomistic Perspective of Nanoscale Laser Ablation
Materials irradiated by ultrashort laser pulses can undergo a variety of surface relief and structural modifications due to melting, spallation, and...
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Explicit solvent machine-learned coarse-grained model of sodium polystyrene sulfonate to capture polymer structure and dynamics
Strongly charged polyelectrolytes (PEs) demonstrate complex solution behavior as a function of chain length, concentrations, and ionic strength. The...
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Modeling of the Interaction of Cytochrome c with the Lipid Bilayer
Abstract—Interactions of horse heart cytochrome c (Cyt c ) with the lipid bilayer consisting of tetraoleoyl cardiolipin molecules were studied by...
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Tuning the Molecular Structure and Transport Property of [bmim][Tf2N] Using Electric Field
In this work, the effects of electric field on the microstructure and transport property of [bmim][Tf 2 N] were simulated by molecular dynamics method...
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Computational Methods on Atomistic/Microscopic Scale
On the atomistic and microscopic scale, the possible conformations (the spatial arrangements) of particles—besides their energy—begins to play a...
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Anomalous diffusion of lithium-anion clusters in ionic liquids
AbstractLithium-ion transport is significantly retarded in ionic liquids (ILs). In this work, we performed extensive molecular dynamics simulations...
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Predicting mechanical failure of polycrystalline dual-phase nickel-based alloys by numerical homogenization using a phase field damage model
Brazing of nickel-based alloys plays a major role in the assembly of turbine components, e.g., abradable sealing systems. In a brazed joint of...
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Molecular dynamics study on structures and adsorption capacity of activated carbon prepared from corn straw and sewage sludge by molten salt method
Activated carbon was prepared from corn straw and sewage sludge by molten salt method, and its structures and adsorption capacity were studied. When...
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Structural Bioinformatics Study of the Structural Basis of Substrate Specificity of Purine Nucleoside Phosphorylase from Thermus thermophilus
AbstractMolecular dynamics simulations were performed for wild-type purine nucleoside phosphorylase in complexes with two substrates (adenosine and...
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Experimental Measurements and Molecular Simulations on the Liquid Density and Viscosity of Pentaerythritol Tetraacetate
Pentaerythritol tetraacetate (PEC2) and its homologs are widely used in many applications, like mechanical lubricants, engine oils, hydraulic oils,...
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A molecularly informed field-theoretic study of the complexation of polycation PDADMA with mixed micelles of sodium dodecyl sulfate and ethoxylated surfactants
AbstractThe self-assembly and phase separation of mixtures of polyelectrolytes and surfactants are important to a range of applications, from...
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Adaptive grid implementation for parallel continuum mechanics methods in particle simulations
In this tutorial review paper, we present our minimally invasive approach for integrating dynamically adaptive tree-structured grids into existing...
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Molecular Perspective on Solutions and Liquid Mixtures from Modelling and Experiment
Liquid solutions and mixtures are part of our everyday lives and also important for their chemical and industrial applications. While considered...