Molecular Dynamics Simulation - Science topic

Non-Arrhenius grain boundary migration, sometimes referred to as antithermal migration where temperature and GB velocity values are inversely related to each other, is examined in an incoherent twin Σ3 [111] 60° (11 8 5) nickel grain boundary. Molecular dynamics is used to simulate migration and examine the effect of various factors on the migratio...

Ga2O3 has gained intensive interests of research and application as an ultrawide bandgap semiconductor. Epitaxial growth technique of the β-Ga2O3 thin film possesses a fundamental and vital role in the Ga2O3-based device fabrication. In this work, epitaxial growth mechanisms of β-Ga2O3 with four low Miller-index facets, namely (100), (010), (001),...

Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical...

We provide a theoretical description of dynamical heterogeneities in glass-forming liquids, based on the premise that relaxation occurs via local rearrangements coupled by elasticity. In our framework, the growth of the dynamical correlation length ξ and of the correlation volume χ4 are controlled by a zero-temperature fixed point. We connect this...

Some calcium channels selectively permeate Ca²⁺, despite the high concentration of monovalent ions in the surrounding environment, which is essential for many physiological processes. Without atomistic and dynamical ion permeation details, the underlying mechanism of Ca²⁺ selectivity has long been an intensively studied, yet controversial, topic. T...

To solve the adhesion problem between molten aluminum and vacuum ladle liner during the electrolytic aluminum production process, the wetting state and adhesion properties of molten aluminum droplets on substrate surfaces with different nanopillars are investigated based on molecular dynamics. The results show that the adhesion strength of molten a...

Since surface contaminants can make optical components such as fused silica highly susceptible to damage, how to maintain the cleanliness of fused silica is an effective way to improve the laser damage threshold. In this study, molecular dynamics techniques were employed to investigate the effect of surface roughness of fused silica on the adsorpti...

Nanopores have recently been used to identify and fingerprint proteins. However, because proteins, unlike DNA, do not have a uniform charge, the electrophoretic force cannot in general be used to translocate or linearize them. Here we show that the introduction of sets of charges in the lumen of the CytK nanopore spaced by ~1 nm creates an electroo...

We performed ab initio molecular dynamics simulations for pressures and temperatures from 300–5000 GPa and 3000–30 000 K in order to determine the equation of state of solid and liquid iron. By employing a thermodynamic integration technique, we derive the ab initio entropy and Gibbs free energy of both phases, which allows us to construct solid an...

The amyloid aggregation of α-synuclein (αS), related to Parkinson’s disease, can be catalyzed by lipid membranes. Despite the importance of lipid surfaces, the 3D-structure and orientation of lipid-bound αS is still not known in detail. Here, we report interface-specific vibrational sum-frequency generation (VSFG) experiments that reveal how monome...

The mechanical properties of calcium-silicate-hydrate (C-S-H) gels in cementitious materials are mainly realized by nanoindentation experiments. There is limited research on the dynamic response of the molecular structure of C-S-H under nanoindentation conditions. This study simulated the nanoindentation on the C-S-H gel samples by the molecular dy...

Aggregation‐induced emission (AIE) is a phenomenon where a molecule that is weakly or non‐luminescent in a diluted solution becomes highly emissive when aggregated. AIE luminogens (AIEgens) hold promise in diverse applications like bioimaging, chemical sensing, and optoelectronics. Investigation in AIE luminescence is also critical for understandin...

Fluorinated polyimides incorporated with triptycene units have gained growing attention over the last decade since they present potentially interesting selectivities and a higher free volume with respect to their triptycene-free counterparts. This work examines the transport of single-gas and mixed-gas N2 and CH4 in the triptycene-based 6FDA-BAPT h...

The effect of oscillatory shear deformation on the fatigue life, yielding transition, and flow localization in metallic glasses is investigated using molecular dynamics simulations. We study a well-annealed Cu-Zr amorphous alloy subjected to periodic shear at room temperature. We find that upon loading for hundreds of cycles at strain amplitudes ju...

The reaction dynamics of excited-state intramolecular proton transfer (ESIPT) tautomerism in 10-hydroxybenzoquinoline (HBQ), 1-hydroxyanthraquinone (HAQ), methyl salicylate (MS) and 4-methyl-2,6-diformyl phenol (MFOH) has been investigated by quantum mechanics/molecular mechanics–molecular dynamics (QM/MM–MD) simulation with four different solvents...

Sorghum is one of the four major C4 crops that are considered to be tolerant to environmental extremes. Sorghum shows distinct growth responses to temperature stress depending on the sensitivity of the genetic background. About half of the transcripts in sorghum exhibit diurnal rhythmic expressions emphasizing significant coordination with the envi...

The thermal conductivity of graphene is in the range of 3000–5000 W m⁻¹ K⁻¹, showing great potential in high thermal conductivity devices. However, the thermal conductivity of graphene-reinforced polymer is typically lower than 10 W m⁻¹ K⁻¹, which is far from theoretical expectations. To understand the mechanisms of heat transfer in graphene-reinfo...

The proton–activated chloride (PAC) channel plays critical roles in ischemic neuron death, but its activation mechanisms remain elusive. Here, we investigated the gating of PAC channels using its novel bifunctional modulator C77304. C77304 acted as a weak activator of the PAC channel, causing moderate activation by acting on its proton gating. Howe...

The principle of maximum entropy provides a canonical way to include measurement results into a thermodynamic ensemble. Observable features of a thermodynamic system, which are measured as averages over an ensemble are included into the partition function by using Lagrange multipliers. Applying this principle to the system's energy leads to the wel...

Despite the accumulating evidence linking the development of Alzheimer’s disease (AD) to the aggregation of Aβ peptides and the emergence of Aβ oligomers, the FDA has approved very few anti-aggregation-based therapies over the past several decades. Here, we report the discovery of an Aβ peptide aggregation inhibitor: an ultra-small nanodot called C...

The peridynamic (PD) theory is a nonlocal reformulation of mechanics with various advantages over common approaches, mainly local continuum mechanics and molecular dynamics (MD). PD theory can capture phenomena at different dimensions, including nanoscale. However, limited studies have been performed by this theory in nanoscale, which have generall...

α-amyloids present a novel self-assembly principle that can be utilized to prepare functional biomaterials. Evidence of α-amyloid formation in the active core of the human LL-37 protein (comprising residues 17 to 29) was associated with this peptide’s membranolytic property. Though mechanistic pathways of β-amyloid formation are known, such studies...

The Laplace–Beltrami problem on closed surfaces embedded in three dimensions arises in many areas of physics, including molecular dynamics (surface diffusion), electromagnetics (harmonic vector fields), and fluid dynamics (vesicle deformation). Using classical potential theory, the Laplace–Beltrami operator can be pre-/post-conditioned with an inte...

A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grou...

Oxidation results in the formation of an oxide film whose properties and structure can be tailored by controlling the oxidation conditions. Reactive molecular dynamics simulations were performed to study thermal oxidation of polycrystalline Al substrates as a function of O2 density and temperature. The structural, chemical, and topological aspects...

Representation learning (RL) is a universal technique for deriving low-dimensional disentangled representations from high-dimensional observations, aiding a multitude of downstream tasks. RL has been extensively applied to various data types, including images and natural language. Here, we analyze molecular dynamics (MD) simulation data of biomolec...

Evidence shows that charge carriers in organic semiconductors self-localize because of dynamic disorder. Nevertheless, some organic semiconductors feature reduced mobility at increasing temperature, a hallmark for delocalized band transport. Here we present the temperature-dependent mobility in two record-mobility organic semiconductors: dinaphtho[...

Data-driven interatomic potentials have emerged as a powerful tool for approximating ab initio potential energy surfaces. The most time-consuming step in creating these interatomic potentials is typically the generation of a suitable training database. To aid this process hyperactive learning (HAL), an accelerated active learning scheme, is present...

Variations of the threshold of swift heavy ion track formation with the ion energy and mass are studied here. We apply the hybrid multiscale approach combining TREKIS-3 code describing the electronic kinetics with the classical molecular dynamics tracing the evolution of the excited lattice. The results demonstrate that with a lowering of the energ...

Alchemical free energy methods can be used for the efficient computation of relative binding free energies during preclinical drug discovery stages. In recent years, this has been facilitated further by the implementation of workflows that enable non-experts to quickly and consistently set up the required simulations. Given the correct input struct...

Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing and elongation processivity. Spt5 was also recognized for its roles in transcription of expanded-repeat genes that are related to neurogenerative diseases. Recently, a set of Spt5-Pol II small mo...

Mechanical force is critical for the interaction between an alpha beta T cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 prese...

In recent years, certain molecular crystals have been reported to possess surprising flexibility by undergoing significant elastic or plastic deformation in response to mechanical loads. However, despite this experimental evidence, there currently exists no atomistic mechanism to explain the physical origin of this phenomenon from numerical simulat...

Using the molecular dynamics simulation method, nanoindentation simulation was carried out on a variety of nanotwin Cu-Ag alloys with different gradient distribution structures and twin spacing to study the mechanical properties and deformation mechanism of nanotwin Cu-Ag alloys with a grain size of 15 nm. The deformation, failure process, and micr...

The two-states Markovv-states-model of molecular dynamics is newly analyt-ically studied. The total reward of the path integral of the reaction within acrisp Markovv landscape is proven to be expressed as a Laplace integral (kernel)after the opportune Radon measure. The evolution of the eigenvalues is newlyexactly analytical calculated; the corresp...

During macroautophagy, cytoplasmic constituents are engulfed by autophagosomes. Lysosomes fuse with closed autophagosomes but not with unclosed intermediate structures. This is achieved in part by the late recruitment of the autophagosomal SNARE syntaxin 17 (STX17) to mature autophagosomes. However, how STX17 recognizes autophagosome maturation is...

Coarse-grained (CG) force fields are essential for molecular dynamics simulations of biomolecules, striking a balance between computational efficiency and biological realism. These simulations employ simplified models grouping atoms into interaction sites, enabling the study of complex biomolecular systems over biologically relevant timescales. Eff...

Machine learning interatomic potentials (MLIPs) that enable accurate simulations of materials at scales beyond conventional first-principles approaches have played increasingly important roles in understanding and design of materials. However, MLIPs are only as accurate and robust as the data they are trained on. In this work, we present DImensiona...

Atomic oxygen (AO), which is one of the most predominant and conspicuous space environmental factors in the low earth orbit, leads to severe deterioration of polymeric materials in spacecraft. The AO flux density and ambient temperature vary while a craft orbits in space; thus, it is necessary to pay close attention to the flux density and temperat...

The potential of B20 cluster decorated with alkali metals (AM = Li, Na, and K) and alkaline earth metals (AEM = Ca, Mg, and Be) to adsorb hydrogen molecules is investigated using density functional theory (DFT). The Bader’s topological parameters suggest the presence of non-bonded interaction between the bare structures and H2 molecules. Global rea...

Almost 80 co-crystal structures of KRAS switch-II pocket (SII-P) targeting inhibitors are currently available in the RCSB Protein Data Bank. These publicly available structures are invaluable tools that have led to a more in-depth understanding of KRAS SII-P pocket, which is crucial for targeted drug design efforts. The binding modes (co-crystal st...

Machine learning methods can be used to predict the properties of materials from their structure. This can be particularly useful in cases where other standard methods for finding material properties are time and resources consuming to use on large sample spaces. In this work, we study the strength of α-quartz crystals with a porous layer created b...

Thin sheets respond to confinement by smoothly wrinkling or by focusing stress into small, sharp regions. From engineering to biology, geology, textiles, and art, thin sheets are packed and confined in a wide variety of ways, and yet fundamental questions remain about how stresses focus and patterns form in these structures. Using experiments and m...

The Derjaguin–Landau–Verwey–Overbeek (DLVO) theory, introduced more than 70 years ago, is a hallmark of colloidal particle modeling. For highly charged particles in the dilute regime, it is often supplemented by Alexander’s prescription (Alexander et al. in J Chem Phys 80:5776, 1984) for using a renormalized charge. Here, we solve the problem of th...

This work addresses the issue of laser-induced white light generation by nano- and micro-diamond powder and the accompanying redox processes occurring at the surface of the particles. The broadband white light is generated by near infra-red continuous wave laser (975 nm) on micro and nano-diamond powders sealed in lightbulb-like devices. It is show...

In this article, the influence of crystallographic orientation on the mechanical properties of pristine nickel (Ni) during uniaxial tensile deformation was explored by utilizing molecular dynamics simulations. To study the influence of [0 01] and [11 8 5] crystal orientations on the mechanical properties and microstructural evolution of pristine Ni...

Hardness of nanostructured metallic multilayers (NMMs) are often understood from their dependence on individual layer thickness (h), yet little is known about the impacts exerted by other microstructural factors. In this work, the effects of residual stress and interface coherency on the deformation mechanisms of Al/Ti NMMs with h = 2.5–52 nm were...

The corrosion of materials remains a critical challenge with significant economic and infrastructural impacts. A comprehensive understanding of adsorption characteristics of phytochemicals can facilitate the effective design of high-performing environmentally friendly inhibitors. This study conducted a computational exploration of hydroxytyrosol (H...

The spike glycoprotein receptor-binding domain (RBD) of SARS-CoV-2 facilitates viral binding to the ACE2 receptor and mediates viral infectivity. The Delta and Omicron variants of concern are the most infectious strains, presenting mutated amino acid residues in their spike RBD. The Omicron variant quickly dominated the COVID-19 pandemic, indicatin...

The structure and dynamics of copolymers of 2-hydroxyethyl methacrylate (HEMA) with 2-methacryloyloxyethyl phosphorylcholine (MPC) were studied by molecular dynamics simulations. In total, 20 systems were analyzed. They differed in numerical fractions of the MPC in the copolymer chain, equal to 0.26 and 0.74, in the sequence of mers, block and rand...

The resulting microstructure after the sintering process determines many materials properties of interest. In order to understand the microstructural evolution, simulations are often employed. One such simulation method is the phase-field method, which has garnered much interest in recent decades. However, the method lacks a complete model for sint...

Amyloid fibrils have been associated with human disease for many decades, but it has also become apparent that they play a functional, non-disease-related role in e.g. bacteria and mammals. Moreover, they have been shown to possess interesting mechanical properties that can be harnessed for future man-made applications. Here, the mechanical behavio...

The quantum thermal average is a central topic in quantum physics and can be represented by the path integrals. For the computational perspective, the path integral representation (PIR) needs to be approximated in a finite-dimensional space, and the convergence of such approximation is termed as the convergence of the PIR. In this paper, we establi...

Pharmacophore modeling is an innovative technology to explore and extract potential interactions between ligand-protein complexes. On the other hand, virtual screening is an in-silico technique that uses pharmacophore models to analyze extensive databases of compounds or approved drugs to evaluate interactions. These techniques enable to discover,...

Inulosucrase from Lactobacillus reuteri 121 (LrInu) exhibits promise in the synthesis of prebiotic inulin and fructooligosaccharides. However, for its use in industry, LrInu’s thermostability is a crucial consideration. In this study, the computational program FireProt was used to predict the thermostable variants of LrInu. Using rational criteria,...

In the present paper, the dislocation-precipitate interaction in the Inconel 718 superalloy is studied by means of molecular dynamics simulation. The atomistic model composed of the ellipsoidal Ni3Nb precipitate (γ″ phase) and the Ni matrix is constructed, and tensile tests on the composite Ni3Nb@Ni system along different loading directions are sim...

Owing to structural defects, stress concentration often occurs in polymer network materials (PEMs) that greatly alters the overall mechanical properties. Herein, the role of dangling chain defects in stress concentration for PEMs was studied by using coarse-grained molecular dynamics simulation. It is found that the presence of dangling chains coul...

The aim of the current research was to explore the influence of bismuth (Bi) nanoparticles on the single-crystal iron (Fe) nano-cutting process using molecular dynamics (MD) simulations. The existence of Bi nanoparticles in the workpiece affected the variation of cutting force, Von_mises stress distribution and dislocation generation during nano-cu...

The present study aimed to investigate the mechanism of TiAl formation through molecular dynamics simulation (MDS) and spark plasma sintering (SPS) methods. The results of the MDS method suggested that TiAl3 is the first intermetallic compound formed by the diffusion of Ti(s) and Al(l) atoms into their interface at 1340 K, followed by the formation...

Room temperature ionic liquids typically contain asymmetric organic cations. The asymmetry is thought to enhance disorder, thereby providing an entropic counter-balance to the strong, enthalpic, ionic interactions, and leading, therefore, to lower melting points. Unfortunately, the synthesis and purification of such asymmetric cations is typically...

We describe the parameterization of a tungsten-hydrogen empirical potential designed for use with large-scale molecular dynamics simulations of highly irradiated tungsten containing hydrogen isotope atoms, and report test results. Particular attention has been paid to getting good elastic properties, including the relaxation volumes of small defect...