Full Atomistic Molecular Dynamics Research Articles

Unusually low and density-insensitive thermal conductivity of three-dimensional gyroid graphene.

Graphene has excellent mechanical, thermal and electrical properties. However, there are limitations in utilizing monolayers of graphene for mechanical engineering applications due to its atomic thickness and lack of bending rigidity. Synthesizing graphene aerogels or foams is one approach to utilize graphene in three-dimensional bulk forms. Recently, graphene with a gyroidal geometry has been proposed. A gyroid is a triply periodic minimal surface that allows graphene sheets to form a three-dimensional structure. Its light weight and high mechanical strength suggests that the graphene that constitutes this geometry can synergistically contribute to the mechanics of the bulk material. However, it is not clear whether gyroid graphene can preserve the high thermal conductivity of pristine graphene sheets. Here, we investigate the thermal conductivities of gyroid graphene with different porosities by using full-atom molecular dynamics simulations. In contrast to its excellent mechanical properties, we find that the thermal conductivity of gyroid graphene is more than 300 times lower than that of pristine graphene, with a bulk density of only about one-third of that of graphene. We derive a scaling law showing that the thermal conductivity does not vary much with different bulk densities, which contrasts the behavior of conventional porous materials. Our analysis shows that the poor thermal conductivity of gyroid graphene can be attributed to defects and curvatures of graphene, which increase with the density, resulting in the reduction of a phonon mean free path by phonon scattering. Our study shows that three-dimensional porous graphene has potential that may be utilized in designing new lightweight structural materials with low and density-insensitive thermal properties and superior mechanical strength.

FEM analysis of metal matrix nanocomposites reinforced with off-line atomistically-informed equivalent nanofillers

With ever increasing the applications of metal matrix nanocomposites (MMNCs) reinforced with carbon nanofillers, demand for accurate and effective modeling techniques in this area has been increased in recent years. To provide such a route, this study is dedicated to apply information form interfacial atomic interactions in modified continuum models implemented to analyze the mechanical behavior of these nanocomposites. In the proposed methodology, the metal matrix is considered as a continuous medium. Meanwhile, to capture the atomic-scale phenomena governing the problem, the carbon nanofiller, local metal atoms neighboring it, and the nanofiller/metal interface are analyzed using molecular dynamics (MD) simulations. Subsequently, employing the equivalent continuum modeling (ECM) concept, geometrical and mechanical characteristics of the equivalent nanofiller is obtained in each case and introduced in a finite element analysis (FEA). It is demonstrated that the atomistically informed FEA can successfully reproduce the results of full atomistic MD simulations with ignorable run-time compared to that of this method. Finally, constructing several computational cells with different metal matrices and reinforcing agents, the developed MD/FE multiscale approach is utilized to capture the influences of temperature, nanofiller geometry and orientation, its volume fraction and interfacial interactions on the axial elastic constants of these nanocomposites.

Kunitz-Type Peptide HCRG21 from the Sea Anemone Heteractis crispa Is a Full Antagonist of the TRPV1 Receptor.

Sea anemone venoms comprise multifarious peptides modulating biological targets such as ion channels or receptors. The sequence of a new Kunitz-type peptide, HCRG21, belonging to the Heteractis crispa RG (HCRG) peptide subfamily was deduced on the basis of the gene sequence obtained from the Heteractis crispa cDNA. HCRG21 shares high structural homology with Kunitz-type peptides APHC1–APHC3 from H. crispa, and clusters with the peptides from so named “analgesic cluster” of the HCGS peptide subfamily but forms a separate branch on the NJ-phylogenetic tree. Three unique point substitutions at the N-terminus of the molecule, Arg1, Gly2, and Ser5, distinguish HCRG21 from other peptides of this cluster. The trypsin inhibitory activity of recombinant HCRG21 (rHCRG21) was comparable with the activity of peptides from the same cluster. Inhibition constants for trypsin and α-chymotrypsin were 1.0 × 10−7 and 7.0 × 10−7 M, respectively. Electrophysiological experiments revealed that rHCRG21 inhibits 95% of the capsaicin-induced current through transient receptor potential family member vanilloid 1 (TRPV1) and has a half-maximal inhibitory concentration of 6.9 ± 0.4 μM. Moreover, rHCRG21 is the first full peptide TRPV1 inhibitor, although displaying lower affinity for its receptor in comparison with other known ligands. Macromolecular docking and full atom Molecular Dynamics (MD) simulations of the rHCRG21–TRPV1 complex allow hypothesizing the existence of two feasible, intra- and extracellular, molecular mechanisms of blocking. These data provide valuable insights in the structural and functional relationships and pharmacological potential of bifunctional Kunitz-type peptides.

Systematic study of glass transition in low-molecular phthalonitriles: Insight from computer simulations.

Phthalonitrile compounds with Si bridges were recently suggested for producing thermosetting polymer composites with reduced Tg and thus expanded processing range. The detailed experimental investigation of this class of phthalonitriles is still difficult due to development time and costs limitations and the need to take into account the structural changes during the crosslinking. In this paper, we try to overcome these limitations using computer simulations. We performed full-atomistic molecular dynamics simulations of various phthalonitrile compounds to understand the influence of molecular structure on the bulk glass temperature Tg. Two molecular properties affect Tg of the resulting bulk compound: the size of the residue and the length of the Si bridge. The larger residues lead to higher Tgs, while compounds with longer Si bridges have lower Tgs. We have also studied relaxation mechanisms involved in the classification of the samples. Two different factors influence the relaxation mechanisms: energetic, which is provided by the rigidity of molecules, and entropic, connected with the available volume of the conformational space of the monomer.

Multiresolution molecular mechanics: Implementation and efficiency

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

Molecular dynamics simulation of the structure of mixed ligand shells stabilizing cadmium selenide nanoparticle surfaces with different curvatures

A full-atomic molecular dynamics simulation has been performed for a ligand shell of colloidal cadmium selenide quantum dots. Trioctylphosphine, trioctylphosphine oxide, octadecylphosphonic acid, and hexadecylamine have been used as ligands. For a mixture of the two former ligands, the effect of surface curvature on the fraction of surface ions of quantum dots bonded to ligands has been studied. It has been shown that, for particles with radii of 1.9 and 4.5 nm, every second and approximately third cadmium atom, respectively, is bonded to trioctylphosphine oxide. Partial introduction of octadecylphosphonic acid and hexadecylamine may increase the fraction of bonded surface atoms by more than two times.

Programmed shape-dependence of shape memory effect of oriented polystyrene: A molecular dynamics study

Oriented polystyrene (PS) has attracted attention due to its capability of sequential self-folding behaviors by infrared (IR) light heating. It has been seen that temporal changes of the shape and properties of PS are affected by its pre-defined molecular structure. In this study, full atomistic molecular dynamics (MD) simulations are carried out to study the effect of initially applied strain on the thermoelastic properties and shape recovery behaviors of the oriented PS. The shape memory creation procedure (SMCP) is described by long-time simulation and initial strains between 15% and 100% are applied by in-plane tensile loadings. As the extent of pre-stretching increases, the anisotropy of elastic modulus and linear coefficient of thermal expansion (CTE) increase primarily due to the molecular alignment. The shape fixity ratio increases by up to 24% and the recovery ratio decreases by up to 32% by increasing the initial strain. In particular, the shape recovery ratio is mainly affected by the orientational order parameter of the oriented PS. The rate of the recoveries of the thermomechanical properties and shape reduce for a more pre-stretched PS. The retardation of conformational transformation comes from a reduction in the sizes of free volume elements. The results demonstrate a microstructure-property relationship which is important in designing the self-folding behaviors of oriented PS.

A Correlation between the Activity of Candida antarctica Lipase B and Differences in Binding Free Energies of Organic Solvent and Substrate

The ability of enzymes to operate in organic solvent is now widely accepted and is the basis for extensive research in enzymology. The challenge is to select the solvent media that allows the modulation of enzyme activity. For a rational selection of a solvent, it is necessary to understand the effect of organic solvent molecules on enzyme structure and the enzymatic reaction on a molecular level. To gain such insight, we combined experimental kinetics studies with full atomic molecular dynamics simulations and found a correlation between the activity of Candida antarctica lipase B (CALB) [for the esterification reaction between butyric acid and ethanol at a fixed water activity] and the binding of the solvent/substrate molecules in the active site region of CALB. We have investigated the influence of four organic solvents—hexane (HEX), methyl tertiary butyl ether (MTBE), acetonitrile (ACN), and tertiary butanol (TBU)—on the catalytic activity of CALB for the esterification reaction. The solvents have bee...

Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPC) and 1,2‐distearoyl‐sn‐glycero‐3‐phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel‐like (L β ′ or P β ′) phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel‐like phase into the completely liquid‐crystalline phase (L α ). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half‐maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness) can be used as order parameters for the membrane phase transition.

Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 Variant

M.HhaI is a DNA methyltransferase from Haemophilus hemolyticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the C5 position of a cytosine. This enzyme is a paradigmatic model for C5 DNA methyltransferases due to its major homology to mammalian enzymes and to the availability of high-resolution structures of the DNA–enzyme complex. In spite of the number of experimental and theoretical analyses carried out for this system, many mechanistic details remain unraveled. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex, where the target cytosine base is flipped out into the active site for both the wild type and Glu119Gln mutant. The relaxed structure was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanism using the string method. Exploration of multidimensional free energy surfaces allowed determining a complete picture of the reaction mechanism, in agreement with...

Controlled 3D Carbon Nanotube Structures by Plasma Welding

3D interconnected carbon nanotubes (CNTs) are synthesized using an industrially scalable spark plasma technique. At high electric field and elevated temperature under sufficient stress the nanotubes are welded together to form a solid block. The detailed spectroscopic and microscopic analyses show successful welding of the CNTs and formation of interconnected networks. The mechanical characteristics of the 3D CNT block show a high stiffness and yield strength. A full atomistic molecular dynamics simulation elucidates the CNT welding mechanism. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Field-induced stacking transition of biofunctionalized trilayer graphene

Trilayer graphene (TLG) is attracting a lot of attention as their stacking structures (i.e., rhombohedral vs. Bernal) drastically affect electronic and optical properties. Based on full-atom molecular dynamics simulations, we here predict electric field-induced rhombohedral-to-Bernal transition of TLG tethered with proteins. Furthermore, our simulations show that protein's electrophoretic mobility and diffusivity are enhanced on TLG surface. This phenomenon of controllable TLG stacking transition will contribute to various applications including biosensing.

Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.

DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.

Computer simulation of ligand shells of colloidal cadmium selenide quantum dots

The full-atomic molecular dynamics approach has been employed to study the structure and composition of ligand shells of colloidal cadmium selenide quantum dots produced by high-temperature colloidal synthesis in a trioctylphosphine–trioctylphosphine oxide mixture. The influence of solvents (chloroform and methanol) on the composition of the shells has been investigated. The number of ligand molecules optimal for complete covering the surface of a considered particle without its deformation has been found. The fraction of passivated surface ions has been calculated.

Molecular Dynamics Force-Field Refinement against Quasi-Elastic Neutron Scattering Data.

Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulation due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. Also, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.

A novel MD-based procedure to obtain the interphase Young’s modulus in nanocomposites

Previous numerical and experimental investigations have shown that the performance of polymer-based composites is greatly affected by properties of the interphase region and its geometrical characteristics. Although, it has been well-established that there is a gradient in the interphase elastic constants, no full atomistic molecular dynamics (MD) based work has been done to capture this, yet. Therefore, the focus of this study is to develop a novel MD-based procedure to attain the changes in the Young’s modulus of the interphase and thus, its mean value in graphene/polymer nanocomposites. To this end, knowing the existence of a correlation between the polymer density and its modulus, first, the radial distribution function (RDF) of polymer atoms with respect to graphene ones is captured to find the density gradient in the interphase. Then, distinct computational cells having pure polymer at different densities are constructed to resemble the various interphase zones. Finally, conducting proper uniaxial tensile tests on these cells, the Young’s modulus of each interphase zone is obtained and implemented in an average method to compute the overall interphase modulus. The trend predicted by this method for variations in the interphase properties and its thickness is completely in good agreement with the available experimental results.

Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA

Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.

New aspects on the metal reinforcement by carbon nanofillers: A molecular dynamics study

Recently, metal-based composites reinforced with carbon nanofillers such as graphene sheets (SLGSs) and carbon nanotubes (CNTs) were proposed to combine the properties of metals. These nanofillers have led to novel materials for a variety of applications. Although there are various experimental and numerical studies in this regard, there is a lack of fundamental understanding of how the geometrical characteristics of these different nanofillers affect their mechanical properties. Here, we report a series of full atomistic molecular dynamics (MD) simulations aimed to assess the issue. Two distinct computational cells, SLGS/Cu and CNT/Cu samples, that have copper as the matrix material, are examined under identical conditions to explore the role of nanofiller geometry on the elastic constants of these nanocomposites. Moreover, the temperature dependence of the axial Young's modulus for each case is investigated via MD simulations. Finally, we also studied the effect of graphene/matrix interfacial interactions on the elastic constants of metal nanocomposites by comparing the results of the SLGS/Cu case with the ones determined for a similar SLGS/Ni sample. Our results reveal that graphene should be the nanomaterial of choice to strengthen metal matrices.

When is 6 less than 5? Penta- to hexa-graphene transition

Penta-graphene is a recently proposed graphene allotrope consisting of repeating pentagons. Here, we characterize the small-strain mechanical properties of finite penta-graphene using full atomistic molecular dynamics (MD). Using tensile tests, the uniaxial yield strength (12.7 N/m) and stiffness (approximately 378.3 N/m) are characterized. Extreme strain is observed at ultimate failure (> 50%), with an associated elastic toughness on the order of 5.4 J/m2. In addition, the bond structure of penta-graphene enables a structural transition from a repeating penta- to hexa-form, e.g., the common hexagonal-based sp2-bonding structure of graphene. We show that penta-graphene can be transitioned to a hexagonal energy-reducing graphene form, via applied strain or temperature. The pentagon-based structure begins to degenerate to a graphene-like hexagonal structure at a critical strain of 5.1%, as the system transitions to a lower energy structure. Beyond this critical strain, the system behaves plastically, and does not revert to initial conditions upon stress removal. The hexagonal form (6-ring) represents a lower energy state than the pentagonal form (5-ring). We further observe conformational changes occur due to thermal energy, leading to a transition at T > 600 K. Post-transition, the system behavior reflects that of graphene with lattice defects. This represents a new paradigm of nanomaterials, whereby one material (graphene) can emerge from another metastable form (penta-graphene).