Dynamic Transition in the Structure of an Energetic Crystal during Chemical Reactions at Shock Front Prior to Detonation

Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front

Left Transperitoneal Adrenalectomy with a Laparoendoscopic Single-Site Surgery Combined Technique: Initial Case Reports

Laparoendoscopic single-site surgery (LESS) is a step toward the development of minimally invasive surgery. It is initially difficult for surgeons with limited experience to perform the surgery. We describe two cases of left adrenalectomy with a LESS combined with the addition of an accessory port. After a 2.5-cm skin incision was made at the level of the paraumbilicus to insert the primary 12-mm trocar for the laparoscope, a 5-mm nonbladed trocar was placed through the skin incision side-by-side with the primary trocar. A second 3-mm nonbladed trocar was then placed along the anterior axillary line; a multichannel trocar was not used as a single port. Both adrenalectomies were completed successfully. In patients with a minor adrenal tumor, a combined technique using LESS and an additional port is easier than LESS alone and may, therefore, be a bridge between the conventional laparoscopic approach and LESS

Alteration of Membrane Physicochemical Properties by Two Factors for Membrane Protein Integration

After a nascent chain of a membrane protein emerges from the ribosomal tunnel, the protein is integrated into the cell membrane. This process is controlled by a series of proteinaceous molecular devices, such as signal recognition particles and Sec translocons. In addition to these proteins, we discovered two endogenous components regulating membrane protein integration in the inner membrane of Escherichia coli. The integration is blocked by diacylglycerol (DAG), whereas the blocking is relieved by a glycolipid named membrane protein integrase (MPIase). Here, we investigated the influence of these integration-blocking and integration-promoting factors on the physicochemical properties of membrane lipids via solid-state NMR and fluorescence measurements. These factors did not have destructive effects on membrane morphology because the membrane maintained its lamellar structure and did not fuse in the presence of DAG and/or MPIase at their effective concentrations. We next focused on membrane flexibility. DAG did not affect the mobility of the membrane surface, whereas the sugar chain in MPIase was highly mobile and enhanced the flexibility of membrane lipid headgroups. Comparison with a synthetic MPIase analog revealed the effects of the long sugar chain on membrane properties. The acyl chain order inside the membrane was increased by DAG, whereas the increase was cancelled by the addition of MPIase. MPIase also loosened the membrane lipid packing. Focusing on the transbilayer movement, MPIase reduced the rapid flip-flop motion of DAG. On the other hand, MPIase could not compensate for the diminished lateral diffusion by DAG. These results suggest that by manipulating the membrane lipids dynamics, DAG inhibits the protein from contacting the inner membrane, whereas the flexible long sugar chain of MPIase increases the opportunity for interaction between the membrane and the protein, leading to membrane integration of the newly formed protein

An extended-Lagrangian scheme for charge equilibration in reactive molecular dynamics simulations

a b s t r a c t Reactive molecular dynamics (RMD) simulations describe chemical reactions at orders-of-magnitude faster computing speed compared with quantum molecular dynamics (QMD) simulations. A major computational bottleneck of RMD is charge-equilibration (QEq) calculation to describe charge transfer between atoms. Here, we eliminate the speed-limiting iterative minimization of the Coulombic energy in QEq calculation by adapting an extended-Lagrangian scheme that was recently proposed in the context of QMD simulations, Souvatzis and Niklasson (2014). The resulting XRMD simulation code drastically improves energy conservation compared with our previous RMD code, , while substantially reducing the time-to-solution. The XRMD code has been implemented on parallel computers based on spatial decomposition, achieving a weak-scaling parallel efficiency of 0.977 on 786,432 IBM Blue Gene/Q cores for a 67.6 billion-atom system

Application of First-Principles-Based Artificial Neural Network Potentials to Multiscale-Shock Dynamics Simulations on Solid Materials

The use of artificial neural network (ANN) potentials trained with first-principles calculations has emerged as a promising approach for molecular dynamics (MD) simulations encompassing large space and time scales while retaining first-principles accuracy. To date, however, the application of ANN-MD has been limited to near-equilibrium processes. Here we combine first-principles-trained ANN-MD with multiscale shock theory (MSST) to successfully describe far-from-equilibrium shock phenomena. Our ANN-MSST-MD approach describes shock-wave propagation in solids with first-principles accuracy but a 5000 times shorter computing time. Accordingly, ANN-MD-MSST was able to resolve fine, long-time elastic deformation at low shock speed, which was impossible with first-principles MD because of the high computational cost. This work thus lays a foundation of ANN-MD simulation to study a wide range of far-from-equilibrium processes

Embrittlement of Metal by Solute Segregation-Induced Amorphization

Impurities segregated to grain boundaries of a material essentially alter its fracture behavior. A prime example is sulfur segregation-induced embrittlement of nickel, where an observed relation between sulfur-induced amorphization of grain boundaries and embrittlement remains unexplained. Here, $48×10^6$-atom reactive-force-field molecular dynamics simulations provide the missing link. Namely, an order-of-magnitude reduction of grain-boundary shear strength due to amorphization, combined with tensile-strength reduction, allows the crack tip to always find an easy propagation path.Engineering and Applied SciencesPhysic

10th Anniversary of Catalysts: Molecular Catalysis

On the occasion of this Special Issue, I would like to present an editorial message on this good occasion [...

Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis

Reactive molecular dynamics (MD) simulation is a powerful research tool for describing chemical reactions. We eliminate the speed-limiting charge iteration in MD with a novel extended-Lagrangian scheme. The extended-Lagrangian reactive MD (XRMD) code drastically improves energy conservation while substantially reducing time-to-solution. Furthermore, we introduce a new polarizable charge equilibration (PQEq) model to accurately predict atomic charges and polarization. The XRMD code based on hybrid message passing+multithreading achieves a weak-scaling parallel efficiency of 0.977 on 786 432 IBM Blue Gene/Q cores for a 67.6 billion-atom system. The performance is portable to the second-generation Intel Xeon Phi, Knights Landing. Blue Gene/Q simulations for the computational synthesis of materials via novel exfoliation mechanisms for synthesizing atomically thin transition metal dichalcogenide layers will dominate nanomaterials science in this century