Institute of Applied Physics

Abstract We investigate, via quantum molecular dynamics simulations, the structural and transport properties of ammonia along the principal Hugoniot for temperatures up to 10 eV and densities up to 2.6 g/cm 3 . With the analysis of the molecular dynamics trajectories by use of the bond auto-correlation function, we identify three distinct pressure-temperature regions for local chemical structures of ammonia. We derive the diffusivity and viscosity of strong correlated ammonia with high accuracy through fitting the velocity and stress-tensor autocorrelation functions with complex functional form which includes structures and multiple time scales. The statistical error of the transport properties is estimated. It is shown that the diffusivity and viscosity behave in a distinctly different manner at these three regimes and thus present complex features. In the molecular fluid regime, the hydrogen atoms have almost the similar diffusivity as nitrogen and the viscosity is dominated by the kinetic contribution. When entering into the mixture regime, the transport behavior of the system remarkably changes due to the stronger ionic coupling, and the viscosity is determined to decrease gradually and achieve minimum at about 2.0 g/cm 3 on the Hugoniot. In the plasma regime, the hydrogen atoms diffuse at least twice as fast as the nitrogen atoms.

Alloys that have high strengths at high temperatures are crucial for a variety of important industries including aerospace. Alloys with ordered superlattice structures are attractive for this purpose but generally suffer from poor ductility and rapid grain coarsening. We discovered that nanoscale disordered interfaces can effectively overcome these problems. Interfacial disordering is driven by multielement cosegregation that creates a distinctive nanolayer between adjacent micrometer-scale superlattice grains. This nanolayer acts as a sustainable ductilizing source, which prevents brittle intergranular fractures by enhancing dislocation mobilities. Our superlattice materials have ultrahigh strengths of 1.6 gigapascals with tensile ductilities of 25% at ambient temperature. Simultaneously, we achieved negligible grain coarsening with exceptional softening resistance at elevated temperatures. Designing similar nanolayers may open a pathway for further optimization of alloy properties.

Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50 GPa, excluding the vapor stability region. The computational efficiency of the model makes it possible to predict its phase diagram using molecular dynamics. Satisfactory overall agreement with experimental results is obtained. The fluid phases, molecular and ionic, and all the stable ice polymorphs, ordered and disordered, are predicted correctly, with the exception of ice III and XV that are stable in experiments, but metastable in the model. The evolution of the atomic dynamics upon heating, as ice VII transforms first into ice VII^{''} and then into an ionic fluid, reveals that molecular dissociation and breaking of the ice rules coexist with strong covalent fluctuations, explaining why only partial ionization was inferred in experiments.

This study uses sharp, differential air quality changes across sites attributable to geographic variation in the effects of the 1981-82 recession to estimate the relationship between infant mortality and particulates air pollution. It is shown that in the narrow period of 1980-82, there was substantial variation across counties in changes in particulates pollution, and that these differential pollution reductions appear to be orthogonal to changes in a multitude of other factors that may be related to infant mortality.

We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called the Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application, we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task.

Diffraction line broadening observed for the biological apatite is ascribed to small crystallite dimensions and lattice imperfections. However, it is rather difficult to separate the individual contribution of each factor. Therefore in numerous works a total inverse width of a diffraction peak is only used as a size/strain parameter. Several authors determine the bioapatite crystallite size ignoring the lattice strain. As is shown in the present paper, this problem can be resolved for oriented specimens. The crystallite size and lattice strain were calculated by two independent methods: Fourier analysis and approximation with threefold convolution of X-ray lines. The approach proposed can be useful in the investigations into structural aspects of the bone apatite and its synthetic analogues as the crystal size is related to surface defects and the lattice strain to lattice imperfections.

OBJECTIVE: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected CNS infections. METHODS: In a prospective pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from 10 patients with neurologic problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. RESULTS: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in 3 patients for whom validation techniques confirmed the pathogens identified by NGS. Although NGS was unable to identify with precision infectious agents in the remaining cases, it contributed to the understanding of neuropathologic processes in 5 others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in 8 of 10 cases, and were noncontributory in the remaining 2. CONCLUSIONS: NGS-guided metagenomic studies of brain, spinal cord, or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.

Exposure of growing batch cultures of Escherichia coli to nine different "model micropollutants" (benzene, cadmium chloride, chlorpyrivos, 2,4-dichloroaniline, dioctylphtalate, hexachlorobenzene, pentachlorophenol, trichloroethylene, and tetrapropylbenzosulfonate) led to the induction of 13 to 39 proteins, as analyzed by two-dimensional gel electrophoresis. Some of these proteins overlapped with heat shock and carbon starvation proteins, but at least 50% were unique to a given chemical. The stress protein induction showed a temporal pattern, indicating sequential gene expression. Chemical stress protein synthesis occurred even at concentrations that had no effect on growth. Thus, the synthesis of these proteins can be a sensitive index of stress and the nature of environmental pollution.

Using first principles calculations, we report for the first time that large nearly neutral aromatic molecules, such as naphthalene and anthracene, and small charge-transfer aromatic molecules, such as TCNQ and DDQ, interact more strongly with metallic single-wall carbon nanotubes (SWNTs) versus their semiconducting counterparts as the molecular orientation of DDQ is taken into account. Hence two new mechanisms for separating metallic and semiconducting SWNTs via noncovalent pi-pi stacking or charge-transfer interaction are suggested.

Abstract Zinc oxide due to specific electrical, optical and acoustic properties is the important semiconductor material, which has many various applications. There is growing interest in ZnO due to its potential applicability for optoelectronic devices such as light‐emitting diodes, laser diodes and detectors for UV wavelength range. ZnO properties are very close to those of widely recognized semiconductor GaN. The band gap of ZnO (3.37 eV) is close to that of GaN (3.39 eV) but ZnO exciton binding energy (60 meV) is twice larger than that of GaN (28 meV). Optically pumped UV lasing have been demonstrated at room temperature using high textured ZnO films. The excitonic gain close to 300 cm –1 was achieved. ZnO thin films are expected to have higher quantum efficiency in UV semiconductor laser than GaN. The physical properties of ZnO are considered. PEMOCVD technology was used to deposit piezoelectric and highly transparent electroconductive ZnO films. Their properties are discussed. The experiments on polycrystalline ZnO films deposited by RF magnetron sputtering at different partial pressure of oxygen are presented. AFM images were studied in tapping mode for deposited films. The investigated films were dielectric ones and had optical transparency within 65‐85% at thickness in the interval 0.2‐0.6 μm. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Abstract The synthesis of discrete nanostructures with a strong, persistent, stable plasmonic circular dichroism (PCD) signal is challenging. We report a seed‐mediated growth approach to obtain discrete Au nanorods with high and stable chiroptical responses (c‐Au NRs) in the visible to near‐IR region. The morphology of the c‐Au NRs was governed by the concentration of l ‐ or d ‐cysteine used. The amino acids encapsulated within the discrete gold nanostructure enhance their PCD signal, attributed to coupling of dipoles of chiral molecules with the near‐field induced optical activity at the hot spots inside the c‐Au NRs. The stability of the PCD signal and biocompatibility of c‐Au NRs was improved by coating with silica or protein corona. Discrete c‐Au NR@SiO 2 with Janus or core–shell configurations retained their PCD signal even in organic solvents. A side‐by‐side assembly of c‐Au NRs induced by l ‐glutathione led to further PCD signal enhancement, with anisotropic g factors as high as 0.048.

A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.

We measure photoelectron angular distributions of noble gases in intense elliptically polarized laser fields, which indicate strong structure-dependent Coulomb asymmetry. Using a dedicated semiclassical model, we have disentangled the contribution of direct ionization and multiple forward scattering on Coulomb asymmetry in elliptical laser fields. Our theory quantifies the roles of the ionic potential and initial transverse momentum on Coulomb asymmetry, proving that the small lobes of asymmetry are induced by direct ionization and the strong asymmetry is induced by multiple forward scattering in the ionic potential. Both processes are distorted by the Coulomb force acting on the electrons after tunneling. Lowering the ionization potential, the relative contribution of direct ionization on Coulomb asymmetry substantially decreases and Coulomb focusing on multiple rescattering is more important. We do not observe evident initial longitudinal momentum spread at the tunnel exit according to our simulation.

This review contains theoretical study of resonant quantum electrodynamics processes in a pulsed laser field. The approximation is examined when the pulse width is considerably greater than the characteristic time of wave oscillations. The lepton’s interaction with the Coulomb potential of a nucleus and each other is considered in the Born approximation. It is demonstrated that the resonant differential cross section of a process in a pulsed light fields may considerably exceed the corresponding cross section in an absence of a laser field. Results obtained may be experimentally verified by the scientific facilities at the SLAC National Accelerator Laboratory and FAIR (Facility for Antiproton and Ion Research, Darmstadt, Germany) project.

Abstract The growing interest in the DNA‐based mesoscale systems of biological and nonbiological nature has encouraged the computational molecular science community to develop coarse‐grained (CG) representationsof the DNA that will be simple enough to permit exhaustive simulations in a reasonable amount of time, yet complex enough to capture the essential physics at play. In the recent years, there have been some major developments in the DNA coarse‐graining area and several fairly sophisticated models are now available that faithfully reproduce key mechanical and chemical properties of the double‐ and single‐stranded DNA. However, there are still many challenges, which limit the applicability of the present models, and much has to be done yet to develop more reliable schemes which would have a predictive power beyond the target domain of the intrinsic parametrization. A development of robust, controllable, and transferrable CG DNA force fields will provide an invaluable tool for gaining physical insights into the molecular nature of complex DNA‐based nanoscale entities such as the chromatin, virus capsids, and DNA nanocomposites. In the present contribution, we provide an overview of the recent developments in the DNA coarse‐graining field. Our aim is to review the existing CG models of the double‐stranded DNA, where a small selection of models, which we believe provide avenues for promising future development, are discussed in some detail. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Mechanics

Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

Abstract This article studies the global well-posedness and long-time dynamics for the nonlinear complex Ginzburg–Landau equation involving fractional Laplacian. The global existence and some uniqueness criterion of weak solutions are given with compactness method. To study the strong solutions with the semigroup method, we generalize some pointwise estimates for the fractional Laplacian to the complex background and study carefully the linear evolution of the equation. Finally, the existence of global attractors is studied. Keywords: Ginzburg–Landau equationfractional Laplacianweak solutionssmooth solutionsglobal attractorsAMS Subject Classification: 35Qxx Acknowledgements Supported by the NNSF of China under Grant No. 11001285.

Chitosan/hydroxyapatite scaffolds could be used for bone regeneration in case the application of auto- or allografts is impossible. The objective of the present work was to characterize and study in vivo biodegradation of simple chitosan/hydroxyapatite scaffolds. For this purpose, a series of chitosan/hydroxyapatite composites has been synthesized in aqueous medium from chitosan solution and soluble precursor salts by a one step coprecipitation method. A study of in vivo behavior of the materials was then performed using model linear rats. Cylindrical-shaped rods made of the chitosan/hydroxyapatite composite material were implanted into tibial bones of the rats. After 5, 10, 15, and 24 days of implantation, histological and histo-morphometric analyses of decalcified specimens were performed to evaluate the stages of biodegradation processes. Calcified specimens were examined by scanning electron microscopy with X-ray microanalysis to compare elemental composition and morphological characteristics of the implant and the bone during integration. Porous chitosan/hydroxyapatite scaffolds have shown osteoconductive properties and have been replaced in the in vivo experiments by newly formed bone tissue.

Numerous theoretical and experimental studies disagree on the impact of surrounding mobile ions on DNA conformational flexibility at high salt content. Specifically, it is not clear how the DNA persistence length varies when concentration of monovalent mobile ions is increased beyond the physiological value of ∼0.1 M. In the present Communication we address this biologically important issue computationally by means of molecular dynamics simulations. We utilize our recently developed chemically accurate coarse-grained model for the double-stranded DNA with explicit mobile ions. We find that in a range of moderate-to-high ionic concentrations, ∼0.1-1 M, DNA persistence length drops noticeably by ∼25%. Our results contradict some experimental works and the celebrated theory of Odijk, Skolnick and Fixman (Skolnick et al., Macromolecules, 1977, 10, 944), suggesting a negligible variation of DNA persistence length at these concentrations. On the other hand, our findings are in near quantitative agreement with a number of other theoretical and experimental studies. Combined with our recent work on elucidating the role of elastic and electrostatic effects in maintaining DNA shape, the results reported here may indicate that conceptually new understanding of DNA rigidity needs to be developed.

BACKGROUND AND PURPOSE: A disordered proliferative process in the vascular wall is thought to underlie the pathogenesis of restenosis after percutaneous transluminal angioplasty and carotid endarterectomy. A growth inhibitory property of overexpressed prostacyclin (PGI2) synthase (PGIS) was recently implicated in the pathological proliferation of vascular smooth muscle cells (VSMC) in vitro. Here, we investigated the effects of increased PGI2 synthesis on the pathological proliferation of VSMCs. METHODS: The cDNA encoding human PGIS was transfected into endothelium-denuded rat carotid arteries after arterial balloon injury with the use of hemagglutinating virus Japan (HVJ). HVJ liposome vector complex without PGIS cDNA was used for vehicle control. The level of 6-keto PGF1alpha, a stable hydrolyzed metabolite of PGI2, the histological distribution of the immunoreactivity for human PGIS and the ratio of neointimal/medial area were analyzed. RESULTS: In the analyses of 6-keto PGF1alpha, the level in the carotid arteries was significantly elevated 3 days after PGIS expression-vector transfection compared with that in the arteries after vehicle transfection. Seven days after human PGIS expression-vector transfection, the PGIS cDNA-transfected neointimal cells were strongly positive for human PGIS immunoreactivity in 81% sections examined. Fourteen days after the injury, the ratio of neointimal/medial area was 1.2+/-0.4 in the PGIS expression-vector transfected group, which was significantly smaller than that of the vehicle control group, 1.7+/-0.5; P<0.01. CONCLUSIONS: It was thus demonstrated that the gene transfer of human PGIS expression-vector into rat carotid arteries resulted in the increased production of human PGI2 in the vascular wall, the expression of human PGIS in the developing neointima and significantly inhibited the neointimal formation generated after balloon injury.