Dynamics and self-assembly of bio-functionalized gold nanoparticles in solution: Reactive molecular dynamics simulations

The self-assembling properties, stability, and dynamics of hybrid nanocarriers (gold nanoparticles (AuNPs) functionalized with cysteine-based peptides) in solution are studied through a series of classical molecular dynamics simulations based on a recently parametrized reactive force field. The results reveal, at the atomic level, all the details regarding the peptide adsorption mechanisms, nanoparticle stabilization, aggregation, and sintering. The data confirm and explain the experimental findings and disclose aspects that cannot be scrutinized by experiments. The biomolecules are both chemisorbed and physisorbed; self-interactions of the adsorbates and formation of stable networks of interconnected molecules on the AuNP surfaces limit substrate reconstructions, protect the AuNPs from the action of the solvent, and prevent direct interactions of the gold surfaces. The possibility of agglomeration of the functionalized nanoparticles, compared with the sintering of the bare supports in a water solution, is demonstrated through relatively long simulations and fast steered dynamics. The analysis of the trajectories reveals that the AuNPs were well stabilized by the peptides. This prevented particle sintering and kept the particles far apart; however, part of their chains could form interconnections (crosslinks) between neighboring gold vehicles. The excellent agreement of these results with the literature confirm the reliability of the method and its potential application to the modeling of more complex materials relevant to the biomedical sector.

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Mixtures of (N2)1−x : (O2) x at High Pressures and Low Temperatures

We performed Raman measurements at 18 K and pressures up to 25 GPa in order to construct a tentative phase diagram of the (N ₂)_1–x :(O ₂)_x –system at low temperatures. We varied the composition of the mixed system over the whole concentration range. Here we focused on the systems with high nitrogen concentration and pressures above 2 GPa. It is known that at room temperature oxygen is highly solvable in the –phase of N ₂. The experimental results show that oxygen suppresses the disorder–order transition –N ₂.     

Analyzing the metallurgical and cultural backgrounds of two Han-dynasty bronze-mirror fragments

Chinese TLV-bronze mirrors dating to the Han dynasty (206 B.C.-220 A.D.) were popular objects of everyday life as well as highly esteemed works of art. The decorated back of the mirror characterizes the culture of this period as well as the excellent early Chinese casting techniques.     

Capillary waveguide optrodes: an approach to optical sensing in medical diagnostics

Glass capillaries with a chemically sensitive coating on the inner surface are used as optical sensors for medical diagnostics. A capillary simultaneously serves as a sample compartment, a sensor element, and an inhomogeneous optical waveguide. Various detection schemes based on absorption, fluorescence intensity, or fluorescence lifetime are described. In absorption-based capillary waveguide optrodes the absorption in the sensor layer is analyte dependent; hence light transmission along the inhomogeneous waveguiding structure formed by the capillary wall and the sensing layer is a function of the analyte concentration. Similarly, in fluorescence-based capillary optrodes the fluorescence intensity or the fluorescence lifetime of an indicator dye fixed in the sensing layer is analyte dependent; thus the specific property of fluorescent light excited in the sensing layer and thereafter guided along the inhomogeneous waveguiding structure is a function of the analyte concentration. Both schemes are experimentally demonstrated, one with carbon dioxide as the analyte and the other one with oxygen. The device combines optical sensors with the standard glass capillaries usually applied to gather blood drops from fingertips, to yield a versatile diagnostic instrument, integrating the sample compartment, the optical sensor, and the light-collecting optics into a single piece. This ensures enhanced sensor performance as well as improved handling compared with other sensors.     

On resolution with short clauses

We investigate properties ofk-resolution, a restricted version of resolution in which one parent clause must have length at mostk. Starting from a unit-preference strategy, we compare minimal proof lengths of unit-resolution and unrestricted resolution. In particular, we show that the speed-up by using resolution is bound by if the shortest unit-resolution refutation needst steps. Next we present an algorithm which decides whether the empty clause can be deduced by 2-resolution from a formula and has time complexity O(length()⁴). Finally we describe effects onk-resolution if a formula is transformed intot-CNF and show that extended 3-resolution is complete and sound.     

Fast approximation algorithms to minimize a special weighted flow-time criterion on a single machine with a non-availability interval and release dates

This paper is the first attempt to successfully design efficient approximation algorithms for the single-machine weighted flow-time minimization problem when jobs have different release dates and weights equal to their processing times under the assumption that one job is fixed (i.e., the machine is unavailable during a fixed interval corresponding to the fixed job). Our work is motivated by an interesting algorithmic application to the generation of valid inequalities in a branch-and-cut method. Our analysis shows that the trivial FIFO sequence can lead to an arbitrary large worst-case performance bound. Hence, we modify this sequence so that a new 2-approximation solution can be obtained for every instance and we prove the tightness of this bound. Then, we propose a fully polynomial-time approximation algorithm with efficient running time for the considered problem. Especially, the complexity of our algorithm is strongly polynomial.     

Iterant recombination with one-norm minimization for multilevel Markov chain algorithms via the ellipsoid method

Recently, it was shown how the convergence of a class of multigrid methods for computing the stationary distribution of sparse, irreducible Markov chains can be accelerated by the addition of an outer iteration based on iterant recombination. The acceleration was performed by selecting a linear combination of previous fine-level iterates with probability constraints to minimize the two-norm of the residual using a quadratic programming method. In this paper we investigate the alternative of minimizing the one-norm of the residual. This gives rise to a nonlinear convex program which must be solved at each acceleration step. To solve this minimization problem we propose to use a deep-cuts ellipsoid method for nonlinear convex programs. The main purpose of this paper is to investigate whether an iterant recombination approach can be obtained in this way that is competitive in terms of execution time and robustness. We derive formulas for subgradients of the one-norm objective function and the constraint functions, and show how an initial ellipsoid can be constructed that is guaranteed to contain the exact solution and give conditions for its existence. We also investigate using the ellipsoid method to minimize the two-norm. Numerical tests show that the one-norm and two-norm acceleration procedures yield a similar reduction in the number of multigrid cycles. The tests also indicate that one-norm ellipsoid acceleration is competitive with two-norm quadratic programming acceleration in terms of running time with improved robustness.     

IRIS: illustrative rendering for integral surfaces

Integral surfaces are ideal tools to illustrate vector fields and fluid flow structures. However, these surfaces can be visually complex and exhibit difficult geometric properties, owing to strong stretching, shearing and folding of the flow from which they are derived. Many techniques for non-photorealistic rendering have been presented previously. It is, however, unclear how these techniques can be applied to integral surfaces. In this paper, we examine how transparency and texturing techniques can be used with integral surfaces to convey both shape and directional information. We present a rendering pipeline that combines these techniques aimed at faithfully and accurately representing integral surfaces while improving visualization insight. The presented pipeline is implemented directly on the GPU, providing real-time interaction for all rendering modes, and does not require expensive preprocessing of integral surfaces after computation.     

Understanding cost drivers of software evolution: a quantitative and qualitative investigation of change effort in two evolving software systems

Making changes to software systems can prove costly and it remains a challenge to understand the factors that affect the costs of software evolution. This study sought to identify such factors by investigating the effort expended by developers to perform 336 change tasks in two different software organizations. We quantitatively analyzed data from version control systems and change trackers to identify factors that correlated with change effort. In-depth interviews with the developers about a subset of the change tasks further refined the analysis. Two central quantitative results found that dispersion of changed code and volatility of the requirements for the change task correlated with change effort. The analysis of the qualitative interviews pointed to two important, underlying cost drivers: Difficulties in comprehending dispersed code and difficulties in anticipating side effects of changes. This study demonstrates a novel method for combining qualitative and quantitative analysis to assess cost drivers of software evolution. Given our findings, we propose improvements to practices and development tools to manage and reduce the costs.