vdW-TSSCDS—An automated and global procedure for the computation of stationary points on intermolecular potential energy surfaces

We present a generalization of the transition state search using chemical dynamics simulations (TSSCDS) methodology (discussed in a previous study) which allows the topographical characterization of intermolecular potential energy surfaces (IPES) for non-covalently bound complexes (vdW-TSSCDS). Starting from a single random input geometry, we show that vdW-TSSCDS is able to globally and automatically locate stationary points of an IPES, even in limiting cases such as extremely flat regions or nontrivial topologies (eg, bifurcation points). The basic idea is the expression of the connectivity matrix in block structure, where diagonal blocks correspond to the isolated fragments and off-diagonal blocks provide the intermolecular connectivity. To this end, we introduce a new definition of bound or not, in a non-covalent sense, utilizing an extra set of van der Waals distances, which encompasses all kinds of non-covalent distances. To discuss the use of the vdW-TSSCDS method, we present a series of 2-body van der Waals systems, namely, Ar-Benzene (3D), N₂-Benzene (6D) and H₂O-Benzene (9D). Finally, we further illustrate its capabilities by presenting some applications for n-body problems (n > 2), (H₂O)₂-Benzene (12D) and (H₂O)₃-Benzene (21D), as well as to a reactive, fully-flexible, system (Benzene-NO₂)⁺ (39D) in which the simultaneous breaking/formation of both covalent and non-covalent interactions takes place.     

Biocompatibility of nitrogen-doped multiwalled carbon nanotubes with murine fibroblasts and human hematopoietic stem cells

Journal of Nanoparticle Research - Workers are increasingly exposed to nanoparticles, mostly via inhalation. Respiratory protection is recommended as an additional control measure. Particulate...     

Controlling the propagation of broadband light pulses by Electromagnetically Induced Transparency

We present an experimental and theoretical investigation, performed on hot sodium atoms in a ladder scheme, showing the control of the absorption and of the propagation velocity of a probe light pulse with a spectral bandwidth as large as 1.8 GHz. The predictions of the theoretical model compare favorably with the experimental results.     

Heuristic approaches for support vector machines with the ramp loss

Recently, Support Vector Machines with the ramp loss (RLM) have attracted attention from the computational point of view. In this technical note, we propose two heuristics, the first one based on solving the continuous relaxation of a Mixed Integer Nonlinear formulation of the RLM and the second one based on the training of an SVM classifier on a reduced dataset identified by an integer linear problem. Our computational results illustrate the ability of our heuristics to handle datasets of much larger size than those previously addressed in the literature.     

Accuracy and efficiency comparison of various nonlinear Kalman filters applied to multibody models

Nonlinear Dynamics - Multibody simulations are already used in many industries to speed up the development of new products. However, improvements in multibody formulations and the continuous...     

Impact of Dye‐Protein Interaction and Silver Nanoparticles on Rose Bengal Photophysical Behavior and Protein Photocrosslinking

The role of recombinant Type‐I human collagen in the free form or forming AgNP@collagen on the photophysical and photochemical behavior of rose Bengal was analyzed. The formation of dye aggregates on the protein surface was experimentally observed and corroborated by docking calculations. The formation of such aggregates is believed to change the main oxidative mechanism from Type‐II (singlet oxygen) to Type‐I (free radical) photosensitization. Remarkably, the presence of AgNP in the form of AgNP@collagen altered the dynamics of dye triplet deactivation, effectively preventing the dye degradation and reducing the extent of protein crosslinked. Both crosslinked rHC and AgNP@collagen were able to support fibroblasts proliferation, but only the material containing silver was resistant to S. epidermidis infection.