Sampling Free Energy Surfaces as Slices by Combining Umbrella Sampling and Metadynamics

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, in order to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories

Graphical Analysis on Text Mining Unstructured Data Using D-Matrix

Fault dependency (D-matrix) is used as a diagnostic model that identifies the fault system data and its causal relationship at the hierarchical system-level. It consists of dependencies and relationship between identified failure modes and symptoms related to a system. Constructing such D-matrix fault detection model is time overwhelming task .A system is proposed that describes associate ontology based text mining on unstructured data using D-matrix for automatically constructing D-matrix by mining many repair verbatim text data (typically written in unstructured text) collected throughout the identification process. And also graphical model generation for each generated D-matrix. Initially we construct fault diagnosis ontology and then text mining techniques are applied to spot dependencies among failure modes and identified symptom. D-matrix is represented in graph so analysis gets easier and faulty parts becomes simply detectable. The proposed methodology are implemented as a prototype tool and validated by using real-life information collected from the automobile domain

One-pot Synthesis of Hierarchical, Micro-macroporous Zeolites with Encapsulated Metal Particles as Sinter-resistant, Bifunctional Catalysts

We report a new one-pot synthesis procedure for hierarchical zeolites with intracrystalline macropores and metal particles encapsulated within the zeolitic walls. The synthesis allows to prepare macroporous zeolites of MFI topology with different heteroatoms (silicalite-1, ZSM-5 and TS-1) and different encapsulated noble metal particles, such as gold, platinum and palladium. The hierarchically structured zeolites contain large macropores with diameters around 400 nm, which are well distributed and interconnected and should significantly enhance mass transport properties. The encapsulation of metal nanoparticles within the zeolitic walls leads to remarkable sinter resistance of the particles. Encapsulated gold nanoparticles (2.6 nm) do not significantly change in size during an 18-hour treatment at 600 °C under air, while non-encapsulated gold particles sinter heavily during the same treatment. Catalytic experiments for the direct epoxidation of propene with hydrogen and oxygen show that both catalytic functions of a macroporous TS-1 sample that encapsulates gold particles are accessible and active. This catalyst displays high activity, although PO selectivity could still be improved. These materials show great potential for use in catalytic applications, due to their bifunctional nature, high sintering resistance, shape selective properties and hierarchical structure

Synthesis of possible room temperature superconductor LK-99:Pb9_9Cu(PO4_4)6_6O

The quest for room-temperature superconductors has been teasing scientists and physicists, since its inception in 1911 itself. Several assertions have already been made about room temperature superconductivity but were never verified or reproduced across the labs. The cuprates were the earliest high transition temperature superconductors, and it seems that copper has done the magic once again. Last week, a Korean group synthesized a Lead Apatite-based compound LK-99, showing a T$_c$ of above 400$^\circ$K. The signatures of superconductivity in the compound are very promising, in terms of resistivity (R = 0) and diamagnetism at T$_c$. Although, the heat capacity (C$_p$) did not show the obvious transition at T$_c$. Inspired by the interesting claims of above room temperature superconductivity in LK-99, in this article, we report the synthesis of polycrystalline samples of LK-99, by following the same heat treatment as reported in [1,2] by the two-step precursor method. The phase is confirmed through X-ray diffraction (XRD) measurements, performed after each heat treatment. The room temperature diamagnetism is not evidenced by the levitation of a permanent magnet over the sample or vice versa. Further measurements for the confirmation of bulk superconductivity on variously synthesized samples are underway. Our results on the present LK-99 sample, being synthesized at 925$^\circ$C, as of now do not approve the appearance of bulk superconductivity at room temperature. Further studies with different heat treatments are though, yet underway.Comment: Short Commun.: 8pages Text + Figs: Comments/suggestion Welcom

Association between various antioxidants in normals and chronic obstructive pulmonary disease, their alteration and impact of smoking and disease on levels of antioxidants

Background: There is total alteration of various antioxidants in response to the oxidative stress, which is one of the major patho-physiologic hallmarks in chronic obstructive pulmonary disease (COPD) development. This study aims to establish the correlation between different antioxidants in normals and COPD, study the alteration in the correlation due to COPD and smoking as well as the impact of COPD and smoking on antioxidants levels.Methods: Study comprises of 96 normals as group I and 96 COPD patients as group II. The antioxidants albumin (Alb), bilirubin (Bil), uric acid (UA) ceruloplasmin (Cp), glutathione peroxidase (GSHPx), catalase (CAT) and superoxide dismutase 3 (SOD3) were estimated.Results: Significant lower serum Alb, UA, SOD3 and increased serum Cp and GSHPx were found in Group II. Significant correlation was found between Alb and UA (r=0.24); Bil and UA (r=0.26); Alb and CAT (r=0.211) and SOD3 and CAT (r=0.318) in normals. However, these correlations were altered in COPD where Alb correlates with Bil (r=0.235); UA with CAT (r=0.203) and SOD3 with GSHPx (r=-0.27). The correlation between SOD3 and CAT remained unaltered. Similar correlation of UA with Alb and Bil was observed in nonsmoker normals and between SOD3 and CAT in smoker normals. In COPD, no correlation was seen in nonsmokers, while in smokers Alb correlates with Bil (r=0.316) and SOD3 with CAT (r=0.317).Conclusions: These alterations may have clinical ramifications in further understanding the pathogenesis of COPD and developing therapeutic approaches