In Silico Exploration of Potential Phytoconstituents from the Bark Extract of Boswellia serrata for Hemorrhoidal Disease: Molecular Docking and Molecular Dynamics Analysis.

Boswellia serrata Roxb. Ex Colebr is a popular medicinal plant used traditionally in herbal medicinal preparations to treat a variety of diseases. The purpose of the present investigation was to investigate the anti-hemorrhoidal property of the bark extract of B. serrata (BS). For this, the sequential Soxhlet extraction method was carried out by using different solvents such as hexane, chloroform, and methanol. After the extraction, the obtained dry extracts were tested for quantitative determinations such as total alkaloid content (TAC), total flavonoid content (TFC), total phenol content (TPC), and total tannin content (TTC) for all the extracts. Moreover, in vitro antioxidant activity was measured using 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity and scavenging activity against 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS). Methanolic bark extract showed the highest TPC (67.10±1.83), TFC (372.73±4.45), TAC (9.732±1.06), and TTC (48.932±1.82), as well as the antioxidant assays DPPH (IC50=9.88 µg/ml) and ABTS (IC50=15.09 µg/ml). In this study, both LC-MS and GC-MS were performed to identify the chemical composition of all the extracts. Consequently, 19 compounds were identified by GC-MS and 27 compounds were identified by LC-MS analysis. The identified phytoconstituent(s) that could potentially interact with the target protein cyclooxygenase-2 (COX-2) (PDB: 4RRW) using molecular dynamics simulation and in silico docking were studied. Three compounds that have passed in drug-likeness and ADME-Tox properties are having more docking score than the standard. In this study, camptothecin, justicidin B, and taxiphyllin are identified as potential lead compounds with anti-hemorrhoidal properties and may be helpful in the process of drug development and discovery of novel drugs. Hence, these results demonstrate that BS is a good source of pharmacologically active components with potential applications against hemorrhoidal disease.

Translational and rotational dynamics of a self-propelled Janus probe in crowded environments.

We computationally investigate the dynamics of a self-propelled Janus probe in crowded environments. The crowding is caused by the presence of viscoelastic polymers or non-viscoelastic disconnected monomers. Our simulations show that the translational as well as rotational mean square displacements have a distinctive three-step growth for fixed values of self-propulsion force, and steadily increase with self-propulsion, irrespective of the nature of the crowder. On the other hand, in the absence of crowders, the rotational dynamics of the Janus probe is independent of self-propulsion force. On replacing the repulsive polymers with sticky ones, translational and rotational mean square displacements of the Janus probe show a sharp drop. Since different faces of a Janus particle interact differently with the environment, we show that the direction of self-propulsion also affects its dynamics. The ratio of long-time translational and rotational diffusivities of the self-propelled probe with a fixed self-propulsion, when plotted against the area fraction of the crowders, passes through a minimum and at higher area fraction merges to its value in the absence of the crowder. This points towards the decoupling of the translational and rotational dynamics of the self-propelled probe at an intermediate area fraction of the crowders. However, such translational-rotational decoupling is absent for passive probes.

d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations.

Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source postprocessing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures in both strong-confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. We also propose and validate a new order parameter for identifying the building blocks of quasi-one-dimensional ice. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture built with nix and employing a YAML-Lua scripting pipeline. The software has been designed to be user-friendly and extensible. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one- and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogeneous ice nucleation on a silver-exposed ß-AgI surface, homogeneous ice nucleation, flat monolayer square ice formation, and freezing of an ice nanotube.

Centering inclusivity in the design of online conferences-An OHBM-Open Science perspective.

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.