Efficient Implementation of Gaussian Process Regression Accelerated Saddle Point Searches with Application to Molecular Reactions.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian.

Compositional Analysis of Fragrance Accords Using Femtosecond Thermal Lens Spectroscopy.

Femtosecond thermal lens spectroscopy (FTLS) is a powerful analytical tool, yet its application to complex, multi-component mixtures like fragrance accords remains limited. Here, we introduce and validate a unified metric, the femtosecond thermal lens integrated magnitude (FTL-IM), to characterize such mixtures. The FTL-IM, derived from the integrated signal area, provides a direct, model-free measure of the total thermo-optical response, including critical convective effects.

Metabolite profiling, antimalarial potentials of using LC-MS and GC-MS: , molecular docking and molecular dynamics.

Purpose: To explore the phytochemical composition of bark and evaluate its potential antimalarial activity through and analyses.

Methods: The bark of was subjected to Soxhlet extraction using petroleum ether, chloroform, and methanol. The quantitative analysis of the extracts was performed to determine total phenolic, flavonoid, and tannin contents.

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.

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.

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.