Because standard molecular dynamics (MD) simulations are unable to access time scales of interest in complex biomolecular systems, it is common to "stitch together" information from multiple shorter trajectories using approximate Markov state model (MSM) analysis. However, MSMs may require significant tuning and can yield biased results. Here, by analyzing some of the longest protein MD data se...

Molecular dynamics with explicit solvent is favored for its ability to more correctly simulate aqueous biological processes and has become routine thanks to increasingly powerful computational resources. However, analysis techniques including Markov state models (MSMs) ignore solvent atoms and focus solely on solute coordinates despite solvent being implicated in myriad biological phenomena. We...

In the increasingly complex prosthetic limbs for upper extremity amputees, more mechanical degrees of freedom are combined with various neural commands to produce versatile human-like movements. Development, testing, and fitting of such neural prosthetic systems and training patients to control them effectively are complex processes that cannot be performed efficiently or safely by ad hoc and t...

We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic states (temperatures, Hamiltonians, etc.) dTRAM provides maximum-likelihood estimates of stationary quantities (probabilities, free energies, expectation values) at any thermodynamic state. In contrast to the weighte...

Introduction (aim) Nigeria currently has one of the highest HIV and AIDS epidemic burden worldwide. Prevalence among key populations is currently, 34.1% (brothel-based sex workers), 21.95 (non-brothel-based), 37.6% (MSMs) and 9.3% for IDUs respectively. A huge gaps exists in the national response to key populations as a result of socio-cultural barriers and unfavorable political and legislative...

Counterfeiting in the pharmaceutical industry has become a serious and underreported problem, particularly in developing countries. This Application Note shows the analysis of antidiabetic drugs of the sulfonylurea class using the Agilent 1220 Infinity Gradient LC system with diode array detector (DAD). Both HPLC and UHPLC methods revealed excellent precision, accuracy and linearity as well as ...

Environmental contaminants can affect human and animal health are thus an issue of concern. Anthony Provatas is a Research Professor the Organics Laboratory Manager at University Connecticut in Center for Sciences Engineering (CESE) Institute Environment; he also Program Chair Board Member Eastern Analytical Symposium (EAS). His research has been focused on effects health. We recently spoke to ...

Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special cas...

A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a m...