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Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes.

As technology moves forward with newer hardware, new computational techniques, and new algorithms, it is important for science to keep up with these advances. Without people maintaining code to the latest standards and modifying the underlying algorithms to closely match the shifting hardware landscape, scientific software easily becomes outdated and deprecated on the latest architectures. Similarly as technology advances and acapability increases so the underlying methods should be adapted, extended or replaced in order to fully realize the scientific potential of the underlying improvements in the hardware. This research focuses on developing faster and higher accuracy free energy prediction methods as well as the development of simulation techniques necessary to improve the sampling efficiency of all atom, condensed phase, molecular dynamics simulations on exa-scale computational hardware. Specifically, it will cover efforts to develop GPU accelerated thermodynamic integration algorithms, low level code optimization on next generation CPU architectures, techniques for more efficient 3D domain decomposition and work to explore more efficient sampling techniques. These methods have been implemented as part of this work within the Amber software package. Additionally, to show the accuracy and performance of the code, comparisons against previous Amber versions as well as existing free energy prediction packages such as Schrodinger's FEP+ will be analyzed and discussed.

Protein-ligand binding is among the most fundamental phenomena underlying all molecular biology, and a greater ability to more accurately and robustly predict the binding free energy of a small molecule ligand for its cognate protein is expected to have vast consequences for improving the efficiency of pharmaceutical drug discovery. We briefly reviewed a number of scientific and technical advances that have enabled alchemical free energy calculations to recently emerge as a preferred approach, and critically considered proper validation and effective use of these techniques. In particular, we characterized a selection bias effect which may be important in prospective free energy calculations, and introduced a strategy to improve the accuracy of the free energy predictions.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Biomolecular and Physical Sciences, Science, Environment, Engineering and Technology, Knowledge of free-energy differences for states of a system provides an essential component in understanding many processes, including solubility, reaction rates, and phase changes. Therefore, the development of efficient, accurate free-energy calculation routines has long been of interest within the field of molecular modelling. Until recently, thermodynamic integration, free-energy perturbation and slow-change techniques were the only approaches available for the calculation of free-energy differences between two states of a system. However, with the discovery of non-equilibrium free-energy relations in the late nineties, new calculation approaches are now possible. This thesis demonstrates the application of these new relations by deriving them from statistical mechanical concepts and applying them to a variety of systems. Although other types of systems are considered, the focus of this work is on the investigation of density changes, as the density of a system is one of its fundamental intrinsic properties, and expansion and compression phenomena are central to many thermodynamic investigations. To investigate the convergence properties of the free-energy calculation methods prior to their application to systems undergoing a density change, a novel transformation between Lennard-Jones systems possessing different potentials is developed and simulations are completed for a variety of transformation parameters. In particular, the accuracy of free-energy calculations as a function of transformation rate is considered, along with a detailed analysis of free-energy convergence as a function of the number of transformations completed.

An in silico screen of the NIH Molecular Library Small Molecule Repository (MLSMR) of 350000 compounds and confirmatory bioassays led to identification of chaetochromin A (1) as an inhibitor of botulinum neurotoxin serotype A (BoNT A). Subsequent acquisition and testing of analogues of 1 uncovered two compounds, talaroderxines A (2) and B (3), with improved activity. These are the first fungal metabolites reported to exhibit BoNT/A inhibitory activity., Published in ACS Medicinal Chemistry Letters, v3 p387-391, 2 Apr 2012.

Prior to applying any interatomic potential, it is important to know the stability of the different phases it describes. In the literature many methods to determine the phase diagram from an interatomic potential are described. Although for pure elements the procedure to obtain the thermodynamic functions is well established, for alloys it is not. In this work a method is developed to determine the phase diagram, i.e. solubility limits and spinodal gap, for the case of miscibility gaps. The method combines Monte Carlo simulations in the isobaric semi-grand canonical ensemble, full thermodynamic integration and Redlich-Kister expansions to parameterize the Gibbs free energy. Besides numerical inaccuracies, this method does not rely on any physical approximations to determine the phase diagram of a given interatomic potential. The method is applied to two different Fe-Cr potentials that are widely used in the literature. The resulting phase diagrams are discussed by comparing them to the experimental one and ones obtained in other works from the same potentials. © 2011 Elsevier B.V. All rights reserved., SCOPUS: ar.j, info:eu-repo/semantics/published

The Neotropical poison frog genus Ranitomeya is revised, resulting in one new genus, one new species, five synonymies and one species classified as nomen dubium. We present an expanded molecular phylogeny that contains 235 terminals, 104 of which are new to this study. Notable additions to this phylogeny include seven of the 12 species in the minuta group, 15 Ranitomeya amazonica, 20 R. lamasi, two R. sirensis, 30 R. ventrimaculata and seven R. uakarii. Previous researchers have long recognized two distinct, reciprocally monophyletic species groups contained within Ranitomeya, sensu Grant et al. 2006: the ventrimaculata group, which is distributed throughout much of the Amazon, and the minuta group of the northern Andes and Central America. We restrict Ranitomeya to the former group and erect a new genus, Andinobates Twomey, Brown, Amézquita & Mejía-Vargas gen. nov., for members of the minuta group. Other major taxonomic results of the current revision include the following: (i) A new species, Ranitomeya toraro Brown, Caldwell, Twomey, Melo-Sampaio & Souza sp. nov., is described from western Brazil. This species has long been referred to as R. ventrimaculata but new morphological and phylogenetic data place it sister to R. defleri. (ii) Examination of the holotype of R. ventrimaculata revealed that this specimen is in fact a member of what is currently referred to as R. duellmani, therefore, Dendrobates duellmani Schulte 1999 is considered herein a junior synonym of D. ventrimaculatus Shreve 1935 (= R. ventrimaculata). (iii) For the frogs that were being called R. ventrimaculata prior to this revision, the oldest available and therefore applicable name is R. variabilis. Whereas previous definitions of R. variabilis were restricted to spotted highland frogs near Tarapoto, Peru, our data suggest that this color morph is conspecific with lowland striped counterparts. Therefore, the definition of R. variabilis is greatly expanded to include most frogs which were (prior

Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or receptor, are characterized by a decrease of free energy. Despite the recent developments in computing power and methodology, it remains challenging to accurately estimate free energy changes. Major issues are still concerned with the accuracy of the underlying model to describe the protein system and how well the calculation in fact emulates the behaviour of the system. This thesis is largely concerned with the quality of current free energy calculation methods as applied to protein-ligand systems. Several methodologies were employed to calculate Gibbs standard free energies of binding for a collection of protein-ligand complexes, for which experimental affinities were available. Calculations were performed using system description with different levels of accuracy and included a continuum approach, which considers the protein and the ligand at the atomic level but includes solvent as a polarizable continuum, and an all-atom approach that relies on molecular dynamics simulations. In most such applications, the effects of ionic strength are neglected. However, the severity of this approximation, in particular when calculating free energies of charged ligands, is not very clear. The issue of incorporating ionic strength in free energy calculations by means of explicit ions was investigated in greater detail and considerable attention was given to the affinities of charged peptides in the presence of explicit counter-ions. A second common approximation is concerned with the description of ligands that exhibit multiple protonation states. Because most of current methods do not model changes in the acid dissociation constants of titrating groups upon binding, protonation equilibria of such ligands are not taken into account in free energy calculations. The implications of this approximation when predicting affinities were analysed. Finally, when calculating free energies of

© 2017, Pleiades Publishing, Ltd. An approach to determining the nucleation barrier and interfacial free energy (surface tension) based on molecular dynamics simulations of structural transformations, in particular, the formation of new phase nuclei, is reported. The approach is based on the thermodynamic integration method, wherein key elements are trajectories characterizing the potential energy change, which are obtained from independent numerical experiments. An important feature of the approach is its applicability to both equilibrium and nonequilibrium systems, as well as the possibility of determining the above thermodynamic characteristics for small new-phase nuclei, with a significant curvature of the surface. For example, we present the temperature dependencies of the surface tension of water droplet nuclei for water vapor nucleation and of the nucleation barrier to crystal nucleation in two model glassy systems, which are computed within the framework of the proposed approach. The calculated values of the surface tension coefficient of water droplet nuclei are compared with the available experimental data.