The Latin Office Hymns in the Lutheran Hymnal

A study of hymns of the Church is most interesting and rewarding to both the historian and the theologian. Hymns reflect the theology of the Church as well as special emphases introduced by theological controversies

The Medieval Sequence and Troupe

The present thesis primarily is an historical research into the origin and development of. the sequence and the trope. From the Table or Contents it may appear that the order of the chapters is a little unusual, for one usually expects an historical account to be presented in chronological order. But because of what we know and what we do not know about the sequence and trope, the outline of the paper begins with the known and proceeds to the unknown. That is why both the sections on the sequence and the trope begin at the Abbey of St. Gall at the time of Charlemagne, and why the section about the origin of\u27 these forms is toward the end of the thesis. However, in the chapter about the origin of the forms one can do no more than present some of the suggested theories, for there is little agreement and it seems that the problem is destined to remain undecided

Appropriation and christianisation of the zodiac motif in the art of the Middle Ages

Концепт зодијака је своју стандардизовану визуелну форму стекао у римској уметности царског периода. Дванаест знакова који су красили представе паганских божанстава, царске и фунерарне споменике, магијске предмете, током средњег века могли су се видети на страницама библијских и литургијских рукописа, на фасадама и у унутрашњости цркава широм Европе. Интердисциплинарним приступом, базираним на методама више друштвених и хуманистичких наука, овај рад настоји да идентификује разлоге који су иницирали транспоновање мотива зодијака из античке уметности и његову реконтекстуaлизацију у хришћанску уметност средњег века, као и историјске, културне, политичке услове који су то омогућили. У ту сврху, пажња је посвећена различитим значењима и формама које је зодијак имао у писаној и визуелној култури старог и средњег века, његовим различитим применама, као и историји оних дисциплина које су имале нарочит утицај на његову популаризацију и рецепцију. С обзиром да је током истраживања уочен синхроницитет између најзначајнијих етапа у развоју и ширењу астрологије и периода интензивиране појаве представа зодијака, у раду се износи преглед историје астрологије, као и различитих ставова које су према њој имали различити хришћански аутори, црквени и световни великодостојници, као и поједине групације од првих векова нове ере до краја средњег века. Упркос бројним конотацијама које су за средњовековне посматраче могле бити негативне, зодијак је уврштен у иконографски репертаор хришћанске уметности захваљујућу својој улози у космолошко-есхатолошким теоријама античке и позноантичке филозофије присутним и у доминантним средњовековним дискурсима о изгледу и структури света. Према њима, овај мотив је означавао границу између небеског и овоземаљског и као такав нашао истакнуто место у декорацији храмова и у оквиру религиозних сцена и иконографских целина.The concept of the zodiac found its standardized visual form in the art of the Roman Imperial age. The Twelve Signs that could be seen decorating images of pagan deities, imperial and funerary monuments, as well as magical objects, could also be seen on the pages of biblical and liturgical manuscripts, on the façades and in the interiors of churches throughout Europe during the Middle Ages. By using an interdisciplinary approach, based on the methods of various disciplines within humanities and social sciences, this dissertation aims to identify causes that initiated the transposition of the Zodiac motif from ancient art and its appropriation into Christian art of the Middle Ages and to illuminate historical, cultural, and political conditions that enabled that process. To that end, we have focused our attention on different meanings and forms of the Zodiac in written and visual cultures of both Antiquity and the Middle Ages, as well as various applications it found, and the histories of those disciplines that had a particular effect on the reception and popularization of this motif. Considering that we have inferred the existence of synchronicity between the major phases in development of astrology and its transmission and periods in art history during which an increased number of representations of the Zodiac occur, we present an overview of the history of astrology, as well as different attitudes towards this divinatory technique expressed by numerous Christian authors, secular and ecclesiastical dignitaries, and certain groups within Christianity, from the first centuries of the common era until the end of the Middle Ages. Despite various connotations which could have posed a negative impression on the medieval viewers, Zodiac was included into the iconographic repertoire of Christian art due to the role it had in cosmological-eschatological theories of antique and late antique philosophers that were included into dominant medieval discourses on the structure of the Universe. The Zodiac, which represented the sphere of the fixed stars- the outer limit of the cosmos, delineated the border between celestial and earthly realms and was thus accorded a prominent position in church decoration and within religious scenes and iconographic ensembles

charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized, and multipurpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms. Due to conceptional differences related to software design and the large amount of numeric data inherent to residue topologies and parameter sets, conversion from one software format to another is not straightforward. Here, we present an automated and validated means to port the CHARMM force field to a format read by the GROMACS engine, harmonizing the different capabilities of the two codes in a self-documenting and reproducible way with a bare minimum of user interaction required. Being based entirely on the upstream data files, the presented approach does not involve any hard-coded data, in contrast with previous attempts to solve the same problem. The heuristic approach used for perceiving the local internal geometry is directly applicable for analogous transformations of other force fields

Exploring RNA structure and dynamics through enhanced sampling simulations

RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided

Insight into Amyloid Structure Using Chemical Probes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86796/1/j.1747-0285.2011.01110.x.pd

Strength of Hydrogen Bond Network Takes Crucial Roles in the Dissociation Process of Inhibitors from the HIV-1 Protease Binding Pocket

To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions

Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods. \ua9 2013 by the author; licensee MDPI, Basel, Switzerland

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μs in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from “pulling” coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives