External Inversion, Internal Inversion, and Reflection Invariance

Having in mind that physical systems have different levels of structure we develop the concept of external, internal and total improper Lorentz transformation (space inversion and time reversal). A particle obtained from the ordinary one by the application of internal space inversion or time reversal is generally a different particle. From this point of view the intrinsic parity of a nuclear particle (`elementary particle') is in fact the external intrinsic parity, if we take into account the internal structure of a particle. We show that non-conservation of the external parity does not necessarily imply non-invariance of nature under space inversion. The conventional theory of beta-decay can be corrected by including the internal degrees of freedom to become invariant under total space inversion, though not under the external one.Comment: 15 pages. An early proposal of "mirror matter", published in 1974. This is an exact copy of the published paper. I am posting it here because of the increasing interest in the "exact parity models" and its experimental consequence

Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints

Carnets de bord en sciences humaines : genèse, dynamique et fin d'une revue

Ce dernier numéro est l'occasion de faire un bilan et d'analyser les raisons qui nous ont conduits à décider de mettre un terme à l'existence d'une revue que nous avons animée pendant près de dix ans. Fidèles à la ligne éditoriale, nous dévoilons les coulisses de la production de Carnets de bord. Chemin faisant, nous nous livrons à un exercice d'auto-analyse susceptible d'éclairer la fragilité de ce genre d'initiatives intellectuelles dans un contexte universitaire où les critères managériaux d'évaluation ont largement gagné du terrain

Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation

Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation

The postpneumonectomy syndrome: clinical presentation and treatment

Background: Postpneumonectomy syndrome (PPS) is a rare complication after pneumonectomy. It consists of an excessive mediastinal shift resulting in compression and stretching of the tracheobronchial tree and the esophagus. The aim of this study was to give a comprehensive overview of diagnosis, variety of symptoms and evaluation of surgical treatment of PPS. Methods: We retrospectively reviewed the charts of all our patients with PPS since 1994 with respect to symptomatology, treatment and outcome. Our results were compared with case reports and case series in the literature. Results: Six women with a median age of 56.5 years (range 49-65) developed PPS after pneumonectomy for the treatment of lung cancer. Four presented with a right PPS and two with a left PPS, respectively. Symptoms consisted of shortness of breath in all patients and dysphagia as well as heartburn in two patients. Correction of PPS required re-exploration of the pneumonectomy space, reposition of the mediastinum followed by the insertion of single silicone prosthesis in five patients or fixation of the mediastinum with a xenopericardial graft in one patient. We could observe an improvement of the FEV(1)/FVC ratio in all our patients and the clinical improvement of shortness of breath was better than we expected by changes of lung function. Four patients returned to their regular activities with a follow-up of four years. We found 73 cases of PPS in the literature, on the right side in 50 patients (68%) and on the left side in 23 patients (32%). Fifty-nine patients (81%) were treated surgically. Symptoms can be suspicious for cardiogenic origin and vary from heartburn to recurrent syncopes. Conclusion: PPS is rare and not predictable. It can occur after right or left pneumonectomy. Symptoms are manifold and result from a shift, leading to compression and stretching of the two conduits located within the mediastinum, the tracheobronchial tree and the esophagus and consists of shortness of breath, stridor and heartburn. Diagnosis must be made by exclusion. Implantation of prosthesis is the most commonly used and effective treatmen

Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin

Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting this issue are provided by electron transfer proteins. The environment provided by the folded protein to the cofactor tunes the metal's electron transport capabilities as envisioned in the entatic hypothesis. To see how the entatic state is achieved one must study how the folding landscape affects and in turn is affected by the metal. Here, we develop a coarse-grained functional to explicitly model how the coordination of the metal (which results in a so-called entatic or rack-induced state) modifies the folding of the metallated Pseudomonas aeruginosa azurin. Our free-energy functional-based approach directly yields the proper nonlinear extra-thermodynamic free energy relationships for the kinetics of folding the wild type and several point-mutated variants of the metallated protein. The results agree quite well with corresponding laboratory experiments. Moreover, our modified free-energy functional provides a sufficient level of detail to explicitly model how the geometric entatic state of the metal modifies the dynamic folding nucleus of azurin

Properties of the energy landscape of network models for covalent glasses

We investigate the energy landscape of two dimensional network models for covalent glasses by means of the lid algorithm. For three different particle densities and for a range of network sizes, we exhaustively analyse many configuration space regions enclosing deep-lying energy minima. We extract the local densities of states and of minima, and the number of states and minima accessible below a certain energy barrier, the 'lid'. These quantities show on average a close to exponential growth as a function of their respective arguments. We calculate the configurational entropy for these pockets of states and find that the excess specific heat exhibits a peak at a critical temperature associated with the exponential growth in the local density of states, a feature of the specific heat also observed in real glasses at the glass transition.Comment: RevTeX, 19 pages, 7 figure

Use of Simulation to Visualize Healthcare Worker Exposure to Aerosol in the Operating Room

Simulation resources offer an opportunity to highlight aerosol dispersion within the operating room environment. We demonstrate our methodology with a supporting video that can offer operating room teams support in their practical understanding of aerosol exposure and the importance of personal protective equipment

On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006