Two-dimensional infrared population transfer spectroscopy for enhancing structural markers of proteins

We propose the possibility of using vibrational population transfer to enhance the structural markers for protein motifs that occur in two-dimensional infrared spectroscopy. We demonstrate the potential of this method by calculating the spectrum of the trpzip2 β-hairpin peptide, a system that is small enough to allow accurate simulation of its two-dimensional infrared spectra, including vibrational population transfer induced by a fluctuating solvent. The results show that under selected experimental conditions, in particular by using perpendicular polarization and finite waiting times, the cross peaks that constitute the well-known Z-shape marker for β-sheet structure in two-dimensional spectra are strongly enhanced. This enhancement is shown to result from vibrational population transfer. It should be possible to use the same technique for enhancing cross peaks in other structures and generally improve structure determination by two-dimensional infrared spectroscopy. The simulated population transfer times are in good agreement with those observed in experiments on typical proteins

Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine

The line shapes detected in coherent femtosecond vibrational spectroscopies contain direct signatures of peptide conformational fluctuations through their effect on vibrational frequencies and intermode couplings. These effects are simulated in trialanine using a Green's function solution of a stochastic Liouville equation constructed for four collective bath coordinates (two Ramachandran angles affecting the mode couplings and two diagonal energies). We find that fluctuations of the Ramachandran angles which hardly affect the linear absorption can be effectively probed by two-dimensional spectra. The signal generated at k(1)+k(2)-k(3) is particularly sensitive to such fluctuations. (C) 2004 American Institute of Physics

XMM-Newton observations of the Small Magellanic Cloud: X-ray outburst of the 6.85 s pulsar XTE J0103-728

A bright X-ray transient was seen during an XMM-Newton observation in the direction of the Small Magellanic Cloud (SMC) in October 2006. The EPIC data allow us to accurately locate the source and to investigate its temporal and spectral behaviour. X-ray spectra covering 0.2-10 keV and pulse profiles in different energy bands were extracted from the EPIC data. The detection of 6.85 s pulsations in the EPIC-PN data unambiguously identifies the transient with XTE J0103-728, discovered as 6.85 s pulsar by RXTE. The X-ray light curve during the XMM-Newton observation shows flaring activity of the source with intensity changes by a factor of two within 10 minutes. Modelling of pulse-phase averaged spectra with a simple absorbed power-law indicates systematic residuals which can be accounted for by a second emission component. For models implying blackbody emission, thermal plasma emission or emission from the accretion disk (disk-blackbody), the latter yields physically sensible parameters. The photon index of the power-law of ~0.4 indicates a relatively hard spectrum. The 0.2-10 keV luminosity was 2x10^{37} with a contribution of ~3% from the disk-blackbody component. A likely origin for the excess emission is reprocessing of hard X-rays from the neutron star by optically thick material near the inner edge of an accretion disk. From a timing analysis we determine the pulse period to 6.85401(1) s indicating an average spin-down of ~0.0017 s per year since the discovery of XTE J0103-728 in May 2003. The X-ray properties and the identification with a Be star confirm XTE J0103-728 as Be/X-ray binary transient in the SMC.Comment: 5 pages, 4 figures, submitted to A&A on 21 Dec. 200

Modeling the Vibrational Dynamics and Nonlinear Infrared Spectra of Coupled Amide I and II Modes in Peptides

The amide vibrational modes play an important role in energy transport and relaxation in polypeptides and proteins and provide us with spectral markers for structure and structural dynamics of these macromolecules. Here, we present a detailed model to describe the dynamic properties of the amide I and amide II modes and the resulting linear and nonlinear spectra. These two modes have large oscillator strengths, and their mutual coupling plays an important role in their relaxation. Using first-principles calculations of NMA-d(7) and a dipeptide in a fluctuating bath described by molecular dynamics simulations, we model the frequencies of the local vibrations as well as the coupling between them. Both the coherent couplings and the fluctuations induced by contact with their environment are taken into account. We apply the resulting model of interacting fluctuating oscillators to study the collective vibrations and the partially coherent transport of vibrational energy through a model a-helix. We find that the instantaneous vibrations are delocalized over a few (up to four) amide units, while the coherences in the helix survive for 0.5-1 ps, leading to coherent transport on a similar time scale.</p

Within You / Without You: Biotechnology, Ontology, and Ethics

As Implantable Cardioverter Defibrillators (ICDs) have become more common, ethical issues have arisen regarding the deactivation of these devices. Goldstein et al., have shown that both patients and cardiologists consider ICD deactivation to be different from the discontinuation of other life-sustaining treatments. It cannot be argued ethically that ICDs raise new questions about the distinction between withholding and withdrawing treatment, and neither the fact that they are used intermittently, nor the duration of therapy, nor the mere fact that they are located inside the body can be considered unique to these devices and morally decisive. However, frequent allusions to the fact that they are located inside the body might provide a clue about what bothers patients and physicians. As technology progresses, some interventions seem to become a part of the patient as a unified whole person, completely replacing body parts and lost physiological functions rather than merely substituting for impaired structure and function. If a life-sustaining intervention can be considered a “replacement”—a part of the patient as a unified whole person—then it seems that deactivation is better classified as a case of killing rather than a case of forgoing a life-sustaining treatment. ICDs are not a “replacement” therapy in this sense. The deactivation of an ICD is best classified, under the proper conditions, as the forgoing of an extraordinary means of care. As technology becomes more sophisticated, however, and new interventions come to be best classified as “replacements” (a heart transplant would be a good example), “discontinuing” these interventions should be much more morally troubling for those clinicians who oppose euthanasia and assisted suicide

Theory of coherent two-dimensional vibrational spectroscopy

Two-dimensional (2D) vibrational spectroscopy has emerged as one of the most important experimental techniques useful to study the molecular structure and dynamics in condensed phases. Theory and computation have also played essential and integral roles in its development through the nonlinear optical response theory and computational methods such as molecular dynamics (MD) simulations and electronic structure calculations. In this article, we present the fundamental theory of coherent 2D vibrational spectroscopy and describe computational approaches to simulate the 2D vibrational spectra. The classical approximation to the quantum mechanical nonlinear response function is invoked from the outset. It is shown that the third-order response function can be evaluated in that classical limit by using equilibrium or non-equilibrium MD simulation trajectories. Another simulation method is based on the assumptions that the molecular vibrations can still be described quantum mechanically and that the relevant molecular response functions are evaluated by the numerical integration of the Schrodinger equation. A few application examples are presented to help the researchers in this and related areas to understand the fundamental principles and to use these methods for their studies with 2D vibrational spectroscopic techniques. In summary, this exposition provides an overview of current theoretical efforts to understand the 2D vibrational spectra and an outlook for future developments. c.Published under license by AIP Publishing

A Robust AFPTAS for Online Bin Packing with Polynomial Migration

In this paper we develop general LP and ILP techniques to find an approximate solution with improved objective value close to an existing solution. The task of improving an approximate solution is closely related to a classical theorem of Cook et al. in the sensitivity analysis for LPs and ILPs. This result is often applied in designing robust algorithms for online problems. We apply our new techniques to the online bin packing problem, where it is allowed to reassign a certain number of items, measured by the migration factor. The migration factor is defined by the total size of reassigned items divided by the size of the arriving item. We obtain a robust asymptotic fully polynomial time approximation scheme (AFPTAS) for the online bin packing problem with migration factor bounded by a polynomial in $\frac{1}{\epsilon}$. This answers an open question stated by Epstein and Levin in the affirmative. As a byproduct we prove an approximate variant of the sensitivity theorem by Cook at el. for linear programs