On the Convergence of QM/MM Energies

We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a second-sphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as a reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarization of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on the contrary, they are sensitive to the charge-redistribution scheme and may cause large errors if charges are close to the junctions. In fact, the best results were obtained with a mechanical embedding approach that does not employ any correction scheme and ignores polarization. It gives a mean unsigned error for 40 QM systems of different sizes of 7 kJ/mol with a maximum error of 28 kJ/mol. The errors can be significantly decreased if bonds between the QM and MM system (junctions) are moved one residue away from all active-site residues. Then, most QM/MM variants give mean unsigned errors of 5-9 kJ/mol, maximum errors of 16-35 kJ/mol, and only five to seven residues give an error of over 5 kJ/mol. In general, QM/MM calculations converge faster with system size than pure QM calculations

X-Ray, FUV, and UV Observations of alpha Centauri B: Determination of Long-term Magnetic Activity Cycle and Rotation Period

We have been carrying out a study of stellar magnetic activity, dynamos, atmospheric physics, and spectral irradiances from a sample of solar-type G0-5 V stars with different ages. One of the major goals of this program is to study the evolution of the Sun's X-ray through NUV spectral irradiances with age. Of particular interest is the determination of the young Sun's elevated levels of high-energy fluxes because of the critical roles that X-ray through FUV emissions play on the photochemical and photoionization evolution of early, young planetary atmospheres and ionospheres. Motivated by the current exoplanetary search missions that are hunting for earth-size planets in the habitable zones of nearby main-sequence G-M stars, we are expanding our program to cooler, less luminous, but much more numerous main-sequence K-type stars, such as alpha Centauri B. The long life (2-3x longer than our Sun) and slow evolution of K stars provide nearly constant energy sources for possible hosted planets. Presented here are X-ray, UV, and recently acquired FUV observations of the K1 V star alpha Cen B. These combined high-energy measures provide a more complete look into the nature of alpha Cen B's magnetic activity and X-UV radiances. We find that alpha Cen B has exhibited significant long-term variability in X-ray through NUV emission fluxes, indicating a solar-like long-term activity cycle of P_cycle = 8.84 years. In addition, analysis of the short-term rotational modulation of mean light due to the effects of magnetically active regions has yielded a well-determined rotation period of P_rotation = 36.2 days. alpha Cen B is the only old main-sequence K star with a reliably determined age and rotation period, and for early K-stars, is an important calibrator for stellar age/rotation/activity relations

The influence of binary stars on the kinematics of low-mass galaxies

In this paper, the influence of binary stars on the measured kinematics of dwarf galaxies is investigated. Using realistic distributions of the orbital parameters (semi-major axis, eccentricity, ...), analytical expressions are derived for the changes induced by the presence of binary stars in the measured velocity moments of low-mass galaxies (such as the projected velocity dispersion and the 4th order Gauss-Hermite coefficient h4). It is shown that there is a noticeable change in the observed velocity dispersion if the intrinsic velocity dispersion of a galaxy is of the same order as the binary velocity dispersion. The kurtosis of the line-of-sight velocity distribution (LOSVD) is affected even at higher values of the intrinsic velocity dispersion

Radial Velocity Studies of Close Binary Stars.VI

Radial-velocity measurements and sine-curve fits to the orbital velocity variations are presented for the sixth set of ten close binary systems: SV Cam, EE Cet, KR Com, V410 Cyg, GM Dra, V972 Her, ET Leo, FS Leo, V2388 Oph, II UMa. All systems except FS Leo are double-lined spectroscopic binaries. The type of FS Leo is unknown while SV Cam is a close, detached binary; all remaining systems are contact binaries. Eight binaries (all except SV Cam and V401 Cyg) are the recent photometric discoveries of the Hipparcos satellite project. Five systems, EE Cet, KR Com, V401 Cyg, V2388 Oph, II UMa, are members of visual/spectroscopic triple systems. We were able to observe the close binary system EE Cet separately of its companion, but in the remaining four systems we could separate the spectral components only through the use of the broadening-function approach. Several of the studied systems are prime candidates for combined light and radial-velocity synthesis solutions.Comment: AASTeX5, 5 figures, 2 tables, modified after the AJ revie

The 7.5 Magnitude Limit Sample of Bright Short-Period Binary Stars. I. How Many Contact Binaries Are There?

A sample of bright contact binary stars (W UMa-type or EW, and related: with beta Lyr light curves, EB, and ellipsoidal, ELL - in effect, all but the detached, EA), to the limit of Vmax = 7.5 magnitude is deemed to include all discoverable short-period (P<1 days) binaries with photometric variation larger than about 0.05 magnitude. Of the 32 systems in the final sample, 11 systems have been discovered by the Hipparcos satellite. The combined spatial density is evaluated at (1.02+/-0.24)x10^-5 pc^-3. The Relative Frequency of Occurrence (RFO), defined in relation to the Main Sequence stars, depends on the luminosity. An assumption of RFO~1/500 for MV>+1.5 is consistent with the data, although the number statistics is poor with the resulting uncertainty in the spatial density and the RFO by a factor of about two. The RFO rapidly decreases for brighter binaries to a level of 1/5,000 for MV<+1.5 and to 1/30,000 for MV<+0.5. The high RFO of 1/130, previously determined from the deep OGLE-I sample of Disk Population W UMa-type systems towards Baade's Window, is inconsistent with and unconfirmed by the new results. Possible reasons for the large discrepancy are discussed. They include several observational effects, but also a possibility of a genuine increase in the contact-binary density in the central parts of the Galaxy.Comment: AASTeX5, 11 figures, 3 tables. Table 1 is very wide; in case of problems send e-mail to [email protected] for a raw text versio

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