Non-Reversibility of Molecular Dynamics Trajectories

We study the non-reversibility of molecular dynamics trajectories arising from the amplification of rounding errors. We analyse the causes of such behaviour and give arguments, indicating that this does not pose a significant problem for Hybrid Monte Carlo computations. We present data for pure SU(3) gauge theory and for QCD with dynamical fermions on small lattices to illustrate and to support some of our ideas.Comment: 3 pages LATEX, 4 color figures included using epsf. Talk presented at LATTICE96(algorithms

Tuning the generalized Hybrid Monte Carlo algorithm

We discuss the analytic computation of autocorrelation functions for the generalized Hybrid Monte Carlo algorithm applied to free field theory and compare the results with numerical results for the $O(4)$ spin model in two dimensions. We explain how the dynamical critical exponent $z$ for some operators may be reduced from two to one by tuning the amount of randomness introduced by the updating procedure, and why critical slowing down is not a problem for other operators.Comment: 4 pages, to be published in the Proceedings of Lattice 95, uuencoded PostScript fil

Amplification of the androgen receptor may not explain the development of androgen-independent prostate cancer

Objective To examine the role of androgen receptor (AR) gene amplification and aneusomy of the X chromosome in the development of antiandrogen-resistant prostate cancer. Patients and methods Twenty patients with prostate cancer resistant to androgen-deprivation therapy were selected for study. The records of patients with tumours before and after antiandrogen therapy, and with a full clinical follow-up, were retrieved. AR gene amplification and X chromosome copy number were assessed by fluorescence in situ hybridization using a labelled probe at locus Xq11-13 for the AR gene and a labelled a-satellite probe for the X chromosome. At least 20 nuclei were scored over three tumour areas by two independent observers. Results Aneusomy of the X chromosome was reported respectively in seven (35%) and 11 (55%) tumours before and after hormone relapse, the AR gene copy number was increased in seven (35%) and 13 (65%), respectively, and AR gene amplification was detected in one (5%) and three (15%), respectively. Neither increased AR copy number nor AR amplification in primary tumours precluded a biological response to androgen-deprivation therapy. Conclusion The rate of AR gene amplification is too low to be solely responsible for the development of antiandrogen-resistant prostate cancer. Also, the presence of amplified AR and cells aneusomic for the X chromosome in primary tumours that respond to androgen-deprivation therapy suggests that an increase in AR gene copy number does not prevent a tumour from responding to this therapy. Therefore other mechanisms which could cause hormone-refractory prostate cancer must be investigated before it is understood why so many patients relapse with this disease

The overlap operator as a continued fraction

We use a continued fraction expansion of the sign-function in order to obtain a five dimensional formulation of the overlap lattice Dirac operator. Within this formulation the inverse of the overlap operator can be calculated by a single Krylov space method where nested conjugate gradient procedures are avoided. We show that the five dimensional linear system can be made well conditioned using equivalence transformations on the continued fractions. This is of significant importance when dynamical overlap fermions are simulated.Comment: 3 pages, 1 figure, talk presented by U. Wenger at Lattice2001(chiral

QCD with dynamical Wilson fermions at β=5.5\beta=5.5

We study QCD with two flavors of dynamical Wilson fermions at $\beta = 5.5$ and three values of $\kappa$. The corresponding pion masses are 0.375, 0.324 and 0.262 in lattice units, with pion to rho mass ratios of 0.76, 0.71 and 0.62, respectively. We use the configurations to compute the heavy quark potential, leading to lattice spacings of 0.110, 0.105 and 0.099 fm, and to compute spectroscopy for several different valence quark $\kappa$'s.Comment: LaTex 4 pages, 4 figures. Talk presented at LATTICE96(spectrum

Radar studies of the vertical distribution of insects migrating over southern Britain: the influence of temperature inversions on nocturnal layer concentrations

Insects migrating over two sites in southern UK (Malvern in Worcestershire, and Harpenden in Hertfordshire) have been monitored continuously with nutating vertical-looking radars (VLRs) equipped with powerful control and analysis software. These observations make possible, for the first time, a systematic investigation of the vertical distribution of insect aerial density in the atmosphere, over temporal scales ranging from the short (instantaneous vertical profiles updated every 15 min) to the very long (profiles aggregated over whole seasons or even years). In the present paper, an outline is given of some general features of insect stratification as revealed by the radars, followed by a description of occasions during warm nights in the summer months when intense insect layers developed. Some of these nocturnal layers were due to the insects flying preferentially at the top of strong surface temperature inversions, and in other cases, layering was associated with higher-altitude temperature maxima, such as those due to subsidence inversions. The layers were formed from insects of a great variety of sizes, but peaks in the mass distributions pointed to a preponderance of medium-sized noctuid moths on certain occasions

On the Dynamics of Light Quarks in QCD

We describe recent results concerning the behavior of lattice QCD with light dynamical Wilson and Staggered quarks. We show that it is possible to reach regions of parameter space with light pions $m_\pi\approx 0.2/a$ using Wilson fermions. If the Hybrid Molecular Dynamics (HMD) algorithm is used with the same parameters it gives incorrect results. We also present preliminary results using a higher-order integration scheme.Comment: 4 pages (all in postscript), proceedings of LAT'9

Instabilities and Non-Reversibility of Molecular Dynamics Trajectories

The theoretical justification of the Hybrid Monte Carlo algorithm depends upon the molecular dynamics trajectories within it being exactly reversible. If computations were carried out with exact arithmetic then it would be easy to ensure such reversibility, but the use of approximate floating point arithmetic inevitably introduces violations of reversibility. In the absence of evidence to the contrary, we are usually prepared to accept that such rounding errors can be made small enough to be innocuous, but in certain circumstances they are exponentially amplified and lead to blatantly erroneous results. We show that there are two types of instability of the molecular dynamics trajectories which lead to this behavior, instabilities due to insufficiently accurate numerical integration of Hamilton's equations, and intrinsic chaos in the underlying continuous fictitious time equations of motion themselves. We analyze the former for free field theory, and show that it is essentially a finite volume effect. For the latter we propose a hypothesis as to how the Liapunov exponent describing the chaotic behavior of the fictitious time equations of motion for an asymptotically free quantum field theory behaves as the system is taken to its continuum limit, and explain why this means that instabilities in molecular dynamics trajectories are not a significant problem for Hybrid Monte Carlo computations. We present data for pure $SU(3)$ gauge theory and for QCD with dynamical fermions on small lattices to illustrate and confirm some of our results.Comment: 28 pages latex with 19 color postscript figures included by eps

The heavy quark potential in QCD with 2 flavors of dynamical quarks

We compute the heavy quark potential on configurations generated by the HEMCGC collaboration with dynamical staggered fermions at $6/g^2 = 5.6$ and with dynamical Wilson fermions at $6/g^2 = 5.3$. The computations are done on $16^3 \times 32$ lattices, corresponding to physical sizes of about 1.6 and 2.3 fm, respectively. Up to the distances probed no sign of string breaking is detectable. We also compute the recently proposed scale $r_0$ defined by $r_0^2 F(r_0) = 1.65$.Comment: 8 pages with 3 figures. uuencoded postscript file. FSU-SCRI-94-0