Generating Generalized Distributions from Dynamical Simulation

We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare' thermostats for two specific classes of distributions; namely, those that are functions of the system Hamiltonian and those for which position and momentum are statistically independent. As an example, we propose a generalized variable temperature distribution that designed to accelerate sampling in molecular systems.Comment: 10 pages, 3 figure

A molecular-dynamics algorithm for mixed hard-core/continuous potentials

We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator splitting techniques similar to those that have been used successfully to generate a variety molecular-dynamics integrators. In numerical experiments, the Impulsive Verlet method is shown to be superior to previous methods with respect to stability and energy conservation in long simulations.Comment: 18 pages, 6 postscript figures, uses rotate.st

THE RELATIONSHIP BETWEEN RESIDUAL VIREMIA AND CHRONIC INFLAMMATION IN PATIENTS ON LONG-TERM ANTIRETROVIRAL THERAPY

Since the development of combination antiretroviral therapy, morbidity and mortality due to AIDS-related malignancies has declined significantly. In most patients, daily administration of a multidrug antiretroviral regimen is sufficient to suppress viral replication and reduce immune activation and inflammation. In spite of this, residual viremia persists for many years in the vast majority of patients, and immune activation remains higher than pre-infection baseline. Chronic immune activation and inflammation are associated with a variety of adverse health consequences including higher risks of cancer, heart disease, liver, and kidney problems. Moreover, these risks are not normalized to those of healthy individuals when patients are on long-term antiretroviral therapy. Due to the deleterious effects of chronic inflammation, it is desirable to develop treatments aimed at reducing immune activation in patients on suppressive antiretroviral therapy. Unfortunately, the variables that drive chronic inflammation are unclear, but could result from multiple factors including antigenic stimulation via residual viremia, microbial translocation from the gut into the blood due to damage of the gastrointestinal tract, and a reduction in the ability of the immune system to mount rapid immune responses against commonly encountered pathogens. In order to better control chronic immune activation, the variables that influence it must first be determined. iv In this thesis, I report on two studies of residual viremia in the context of immune activation. The first is a report of virologic data derived from a clinical trial of patients with sub-optimal reconstitution of the CD4+ T cell compartment. The second is a study regarding the relationship between immune activation, residual viremia, and CD4+ T cell count in the context of regulatory T cells. Neither study found a correlation between immune activation and residual viremia, indicating that immune activation may not be not driven by continuous antigenic stimulation provided by persistent virion production

Study of physiological tolerance to centrifugation Final report

Physiological effects and acceleration tolerances after weightlessness based on space environment simulation with human centrifuges and bed res

Secret Reception

Secret Reception combines art and bioacoustics to creatively engage the public in questions about sound reception in more-than-human worlds. This sonic art installation offers new paradigms for hearing through the design of haptic objects and tactile interfaces that use vibration to transmit sonic information. Drawing on scientific research that examines how insects detect sound through body parts, we transpose insect hearing to the human listening experience using sonic impulses that emulate the way insects receive them

Dynamical excitations in the collision of 2D Bose-Einstein condensates

We carry out simulations of the collision of two components of an adiabatically divided, quasi-2D BEC. We identify under, over and critically damped regimes in the dipole oscillations of the components according to the balance of internal and centre-of-mass (c.m.) energies of the components and investigate the creation of internal excitations. We distinguish the behaviour of this system from previous studies of quasi-1D BEC's. In particular we note that the nature of the internal excitations is only essentially sensitive to an initial phase difference between the components in the overdamped regime.Comment: 17 pages, 9 figure

Mechanochemical Coupling in Flagella : II. Effects of viscosity and thiourea on metabolism and motility of Ciona spermatozoa

The relation between oxygen consumption and motility of Ciona spermatozoa has been measured by using pH stats to measure the acid production of spermatozoa swimming in dilute suspensions where their motility can be analyzed accurately, and calibrating the acid production by measuring it simultaneously with measurements of oxygen consumption, using more concentrated sperm suspensions. When the motility of the spermatozoa is inhibited by thiourea or by increased viscosity, their oxygen consumption decreases in proportion to the decrease in beat frequency. 80–85 % of their oxygen consumption appears to be tightly coupled to motility. The amount of movement-coupled oxidative metabolism per beat remains nearly constant, even when there are significant changes in the energy required per beat for movement against the viscous resistance of the medium. This implies that under these conditions, where the radius of curvature of flagellar bending remains constant, the amount of ATP used is determined by a stoichiometric relation to bending rather than by the energy requirement. The movement-coupled oxidative metabolism appears to be sufficient to generate approximately two molecules of ATP per beat for each molecule of the flagellar ATPase, dynein