Design of Force Fields from Data at Finite Temperature

We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs substantially from the ground state. We apply our method to systems modeling proteins and demonstrate that the correct potentials can be recovered even in the presence of thermal noise.Comment: 10 pages, 1 postcript figure, Late

In-office needle arthroscopic assessment after primary ACL repair. Short-term results in 15 patients

Purpose: In-office needle arthroscopy has been reported as a diagnostic tool for different knee pathologies. In addi- tion, ACL repair has seen a resurgence with the advent of innovative orthopedic devices. The aim of this study was to assess clinical, radiological, and in-office needle arthroscopic findings in 15 adult patients who underwent acute (within 14 days from injury) anterior cruciate ligament (ACL) repair. Methods: Fifteen patients voluntarily participated in the study. A second-look arthroscopy was performed with an in-office needle arthroscopy at an average of 7.2 months after the primary repair. The parameters included in the investigation were the continuity of the anatomical footprint of the repaired ACL, subjective assessment of the ACL tension with the probe, and synovial coverage of the ACL. All patients had a Magnetic Resonance Imaging (MRI) at 6 months after repair and an arthrometric evaluation with the KT-1000. Clinical evaluation with the scores, Tegner Lysholm Knee Scoring Scale (TLKSS), the Knee Injury and Osteoarthritis Outcome Score (KOOS), and International Knee Documentation Committee (IKDC) was performed at the final follow-up of 2 years. Moreover, a correlation between the characteristics of ACL appearance at the time of the second look in-office needle arthroscopy, MRI and KT-1000 was performed. Results: The mean TLKSS was 97.86, the mean KOOS was 98.08 and the mean subjective IKDC was 96.71. The objec- tive IKDC was A in 10 patients and B in 5 patients. ACL healing was graded as A in 11 patients and B in 4 patients. Synovial coverage was graded as good in 10 patients and fair in 5 while MRI assessment showed a type I ACL in 10 patients, type II in 4 patients and type III in 1 patient. Conclusion: In-office needle arthroscopy is a reliable tool to assess the condition of a repaired ACL. In addition, ACL repair performed in acute proximal tears demonstrated excellent clinical results

Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models

Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.Comment: 9 pages, 2 tables and 5 figure

Protein dynamics with off-lattice Monte Carlo moves

A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte Carlo moves are used: single rotations about torsion axes, and cooperative rotations in windows of amide planes, changing the conformation globally and locally, respectively. For local moves Jacobians are used to obtain an unbiased distribution of dihedrals. A molecular dynamics energy function adapted to the protein model is employed. A polypeptide is folded into native-like structures by local but not by global moves.Comment: 10 pages, 4 Postscript figures, uses epsf.sty and a4.sty; scheduled tentatively for Phys.Rev.E issue of 1 March 199

Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Recent Studies in Andean Prehistory and Protohistory: Papers from the Second Annual Northeast Conference on Andean Archaeology and Ethnohistory

The contributions in this volume represent nine of the twenty-three papers presented at the Second Annual Northeast Conference on Andean Archaeology and Ethnohistory (NCAAE) held at the American Museum of Natural History on November 19-20, 1983. Papers include The Preceramic and Formative Period Occupations in the Cordillera Negra: Preliminary Report by Michael A. Malpass, The Early Horizon--Early Intermediate Period Transition: A View from the Nepena and Viru Valleys by Richard E. Daggett, Paracas in Chincha and Pisco: A Reappraisal of the Ocucaje Sequence by Dwight T. Wallace, Impressions in Metal: Reconstructing Burial Context at Loma Negra, Peru by Anne-Louise Schaeffer, The Moche Moon by Elizabeth P. Benson, Archaeological Investigation in the Andean Piedmont and High Llanos of Western Venezuela: A Preliminary Report by Charles S. Spencer and Elsa M. Redmond, Pachacamac--An Andean Oracle Under Inca Rule by Thomas C. Patterson, The Spanish League and Inca Sites: A Reassessment of the Itinerary of Juan de Matienzo through N.W. Argentina by Gordon C. Pollard, and Written Sources on Andean Cosmogony by George Kubler.https://digitalcommons.library.umaine.edu/andean_past_special/1001/thumbnail.jp

Tradeoffs in jet inlet design: a historical perspective

The design of the inlet(s) is one of the most demanding tasks of the development process of any gas turbine-powered aircraft. This is mainly due to the multi-objective and multidisciplinary nature of the exercise. The solution is generally a compromise between a number of conflicting goals and these conflicts are the subject of the present paper. We look into how these design tradeoffs have been reflected in the actual inlet designs over the years and how the emphasis has shifted from one driver to another. We also review some of the relevant developments of the jet age in aerodynamics and design and manufacturing technology and we examine how they have influenced and informed inlet design decision

Boundary-Layer-Ingesting Inlet Flow Control

This paper gives an overview of a research study conducted in support of the small-scale demonstration of an active flow control system for a boundary-layer-ingesting (BLI) inlet. The effectiveness of active flow control in reducing engine inlet circumferential distortion was assessed using a 2.5% scale model of a 35% boundary-layer-ingesting flush-mounted, offset, diffusing inlet. This experiment was conducted in the NASA Langley 0.3-meter Transonic Cryogenic Tunnel at flight Mach numbers with a model inlet specifically designed for this type of testing. High mass flow actuators controlled the flow through distributed control jets providing the active flow control. A vortex generator point design configuration was also tested for comparison purposes and to provide a means to examine a hybrid vortex generator and control jets configuration. Measurements were made of the onset boundary layer, the duct surface static pressures, and the mass flow through the duct and the actuators. The distortion and pressure recovery were determined by 40 total pressure measurements on 8 rake arms each separated by 45 degrees and were located at the aerodynamic interface plane. The test matrix was limited to a maximum free-stream Mach number of 0.85 with scaled mass flows through the inlet for that condition. The data show that the flow control jets alone can reduce circumferential distortion (DPCPavg) from 0.055 to about 0.015 using about 2.5% of inlet mass flow. The vortex generators also reduced the circumferential distortion from 0.055 to 0.010 near the inlet mass flow design point. Lower inlet mass flow settings with the vortex generator configuration produced higher distortion levels that were reduced to acceptable levels using a hybrid vortex generator/control jets configuration that required less than 1% of the inlet mass flow

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation