Some ideas and questions regarding space station design for human use

Design concepts for interior utility of space station crew areas are offered. Planning of a living environment that maintains elements of humanity is stressed

Monte Carlo study of cooperativity in homopolypeptides

©1992 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/9412/1DOI:10.1063/1.463317A discretized model of globular proteins is employed in a Monte Carlo study of the helix-coil transition of polyalanine and the collapse transition of polyvaline. The present lattice realization permits real protein crystal structures to be represented at the level of 1 A resolution. Furthermore, the Monte Carlo dynamic scheme is capable of moving elements of assembled secondary and supersecondary structure. The potentials of mean force for the interactions are constructed from the statistics of a set of high resolution x-ray structures of nonhomologous proteins. The cooperativity of formation of ordered structures is found to be larger when the major contributions to the conformational energy of the low temperature states come from hydrogen bonds and short range conformational propensities. The secondary structure seen in the folded state is the result of an interplay between the short and long range interactions. Compactness itself, driven by long range, nonspecific interactions, seems to be insufficient to generate any appreciable secondary structure. A detailed examination of the dynamics of highly helical model proteins demonstrates that all elements of secondary structure are mobile in the present algorithm, and thus the folding pathways do not depend on the use of a lattice approximation. Possible applications of the present model to the prediction of protein 3D structures are briefly discussed

Monte Carlo dynamics of diamond-lattice multichain systems

©1986 American Institute of Physics. The electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?APCPCS/137/241/1DOI:10.1063/1.35530Presented at the 1985 La Jolla Workshop on Polymer Flow Interaction.We present preliminary results of Monte Carlo studies on the dynamics of multichain diamond-lattice systems at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three or four bond kink motions. The single bead autocorrelation function exhibits "slow" mode relaxation behavior with a g(t)∝ tβ. There is a smooth crossover from Rouse-like dynamics, β=1/2, at low density to smaller values of β at higher density and β=0 at the glass transition density (φG≅0.92). The simulation provides a self-diffusion coefficient D ∝ n-2, with n the number of beads, in agreement with experiment. A phenomenological model, different from the widely accepted reptation picture, is proposed

EFICAz²: enzyme function inference by a combined approach enhanced by machine learning

©2009 Arakaki et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/10/107doi:10.1186/1471-2105-10-107Background: We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment. Results: We have developed two new EFICAz components, analogs to the two FDR-based components, where the discrimination between homo and heterofunctional members is based on the evaluation, via Support Vector Machine models, of all the aligned positions between the query sequence and the multiple sequence alignments associated to the enzyme families. Benchmark results indicate that: i) the new SVM-based components outperform their FDR-based counterparts, and ii) both SVM-based and FDR-based components generate unique predictions. We developed classification tree models to optimally combine the results from the six EFICAz components into a final EC number prediction. The new implementation of our approach, EFICAz², exhibits a highly improved prediction precision at MTTSI < 30% compared to the original EFICAz, with only a slight decrease in prediction recall. A comparative analysis of enzyme function annotation of the human proteome by EFICAz² and KEGG shows that: i) when both sources make EC number assignments for the same protein sequence, the assignments tend to be consistent and ii) EFICAz² generates considerably more unique assignments than KEGG. Conclusion: Performance benchmarks and the comparison with KEGG demonstrate that EFICAz² is a powerful and precise tool for enzyme function annotation, with multiple applications in genome analysis and metabolic pathway reconstruction. The EFICAz² web service is available at: http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.htm

Temperature dependent polariton emission from strongly coupled organic semiconductor microcavities

We investigated the absorption and photoluminescence (PL) of J-aggregates of a cyanine dye both in a thin film format and when used as the active layer in a strongly-coupled microcavity. We show that as temperature is reduced, the absorption linewidth of the J-aggregates narrows and shifts to higher energy. When the J-aggregate is placed in a microcavity we find that the energy of the polariton modes also shifts to higher energies as temperature is reduced. We compare the intensity of PL emission from the upper and lower branches at resonance as a function of temperature, and find that it can be described by an activation energy of 25 meV. PL emission spectra at resonance also suggest that uncoupled excitons inside the microcavity populate the upper polariton branch states

Effect of double bonds on the dynamics of hydrocarbon chains

©1992 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/1240/1DOI:10.1063/1.463250Brownian dynamics simulations of isolated 18-carbon chains have been performed, both for saturated and unsaturated hydrocarbons. The effect of one or several (nonconjugated) double bonds on the properties of the chains is discussed in terms of both equilibrium and dynamic properties. The introduction of a cis double bond increases the relaxation rates of the unsaturated chain with respect to the saturated alkane. On the other hand, coupling effects in the torsional transitions around a trans double bond make the dynamics of this unsaturated chain very similar to the saturated one. Based on these results, the parameters and moves of a dynamic Monte Carlo algorithm are tuned to reproduce the observed behavior, providing an efficient method for the study of more complicated systems

Dmitri Shalin Interview with Arlene Skolnick about Erving Goffman entitled Remembering Erving Goffman

These conversations with Dr. Arlene Skolnick were recorded over the phone on August 7 and August 30, 2010. After Dmitri Shalin transcribed the conversations, Dr. Skolnick edited the transcript and approved posting the present version in the Goffman Archives. Breaks in the conversation flow are indicated by ellipses. Supplementary information and additional materials inserted during the editing process appear in square brackets. Undecipherable words and unclear passages are identified in the text as “[?]”

A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants

First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.Presented at DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, March 20-21, 1995.A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al

Irving Skolnick, transcript only

Transcript of an interview with Irving Skolnick by Lucille Brown of Union College. Irving was born in Bratslav, Ukraine in 1902.https://digitalworks.union.edu/berkoralhistories/1020/thumbnail.jp

High-occupancy effects and stimulation phenomena in semiconductor microcavities

This paper describes recent work on high-occupancy effects in semiconductor microcavities, with emphasis on the variety of new physics and the potential for applications that has been demonstrated recently. It is shown that the ability to manipulate both exciton and photon properties, and how they interact together to form strongly coupled exciton-photon coupled modes, exciton polaritons, leads to a number of very interesting phenomena, which are either difficult or impossible to achieve in bulk semiconductors or quantum wells. The very low polariton density of states enables state occupancies greater than one to be easily achieved, and hence stimulation phenomena to be realized under conditions of resonant excitation. The particular form of the lower polariton dispersion curve in microcavities allows energy and momentum conserving polariton-polariton scattering under resonant excitation. Stimulated scattering of the bosonic quasi-particles occurs to the emitting state at the center of the Brillouin zone, and to a companion state at high wave vector. The stimulation phenomena lead to the formation of highly occupied states with macroscopic coherence in two specific regions of k space. The results are contrasted with phenomena that occur under conditions of nonresonant excitation. Prospects to achieve "polariton lasing" under nonresonant excitation, and high-gain, room-temperature ultrafast amplifiers and low-threshold optical parametric oscillator under resonant excitation conditions are discussed