Dynamical chaos and power spectra in toy models of heteropolymers and proteins

The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically non-chaotic. A choice of a distance of the initial conformation from the native state affects the way in which a separation between the twin trajectories behaves in time. This observation allows one to determine the size of a folding funnel in good folders. We study the energy landscapes of the toy models by determining the power spectra and fractal characteristics of the dependence of the potential energy on time. For good folders, folding and unfolding trajectories have distinctly different correlated behaviors at low frequencies.Comment: 8 pages, 9 EPS figures, Phys. Rev. E (in press

Identifying and improving reusability based on coupling patterns

Open Source Software (OSS) communities have not yet taken full advantage of reuse mechanisms. Typically many OSS projects which share the same application domain and topic, duplicate effort and code, without fully leveraging the vast amounts of available code. This study proposes the empirical evaluation of source code folders of OSS projects in order to determine their actual internal reuse and their potential as shareable, fine-grained and externally reusable software components by future projects. This paper empirically analyzes four OSS systems, identifies which components (in the form of folders) are currently being reused internally and studies their coupling characteristics. Stable components (i.e., those which act as service providers rather than service consumers) are shown to be more likely to be reusable. As a means of supporting replication of these successful instances of OSS reuse, source folders with similar patterns are extracted from the studied systems, and identified as externally reusable components

An evaluation of a service program in reading in grades one through six,

Includes tests in separate folders in back of dissertation. Thesis (M.A.)--Boston Universit

Content of Folders

This document describes the content of the archives folders of the Dorothy Cramer Hansen collection of Silent Film Scores.https://thekeep.eiu.edu/dorothy_hansen_collection/1001/thumbnail.jp

Folding and Design in Coarse-Grained Protein Models

Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders are discussed. Similar patterns for non-randomness are found for real proteins. Dynamical parameter MC methods, such as the tempering and multisequence algorithms, are essential in order to obtain these results. Also, a new MC method for design, the inverse of folding, is presented. Here, one maximizes conditional probabilities rather than minimizing energies. By construction, this method ensures that the designed sequences represent good folders thermodynamically.Comment: LATTICE 99 (Spin Models), 3 pages, 1 figure, espcrc2.st

Royalties (4 folders)

For more information about this item, visit https://archivesspace.mit.edu/repositories/2/archival_objects/30900

Selecting fast folding proteins by their rate of convergence

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using only the very initial parts of the dynamical trajectories. It does not require any preliminary knowledge of the native state and can be applied to different kinds of models, including atomistic descriptions. We tested the method within both the lattice and off-lattice model frameworks and obtained several so far unknown good folders. The unbiased algorithm also allows to determine the optimal folding temperature and takes at least 3--4 orders of magnitude less time steps than those needed to compute folding times

Folders in group chat

While communicating in a group chat, whether on a computer, smartphone, or any other digital device, it is sometimes hard to find data, such as images, links, files, etc., that was sent a long time ago in the conversation thread by one of the participants of the group chat. In such a case, it is usually necessary to scroll back through the conversation thread and analyze all the data appearing in the thread so as to find the required information. This approach can be cumbersome, time-consuming, and often ineffective. As an alternative, a user can try to remember key words associated with such data to search using a built-in search engine. However, this alternative approach is also often ineffective given the difficulties of remembering exact one-to-one word matches in a filename or conversation from long ago. In order to solve said problem, all data that is sent by a particular participant can be stored in participant-specific or sender-specific folder as part of the group chat user interface. For example, in a group chat that has five participants, personalized folders that are specific to each of four other participants can be place in an screen panel, along with any other information or data. During group chats, all data that is sent by each participant can be stored in these participant-specific folders. In the case where a participant needs to find some data, such as a report that he can’t remember the exact filename of, and he knows who sent the report, he can open the participant-specific folder that is associated with the known sender in the group chat user interface and easily find what he needs. Since these folders contain data that is limited to a particular sender, the amount of data to search through is far less than what it would be from all the participants and much easier to navigate through. As another example, such personalized folders can be shown in a menu of the group chat, or in any other place. As another example, this participant-specific folder with all data that was sent by a particular user can be shown in the user profile information along with his contact information, title, and/or any other data. The examples above are not limiting and the participant-specific folders can be placed anywhere in a collaboration environment or other communication tool based on UI/UX needs and preferences