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MOIL: A program for simulations of macromolecules

Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Haiying Li, Gennady Verkhivker, Chen Keasar, Jing Zhang, Alex Ulitsky
1995 Computer Physics Communications  
A flexible data structure enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field. The supplied parameter set has proteins in mind.  ...  A package of computer programs for molecular dynamics simulations-MOIL-is described.  ...  Acknowledgements This development of MOIL was supported by grants from the NIH, the DOE and Israel Science Foundation. RE is an Alon fellow in Israel and West scholar in the University of Illinois.  ... 
doi:10.1016/0010-4655(95)00047-j fatcat:uwdjaffbjjbb7f7wl3vjum6z2e

Modeling & Analysis

2003 NeuroImage  
Preliminary results from a analogous study of an event-related motor paradigm suggest that 1/n does not fit the empirical data as well as the block data.  ...  Abstract INTRODUCTION With linear regression models of fMRI time series (e.g., SPM99), the asymptotic theory has been well studied.  ...  Acknowledgement This study was conducted by the authors on behalf of the NEST-DD consortium with support from the European Commission (Framework V).  ... 
doi:10.1016/s1053-8119(05)70006-9 fatcat:zff2suxcofbxvetfrwfwcxi3zm

Quantum computation and communication in strongly interacting systems [article]

Bobby Antonio
2016 arXiv   pre-print
We then present novel ways to create three-qubit Toffoli and Fredkin gates in a single step using linear arrays of qubits, including an assessment of how well these gates could perform, for quantum or  ...  This includes an analysis of the effect of control errors and magnetic field fluctuations on the gate.  ...  In this study we will use the path integral instanton (or many-dimensional WKB) method (for an overview of this method, see for example [280] ).  ... 
arXiv:1604.05655v1 fatcat:bfb2bpc6mbbn5awlb5kjwq7aem

GROMACS 2021.6 Manual

Lindahl, Abraham, Hess, Van Der Spoel
2022 Zenodo  
Full documentation for the GROMACS 2021.6 patch release version.  ...  The dimensions of the box are such that an atom will interact with itself (when using periodic boundary conditions), thus violating the minimum image convention.  ...  For atom i the vector i-1, i+1 is used together with an axis.  ... 
doi:10.5281/zenodo.6801839 fatcat:5mkxexd7vjf7fhxssntr7g5o2m

Execution Models [chapter]

2006 Service-Oriented Computing  
When that property is violated, it means we cannot partition the values into those that map well to each other. Exercise 6.8 asks you to study these value maps more closely.  ...  We may still need a protocol such as 2PC to ensure atomicity, but we may not care about violations of compositional serializability.  ...  Subspaces of URN must also be registered with IANA by the organization that wishes to serve as the authority for making URN assignments within that subspace.  ... 
doi:10.1002/0470091509.ch10 fatcat:2jdemglma5gtre5xkxtzck45am

Loop quantum gravity

Dah-Wei Chiou
2015 International Journal of Modern Physics D  
The canonical formulation of LQG, as the central topic of the article, is presented in a logically orderly fashion with moderate details, while the spin foam theory, black hole thermodynamics, and loop  ...  This article presents an "in-a-nutshell" yet self-contained introductory review on loop quantum gravity (LQG) -- a background-independent, nonperturbative approach to a consistent quantum theory of gravity  ...  Deep gratitude goes to Chih-Wei Chang for having inspiring discussions with the author on quantum gravity and providing him with a comfortable office at CCMS.  ... 
doi:10.1142/s0218271815300050 fatcat:tfd2mwyklzgutkomutmohhv44e

No return to classical reality

David Jennings, Matthew Leifer
2015 Contemporary physics (Print)  
must be an objective property of an individual quantum system.  ...  At a fundamental level, the classical picture of the world is dead, and has been dead now for almost a century.  ...  DJ thanks Sania Jevtic for useful comments on an earlier draft.  ... 
doi:10.1080/00107514.2015.1063233 fatcat:7dl4mh274fcchm27tx6zssurxm

Can robots make good models of biological behaviour?

B Webb
2001 Behavioral and Brain Sciences  
The explication and justification of this approach are here placed within a framework for describing and comparing models in the behavioural and biological sciences.  ...  First, simulation models--the representation of a hypothesis about a target system--are distinguished from several other relationships also termed "modelling" in discussions of scientific explanation.  ...  ACKNOWLEDGMENT We thank the National Science Foundation and the Gatsby Foundation for the support of the Telluride Workshop on Neuromorphic Engineering where this work was performed.  ... 
pmid:12412325 fatcat:xzdirg5xezamdpqc5k42qydf3m

1 Keynote address by Nobel Laureate Phillip A. Sharp the 21st century opened with a revolution in RNA biology

Phillip A. Sharp
2015 Journal of Biomolecular Structure and Dynamics  
Excitingly, these insights and others are now being translated into new treatments for diseases and control of plant pathogens. 2 His Nobel Lecture and his speculative commentary on "What does the Future  ...  Of particular note is the emerging understanding of the wide ranging roles of non-coding RNAs.  ...  DNA sequences that interfere with transcription: Implications for genome function and stability. Chemical Reviews, 113, 8620-8637. Belotserkovskii Authors thank TATA-OSDD, J. C.  ... 
doi:10.1080/07391102.2015.1032624 fatcat:w7iil7k3ize77bjkthcyi52ohy

Certifying Unstability of Switched Systems Using Sum of Squares Programming

Benoît Legat, Pablo Parrilo, Raphaël Jungers
2020 SIAM Journal of Control and Optimization  
In a similar manner as for the linear case, we can compute a balanced realization from these two empirical Gramians.  ...  Acknowledgement This abstract presents research results of the Belgian Programme on Interuniversity Poles of Attraction, initiated by the Belgian state, the Prime Minister's office for Science, Technology  ...  2) Is the variation between cows too large for oestrus detection via an electronic nose with a single decision model [2] ?  ... 
doi:10.1137/18m1173460 fatcat:ytlzbwk7vbampbuyo6snenz33m


2019 Seibutsu Butsuri  
The elements could represent proteins in an abstractive form.  ...  The gmfit has improved to perform a partial fitting of an atomic model in a subspace of the 3D map, using masking function. 2SCA-5 Development of a deep-learning-based method to identify "good" regions  ...  In this study, we tried to develop an automated real-time microliter-scale high throughput screening (MSHTS) system for Aβ aggregation inhibitors using quantum-dot (QD) nanoprobes.  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

Can robots make good models of biological behaviour?

Barbara Webb
2001 Behavioral and Brain Sciences  
Level: the elemental units of the model in the hierarchy from atoms to societies. 3. Generality: the range of biological systems the model can represent. 4.  ...  Abstraction: the complexity, relative to the target, or amount of detail included in the model. 5.  ...  Georgio Metta, a postdoctoral associate at MIT Artificial Intelligence Lab, has been supported with a grant by DARPA as part of the "Natural Tasking of Robots Based on Human Interaction Cues" project under  ... 
doi:10.1017/s0140525x01000127 fatcat:paszkdmgg5azlplbfzfyfh3z7u

LIPIcs, Volume 7, ICLP'10, Complete Volume [article]

Manuel Hermenegildo, Torsten Schaub
Preliminary Results Accomplished With the system ASPARTIX, we provide ASP encodings for most of the semantics and frameworks proposed so far.  ...  It serves as an interpreter which takes an AF given as input.  ...  An abstract constraint program (ACP) consists of rules of the form π ← π 1 , . . . , π n where π and each π i is an abstract constraint atom.  ... 
doi:10.4230/lipics.iclp.2010 fatcat:j7jd7dpsffbs7plm5qa6qi2wem

The neural bases of normalising for accented speech: A repetition suppression functional magnetic resonance imaging study

Patti Adank, Peter Hagoort
2008 Journal of the Acoustical Society of America  
Where the flap allophone of "t" and "d" is expected in American English, one frequently sees an approximant-like or even vocalic pattern, rather than a clear flap.  ...  indicate that all three of these characteristics do affect listeners' percept of a consonant, but not sufficiently to completely account for the percept.  ...  Comparative Study of Wideband Subspace Direction of Arrival (DOA) estimation methods.  ... 
doi:10.1121/1.2934685 fatcat:qqmjcl5gjzcj7kssv2pi6efwti

Smarandache Function Journal, 13 [article]

Sabin Tabirca, Tatiana Tabirca
2002 Zenodo  
SNJ is a referred journal: reviewed, indexed, cited, concerning any of Smarandache type functions, numbers, sequences, integer algorithms, paradoxes, Non-Euclidean geometries, etc.  ...  It is a well known fact that (2) Pn>nlogn, for any positive integer n (see [1]).  ...  By (2), we get 239 On the other hand, since P n+ I > n+ 1, we get (4) ex p ( ~ -~ + ~::11 }-ex{~ -~ +1)<ex P (1.5) The combination of (3) and (4) yields (5) Thus, by (5) , we get (1) immediately  ... 
doi:10.5281/zenodo.8968 fatcat:mjrkjhc25vdr5ova23qlszcua4
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