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» Theory and Construction of Molecular Computers
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TEI
2009
ACM
103views Hardware» more  TEI 2009»
14 years 2 months ago
A tangible construction kit for exploring graph theory
Graphs are a versatile representation of many systems in computer science, the social sciences, and mathematics, but graph theory is not taught in schools. We present our work on ...
Eric Schweikardt, Nwanua Elumeze, Michael Eisenber...
JCC
2011
87views more  JCC 2011»
13 years 2 months ago
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...
Djurre H. De Jong, Lars V. Schäfer, Alex H. D...
TCS
2008
13 years 7 months ago
Constructibility and decidability versus domain independence and absoluteness
We develop a unified framework for dealing with constructibility and absoluteness in set theory, decidability of relations in effective structures (like the natural numbers), and ...
Arnon Avron
JCC
2006
103views more  JCC 2006»
13 years 7 months ago
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Oliver F. Lange, Lars V. Schäfer, Helmut Grub...
JCB
2007
168views more  JCB 2007»
13 years 7 months ago
Fast Molecular Shape Matching Using Contact Maps
In this paper, we study the problem of computing the similarity of two protein structures ring their contact-map overlap. Contact-map overlap abstracts the problem of computing th...
Pankaj K. Agarwal, Nabil H. Mustafa, Yusu Wang