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ICASSP
2011
IEEE
8 years 15 hour ago
Fast adaptive variational sparse Bayesian learning with automatic relevance determination
In this work a new adaptive fast variational sparse Bayesian learning (V-SBL) algorithm is proposed that is a variational counterpart of the fast marginal likelihood maximization ...
Dmitriy Shutin, Thomas Buchgraber, Sanjeev R. Kulk...
JCC
2011
87views more  JCC 2011»
8 years 3 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...
JCC
2011
105views more  JCC 2011»
8 years 3 months ago
Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
Abstract: Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have b...
Michele Seeber, Angelo Felline, Francesco Raimondi...
JCC
2008
99views more  JCC 2008»
8 years 6 months ago
Assessment of programs for ligand binding affinity prediction
: The prediction of the binding free energy between a ligand and a protein is an important component in the virtual screening and lead optimization of ligands for drug discovery. T...
Ryangguk Kim, Jeffrey Skolnick
BMCBI
2004
116views more  BMCBI 2004»
8 years 8 months ago
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure p
Background: A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy mini...
Kishore J. Doshi, Jamie J. Cannone, Christian W. C...
MCS
2006
Springer
8 years 8 months ago
Lattice Boltzmann simulations of drop dynamics
We present a free energy lattice Boltzmann approach to modelling the dynamics of liquid drops on chemically patterned substrates. We start by describing a choice of free energy th...
H. Kusumaatmaja, A. Dupuis, Julia M. Yeomans
MCS
2006
Springer
8 years 8 months ago
A phase-field method for interface-tracking simulation of two-phase flows
For interface-tracking simulation of two-phase flows, we propose a new computational method, NS-PFM, combining Navier-Stokes (NS) equations with phase-field model (PFM). Based on ...
Naoki Takada, Masaki Misawa, Akio Tomiyama
JAIR
2006
143views more  JAIR 2006»
8 years 8 months ago
Convexity Arguments for Efficient Minimization of the Bethe and Kikuchi Free Energies
Loopy and generalized belief propagation are popular algorithms for approximate inference in Markov random fields and Bayesian networks. Fixed points of these algorithms have been...
Tom Heskes
BMCBI
2006
141views more  BMCBI 2006»
8 years 8 months ago
Identification of consensus RNA secondary structures using suffix arrays
Background: The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. How...
Mohammad Anwar, Truong Nguyen, Marcel Turcotte
CPHYSICS
2008
90views more  CPHYSICS 2008»
8 years 8 months ago
Optimum bias for fast-switching free energy calculations
We derive the bias function that minimizes the statistical error of free energy differences calculated in work-biased fast-switching simulations. The optimum bias function is comp...
Harald Oberhofer, Christoph Dellago
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