253 citations
- National Center for Biotechnology InformationUS9 papers
- National Institute of Diabetes and Digestive and Kidney DiseasesUS7 papers
- Jožef Stefan InstituteSI5 papers
- University of LjubljanaSI5 papers
- Howard UniversityUS4 papers
- The University of Texas at AustinUS4 papers
- University of California, Santa BarbaraUS4 papers
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentUS2 papers
- Harvard UniversityUS2 papers
- Institute of Mathematics, Physics, and MechanicsSI2 papers
- University at Buffalo, State University of New YorkUS2 papers
- University of WashingtonUS2 papers
38 papers
Estimating the Gumbel scale parameter for local alignment of random sequences by importance sampling with stopping times
Yonil Park, Sergey Sheetlin, John L. Spouge
The gapped local alignment score of two random sequences follows a Gumbel distribution. If computers could estimate the parameters of the Gumbel distribution within one second, the…
Exceptional error minimization in putative primordial genetic codes
Artem S. Novozhilov, Eugene V. Koonin
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously…
Comment on "On the Crooks fluctuation theorem and the Jarzynski equality" [J. Chem. Phys. 129, 091101 (2008)]
Artur B. Adib
It has recently been argued that a self-consistency condition involving the Jarzynski equality (JE) and the Crooks fluctuation theorem (CFT) is violated for a simple Brownian proce…
Weak and Strong-Coupling Electrostatic Interactions between Asymmetrically Charged Planar Surfaces
M. Kanduc, M. Trulsson, A. Naji +3
We compare weak and strong coupling theory of counterion-mediated electrostatic interactions between two asymmetrically charged plates with extensive Monte-Carlo simulations. Analy…
Epidemics with general generation interval distributions
Joel Miller, Bahman Davoudi, Rafael Meza +2
We study the spread of susceptible-infected-recovered (SIR) infectious diseases where an individual's infectiousness and probability of recovery depend on his/her "age" of infectio…
How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins?
E. P. O'Brien, G. Morrison, B. R. Brooks +1
Single molecule Forster resonance energy transfer (FRET) experiments are used to infer the properties of the denatured state ensemble (DSE) of proteins. From the measured average F…