Related papers: Modelling Biochemical Operations on RNA Secondary …
In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure…
Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using…
We reply to the Comment by Hartmann (cond-mat/9908132) on our paper Phys. Rev. Lett. 84 (2000) 2026 (also cond-mat/9907125).
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
The purpose of this report is a study of the algebraic approach possibilities to reconstruct images. This approach is reduced to solution of the large system of linear algebraic equations. We also point out some possible further…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
We investigate several important issues regarding the Random Batch Method (RBM) for second order interacting particle systems. We first show the uniform-in-time strong convergence for second order systems under suitable contraction…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
In this paper I present some of the most representative biological models applied to robotics. In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
A series of MnO2 unique nanostructures were synthesized by a facile hydrothermal method with microwave-assisted procedures. A novel nanostructure formation mechanism has been proposed, that MnO6 octahedral nuclei and molecular layers can be…
Electrochemical biosensors ("E-AB" or "E-DNA" type sensors) that utilize square-wave voltammetry originated in academic labs with a few standard experimental configurations for the electrochemical cell and data analysis. We report here on…
Although algebraic structures are frequently analyzed using unary and binary operations, they can also be effectively defined and unified through ternary operations. In this context, we introduce structures that contain two constants and a…