Biomolecules
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
A disease that caused by dengue virus (DENV) has become the major health problem of the world. Nowadays, no effective treatment is available to overcome the disease due to the level of dengue virus pathogeneses. A novel treatment method…
Statistics of Poincar\'e recurrences is studied for the base-pair breathing dynamics of an all-atom DNA molecule in realistic aqueous environment with thousands of degrees of freedom. It is found that at least over five decades in time the…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Protein-nucleic acid complexes are important for many cellular processes including the most essential function such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown…
Although significant insight has been gained into biochemical, genetic and structural features of oxidative phosphorylation (OXPHOS) at the single-enzyme level, relatively little was known of how the component complexes function together in…
To study how plants respond to conditions under which the carbohydrates needed for growth and development are exhausted, this project focuses on cloning and functional characterization of a cytosolic protein kinase, STY46 that may…
We analyze the translocation of a charged particle across an Alpha-Hemolysin (aHL) pore in the framework of a driven diffusion over an extended energy barrier generated by the electrical charges of the aHL. A one-dimensional electrostatic…
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via…
Peptide Nucleic Acids (PNA) are non-natural oligonucleotides mimics. {\gamma}-PNA backbone are formed by standard nucleic acids nucleobases connected by a neutral N-(2-aminoethyl)glycine backbone linked by a peptide bond. In this study, we…
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical…
The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a…
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein…
A modified ssDNA SELEX protocol was developed in order to evolve a randomized library of imidazole modified ssDNA sequences towards sequences that mediate the formation of gold nanoparticles from Au3+ precursor ions in aqueous solution.…
Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the…
When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model.…
Protein structure prediction remains to be an open problem in bioinformatics. There are two main categories of methods for protein structure prediction: Free Modeling (FM) and Template Based Modeling (TBM). Protein threading, belonging to…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological…