Related papers: Synonymous mutations reduce genome compactness in …
Recent outbreaks of infectious diseases have been monitored closely from an epidemiological and microbiological perspective. Extracting from this wealth of data the information that is relevant for the evolution of the pathogen and predict…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular…
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation…
We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC)…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
A simplified model of clonal plant growth is formulated, motivated by observations of spatial structures in Posidonia oceanica meadows in the Mediterranean Sea. Two levels of approximation are considered for the scale-dependent feedback…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
Sexual reproduction is not always synonymous with the existence of two morphologically different sexes; isogamous species produce sex cells of equal size, typically falling into multiple distinct self-incompatible classes, termed mating…
Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that…
Nearly neutral theory predicts that evolutionary processes will differ in small populations compared to large populations, a key point of concern for endangered species. The nearly-neutral threshold, the span of neutral variation, and the…
Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The…
BRCA genes, comprising BRCA1 and BRCA2 play indispensable roles in preserving genomic stability and facilitating DNA repair mechanisms. The presence of germline mutations in these genes has been associated with increased susceptibility to…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…