Related papers: Modeling the dynamics of bivalent histone modifica…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end…
The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the…
Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be…
The catalytic properties of Pt2XSe3 (X = Hg, Zn) in hydrogen-electrode- (HER-) based catalysts have been investigated based on state-of-the-art ab initio simulations. Our results show that the late transition metal sites (Hg and Zn) exhibit…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere…
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the…
A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the…
We investigate the hydrodynamic stability and the formation of patterns in a continuum model of epithelial layers, able to account for the interplay between mechanical activity, lateral adhesion and the $6-$fold orientational order…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin…
From fundamental discovery to practical application, advances in the optical and quantum sciences rely upon precise control of light-matter interactions. Systems of coupled optical cavities are ubiquitous in these efforts, yet design and…
A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…
We investigate the energetic ground states of a model two-phase system with 1/r^3 dipolar interactions in two dimensions. The model exhibits spontaneous formation of two kinds of periodic domain structure. A striped domain structure is…
Eukaryotic cells demonstrate a wide variety of dynamic patterns of filamentous actin (F-actin) and its regulators. Some of these patterns play important roles in cell functions, such as distinct motility modes, which motivate this study. We…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…