相关论文: Sliding Columnar Phase of DNA-Lipid Complexes
We show that a long DNA molecule can form a novel condensed phase of matter, the pseudoscalar liquid crystal, that consists of aperiodically ordered DNA fragments in right-handed B and left-handed Z forms. We discuss the possibility of…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
We have discovered two novel types of planar defects that appear in heteroepitaxial YBa$_2$Cu$_3$O$_{7-\delta}$ (YBCO123) thin films, grown by pulsed-laser deposition (PLD) either with or without a La$_{2/3}$Ca$_{1/3}$MnO$_3$ (LCMO)…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
This article examines the dynamic phase transitions and pattern formations attributed to binary systems modeled by the Cahn-Hilliard equation. In particular, we consider a two-dimensional lattice structure and determine how different…
Composed of microscopic layers that stack along one direction while maintaining fluid-like positional disorder within layers, smectics are excellent systems for exploring topology, defects and geometric memory in complex confining…
We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
We study a model lipid bilayer composed of a mixture of two incompatible lipid types which have a natural tendency to segregate in the absence of membrane fluctuations. The membrane is mechanically characterized by a local bending rigidity…
We report a molecular dynamics (MD) study of the collective dynamics of a simple monatomic liquid -interacting through a two body potential that mimics that of lithium- across the liquid-glass transition. In the glassy phase we find…
Using high-resolution confocal rheometry, we study the shear profiles of well-entangled DNA solutions under large amplitude oscillatory shear (LAOS) in a rectilinear planar shear cell. With increasing Weissenberg number (Wi), we observe…
The self-assembly of monoacyl lipids in solution is studied employing a model in which the lipid's hydrocarbon tail is described within the Rotational Isomeric State framework and is attached to a simple hydrophilic head. Mean-field theory…
Small angle neutron scattering (SANS) on the unilamellar vesicle populations (diameter 500 and 1000 angstrom) was used to characterize lipid vesicles from dimyristoylphosphatidylcholine (DMPC) at three phases (gel, ripple, and liquid).…
In the frameworks of algebraic topology {\alpha}-helix and different DNA-conformations are determined as the local latticed packing, confined by peculiar minimal surfaces which are similar to helicoids. These structures are defined by…
Common models for two-phase lipid bilayer membranes are based on an energy that consists of an elastic term for each lipid phase and a line energy at interfaces. Although such an energy controls only the length of interfaces, the membrane…