The microphase separation of hydrated perfluorinated sulfonic acid membrane Nafion was investigated using Dissipative Particle Dynamics (DPD). The nafion as a polymer was modelled by connecting coarse grained beads which corresponds to the hydrophobic backbone of polytetrafluoroethylene and perfluorinated side chains terminated by hydrophilic end particles of sulfonic acid groups [1, 2]. Each f...

Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesia...

More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability...

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand c...

Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a mode...

An increasing amount of information is being collected in structured, evolving, curated databases, driving the question of how information extracted from such datasets via queries should be cited. Unlike traditional research products, such books and journals, which have a fixed granularity, data citation is a challenge because the granularity varies. Different portions of the database, with var...

Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created...