Learn More
Defining the extent of epistasis – the non-independence of the effects of mutations – is essential for understanding the relationship of genotype, phenotype, and fitness in biological systems. The applications cover many areas of biological research, including biochemistry, genomics, protein and systems engineering, medicine, and evolutionary biology.(More)
Mesoscopic simulations and electron microscopy of N-BAR domain-induced liposome remodeling are used to characterize the process of liposome tubulation and vesiculation. The overall process of membrane remodeling is found to involve complex couplings among the N-BAR protein density, the degree of N-BAR oligomerization, and the membrane density. A comparison(More)
Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarse-graining (MS-CG) method [J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys.(More)
Coarse-grained (CG) models of biomolecules have recently attracted considerable interest because they enable the simulation of complex biological systems on length-scales and timescales that are inaccessible for atomistic molecular dynamics simulation. A CG model is defined by a map that transforms an atomically detailed configuration into a CG(More)
This work develops a method for the construction of multiscale coarse-grained (MS-CG) force fields at different temperatures based on available atomistic data at a given reference temperature. The validity of this theory is demonstrated numerically by applying it to construct MS-CG models of the Lennard-Jones liquid and simple point charge water model(More)
Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid shell, which is composed of approximately 1500 copies of CA proteins, are constructed and their stability is examined. A key interaction between carboxyl and hexameric amino terminal domains is shown to(More)
We show that the time-dependent single electron, nuclear density matrix of an interacting electronic system coupled to nuclear degrees of freedom can be exactly reproduced by that of an electronic system with arbitrarily specified electron-electron interactions coupled to the same nuclear degrees of freedom, given the initial density matrix of the(More)
We report density functional theory calculations of electron-hole pair induced vibrational lifetimes of diatomic molecules adsorbed on metal surfaces. For CO on Cu(100), Ni(100), Ni(111), Pt(100), and Pt(111), we find that the C-O internal stretch and the bending modes have lifetimes in the 1-6 ps range, and that the CO-surface stretch and the frustrated(More)
The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing(More)