Despite significant progress in recent years, ab initio folding is still one of the most challenging problems in structural biology. This paper presents a probabilistic graphical model for ab initio folding, which employs Conditional Random Fields (CRFs) and directional statistics to model the relationship between the primary sequence of a protein and its three-dimensional structure. Different ...

The FALC-Loop web server provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures or to model segments of designed sequences. The FALC method is computationall...

• Ab initio simulation of Nanowire at cryogenic temperature. Robust ab simulation. Subthreshold slope nanowire with gate length = 10 nm. In this paper, we propose a methodology for robust and accurate ab-initio quantum transport down to 3 K an n -type Si nanowire. This is important understand the subthreshold swing (SS) We show that L G nm, SS fully dominated by direct tunneling temperature, wh...

We present a linear scaling 3 dimensional fragment (LS3DF) method that uses a novel decomposition and patching scheme to do ab initio density functional theory (DFT) calculations for large systems. This method cancels out the artificial boundary effects that arise from the spatial decomposition. As a result, the LS3DF results are essentially the same as the original full-system DFT results with...

We explore the use of ab initio, density-functional methods for the study of large-scale materials problems. Three examples are presented: (i) the interplay of surface and edge reconstructions in long silicon nanowires, where we examine the effects on electrical and mechanical properties; (ii) the calculation of solvation effects based on ab initio dielectric models, where we derive the dielect...

The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite ...

For I-(H 2 O) 4 cluster, it has long believed that the C 4 symmetry structure is most stable isomer at low temperature. However, calculated vibrational spectra values using ab initio disagree with experimental values. Therefore, we calculated the structure of I-(H 2 O) 4 using extensive ab initio calculation. Hence, we found most stable isomer for I-(H 2 O) 4 at low temperature. The isomer has ...

We have performed ab initio calculations of the frequency shift induced by a static electric field on the cesium clock hyperfine transition. The calculations are used to find the frequency shifts due to blackbody radiation. Our result (δν/E = −2.26(2) × 10Hz/(V/m)) is in good agreement with early measurements and ab initio calculations performed in other groups. We present arguments against rec...

We survey approaches to nonrelativistic density functional theory (DFT) for nuclei using progress toward ab initio DFT for Coulomb systems as a guide. Ab initio DFT starts with a microscopic Hamiltonian and is naturally formulated using orbital-based functionals, which generalize the conventional local-density-plus-gradients form. The orbitals satisfy single-particle equations with multiplicati...