Related papers: Serine Proteases: an Ab Initio Molecular Dynamics …
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
We present a density-functional theory trend study addressing the binding of the trans-cis conformational switch azobenzene (C6H5-N=N-C6H5) at three coinage metal surfaces. From the reported detailed energetic, geometric, and electronic…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
Hyaluronan, a sugar polymer found outside the plasma membrane, is a critical component of the extracellular matrix (ECM) scaffold. Hyaluronan's length and moderate negative charge aid in ECM entanglement and solubility. This allows it to…
Despite the well-established presence of amorphous compounds on planetary bodies such as the Moon and Mercury due to space weathering, the direct effect of atomic arrangement on the surface binding energies (SBEs) of elements on these…
We perform a first principles band calculation for a group of quasi-two-dimensional organic conductors \beta-(BDA-TTP)2MF6 (M=P, As, Sb, Ta). The ab-initio calculation shows that the density of states (DOS) is correlated with the band width…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
The atomistic structure and energetics of the Sigma 13 (10-14)[1-210] symmetrical tilt grain boundary in alpha-Al2O3 are studied by first-principles calculations based on the local-density-functional theory with a mixed-basis…
We consider how the infrared intensity of an O-H stretch in a hydrogen bonded complex varies as the strength of the H-bond varies from weak to strong. We obtain trends for the fundamental and overtone transitions as a function of…
The modified static exchange model (MSEM) recently introduced by Ray [1] to study two-atomic collision processes at low and cold-energies, is used for detailed analysis of the long-range effects due to induced dipole-dipole van der Waals…
Protein phosphorylation cycles are important mechanisms of the post translational modification of a protein and as such an integral part of intracellular signaling and control. We consider the sequential phosphorylation and…
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…
To explain recent experiment showing the role of odd fullerenes in formation of abundant fullerene isomers a reactive molecular dynamics (MD) study has been performed. Three types of bond rearrangement reactions are found by MD simulations…
Series of molecular dynamics simulations for 2-propanol-water mixtures, as a function of temperature (between freezing and room temperature) and composition (xip= 0, 0.5, 0.1 and 0.2) have been performed for temperatures reported in the…
We analyze a $XXZ$ spin-1/2 chain which is driven dissipatively at its boundaries. The dissipative driving is modelled by Lindblad jump operators which only act on both boundary spins. In the limit of large dissipation, we find that the…
We report vibrational sum frequency generation spectra from supported lipid bilayers in which the OH and the CH stretching signals are probed at different salt concentrations. Atomistic simulations show a negligible impact of salt on the OH…
We study generalizations of the singlet-sector amplitude-product (AP) states in the valence-bond basis of S=1/2 quantum spin systems. In the standard AP states, the weight of a tiling of the system into valence bonds (singlets of two spins)…
We study spin transport in the one-dimensional anisotropic S = 1 Heisenberg model. Particular emphasis is given to dynamics at infinite temperature, where current autocorrelations and spatio-temporal correlation functions are obtained by…
Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include…