Fairclothlawrence8545

We have constructed efficient coarse-grained (CG) models of poly(ethylene terephthalate) (PET), using three mapping schemes, in which a repeat unit is lumped into either three or four beads. The CG potentials are parameterized to reproduce target distributions of an underlying accurate atomistic model [H. Eslami and F. Müller-Plathe, Macromolecules 42, 8241-8250 (2009)]. The CG simulations allow equilibration of long PET chains at all length scales. The CG results on the density of PET in melt and glassy states, chain dimension, local packing, and structure factor are in good agreement with experiment. We have established a link between the glass transition temperature and the local movements including conformational transitions and mean-square displacements of chain segments. Temperature transferabilities of the three proposed models were studied by comparing CG results on the static and thermodynamic properties of a polymer with atomistic and experimental findings. One of the three CG models has a good degree of transferability, following all inter- and intra-structural rearrangements of the atomistic model, over a broad range of temperature. Furthermore, as a distinct point of strength of CG, over atomistic, simulations, we have examined the dynamics of PET long chains, consisting of 100 repeat units, over a regime where entanglements dominate the dynamics. Performing long-time (550 ns) CG simulations, we have noticed the signature of a crossover from Rouse to reptation dynamics. However, a clear separation between the Rouse and the reptation dynamics needs much longer time simulations, confirming the experimental findings that the crossover to full reptation dynamics is very protracted.All-atom molecular dynamics (MD) simulations of bio-macromolecules can yield relatively accurate results while suffering from the limitation of insufficient conformational sampling. On the other hand, the coarse-grained (CG) MD simulations efficiently accelerate conformational changes in biomolecules but lose atomistic details and accuracy. Here, we propose a novel multiscale simulation method called the adaptively driving multiscale simulation (ADMS)-it efficiently accelerates biomolecular dynamics by adaptively driving virtual CG atoms on the fly while maintaining the atomistic details and focusing on important conformations of the original system with irrelevant conformations rarely sampled. Herein, the "adaptive driving" is based on the short-time-averaging response of the system (i.e., an approximate free energy surface of the original system), without requiring the construction of the CG force field. We apply the ADMS to two peptides (deca-alanine and Ace-GGPGGG-Nme) and one small protein (HP35) as illustrations. The simulations show that the ADMS not only efficiently captures important conformational states of biomolecules and drives fast interstate transitions but also yields, although it might be in part, reliable protein folding pathways. Remarkably, a ∼100-ns explicit-solvent ADMS trajectory of HP35 with three CG atoms realizes folding and unfolding repeatedly and captures the important states comparable to those from a 398-µs standard all-atom MD simulation.Formic acid adsorption and decomposition on clean Cu(100) and two atomic oxygen pre-covered Cu(100) surfaces have been studied using surface science techniques including scanning tunneling microscopy, low-energy electron diffraction, x-ray photoelectron spectroscopy, and infrared reflection-absorption spectroscopy. The two atomic oxygen pre-covered Cu(100) surfaces include an O-(22 ×2)R45° Cu(100) surface and an oxygen modified Cu(100) surface with a local O-c(2 × 2) structure. The results show that the O-(22 ×2)R45° Cu(100) surface is inert to the formic acid adsorption at 300 K. After exposing to formic acid at 300 K, bidentate formate formed on the clean Cu(100) and local O-c(2 × 2) area of the oxygen modified Cu(100) surface. However, their adsorption geometries are different, being vertical to the surface plane on the former surface and inclined with respect to the surface normal with an ordered structure on the latter surface. The temperature programmed desorption spectra indicate that the formate species adsorbed on the clean Cu(100) surface decomposes into H2 and CO2 when the sample temperature is higher than 390 K. Differently, the proton from scission of the C-H bond of formate reacts with the surface oxygen, forming H2O on the oxygen modified Cu(100) surface. The CO2 signal starts increasing at about 370 K, which is lower than that on clean Cu(100), indicating that the surface oxygen affiliates formate decomposition. Combining all these results, we conclude that the surface oxygen plays a crucial role in formic acid adsorption and formate decomposition.We derive a matrix formalism for the simulation of long range proton dynamics for extended systems and timescales. On the basis of an ab initio molecular dynamics simulation, we construct a Markov chain, which allows us to store the entire proton dynamics in an M × M transition matrix (where M is the number of oxygen atoms). In this article, we start from common topology features of the hydrogen bond network of good proton conductors and utilize them as constituent constraints of our dynamic model. We present a thorough mathematical derivation of our approach and verify its uniqueness and correct asymptotic behavior. We propagate the proton distribution by means of transition matrices, which contain kinetic data from both ultra-short (sub-ps) and intermediate (ps) timescales. This concept allows us to keep the most relevant features from the microscopic level while effectively reaching larger time and length scales. We demonstrate the applicability of the transition matrices for the description of proton conduction trends in proton exchange membrane materials.We report the high-resolution photoelectron spectra of negative gallium anions obtained via the slow-electron velocity-map imaging method. The electron affinity of Ga is determined to be 2429.07(12) cm-1 or 0.301 166(14) eV. The fine structures of Ga are well resolved 187.31(22) cm-1 or 23.223(27) meV for 3P1 and 502.70(28) cm-1 or 62.327(35) meV for 3P2 above the ground state 3P0, respectively. The photoelectron angular distribution for photodetachment from Ga-(4s24p2 3P0) to Ga(4s25s 2S1/2) is measured. EGFR inhibitor An unexpected perpendicular distribution instead of an isotropic distribution is observed, which is due to a resonance near 3.3780 eV.