Suk Min Shin

We use a minimal model to study the effects of the upper electronic states on the rate of a charge transfer reaction. The model consists of three ions and an electron, all strung on a line. The two ions at the ends of the structure are held fixed, but the middle ion and the electron are allowed to move in one dimension, along the line joining them. The system has two bound states, one in which the electron ties the movable ion to the fixed ion at the left, and the other in which the binding take

We report the results of molecular dynamics simulations of liquid-supported monolayers of three partially fluorinated amphiphile molecules, namely CF3(CF2)9CH2COOH, CF3(CF2)6CH2(CF2)3COOH, and CF3(CF2)6(CH2)4COOH. These studies were undertaken to provide information on the interplay between molecular flexibility and the packing structure in a monolayer so as to better interpret the results of recent experiments. The qualitative aspects of the predictions of the simulations are consistent with th

We have developed a multiple time scale (MTS) quantum wavepacket propagation algorithm for the electron−nuclear dynamics in which the electron and nuclear motions are followed simultaneously. The large mass disparity between the electron and the nuclear degrees of freedom poses a problem when one propagates the total wavefunction using a single time step. The standard split operator propagation method requires a small time step to be used for stable propagation of the fast electronic degrees of

Soluble oligomers of Alzheimer's amyloid beta protein (Abeta) may act as effectors of neurotoxicity in early stages of Alzheimer's disease. Detailed information about the structure of Abeta in atomistic level and the dynamics of assembly of monomeric Abeta into oligomeric structures is rather elusive. We have performed replica exchange molecular dynamics (REMD) simulations on the formation of the dimer and trimer of Abeta10-35 peptide. We have observed spontaneous formation of several basic stru

We studied the oligomerization of Alzheimer amyloid beta peptide (Abeta) using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with Abeta(10-35) dimers, trimers, and tetramers. Extensive REMD simulations illustrated several possible oligomer conformations. As the size of the oligomer increased from a dimer to a tetramer, the number of possible configurations was reduced. We identified all the possible conformations for each oligomer and characterized their t

In this communication, we have demonstrated that molecular dynamics simulations using a GB implicit solvation model with the all-atom based force field (CHARMM19) can describe the spontaneous folding of small peptides in aqueous solution. The native structures of peptides with various structural motifs (beta-hairpin, beta-sheet, and betabetaalpha-moiety) were successfully predicted within reasonable time scales by MD simulations at moderately elevated temperatures. It is expected that the presen

We report the results of new molecular dynamics simulations of liquid-supported monolayers of perfluorinated and partially fluorinated amphiphiles such as F(CF2)11COOH and F(CF2)10CH2COOH. The new simulations include a representation of the superhelical structure of the perfluoroalkane portion of the amphiphile chain in the intramolecular potential energy; in addition, the calculation of the collective tilt angle of the monolayer is improved to include the effect of the azimuthal distribution of

A homology model builder using simple restraining potentials based on spline-interpolated quadratic functions is developed and interfaced with CHARMM package. The continuity and stability of the potential function were validated, and the parameters were optimized using the CASP7 targets. The performance of the model builder was benchmarked to the Modeller program using the template-based modeling targets in CASP9. The benchmark results show that, while our builder yields the structures with slig

The potential energy surface for the Ar...CO van der Waals complex is calculated by the supermolecular approach using fourth-order Mo/ller–Plesset perturbation theory (MP4) with a large basis set containing bond functions. The Hartree–Fock potentials are repulsive for all configurations considered. The second-order correlation energy accounts for most of the dispersion interactions. The MP4 potential energy surface is characterized by a global minimum of −96.3 cm−1 at Re=3.743 Å and θe=98° with

We describe an extension of the generalized regular solution model of a liquid supported monolayer of long chain amphiphile molecules in which chain–chain interactions outside the surface layer are included as well as the effects of chain flexibility in the surface and in the space above the surface layer. Self-consistent equations for the distribution of molecular configurations and the surface density and pressure are derived by using a model free energy expression. Two first order fluid–fluid

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComment on the influence of molecular flexibility on molecular packing in Langmuir monolayersSeokmin Shin and Stuart A. RiceCite this: Langmuir 1994, 10, 1, 262–266Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://doi.org/10.1021/la00013a039RIGHTS & PERMISSIONSArticle Views94Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text a

The detailed mechanism of the pathology of α-synuclein in the Parkinson's disease has not been clearly elucidated. Recent studies suggested a possible chaperone-like role of the acidic C-terminal region of α-synuclein in the formation of amyloid fibrils. It was also previously demonstrated that the α-synuclein amyloid fibril formation is accelerated by mutations of proline residues to alanine in the acidic region. We performed replica exchange molecular dynamics simulations of the acidic and non

We present a diabatic approach to the dynamics of electronically adiabatic chemical reactions. A method is proposed for constructing diabatic surfaces from a single adiabatic potential surface. By using diabatic surfaces we can choose natural coordinate systems for both the reactant and product arrangements. The diabatic approach can be easily adapted to exact quantum mechanical calculations based on variational scattering formulations. The square integrable basis functions are obtained by diago