Event Title
Location
Cherry Auditorium, Kirk Hall
Start Date
2-14-2013 1:00 PM
Description
Many molecular characteristics would be interesting to know but are not easy to access through experiments. What molecule arrangements are most effective for transmitting or damping applied forces? What configurations of a binding site enable or block substrate adsorption? Such questions can be investigated computationally through molecular simulations: large scale calculations that apply statistical mechanics toward quantifying the properties and mechanisms that occur in atomic and molecular systems.
Molecular dynamics and Monte Carlo methods provide large numbers of representative molecule configurations (an "ensemble"), and statistical weighting over an ensemble provides the desired results as a numerical average. Improvements in force fields, algorithms, and computing power have enabled molecular simulations to advance far beyond simple systems, such as hard spheres and idealized slit pores.
The seminar will describe several simulations of "real world" systems from the PI's lab. Computational models of bitumens developed in the group provide recipes for molecule types and compositions that exhibit physical, chemical, and mechanical properties comparable to those of asphalts used in roads. Molecular simulations of these model bitumens have quantified the rates of single molecule relaxations amidst overall spontaneous system-wide force relaxations. Methods for analyzing accessible volume that were developed in the group have been applied by collaborators within large-scale screening of metal-organic frameworks, which are adsorbents with applications such as size separation of vapor mixtures. In one biological system, Monte Carlo simulations have relaxed anticipated binding sites for likely sulfate donors and acceptors within SULT4A1 protein. In another, Monte Carlo simulations have provided initial estimates of probable chain conformations for a short peptide. Ongoing work also includes using conformational analysis to model the forces on elastomers.
Molecular Simulations of "Real World" Systems
Cherry Auditorium, Kirk Hall
Many molecular characteristics would be interesting to know but are not easy to access through experiments. What molecule arrangements are most effective for transmitting or damping applied forces? What configurations of a binding site enable or block substrate adsorption? Such questions can be investigated computationally through molecular simulations: large scale calculations that apply statistical mechanics toward quantifying the properties and mechanisms that occur in atomic and molecular systems.
Molecular dynamics and Monte Carlo methods provide large numbers of representative molecule configurations (an "ensemble"), and statistical weighting over an ensemble provides the desired results as a numerical average. Improvements in force fields, algorithms, and computing power have enabled molecular simulations to advance far beyond simple systems, such as hard spheres and idealized slit pores.
The seminar will describe several simulations of "real world" systems from the PI's lab. Computational models of bitumens developed in the group provide recipes for molecule types and compositions that exhibit physical, chemical, and mechanical properties comparable to those of asphalts used in roads. Molecular simulations of these model bitumens have quantified the rates of single molecule relaxations amidst overall spontaneous system-wide force relaxations. Methods for analyzing accessible volume that were developed in the group have been applied by collaborators within large-scale screening of metal-organic frameworks, which are adsorbents with applications such as size separation of vapor mixtures. In one biological system, Monte Carlo simulations have relaxed anticipated binding sites for likely sulfate donors and acceptors within SULT4A1 protein. In another, Monte Carlo simulations have provided initial estimates of probable chain conformations for a short peptide. Ongoing work also includes using conformational analysis to model the forces on elastomers.
Comments
Downloadable file is a PDF of the original event flier.