We present a new approach to computer modeling of solvation free energies of oil in water. Informed by the behavior of TIP3P waters around simple Lennard-Jones spheres, Semi-Explicit assembly is a fast implicit approach for computing the nonpolar solvation properties of arbitrary solutes. By summing interactions from whole regions of the solute molecule, this method solves problems that appear as nonadditivities in traditional g A approaches. Semi-Explicit assembly involves little parameter fitting because the solute and water properties come from existing force fields. We test the predictions on alkanes, alkynes, linear and planar polyaromatic hydrocarbons, and on a general set of 504 molecules previously explored by explicit solvent simulations. We find that not all hydrocarbons are the same. Hydrocarbons have 'hot spots', places where firstshell waters interact more strongly with the molecule than at other locations. By accounting for these 'hot spots', Semi-Explicit assembly attains the physical accuracies of explicit solvent models, but because of the pre-computations and the regional additivities, it is nearly as fast to compute as g A methods.
Actin binding proteins (ABPs) organize F-actin into ensembles_generally bundles or networks_thereby affecting actin cytoskeletal function and dynamics. They also participate in binding F-actin to the cell membrane. Some ABPs, e.g. a-actinin, fascin, bind F-actin into parallel bundles whose inter-filament spacing, which depends upon the ABP length and distance between its actinbinding domains, may or may not allow F-actin to interact with other proteins, e.g. myosin. Other, generally longer, ABPs, e.g. filamins, bind F-actin into compliant, albeit tightly-entangled, orthogonal networks imbued with gellike mechanical properties, as a result of the 2D-rotational flexibility of the V-shaped ABP hinges. As the actin structure in non-muscle cells is complex and dynamic, a couple of features have been made to build the 3D model: determination of the representative model space that contains enough number of actin filaments to model the typical actin-actin interactions over larger scales; identification of the average effect of actin crosslinking in the model space, including the possible links and number of actin filaments in the neighborhood with respect to actin length, length distribution, and number density; construction of the fundamental elements that repeat in the crosslinked structures and maintain the physical constraints of bundles and networks; application of Bell's model to back out the passive force and bond lifetime of actin structure under load. Myosin mini-filaments work together with actin filaments in non-muscle cells during cell migration and division. Instead of providing passive load bearing like ABPs, myosin filaments walk along F-actins to generate contraction forces. This model is being integrated with the presence of myosin mini-filaments and the relative interactions, into a larger model for the production and transmission of biochemically-mediated intracellular forces, and actin cytoskeleton dynamics in whole cells.
We present a new approach to computer modeling of solvation free energies of oil in water. Informed by the behavior of TIP3P waters around simple Lennard-Jones spheres, Semi-Explicit assembly is a fast implicit approach for computing the nonpolar solvation properties of arbitrary solutes. By summing interactions from whole regions of the solute molecule, this method solves problems that appear as nonadditivities in traditional g A approaches. Semi-Explicit assembly involves little parameter fitting because the solute and water properties come from existing force fields. We test the predictions on alkanes, alkynes, linear and planar polyaromatic hydrocarbons, and on a general set of 504 molecules previously explored by explicit solvent simulations. We find that not all hydrocarbons are the same. Hydrocarbons have 'hot spots', places where firstshell waters interact more strongly with the molecule than at other locations. By accounting for these 'hot spots', Semi-Explicit assembly attains the physical accuracies of explicit solvent models, but because of the pre-computations and the regional additivities, it is nearly as fast to compute as g A methods.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.