Publisher's Note: “Catch bond-like kinetics of helix cracking: Network analysis by molecular dynamics and Milestoning” [J. Chem. Phys. 139, 121902 (2013)]

Kreuzer, Steven M.; Moon, Tessie J; Elber, Ron

doi:10.1063/1.4824427

Cited by 3 publications

(6 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Anchors can be determined by prior thermodynamic sampling (e.g. by replica exchange[41,42]), by reaction path calculations [43,44], or by chemical intuition[34,45]. For example, studies of peptide folding and unfolding in an explicit solvent use only the backbone dihedral angles of the peptide as the coarse variables [42,46].…”

Section: Milestoningmentioning

confidence: 99%

Computational study of peptide permeation through membrane: searching for hidden slow variables

Cárdenas

Elber

2013

Molecular Physics

Self Cite

View full text Add to dashboard Cite

Atomically detailed molecular dynamics trajectories in conjunction with Milestoning are used to analyze the different contributions of coarse variables to the permeation process of a small peptide (N-acetyl-L-tryptophanamide, NATA) through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane. The peptide reverses its overall orientation as it permeates through the biological bilayer. The large change in orientation is investigated explicitly but is shown to impact the free energy landscape and permeation time only moderately. Nevertheless, a significant difference in permeation properties of the two halves of the membrane suggests the presence of other hidden slow variables. We speculate, based on calculation of the potential of mean force, that a conformational transition of NATA makes significant contribution to these differences. Other candidates for hidden slow variables may include water permeation and collective motions of phospholipids.

show abstract

Section: Milestoningmentioning

confidence: 99%

Computational study of peptide permeation through membrane: searching for hidden slow variables

Cárdenas

Elber

2013

Molecular Physics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Matching fluxes between interfaces is used by a number of different methods, such as the Transition Interface Sampling, [10] Partial Paths Transition Interface Sampling, [11] and Forward Flux [8] in addition to Milestoning. [30,45,46] Exploration of the coarse space need not be exhaustive and it can be sampled with different techniques. More recently, extensions of Transition Interface Sampling, Weighted Ensemble, and Forward Flux to more than one reaction coordinate have been described.…”

Section: Discussionmentioning

confidence: 99%

“…This set can be generated in multiple ways and need not be accurate or Boltzmann-weighted. Structures can be selected from high-temperature MD simulation, replica exchange trajectories, [29] a single very long MD trajectory, [30] reaction path calculations, [27,31] and more. [4] The set is required to be sufficiently dense, such that short trajectories can connect all domains of different anchors.…”

Section: Sampling the Coarse Spacementioning

confidence: 99%

Molecular Dynamics at Extended Timescales

Elber¹,

Cárdenas²

2014

Israel Journal of Chemistry

Self Cite

View full text Add to dashboard Cite

The use of short time trajectory fragments to enhance sampling of kinetics is discussed. It is argued that partitioning of phase space with interfaces that are called milestones and conducting a large number of short time trajectories between these interfaces is a highly efficient and accurate method to calculate thermodynamics and kinetics. The method of Milestoning, which is a theory and an algorithm, enables the rapid calculations of fluxes, stationary distributions, and moments of the mean first passage time. It is based on sub‐nanosecond trajectories between cell partitions (milestones) that are defined in coarse space. While the method was applied in the past to highly complex systems, we illustrate it here on a pedagogical two‐dimensional system using dividers of Voronoi cells as milestones.

show abstract

“…Because the present manuscript does not deal with the partition of space into the aforementioned cells and takes the partition as given, we briefly discuss below how such partitions are obtained in practice for a real molecular system. [12][13][14] We first construct a sparse sampling of space that consists of a set of configurations (in full or coarse space), which we call anchors that must cover (albeit sparsely) the relevant landscape. Anchors can be extracted using a number of approaches.…”

Section: Introductionmentioning

confidence: 99%

“…where n j ðx j Þ is the unit vector normal to the milestone M j at the point x j . We can substitute the expression for h ðnÞ ij into (12) and (13) to get the weights w ðn11Þ j and the densities f where, as in (17), the indices f go through all the milestones in the boundary of the product set P.…”

mentioning

confidence: 99%

Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning

Bello-Rivas

Elber

2015

J Comput Chem

Self Cite

View full text Add to dashboard Cite

We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two-dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly-solvable one-dimensional model, and with the results from the rough one-dimensional energy model introduced by Zwanzig.

show abstract

Publisher's Note: “Catch bond-like kinetics of helix cracking: Network analysis by molecular dynamics and Milestoning” [J. Chem. Phys. 139, 121902 (2013)]

Cited by 3 publications

References 0 publications

Computational study of peptide permeation through membrane: searching for hidden slow variables

Computational study of peptide permeation through membrane: searching for hidden slow variables

Molecular Dynamics at Extended Timescales

Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning

Contact Info

Product

Resources

About