相关论文: Heterogeneous path ensembles for conformational tr…
In this note, we address formally the issue of symmetry for probabilities of different dynamical pathways in the forward and reverse directions of a conformational transition. Our discussion is based on a decomposition of equilibrium into…
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex…
Solid-solid phase transitions are ubiquitous in nature, but the kinetic pathway of anisotropic particle systems remains elusive, where the coupling between translational and rotational motions plays a critical role in various kinetic…
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
Cryogenic electron microscopy (cryo-EM) provides a unique opportunity to study the structural heterogeneity of biomolecules. Being able to explain this heterogeneity with atomic models would help our understanding of their functional…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
Simulations that couple different classical molecular models in an adaptive way by changing the number of degrees of freedom on the fly, are available within reasonably consistent theoretical frameworks. The same does not occur when it…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
We explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between…
We study the trajectories of a solution $X_t$ to an It\^o stochastic differential equation in $\Rm^d$, as the process passes between two disjoint open sets, $A$ and $B$. These segments of the trajectory are called transition paths or…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
A biological pathway represents a set of genes that serves a particular cellular or a physiological function. The genes within the same pathway are expected to function together and hence may interact with each other. It is also known that…