Using Markov state models to study self-assembly.

نویسندگان

  • Matthew R Perkett
  • Michael F Hagan
چکیده

Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguished by their undirected graphs, which are defined by strong subunit interactions. Spatial inhomogeneities of free subunits are accounted for using a recently developed Gaussian-based signature. Simplifications to this state identification are also investigated. The feasibility of this approach is demonstrated on two different coarse-grained models for virus self-assembly. We find good agreement between the dynamics predicted by the MSMs and long, unbiased simulations, and that the MSMs can reduce overall simulation time by orders of magnitude.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Estimating Stock Price in Energy Market Including Oil, Gas, and Coal: The Comparison of Linear and Non-Linear Two-State Markov Regime Switching Models

A common method to study the dynamic behavior of macroeconomic variables is using linear time series models; however, they are unable to explain nonlinear behavior of the series. Given the dependency between stock market and derivatives, the behavior of the underlying asset price can be modeled using Markov switching process properties and the economic regime significance. In this paper, a two-...

متن کامل

Comparative study of predictive ability of AIDS incidence in HIV positive people using Markov model according to two criteria, WHO and CDC in CD4 cell categorization

Background: The Multi state Markov models have extensively application with categorization of laboratory marker of CD4 cells for evaluation of HIV disease progression. These models with different states result in different effects of covariates and prediction of HIV disease trend. The main purpose of this study was comparison of four and five states models with the three- state in order to sele...

متن کامل

Recent advances in coarse-grained modeling of virus assembly.

[37] M. R. Perkett, M. F. Hagan, Using Markov state models to study self-assembly, J. Chem. Phys. 140 (21) (2014) 214101. doi:10.1063/1.4878494.

متن کامل

Study of Cis–trans Isomerization Mechanism of [3-(3-Aminomethyl) Phenylazo] Phenyl Acetic Acid as a Causative Role in Alzheimer Using Density Functional Theory

Amyloid-β (Aβ) self-assembly into cross-β amyloidfibrils is implicated in a causative role in Alzheimer’s disease pathology.Uncertainties persist regarding the mechanisms of amyloid self assembly and the role of metastable prefibrillar aggregates. Aβ fibrilsfeature a sheet-turn-sheet motif in the constituent β-strands; as such, turn nucleation has been proposed as a rate-limiting step in the se...

متن کامل

Study of Cis–trans Isomerization Mechanism of [3-(3-Aminomethyl) Phenylazo] Phenyl Acetic Acid as a Causative Role in Alzheimer Using Density Functional Theory

Amyloid-β (Aβ) self-assembly into cross-β amyloidfibrils is implicated in a causative role in Alzheimer’s disease pathology.Uncertainties persist regarding the mechanisms of amyloid self assembly and the role of metastable prefibrillar aggregates. Aβ fibrilsfeature a sheet-turn-sheet motif in the constituent β-strands; as such, turn nucleation has been proposed as a rate-limiting step in the se...

متن کامل

Applying Semi-Markov Models for forecasting the Triple Dimensions of Next Earthquake Occurrences: with Case Study in Iran Area

  In this paper Semi-Markov models are used to forecast the triple dimensions of next earthquake occurrences. Each earthquake can be investigated in three dimensions including temporal, spatial and magnitude. Semi-Markov models can be used for earthquake forecasting in each arbitrary area and each area can be divided into several zones. In Semi-Markov models each zone can be considered as a sta...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • The Journal of chemical physics

دوره 140 21  شماره 

صفحات  -

تاریخ انتشار 2014