Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics

نویسندگان

  • Peter Minary
  • Glenn J. Martyna
  • Mark E. Tuckerman
چکیده

Related Articles Behavior of peptides combining 1 alanine residue and 8 glycine residues on papain associated with structural fluctuations J. Appl. Phys. 110, 114701 (2011) Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble J. Chem. Phys. 135, 204101 (2011) Differential geometry based solvation model. III. Quantum formulation J. Chem. Phys. 135, 194108 (2011) Thermal conductivity of bovine serum albumin: A tool to probe denaturation of protein Appl. Phys. Lett. 99, 163702 (2011) Inertial focusing of non-spherical microparticles Appl. Phys. Lett. 99, 044101 (2011)

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

Mechanical Characteristics and Failure Mechanism of Nano-Single Crystal Aluminum Based on Molecular Dynamics Simulations: Strain Rate and Temperature Effects

Besides experimental methods, numerical simulations bring benefits and great opportunities to characterize and predict mechanical behaviors of materials especially at nanoscale. In this study, a nano-single crystal aluminum (Al) as a typical face centered cubic (FCC) metal was modeled based on molecular dynamics (MD) method and by applying tensile and compressive strain loadings its mechanical ...

متن کامل

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that ...

متن کامل

Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.

As the major component of membrane proteins, transmembrane helices embedded in anisotropic bilayer environments adopt preferential orientations that are characteristic or related to their functional states. Recent developments in solid-state nuclear magnetic resonance (SSNMR) spectroscopy have made it possible to measure NMR observables that can be used to determine such orientations in a nativ...

متن کامل

The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics

Numerical algorithms are developed for the centroid molecular dynamics (centroid MD) method to calculate dynamical time correlation functions for general many-body quantum systems. Approaches based on the normal mode path integral molecular dynamics and staging path integral Monte Carlo methods are described to carry out a direct calculation of the force on the centroid variables in the centroi...

متن کامل

Exact low-force kinetics from high-force single-molecule unfolding events.

Mechanical forces play a key role in crucial cellular processes involving force-bearing biomolecules, as well as in novel single-molecule pulling experiments. We present an exact method that enables one to extrapolate, to low (or zero) forces, entire time-correlation functions and kinetic rate constants from the conformational dynamics either simulated numerically or measured experimentally at ...

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:

دوره   شماره 

صفحات  -

تاریخ انتشار 2011