Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system

The following article appeared in J. Chem. Phys. 139, 174107 (2013) and may be found at http://scitation.aip.org/content/aip/journal/jcp/139/17/10.1063/1.482705

Comment on “Preserving the Boltzmann ensemble in replica-exchange molecular dynamics” [J. Chem. Phys.129, 164112 (2008)]

A brief discussion of the ergodic description of constant temperature molecular dynamics (MD) is provided; the discussion is based on the analysis of criticisms raised in a recent paper [B. Cooke and S. C. Schmidler, J. Chem. Phys.129, 164112 (2008)]. In the paper, the following criticisms relating to the basic concepts of constant temperature MD are made in mathematical manners: (I) the Nosé–Hoover (NH) equation is not measure-preserving; (II) NH system and NH chain system are not ergodic under the Boltzmann measure; and (III) the Nosé Hamiltonian system as well as the Nosé–Poincaré Hamiltonian system is not ergodic. In this comment, I show the necessity for the reconsideration of these criticisms. The NH equation is measure-preserving, where the measure carries the Boltzmann–Gibbs density; this fact provides the compatibility between MD equation and the Boltzmann–Gibbs distribution. The arguments advanced in support of the above criticisms are unsound; ergodicities of those systems are still not theoretically judged. I discuss exact ergodic-theoretical expressions appropriate for constant temperature MD, and explain the reason behind the incorrect recognitions.The following article appeared in J. Chem. Phys. 132, 127101 (2010) and may be found at http://scitation.aip.org/content/aip/journal/jcp/132/12/10.1063/1.329942

Coupled Nosé-Hoover equations of motions without time scaling

The Nosé-Hoover (NH) equation of motion is widely used in molecular dynamics simulations. It enables us to set a constant temperature and produce the canonical distribution for a target physical system. For the purpose of investigating the physical system under fluctuating temperature, we have introduced a coupled Nosé-Hoover equation in our previous work [J. Phys. A 48 455001 (2015)]. The coupled NH equation implements a fluctuating heat-bath temperature in the NH equation of the physical system, and also keeps a statistically complete description via an invariant measure of the total system composed of the physical system and a "temperature system" . However, a difficulty lies in that the time development of the physical system may not correspond to the realistic physical process, because of the need of a scaled time average to compute thermodynamical quantities. The current work gives a solution by presenting a new scheme, which is free from the scaled time but retains the statistical description. By use of simple model systems, we validate the current scheme and compare with the original scheme. The sampling property of the current scheme is also clari fied to investigate the effect of function setting used for the distribution of the total system.This is an author-created, un-copyedited version of an article accepted for publication/published in Journal of Physics A : Mathematical and Theoretical. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://dx.doi.org/10.1088/1751-8113/50/1/015002

Double density dynamics : realizing a joint distribution of a physical system and a parameter system

This is an author-created, un-copyedited version of an article accepted for publication/published in Journal of Physics A : Mathematical and Theoretical. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://doi.org/10.1088/1751-8113/48/45/455001

Numerical Integration Techniques Based on a Geometric View and Application to Molecular Dynamics Simulations

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A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

The dynamic cross correlation (DCC) analysis is a popular method for analyzing the trajectories of molecular dynamics (MD) simulations. However, it is difficult to detect correlative motions that appear transiently in only a part of the trajectory, such as atomic contacts between the side-chains of amino acids, which may rapidly flip. In order to capture these multi-modal behaviors of atoms, which often play essential roles, particularly at the interfaces of macromolecules, we have developed the "multi-modal DCC (mDCC)" analysis. The mDCC is an extension of the DCC and it takes advantage of a Bayesian-based pattern recognition technique. We performed MD simulations for molecular systems modeled from the (Ets1)2-DNA complex and analyzed their results with the mDCC method. Ets1 is an essential transcription factor for a variety of physiological processes, such as immunity and cancer development. Although many structural and biochemical studies have so far been performed, its DNA binding properties are still not well characterized. In particular, it is not straightforward to understand the molecular mechanisms how the cooperative binding of two Ets1 molecules facilitates their recognition of Stromelysin-1 gene regulatory elements. A correlation network was constructed among the essential atomic contacts, and the two major pathways by which the two Ets1 molecules communicate were identified. One is a pathway via direct protein-protein interactions and the other is that via the bound DNA intervening two recognition helices. These two pathways intersected at the particular cytosine bases (C110/C11), interacting with the H1, H2, and H3 helices. Furthermore, the mDCC analysis showed that both pathways included the transient interactions at their intermolecular interfaces of Tyr396-C11 and Ala327-Asn380 in multi-modal motions of the amino acid side chains and the nucleotide backbone. Thus, the current mDCC approach is a powerful tool to reveal these complicated behaviors and scrutinize intermolecular communications in a molecular system

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics : Analysis of the accuracy and application to liquid systems

The following article appeared in J. Chem. Phys. 140, 194307 (2014) and may be found at http://scitation.aip.org/content/aip/journal/jcp/140/19/10.1063/1.487569