Qun Ma

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ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections(More)
This paper shows that in molecular dynamics (MD) when constant-energy (NVE) simulations of Newton's equations of motion are attempted using the multiple time stepping (MTS) integrator Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the longest step size is a third or possibly a fourth of the period(s) of the fastest motion(s) in the system.(More)
The primary objective of this paper is to explain the derivation of symplectic mollified Verlet-I/r-RESPA (MOLLY) methods that overcome linear and nonlinear instabilities that arise as numerical artifacts in Verlet-I/r-RESPA. These methods allow for lengthening of the longest time step used in molecular dynamics (MD). We provide evidence that MOLLY methods(More)
Molecular dynamics (MD) is widely used in simulations of biomolecular systems such as DNA and proteins, systems which are multiscale in nature. However, current time stepping integrators are not able to address the time scale problems. Multiscale integrators, in which the presence of " fast " modes does not affect the time integration of " slow " modes, are(More)
We introduce the B-spline Mollified Impulse (MOLLY) and the Targeted MOLLY (TM) for molecular dynamics (MD). TM uses targeted Langevin coupling to stabilize B-spline MOLLY. Results show that with a proper choice of parameters, the radial distribution function can be correctly recovered and the self-diffusion co-efficient can be correctly estimated from MD(More)
This paper discusses additional stability limitations of multiple time stepping (MTS) integrators for molecular dynamics (MD) that attempt to bridge time scales. In particular, it is shown that when constant-energy (NVE) simulations of Newton's equations of motion are attempted using the Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the(More)
  • Qun Ma, A Jesús, Izaguirre
  • 2003
by Qun Ma In post-genomic computational biology and bioinformatics, long simulations of the dynamics of molecular systems, particularly biological molecules such as proteins and DNA, require advances in time stepping computational methods. The most severe problem of these algorithms is instability. The objective of this dissertation is to present original(More)
Understanding how urban impervious surfaces (UIS) affect land surface temperatures (LST) on different scales in space and time is important for urban ecology and sustainability. We examined how spatial scales, seasonal and diurnal variations, and bioclimatic settings affected the UIS–LST relationship in mainland China. We took a hierarchical approach(More)
In multivariate calibration using a spectral dataset, it is difficult to optimize nonsystematic parameters in a quantitative model, i.e., spectral pretreatment, latent factors and variable selection. In this study, we describe a novel and systematic approach that uses a processing trajectory to select three parameters including different spectral(More)