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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)
BACKGROUND Previously we showed that BdcA controls Escherichia coli biofilm dispersal by binding the ubiquitous bacterial signal cyclic diguanylate (c-di-GMP); upon reducing the concentration of c-di-GMP, the cell shifts to the planktonic state by increasing motility, decreasing aggregation, and decreasing production of biofilm adhesins. FINDINGS Here we(More)
Phages are the most abundant entity in the biosphere and outnumber bacteria by a factor of 10. Phage DNA may also constitute 20% of bacterial genomes; however, its role is ill defined. Here, we explore the impact of cryptic prophages on cell physiology by precisely deleting all nine prophage elements (166 kbp) using Escherichia coli. We find that cryptic(More)
Although it is well recognized that bacteria respond to environmental stress through global networks, the mechanism by which stress is relayed to the interior of the cell is poorly understood. Here we show that enigmatic toxin-antitoxin systems are vital in mediating the environmental stress response. Specifically, the antitoxin MqsA represses rpoS, which(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)
Lucilia Robineau-Desvoidy (Diptera: Calliphoridae) is a blow fly genus of forensic, medical, veterinary, and agricultural importance. This genus is also famous because of its beneficial uses in maggot debridement therapy (MDT). Although the genus is of considerable economic importance, our knowledge about microbes associated with these flies and how these(More)