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Bug reproduction is critically important for diagnosing a production-run failure. Unfortunately, reproducing a concurrency bug on multi-processors (e.g., multi-core) is challenging. Previous techniques either incur large overhead or require new non-trivial hardware extensions. This paper proposes a novel technique called PRES (probabilistic replay via(More)
We recently developed an all-atom free energy forcefield (PFF01) for protein structure prediction with stochastic optimization methods. We demonstrated that PFF01 correctly predicts the native conformation of several proteins as the global optimum of the free energy surface. Here we review recent folding studies, which permitted the reproducible all-atom(More)
The search for efficient and predictive methods to describe the protein folding process at the all-atom level remains an important grand-computational challenge. The development of multi-teraflop architectures, such as the IBM BlueGene used in this study, has been motivated in part by the large computational requirements of such studies. Here we report the(More)
Dependence of charge transmission through several experimentally studied DNA duplexes on their lowest-frequency acoustic modes, combined with the molecular dynamics in picosecond characteristic time range, has been studied. Based on this analysis we were able to identify the specific acoustic modes responsible for the noticeable increase in DNA charge(More)
Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above.(More)
Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above. We(More)
The hydration and dissociation phenomena of HF(H(2)O)(n)() (n < or = 10) clusters have been studied by using both the density functional theory with the 6-311++G[sp] basis set and the Møller-Plesset second-order perturbation theory with the aug-cc-pVDZ+(2s2p/2s) basis set. The structures for n > or = 8 are first reported here. The dissociated form of the(More)
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