We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...

In this paper a single machine time-dependent scheduling problem with total completion time criterion is considered. There are given n jobs J1,…,Jn and the processing time pi of the ith job is given by pi=a+bisi, where si is the starting time of the ith job (i=1,…,n),bi is its deterioration rate and a is the common base processing time. If all jobs have deterioration rates different and not smaller than a certain constant u>0,...

Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended...