Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
Population balance equation (PBE) models have potential to automate many engineering processes with far-reaching implications. In the pharmaceutical sector, crystallization model-based design can contribute to shortening excessive drug…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
The fluctuation theorems, and in particular, the Jarzynski equality, are the most important pillars of modern non-equilibrium statistical mechanics. We extend the quantum Jarzynski equality together with the Two-Time Measurement Formalism…
The detail structure of energy output and the dynamic characteristics of electric spark discharge process have been studied to calculate the energy of electric spark induced plasma under different discharge condition accurately. A series of…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
Serial-parallel redundancy is a reliable way to ensure service and systems will be available in cloud computing. That method involves making copies of the same system or program, with only one remaining active. When an error occurs, the…
Fork-Join (FJ) queueing models capture the dynamics of system parallelization under synchronization constraints, for example, for applications such as MapReduce, multipath transmission and RAID systems. Arriving jobs are first split into…
Algorithms for scheduling structured parallel computations have been widely studied in the literature. For some time now, Work Stealing is one of the most popular for scheduling such computations, and its performance has been studied in…
Work-stealing is a widely used technique for balancing irregular parallel workloads, and most modern runtime systems adopt lock-free work-stealing deques to reduce contention and improve scalability. However, existing algorithms are…
We derive an analytic expression for the distribution of velocities of multiple interacting active particles which we test by numerical simulations. In clear contrast with equilibrium we find that the velocities are coupled to positions.…
During July 2012, 150 almost identical H-mode plasmas were consecutively created in the Joint European Torus (JET), providing a combined total of approximately 8 minutes of steady-state plasma with 15,000 Edge Localised Modes (ELMs). In…
The constant increase in parallelism available on large-scale distributed computers poses major scalability challenges to many scientific applications. A common strategy to improve scalability is to express the algorithm in terms of…
Rare event simulation and estimation for systems in equilibrium are among the most challenging topics in molecular dynamics. As was shown by Jarzynski and others, nonequilibrium forcing can theoretically be used to obtain equilibrium rare…
In this work, molecular mechanics simulations were performed using a modified embedded-atom method (MEAM) potential to generate the stress-strain responses of a series of n-alkane molecules from ethane (C$_2$H$_6$) to undecane…
Quantum work is usually determined from two projective measurements of the energy at the beginning and at the end of a thermodynamic process. However, this paradigm cannot be considered thermodynamically consistent as it does not account…
We analyze work extraction protocols using the long-lived quantum coherence of a three-level quantum system, which is coupled to a thermal bath through dipole-monopole interactions. We identify situations where persistent quantum coherence…
We discuss the optimized switching free energy simulations in an analogy with the systems which are driven under nonequilibrium feedback control. We find an on-the-fly simulation approach of switching optimization is a special case of the…
We derive a general information-theoretic equality for a system undergoing two projective measurements separated by a general temporal evolution. The equality implies the non-negativity of the mutual information between the measurement…
We combine the formalisms of diagonal entropy and Jarzynski Equality to study the thermodynamic properties of closed quantum systems. Applying this approach to a quantum harmonic oscillator, the diagonal entropy offers a notion of…