Topic
Monte Carlo molecular modeling
About: Monte Carlo molecular modeling is a research topic. Over the lifetime, 11307 publications have been published within this topic receiving 409122 citations.
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TL;DR: In this paper, the authors compared four Monte Carlo (MC) methods for the numerical solution of the general dynamic equation (GDE) in particulate systems and found that when run with a comparable number of particles, all methods compute the size distribution within comparable levels of error.
131 citations
TL;DR: Formulation and fitting of a hidden process model are demonstrated for Sacramento River winter-run chinook salmon and its role in animal population dynamics is demonstrated.
Abstract: Hidden process models are a conceptually useful and practical way to simultaneously account for process variation in animal population dynamics and measurement errors in observations and estimates made on the population. Process variation, which can be both demographic and environmental, is modeled by linking a series of stochastic and deterministic subprocesses that characterize processes such as birth, survival, maturation, and movement. Observations of the population can be modeled as functions of true abundance with realistic probability distributions to describe observation or estimation error. Computer-intensive procedures, such as sequential Monte Carlo methods or Markov chain Monte Carlo, condition on the observed data to yield estimates of both the underlying true population abundances and the unknown population dynamics parameters. Formulation and fitting of a hidden process model are demonstrated for Sacramento River winter-run chinook salmon (Oncorhynchus tshawytsha).
131 citations
TL;DR: In this paper, a method for carrying out Monte Carlo calculations for field theories with fermion degrees of freedom is presented, and results for a simple one-dimensional model are given.
Abstract: A method is presented for carrying out Monte Carlo calculations for field theories with fermion degrees of freedom. As an example of our technique, results for a simple one-dimensional model are given.
131 citations
TL;DR: In this paper, a multi-canonical Monte Carlo method is proposed to sample across an extended space of macro-states, showing that a good approximation to this distribution may be generated efficiently by exploiting measurements of the transition rate between macro states, in simulations launched from sub-dominant macro states.
Abstract: We present a study of the multi-canonical Monte Carlo method which constructs and exploits Monte Carlo procedures that sample across an extended space of macrostates. We examine the strategies by which the sampling distribution can be constructed, showing, in particular, that a good approximation to this distribution may be generated efficiently by exploiting measurements of the transition rate between macrostates, in simulations launched from sub-dominant macrostates. We explore the utility of the method in the measurement of absolute free energies, and how it compares with traditional methods based on path integration. We present new results revealing the behaviour of the magnetization distribution of a critical finite-sized magnet, for magnetization values extending from the scaling region all the way to saturation.
131 citations
TL;DR: In this article, a molecular simulation study of freezing transitions for simple fluids in narrow slit pores was performed using the grand canonical Monte Carlo simulation method, which indicated a first order fluid to solid transition.
Abstract: We report a molecular simulation study of freezing transitions for simple fluids in narrow slit pores. A major stumbling block in previous studies of freezing in pores has been the lack of any method for calculating the free energy difference between the confined solid and liquid phases. Conventional thermodynamic integration methods often fail for confined systems, due to the difficulty in choosing a suitable path of integration. We use a different approach that involves calculating the Landau free energy as a function of a suitable order parameter, using the grand canonical Monte Carlo simulation method. The grand free energy for each phase can then be obtained by one-dimensional integration of the Landau free energy over the order parameter. These calculations are carried out for two types of wall—fluid interaction, a hard wall and a strongly attractive wall modelled on carbon. The grand free energy results for both cases clearly indicate a first order fluid to solid transition. In the case of the attr...
131 citations