Biomedical subjects

Robert H Swendsen

Publications and source records attributed to Robert H Swendsen.

6 recordsLinked to original sources

PubMed2006

Comparison of free energy methods for molecular systems.

We present a detailed comparison of computational efficiency and precision for several free energy difference (DeltaF) methods. The analysis includes both equilibrium and nonequilibrium approaches, and distinguishes between unidirectional and bidirectional methodologies. We are primarily interested in comparing two recently proposed approaches, adaptive integration, and single-ensemble path sampling to more established methodologies. As test cases, we study relative solvation free energies of large changes to the size or charge of a Lennard-Jones particle in explicit water. The results show that, for the systems used in this study, both adaptive integration and path sampling offer unique advantages over the more traditional approaches. Specifically, adaptive integration is found to provide very precise long-simulation DeltaF estimates as compared to other methods used in this report, while also offering rapid estimation of DeltaF. The results demonstrate that the adaptive integration approach is the best overall method for the systems studied here. The single-ensemble path sampling approach is found to be superior to ordinary Jarzynski averaging for the unidirectional, "fast-growth" nonequilibrium case. Closer examination of the path sampling approach on a two-dimensional system suggests it may be the overall method of choice when conformational sampling barriers are high. However, it appears that the free energy landscapes for the systems used in this study have rather modest configurational sampling barriers.

Models, Chemical↗

PubMed2004

Adaptive integration method for Monte Carlo simulations.

We present an adaptive sampling method for computing free energies, radial distribution functions, and potentials of mean force. The method is characterized by simplicity and accuracy, with the added advantage that the data are obtained in terms of quasicontinuous functions. The method is illustrated and tested with simulations on a high density fluid, including a stringent consistency test involving an unusual thermodynamic cycle that highlights its advantages.

Algorithms↗

PubMed2003

Feeling textures through a probe: effects of probe and surface geometry and exploratory factors.

Vibratory roughness perception occurs when people feel a surface with a rigid probe. Accordingly, perceived roughness should reflect probe and surface geometry, exploratory speed, and force. Experiments 1 and 2 compared magnitude estimation of roughness with the bare finger and two types of probes, one designed to eliminate force moments, under the subject's active control. Experiments 3 and 4 varied speed under passive control. Log magnitude was consistently a quadratic function of log spacing between elements in the surface. The location of the function's peak was related to the drop point--that is, the spacing at which the probe can just drop between elements--which is affected by probe tip diameter, element height, and speed. Other parameters of the quadratic were affected by probe type and speed.

Female↗

PubMed2002

Inverse Monte Carlo renormalization group transformations for critical phenomena.

We introduce a computationally stable inverse Monte Carlo renormalization group transformation method that provides a number of advantages for the calculation of critical properties. We are able to simulate the fixed point of a renormalization group for arbitrarily large lattices without critical slowing down. The log-log scaling plots obtained with this method show remarkable linearity, leading to accurate estimates for critical exponents. We illustrate this method with calculations in two- and three-dimensional Ising models for a variety of renormalization group transformations.

Journal Article↗

PubMed2002

Importance of multispin couplings in renormalized Hamiltonians.

We introduce a Monte Carlo approach to the calculation of more distant renormalized interactions with higher accuracy than is possible with previous methods. We have applied our method to study the effects of multispin interactions, which turn out to be far more important than commonly assumed. Even though the individual multispin interactions usually have smaller coupling constants than two-spin interactions, they can dominate the effects of two-spin interactions because they are so numerous.

Journal Article↗

PubMed2002

Sweeny and Gliozzi dynamics for simulations of Potts models in the Fortuin-Kasteleyn representation.

We compare the correlation times of the Sweeny and Gliozzi dynamics for two-dimensional Ising and three-state Potts models, and the three-dimensional Ising model for the simulations in the percolation representation. The results are also compared with Swendsen-Wang and Wolff cluster dynamics. It is found that Sweeny and Gliozzi dynamics have essentially the same dynamical critical behavior. Contrary to Gliozzi's claim [Phys. Rev. E 66, 016115 (2002)], the Gliozzi dynamics has critical slowing down comparable to that of other cluster methods. For the two-dimensional Ising model, both Sweeny and Gliozzi dynamics give good fits to logarithmic size dependences for the correlation times; for two-dimensional three-state Potts model, their dynamical critical exponent z is 0.49+/-0.01; the three-dimensional Ising model has z=0.37+/-0.02.

Journal Article↗